From 5d2455f6a909a328d42d1062a488ccd37b576c6c Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 1 Jun 2026 15:03:46 +0200
Subject: [PATCH 001/256] add test covering a collection input

---
 test/unit/app/tools/test_actions.py | 33 +++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/test/unit/app/tools/test_actions.py b/test/unit/app/tools/test_actions.py
index de6efdca29d..d6ec06b4412 100644
--- a/test/unit/app/tools/test_actions.py
+++ b/test/unit/app/tools/test_actions.py
@@ -51,6 +51,18 @@ TWO_OUTPUTS = """<tool id="test_tool" name="Test Tool">
 </tool>
 """
 
+# Tool with a multiple="true" data parameter – used to test on_string handling for collections.
+MULTIPLE_DATA_TOOL = """<tool id="test_tool" name="Test Tool" version="1.0" profile="26.1">
+    <command>cat "$param1" &lt; $out1</command>
+    <inputs>
+        <param type="data" format="tabular" name="param1" multiple="true" value="" />
+    </inputs>
+    <outputs>
+        <data name="out1" format="data" />
+    </outputs>
+</tool>
+"""
+
 
 def test_on_text_for_numeric_ids():
     def assert_on_text_is(expected, hids):
@@ -83,6 +95,27 @@ def test_on_text_for_dataset_and_collections():
 
 
 class TestDefaultToolAction(TestCase, tools_support.UsesTools):
+    def test_on_text_multiple_true_collection(self):
+        # Create a collection with three datasets
+        hdca = model.HistoryDatasetCollectionAssociation()
+        hdca.id = 999
+        hdca.hid = 55
+        collection = model.DatasetCollection()
+        hdca.collection = collection
+        # add three datasets to the collection
+        hda1 = self.__add_dataset()
+        hda2 = self.__add_dataset()
+        hda3 = self.__add_dataset()
+        model.DatasetCollectionElement(collection=collection, element=hda1)
+        model.DatasetCollectionElement(collection=collection, element=hda2)
+        model.DatasetCollectionElement(collection=collection, element=hda3)
+        collection.collection_type = "list"
+        self.history.dataset_collections.append(hdca)
+        # incoming param with the collection
+        incoming = {"param1": hdca}
+        job, output = self._simple_execute(contents=MULTIPLE_DATA_TOOL, incoming=incoming)
+        assert output["out1"].name == f"Test Tool on collection {hdca.hid}"
+
     def setUp(self):
         self.setup_app()
         history = model.History()

From 4ed0118ebdb66c87f2c1aa80176bee90f30574cb Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 1 Jun 2026 15:04:16 +0200
Subject: [PATCH 002/256] fix

---
 lib/galaxy/tools/actions/__init__.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 50429437766..3088a070043 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -941,8 +941,12 @@ class DefaultToolAction(ToolAction):
 
         for input_name in inp_data:
             data = inp_data[input_name]
+            # Skip collection inputs and any suffixed dataset names derived from them (e.g., "datasets1", "datasets2")
             if input_name in inp_dataset_collections:
                 continue
+            # Also skip if the name starts with a collection input key and the remainder is a numeric suffix
+            if any(input_name.startswith(key) and input_name[len(key) :].isdigit() for key in inp_dataset_collections):
+                continue
             if getattr(data, "hid", None):
                 input_hids.append(data.hid)
         return on_text_for_dataset_and_collections(dataset_hids=input_hids, collection_hids=collection_hids)

From 9960452f0f0b22dcb019e5623ecf7cfb3157c3f6 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 3 Jun 2026 09:44:19 +0200
Subject: [PATCH 003/256] Add utility for workflow file validation

---
 .../Workflow/Import/workflowValidation.ts     | 69 +++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 client/src/components/Workflow/Import/workflowValidation.ts

diff --git a/client/src/components/Workflow/Import/workflowValidation.ts b/client/src/components/Workflow/Import/workflowValidation.ts
new file mode 100644
index 00000000000..19b4f69b4ae
--- /dev/null
+++ b/client/src/components/Workflow/Import/workflowValidation.ts
@@ -0,0 +1,69 @@
+/** Accepted workflow file extensions */
+export const WORKFLOW_FILE_EXTENSIONS = [".ga", ".gxwf.yml", ".gxwf.yaml", ".yml", ".yaml"] as const;
+
+/** Human-readable list of accepted formats for file inputs */
+export const WORKFLOW_FILE_ACCEPT = ".ga, .yml, .yaml";
+
+/**
+ * Check if a filename has a valid workflow file extension.
+ * Supports .ga (Galaxy Archive), .yml/.yaml (Galaxy Workflow Format), and .gxwf.yml/.gxwf.yaml
+ */
+export function hasWorkflowFileExtension(fileName: string): boolean {
+    const lowerName = fileName.toLowerCase();
+    return WORKFLOW_FILE_EXTENSIONS.some((ext) => lowerName.endsWith(ext));
+}
+
+/**
+ * Validate a workflow file by checking its extension and optionally its content.
+ *
+ * For .ga files (JSON format), checks for `"a_galaxy_workflow": "true"`.
+ * For .yml/.yaml files (YAML format), checks for `class: GalaxyWorkflow` or `class: GalaxyWorkflow`.
+ *
+ * Content validation reads only the first 1KB of the file for efficiency.
+ */
+export async function validateWorkflowFile(
+    file: File,
+    options: { checkContent?: boolean } = {},
+): Promise<{ valid: boolean; error?: string }> {
+    if (!hasWorkflowFileExtension(file.name)) {
+        return { valid: false, error: `Invalid file type. Accepted formats: ${WORKFLOW_FILE_ACCEPT}` };
+    }
+
+    if (options.checkContent) {
+        const lowerName = file.name.toLowerCase();
+
+        if (lowerName.endsWith(".ga")) {
+            const hasMarker = await readFileMarker(file, '"a_galaxy_workflow"');
+            if (!hasMarker) {
+                return {
+                    valid: false,
+                    error: "File does not appear to be a Galaxy workflow (.ga). Missing workflow marker.",
+                };
+            }
+        } else if (lowerName.endsWith(".yml") || lowerName.endsWith(".yaml")) {
+            const hasMarker = await readFileMarker(file, "class:");
+            if (!hasMarker) {
+                return {
+                    valid: false,
+                    error: "File does not appear to be a Galaxy workflow (.yml/.yaml). Missing 'class:' marker.",
+                };
+            }
+        }
+    }
+
+    return { valid: true };
+}
+
+/**
+ * Read the first 1KB of a file and check if it contains the given marker string.
+ * This is efficient and avoids loading the entire file into memory.
+ */
+async function readFileMarker(file: File, marker: string): Promise<boolean> {
+    try {
+        const slice = file.slice(0, 1024);
+        const text = await slice.text();
+        return text.includes(marker);
+    } catch {
+        return false;
+    }
+}

From b2f79e1084f4eea9b56a33e1d619c382251380d4 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 3 Jun 2026 09:44:20 +0200
Subject: [PATCH 004/256] Improve file import usability with drag-and-drop and
 validation

---
 .../components/Workflow/Import/FromFile.vue   | 171 +++++++++++++-----
 .../Workflow/Import/FromFileOrUrl.test.ts     |   2 +-
 2 files changed, 126 insertions(+), 47 deletions(-)

diff --git a/client/src/components/Workflow/Import/FromFile.vue b/client/src/components/Workflow/Import/FromFile.vue
index d5fe4ffa9a5..607f9e9b246 100644
--- a/client/src/components/Workflow/Import/FromFile.vue
+++ b/client/src/components/Workflow/Import/FromFile.vue
@@ -1,44 +1,40 @@
 <script setup lang="ts">
+import { faCloudUploadAlt } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import axios from "axios";
-import { BAlert, BForm, BFormFile, BFormGroup } from "bootstrap-vue";
+import { BForm, BFormFile, BFormGroup } from "bootstrap-vue";
 import { computed, type Ref, ref, watch } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { getRedirectOnImportPath } from "@/components/Workflow/redirectPath";
+import { useFileDrop } from "@/composables/fileDrop";
 import { withPrefix } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
+import { validateWorkflowFile, WORKFLOW_FILE_ACCEPT } from "./workflowValidation";
+
+import GAlert from "@/components/BaseComponents/GAlert.vue";
 import GButton from "@/components/BaseComponents/GButton.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
 interface Props {
-    hideSubmitButton?: boolean;
+    /** A file dropped on the parent's method card, to be consumed on mount */
+    droppedFile?: File | null;
 }
 
-const props = withDefaults(defineProps<Props>(), {
-    hideSubmitButton: false,
-});
+const props = defineProps<Props>();
 
 const emit = defineEmits<{
     (e: "input-valid", valid: boolean): void;
 }>();
 
 const loading = ref(false);
-const sourceFile: Ref<string | null> = ref(null);
+const sourceFile: Ref<File | null> = ref(null);
 const errorMessage: Ref<string | null> = ref(null);
-const acceptedWorkflowFormats = ".ga, .yml";
+const dropZoneRef = ref<HTMLElement | null>(null);
+const fileSetViaDrop = ref(false);
 
-const isImportDisabled = computed(() => {
-    return !sourceFile.value;
-});
-
-const importTooltip = computed(() => {
-    return isImportDisabled.value ? "You must provide a workflow file." : "Import workflow from File";
-});
-
-const hasErrorMessage = computed(() => {
-    return errorMessage.value != null;
-});
+const hasErrorMessage = computed(() => errorMessage.value != null);
 
 // Validation state for wizard mode
 const isValid = computed(() => sourceFile.value !== null);
@@ -47,15 +43,65 @@ watch(isValid, (newValue) => {
     emit("input-valid", newValue);
 });
 
-// Hide submit button in wizard mode (or when hideSubmitButton is true)
-const showSubmitButton = computed(() => {
-    return !props.hideSubmitButton;
+// Consume a file dropped on the parent's method card
+if (props.droppedFile) {
+    sourceFile.value = props.droppedFile;
+    fileSetViaDrop.value = true;
+}
+
+// Drop zone handling
+async function onDrop(evt: DragEvent) {
+    if (evt.dataTransfer?.files?.length) {
+        const file = evt.dataTransfer.files[0];
+        if (!file) {
+            return;
+        }
+        const result = await validateWorkflowFile(file, { checkContent: true });
+        if (result.valid) {
+            sourceFile.value = file;
+            fileSetViaDrop.value = true;
+        } else {
+            errorMessage.value = result.error ?? "Invalid workflow file.";
+        }
+    }
+}
+
+const { isFileOverDropZone } = useFileDrop({
+    dropZone: dropZoneRef,
+    onDrop,
+    onDropCancel: () => {},
+    solo: false,
+    idleTime: 10000,
+    ignoreChildrenOnLeave: true,
 });
 
+/** When the user selects a file via the native input, validate it */
+async function onFileInput(file: File | null) {
+    if (!file) {
+        sourceFile.value = null;
+        fileSetViaDrop.value = false;
+        return;
+    }
+    const result = await validateWorkflowFile(file, { checkContent: true });
+    if (result.valid) {
+        sourceFile.value = file;
+        fileSetViaDrop.value = false;
+    } else {
+        sourceFile.value = null;
+        fileSetViaDrop.value = false;
+        errorMessage.value = result.error ?? "Invalid workflow file.";
+    }
+}
+
+/** Clear the current file and reset to the browse state */
+function clearFile() {
+    sourceFile.value = null;
+    fileSetViaDrop.value = false;
+}
+
 const router = useRouter();
 
-async function submit(ev: SubmitEvent) {
-    ev.preventDefault();
+async function submit() {
     const formData = new FormData();
 
     if (sourceFile.value) {
@@ -78,38 +124,71 @@ async function submit(ev: SubmitEvent) {
 
 // Expose method for wizard submit
 async function attemptImport() {
-    await submit(new Event("submit") as SubmitEvent);
+    await submit();
 }
 
 defineExpose({ attemptImport });
 </script>
 
 <template>
-    <BForm class="mt-4 workflow-import-file" @submit="submit">
-        <h2 class="h-sm">Import from a workflow file</h2>
+    <BForm class="mt-4 workflow-import-file" @submit.prevent="submit">
+        <div
+            ref="dropZoneRef"
+            class="workflow-drop-zone"
+            :class="{ 'workflow-drop-zone-active': isFileOverDropZone }"
+            data-galaxy-file-drop-target>
+            <div v-if="!sourceFile" class="mb-3">
+                <FontAwesomeIcon :icon="faCloudUploadAlt" size="3x" class="text-muted" />
+                <p class="mt-2 mb-1 font-weight-medium">Drag a workflow file here</p>
+                <p class="text-muted small mb-2">or</p>
+            </div>
+            <BFormGroup :label="sourceFile ? 'Workflow File' : 'Browse for a file'">
+                <!-- When a file was set via drop, the native file input can't reflect
+                     it programmatically, so we show the filename manually instead. -->
+                <div v-if="fileSetViaDrop && sourceFile" class="text-center py-2">
+                    <span class="font-weight-bold text-break">{{ sourceFile.name }}</span>
+                    <div class="mt-1">
+                        <GButton transparent size="small" @click="clearFile">Choose another</GButton>
+                    </div>
+                </div>
+                <BFormFile
+                    v-show="!fileSetViaDrop"
+                    v-model="sourceFile"
+                    :accept="WORKFLOW_FILE_ACCEPT"
+                    @input="onFileInput" />
+                <span v-if="!sourceFile" class="text-muted small">
+                    Accepted formats: <code>*.ga</code>, <code>*.yml</code>, <code>*.yaml</code>
+                </span>
+            </BFormGroup>
+        </div>
 
-        <BFormGroup label="Archived Workflow File">
-            <BFormFile v-model="sourceFile" :accept="acceptedWorkflowFormats" />
-            If the workflow is in a file on your computer, choose it and then click Import.
-        </BFormGroup>
-
-        <BAlert :show="hasErrorMessage" variant="danger">
+        <GAlert :show="hasErrorMessage" variant="danger">
             {{ errorMessage }}
-        </BAlert>
+        </GAlert>
 
-        <BAlert v-if="loading" show variant="info">
+        <GAlert v-if="loading" variant="info">
             <LoadingSpan message="Loading your workflow, this may take a while - please be patient." />
-        </BAlert>
-
-        <GButton
-            v-if="showSubmitButton"
-            id="workflow-import-button"
-            type="submit"
-            :disabled="isImportDisabled"
-            :title="importTooltip"
-            tooltip
-            color="blue">
-            Import workflow
-        </GButton>
+        </GAlert>
     </BForm>
 </template>
+
+<style scoped lang="scss">
+@import "@/style/scss/theme/blue.scss";
+
+.workflow-drop-zone {
+    border: 2px dashed $border-color;
+    border-radius: $border-radius-large;
+    text-align: center;
+    background-color: $gray-100;
+    padding: 1.5rem;
+    margin-bottom: 1rem;
+    transition:
+        border-color 0.3s ease,
+        background-color 0.3s ease;
+
+    &.workflow-drop-zone-active {
+        border-color: $brand-primary;
+        background-color: lighten($brand-primary, 60%);
+    }
+}
+</style>
diff --git a/client/src/components/Workflow/Import/FromFileOrUrl.test.ts b/client/src/components/Workflow/Import/FromFileOrUrl.test.ts
index f9c759b83be..2bfdaf7f468 100644
--- a/client/src/components/Workflow/Import/FromFileOrUrl.test.ts
+++ b/client/src/components/Workflow/Import/FromFileOrUrl.test.ts
@@ -72,6 +72,6 @@ describe("FromUrl", () => {
 describe("FromFile", () => {
     it("can mount the component", async () => {
         const wrapper = mount(FromFile as object, { localVue });
-        expect(wrapper.find("#workflow-import-button").exists()).toBe(true);
+        expect(wrapper.find("form").exists()).toBe(true);
     });
 });

From 16f4744e92e9f6f77c52cb0f39e64080f28e5de0 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 3 Jun 2026 09:44:20 +0200
Subject: [PATCH 005/256] Streamline import wizard navigation and UI

---
 .../components/Workflow/WorkflowImport.vue    | 93 ++++++++++++++++---
 1 file changed, 79 insertions(+), 14 deletions(-)

diff --git a/client/src/components/Workflow/WorkflowImport.vue b/client/src/components/Workflow/WorkflowImport.vue
index 3c8d1239899..8d3e149be18 100644
--- a/client/src/components/Workflow/WorkflowImport.vue
+++ b/client/src/components/Workflow/WorkflowImport.vue
@@ -1,10 +1,14 @@
 <script setup lang="ts">
+import { faCloudUploadAlt, faFileImport, faIdBadge, faLink, faSearch } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed, nextTick, onMounted, type Ref, ref } from "vue";
 import { useRoute } from "vue-router/composables";
 
 import { useWizard } from "@/components/Common/Wizard/useWizard";
 import type { TrsSelection } from "@/components/Workflow/Import/types";
+import { validateWorkflowFile } from "@/components/Workflow/Import/workflowValidation";
 import { Services } from "@/components/Workflow/services";
+import { useFileDrop } from "@/composables/fileDrop";
 
 import GCard from "@/components/Common/GCard.vue";
 import GenericWizard from "@/components/Common/Wizard/GenericWizard.vue";
@@ -22,6 +26,8 @@ const trsServers: Ref<TrsSelection[]> = ref([]);
 const fileComponent = ref<InstanceType<typeof FromFile>>();
 const urlComponent = ref<InstanceType<typeof FromUrl>>();
 const trsComponent = ref<InstanceType<typeof TrsImport>>();
+const uploadCardRef = ref<HTMLElement | null>(null);
+const droppedFile: Ref<File | null> = ref(null);
 
 // Validation states for each step
 const uploadValid = ref(false);
@@ -30,6 +36,32 @@ const trsSearchValid = ref(false);
 const trsUrlValid = ref(false);
 const trsIdValid = ref(false);
 
+// Drop zone on the "Upload file" method card — allows dropping a workflow file
+// directly on the card to skip straight to the upload step with the file pre-populated
+async function onUploadCardDrop(evt: DragEvent) {
+    if (evt.dataTransfer?.files?.length) {
+        const file = evt.dataTransfer.files[0];
+        if (!file) {
+            return;
+        }
+        const result = await validateWorkflowFile(file, { checkContent: true });
+        if (result.valid) {
+            droppedFile.value = file;
+            selectMethod("upload");
+        }
+        // If invalid, the drop is silently ignored — the user can still click the card
+    }
+}
+
+const { isFileOverDropZone: isFileOverUploadCard } = useFileDrop({
+    dropZone: uploadCardRef,
+    onDrop: onUploadCardDrop,
+    onDropCancel: () => {},
+    solo: false,
+    idleTime: 10000,
+    ignoreChildrenOnLeave: true,
+});
+
 const queryParams = computed(() => ({
     trsId: route.query.trs_id as string | undefined,
     trsUrl: route.query.trs_url as string | undefined,
@@ -153,10 +185,26 @@ onMounted(async () => {
 
 function selectMethod(method: ImportMethod) {
     selectedMethod.value = method;
+    // Navigate to the appropriate step based on the selected method
+    if (method === "upload") {
+        wizard.goTo("upload-file");
+    } else if (method === "fetch") {
+        wizard.goTo("fetch-url");
+    } else if (method === "repository") {
+        wizard.goTo("select-trs-method");
+    }
 }
 
 function selectTrsMethod(method: TrsMethod) {
     selectedTrsMethod.value = method;
+    // Navigate to the appropriate TRS step
+    if (method === "search") {
+        wizard.goTo("trs-search");
+    } else if (method === "url") {
+        wizard.goTo("trs-url");
+    } else if (method === "id") {
+        wizard.goTo("trs-id");
+    }
 }
 
 function onSubmit() {
@@ -202,17 +250,24 @@ function onTrsIdValid(e: boolean) {
             <div v-if="wizard.isCurrent('select-method')" class="method-selection">
                 <div class="row">
                     <div class="col-xl-4 my-5">
-                        <GCard
-                            class="h-100 workflow-import-file-link text-center"
-                            :class="{ selected: selectedMethod === 'upload' }"
-                            :clickable="true"
-                            @click="selectMethod('upload')">
-                            <h4>Upload file</h4>
-                            <p class="text-muted mb-0">
-                                Upload a <code>*.ga</code> file from your computer. These files can be downloaded from
-                                Galaxy servers or workflow repositories.
-                            </p>
-                        </GCard>
+                        <div
+                            ref="uploadCardRef"
+                            class="h-100"
+                            :class="{ 'drop-zone-active': isFileOverUploadCard }"
+                            data-galaxy-file-drop-target>
+                            <GCard
+                                class="h-100 workflow-import-file-link text-center"
+                                :class="{ selected: selectedMethod === 'upload' }"
+                                :clickable="true"
+                                @click="selectMethod('upload')">
+                                <FontAwesomeIcon :icon="faFileImport" size="3x" class="mb-3 text-muted" />
+                                <h4>Upload file</h4>
+                                <p class="text-muted mb-0">
+                                    Upload a <code>*.ga</code> or <code>*.gxwf.yml</code> file from your computer. You
+                                    can also drag and drop a file here.
+                                </p>
+                            </GCard>
+                        </div>
                     </div>
 
                     <div class="col-xl-4 my-5">
@@ -221,10 +276,11 @@ function onTrsIdValid(e: boolean) {
                             :class="{ selected: selectedMethod === 'fetch' }"
                             :clickable="true"
                             @click="selectMethod('fetch')">
+                            <FontAwesomeIcon :icon="faLink" size="3x" class="mb-3 text-muted" />
                             <h4>Fetch URL</h4>
                             <p class="text-muted mb-0">
-                                Fetch a remote <code>*.ga</code> file from any publicly accessible URL. This can be
-                                generated by any Galaxy server, or public repositories like GitHub.
+                                Fetch a remote <code>Galaxy Workflow</code> file from any publicly accessible URL. This
+                                can be generated by any Galaxy server, or public repositories like GitHub.
                             </p>
                         </GCard>
                     </div>
@@ -235,6 +291,7 @@ function onTrsIdValid(e: boolean) {
                             :class="{ selected: selectedMethod === 'repository' }"
                             :clickable="true"
                             @click="selectMethod('repository')">
+                            <FontAwesomeIcon :icon="faCloudUploadAlt" size="3x" class="mb-3 text-muted" />
                             <h4>Import from repository</h4>
                             <p class="text-muted mb-0">
                                 Search and import workflows from our configured workflow repositories ({{
@@ -248,7 +305,7 @@ function onTrsIdValid(e: boolean) {
 
             <div v-else-if="wizard.isCurrent('upload-file')" class="import-form">
                 <div class="container-narrow">
-                    <FromFile ref="fileComponent" @input-valid="onUploadValid" />
+                    <FromFile ref="fileComponent" :dropped-file="droppedFile" @input-valid="onUploadValid" />
                 </div>
             </div>
 
@@ -266,6 +323,7 @@ function onTrsIdValid(e: boolean) {
                             :class="{ selected: selectedTrsMethod === 'search' }"
                             :clickable="true"
                             @click="selectTrsMethod('search')">
+                            <FontAwesomeIcon :icon="faSearch" size="3x" class="mb-3 text-muted" />
                             <h4>Search workflow registries</h4>
                             <p class="text-muted mb-0">Search for workflows across configured GA4GH servers.</p>
                         </GCard>
@@ -277,6 +335,7 @@ function onTrsIdValid(e: boolean) {
                             :class="{ selected: selectedTrsMethod === 'url' }"
                             :clickable="true"
                             @click="selectTrsMethod('url')">
+                            <FontAwesomeIcon :icon="faLink" size="3x" class="mb-3 text-muted" />
                             <h4>TRS URL</h4>
                             <p class="text-muted mb-0">Import directly from any GA4GH server with a TRS URL.</p>
                         </GCard>
@@ -288,6 +347,7 @@ function onTrsIdValid(e: boolean) {
                             :class="{ selected: selectedTrsMethod === 'id' }"
                             :clickable="true"
                             @click="selectTrsMethod('id')">
+                            <FontAwesomeIcon :icon="faIdBadge" size="3x" class="mb-3 text-muted" />
                             <h4>TRS ID</h4>
                             <p class="text-muted mb-0">
                                 When you know the TRS ID for a workflow in one of the configured GA4GH servers.
@@ -355,4 +415,9 @@ function onTrsIdValid(e: boolean) {
     width: 100%;
     max-width: 600px;
 }
+.drop-zone-active {
+    border-radius: 0.3rem;
+    outline: 2px dashed var(--brand-primary, #2c3143);
+    outline-offset: 2px;
+}
 </style>

From 2e76c8e3154a9293dd1b54362e6415a48bfd990d Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 3 Jun 2026 09:44:21 +0200
Subject: [PATCH 006/256] Remove redundant UI elements from import
 sub-components

---
 .../components/Workflow/Import/FromUrl.vue    | 39 ++-----------------
 .../Workflow/Import/TrsIdImport.vue           |  2 -
 .../Workflow/Import/TrsUrlImport.vue          | 30 --------------
 3 files changed, 3 insertions(+), 68 deletions(-)

diff --git a/client/src/components/Workflow/Import/FromUrl.vue b/client/src/components/Workflow/Import/FromUrl.vue
index 4c0658cd5cb..736842ec3b1 100644
--- a/client/src/components/Workflow/Import/FromUrl.vue
+++ b/client/src/components/Workflow/Import/FromUrl.vue
@@ -9,14 +9,6 @@ import { withPrefix } from "@/utils/redirect";
 
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
-interface Props {
-    hideSubmitButton?: boolean;
-}
-
-const props = withDefaults(defineProps<Props>(), {
-    hideSubmitButton: false,
-});
-
 const emit = defineEmits<{
     (e: "input-valid", valid: boolean): void;
 }>();
@@ -25,14 +17,6 @@ const loading = ref(false);
 const sourceURL: Ref<string | null> = ref(null);
 const errorMessage: Ref<string | null> = ref(null);
 
-const isImportDisabled = computed(() => {
-    return !sourceURL.value;
-});
-
-const importTooltip = computed(() => {
-    return isImportDisabled.value ? "You must provide a workflow archive URL." : "Import workflow from URL";
-});
-
 const hasErrorMessage = computed(() => {
     return errorMessage.value != null;
 });
@@ -46,11 +30,6 @@ watch(isValid, (newValue) => {
     emit("input-valid", newValue);
 });
 
-// Hide submit button in wizard mode (or when hideSubmitButton is true)
-const showSubmitButton = computed(() => {
-    return !props.hideSubmitButton;
-});
-
 function autoAppendJson(urlString: string): string {
     const sharedWorkflowRegex = /^(https?:\/\/[\S]+\/u\/[\S]+\/w\/[^\s/]+)\/?$/;
     const matches = urlString.match(sharedWorkflowRegex);
@@ -65,8 +44,7 @@ function autoAppendJson(urlString: string): string {
 
 const router = useRouter();
 
-async function submit(ev: SubmitEvent) {
-    ev.preventDefault();
+async function submit() {
     const formData = new FormData();
 
     if (sourceURL.value) {
@@ -94,14 +72,14 @@ async function submit(ev: SubmitEvent) {
 
 // Expose method for wizard submit
 async function attemptImport() {
-    await submit(new Event("submit") as SubmitEvent);
+    await submit();
 }
 
 defineExpose({ attemptImport });
 </script>
 
 <template>
-    <BForm class="mt-4 workflow-import-url" @submit="submit">
+    <BForm class="mt-4 workflow-import-url" @submit.prevent="submit">
         <h2 class="h-sm">Import from a Galaxy workflow export URL</h2>
 
         <BFormGroup label="Workflow Archive URL">
@@ -122,16 +100,5 @@ defineExpose({ attemptImport });
         <BAlert v-if="loading" show variant="info">
             <LoadingSpan message="Loading your workflow, this may take a while - please be patient." />
         </BAlert>
-
-        <GButton
-            v-if="showSubmitButton"
-            id="workflow-import-button"
-            type="submit"
-            :disabled="isImportDisabled"
-            :title="importTooltip"
-            tooltip
-            color="blue">
-            Import workflow
-        </GButton>
     </BForm>
 </template>
diff --git a/client/src/components/Workflow/Import/TrsIdImport.vue b/client/src/components/Workflow/Import/TrsIdImport.vue
index f6fb5d3f00a..3c33eed25ed 100644
--- a/client/src/components/Workflow/Import/TrsIdImport.vue
+++ b/client/src/components/Workflow/Import/TrsIdImport.vue
@@ -134,8 +134,6 @@ defineExpose({ triggerImport });
 
 <template>
     <div class="workflow-import-trs-id">
-        <h2 class="h-sm">Import from TRS ID</h2>
-
         <div>
             <b>TRS Server:</b>
 
diff --git a/client/src/components/Workflow/Import/TrsUrlImport.vue b/client/src/components/Workflow/Import/TrsUrlImport.vue
index c9f9986c36e..d64a1890d7d 100644
--- a/client/src/components/Workflow/Import/TrsUrlImport.vue
+++ b/client/src/components/Workflow/Import/TrsUrlImport.vue
@@ -2,16 +2,12 @@
 import { BForm, BFormGroup, BFormInput } from "bootstrap-vue";
 import { computed, ref, watch } from "vue";
 
-import GButton from "@/components/BaseComponents/GButton.vue";
-
 interface Props {
     queryTrsUrl?: string;
-    hideSubmitButton?: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
     queryTrsUrl: "",
-    hideSubmitButton: false,
 });
 
 const emit = defineEmits<{
@@ -21,14 +17,6 @@ const emit = defineEmits<{
 
 const trsUrl = ref(props.queryTrsUrl);
 
-const isImportDisabled = computed(() => {
-    return !trsUrl.value;
-});
-
-const importTooltip = computed(() => {
-    return isImportDisabled.value ? "You must provide a TRS URL." : "Import workflow from TRS URL";
-});
-
 // Validation state for wizard mode
 const isValid = computed(() => {
     return trsUrl.value !== null && trsUrl.value !== undefined && trsUrl.value.length > 0;
@@ -42,11 +30,6 @@ watch(
     { immediate: true },
 );
 
-// Hide submit button in wizard mode (or when hideSubmitButton is true)
-const showSubmitButton = computed(() => {
-    return !props.hideSubmitButton;
-});
-
 function submit(ev: SubmitEvent) {
     ev.preventDefault();
 
@@ -67,22 +50,9 @@ defineExpose({ triggerImport });
 
 <template>
     <BForm class="mt-4" @submit="submit">
-        <h2 class="h-sm">Import from TRS URL</h2>
-
         <BFormGroup label="TRS URL:" label-class="font-weight-bold">
             <BFormInput id="trs-import-url-input" v-model="trsUrl" aria-label="TRS URL" type="url" />
             If the workflow is accessible via a TRS URL, enter the URL above and click Import.
         </BFormGroup>
-
-        <GButton
-            v-if="showSubmitButton"
-            id="trs-url-import-button"
-            type="submit"
-            :disabled="isImportDisabled"
-            :title="importTooltip"
-            tooltip
-            color="blue">
-            Import workflow
-        </GButton>
     </BForm>
 </template>

From 3821169a172d9c945b37f3d810f992e2d24bf743 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 3 Jun 2026 15:06:15 +0200
Subject: [PATCH 007/256] Update Selenium tests for workflow import wizard

Simplify workflow and TRS import tests by removing redundant clicks on the "Next" button. The import wizard now automatically navigates to the next step upon selecting an import method
---
 lib/galaxy/selenium/navigates_galaxy.py           | 14 +++++---------
 .../selenium/test_workflow_management.py          | 15 +++++----------
 2 files changed, 10 insertions(+), 19 deletions(-)

diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index 3df6ae39c27..bfb029128bf 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -385,26 +385,23 @@ class NavigatesGalaxy(HasDriverProxy[WaitType]):
         self.navigate_to(self.build_url("workflows/trs_import"))
         self.components.masthead._.wait_for_visible()
         # The wizard auto-navigates to TRS method selection on mount
-        # Click the "Search workflow registries" card then advance the wizard
+        # Clicking the "Search workflow registries" card auto-navigates to the search form
         self.components.workflows.import_trs_search_link.wait_for_and_click()
-        self.components.workflows.import_next_button.wait_for_and_click()
 
     def go_to_trs_by_id(self) -> None:
         self.navigate_to(self.build_url("workflows/trs_import"))
         self.components.masthead._.wait_for_visible()
         # The wizard auto-navigates to TRS method selection on mount
-        # Click the TRS ID sub-card then advance the wizard
+        # Clicking the TRS ID card auto-navigates to the TRS ID form
         self.components.workflows.import_trs_id_link.wait_for_and_click()
-        self.components.workflows.import_next_button.wait_for_and_click()
 
     def go_to_trs_by_url(self) -> None:
         self.navigate_to(self.build_url("workflows/trs_import"))
         self.components.masthead._.wait_for_visible()
         # The wizard auto-navigates to TRS method selection on mount
-        # Click the TRS URL sub-card then advance the wizard
+        # Clicking the TRS URL card auto-navigates to the TRS URL form
         self.components.workflows.import_trs_url_link.wait_for_and_click()
-        self.components.workflows.import_next_button.wait_for_and_click()
-        # Wait for the URL input to be visible after wizard navigates to the form
+        # Wait for the URL input to be visible after wizard auto-navigates to the form
         self.components.trs_import.url_input.wait_for_visible()
 
     def go_to_workflow_sharing(self, workflow_id: str) -> None:
@@ -2030,9 +2027,8 @@ class NavigatesGalaxy(HasDriverProxy[WaitType]):
 
     def workflow_import_submit_url(self, url):
         # Click the "Fetch URL" card to select that import method
+        # (auto-navigates to the URL input step)
         self.components.workflows.import_url_link.wait_for_and_click()
-        # Click the wizard's Next button to proceed to the URL input step
-        self.wait_for_and_click_selector(".wizard-actions .go-next-btn")
         # Enter the URL
         url_element = self.wait_for_selector_visible("#workflow-import-url-input")
         url_element.send_keys(url)
diff --git a/lib/galaxy_test/selenium/test_workflow_management.py b/lib/galaxy_test/selenium/test_workflow_management.py
index 222f1af710e..6cd04a2f50f 100644
--- a/lib/galaxy_test/selenium/test_workflow_management.py
+++ b/lib/galaxy_test/selenium/test_workflow_management.py
@@ -33,28 +33,23 @@ class TestWorkflowManagement(SeleniumTestCase, TestsGalaxyPagers, UsesWorkflowAs
         workflows = self.components.workflows
 
         self.workflow_index_click_import()
+        # Clicking the method card auto-navigates to the upload step
         workflows.import_file_link.wait_for_and_click()
-        # Click Next to navigate to the file upload view
-        self.wait_for_and_click_selector(".wizard-actions .go-next-btn")
         workflows.import_file.assert_no_axe_violations_with_impact_of_at_least("moderate")
 
         self.navigate_to_workflows_import()
+        # Clicking the TRS card auto-navigates to the TRS method selection step
         workflows.import_trs_link.wait_for_and_click()
-        # Click Next to navigate to TRS method selection
-        self.wait_for_and_click_selector(".wizard-actions .go-next-btn")
+        # Clicking the search card auto-navigates to the TRS search form
         workflows.import_trs_search_link.wait_for_and_click()
-        # Click Next to navigate to TRS search view
-        self.wait_for_and_click_selector(".wizard-actions .go-next-btn")
         # moderate violation relating to header ordering
         workflows.import_trs_search.assert_no_axe_violations_with_impact_of_at_least("serious")
 
         self.navigate_to_workflows_import()
+        # Clicking the TRS card auto-navigates to the TRS method selection step
         workflows.import_trs_link.wait_for_and_click()
-        # Click Next to navigate to TRS method selection
-        self.wait_for_and_click_selector(".wizard-actions .go-next-btn")
+        # Clicking the TRS ID card auto-navigates to the TRS ID form
         workflows.import_trs_id_link.wait_for_and_click()
-        # Click Next to navigate to TRS ID view
-        self.wait_for_and_click_selector(".wizard-actions .go-next-btn")
         # ditto - moderate violation relating to header ordering
         workflows.import_trs_id.assert_no_axe_violations_with_impact_of_at_least("serious")
 

From a23fc614af0f75130026848217e0449a0f910981 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 3 Jun 2026 15:33:46 +0200
Subject: [PATCH 008/256] Improve TRS import test reliability

Introduces a centralized helper method to manage clicking the wizard's import button. This ensures the button is enabled and clickable before interaction, accounting for delays in UI validation propagation following user input.
---
 test/integration_selenium/test_trs_import.py | 29 ++++++++++++--------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/test/integration_selenium/test_trs_import.py b/test/integration_selenium/test_trs_import.py
index 9bf28c054c5..185ad9c16cc 100644
--- a/test/integration_selenium/test_trs_import.py
+++ b/test/integration_selenium/test_trs_import.py
@@ -51,6 +51,18 @@ class TestTrsImport(SeleniumIntegrationTestCase):
     def trs_config_dir(cls):
         return cls.temp_config_dir("trs")
 
+    def _click_wizard_import_button(self, wait_for_validation=False):
+        """Click the wizard's Import button after ensuring it's enabled.
+
+        The Import button is disabled until the current step's validation passes.
+        Set wait_for_validation=True to sleep briefly before clicking (needed when
+        user input was just entered and Vue validation hasn't propagated yet).
+        """
+        if wait_for_validation:
+            self.sleep_for(self.wait_types.UX_RENDER)
+        import_button = self.wait_for_selector_clickable(".wizard-actions .go-next-btn.btn-primary:not([disabled])")
+        import_button.click()
+
     def assert_workflow_imported(self, name):
         # surround name with quotes to consider case where name contains colons
         self.workflow_index_search_for(f'"{name}"')
@@ -69,8 +81,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
         full_url = self.build_url(import_url)
         self.driver.get(full_url)
         self.components.workflows.workflow_trs_import.wait_for_visible()
-        # Wait for the wizard's Import button to become enabled and click it
-        self.components.workflows.import_next_button.wait_for_and_click()
+        self._click_wizard_import_button()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.workflow_index_open()
         self.assert_workflow_imported(WORKFLOW_NAME)
@@ -81,8 +92,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
         self.components.trs_search.search_result(
             workflow_name="galaxy-workflow-dockstore-example-1"
         ).wait_for_and_click()
-        # Wait for the wizard's Import button to become enabled and click it
-        self.components.workflows.import_next_button.wait_for_and_click()
+        self._click_wizard_import_button(wait_for_validation=True)
         self.sleep_for(self.wait_types.UX_RENDER)
         self.workflow_index_open()
         self.assert_workflow_imported("Test Workflow")
@@ -94,8 +104,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
         # Select version from dropdown
         version_select = self.components.trs_search.version_select.wait_for_visible()
         Select(version_select).select_by_visible_text("v0.4")
-        # Wait for the wizard's Import button to become enabled and click it
-        self.components.workflows.import_next_button.wait_for_and_click()
+        self._click_wizard_import_button(wait_for_validation=True)
         self.sleep_for(self.wait_types.UX_RENDER)
         self.workflow_index_open()
         self.assert_workflow_imported(WORKFLOW_NAME)
@@ -109,8 +118,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
         self.components.trs_search.select_server(server="workflowhub").wait_for_and_click()
         self.components.trs_search.search.wait_for_and_send_keys(WORKFLOW_NAME)
         self.components.trs_search.search_result(workflow_name=WORKFLOW_NAME).wait_for_and_click()
-        # Wait for the wizard's Import button to become enabled and click it
-        self.components.workflows.import_next_button.wait_for_and_click()
+        self._click_wizard_import_button(wait_for_validation=True)
         self.sleep_for(self.wait_types.UX_RENDER)
         self.workflow_index_open()
         self.assert_workflow_imported(WORKFLOW_NAME)
@@ -146,8 +154,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
         # Select version from dropdown
         version_select = self.components.trs_import.version_select.wait_for_visible()
         Select(version_select).select_by_visible_text("v0.4")
-        # Wait for the wizard's Import button to become enabled and click it
-        self.components.workflows.import_next_button.wait_for_and_click()
+        self._click_wizard_import_button(wait_for_validation=True)
         self.sleep_for(self.wait_types.UX_RENDER)
         self.workflow_index_open()
         self.assert_workflow_imported(WORKFLOW_NAME)
@@ -155,7 +162,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
     def _import_by_trs_url(self, trs_url):
         self.go_to_trs_by_url()
         self.components.trs_import.url_input.wait_for_and_send_keys(trs_url)
-        self.components.trs_import.url_import_button.wait_for_and_click()
+        self._click_wizard_import_button(wait_for_validation=True)
         self.sleep_for(self.wait_types.UX_RENDER)
         self.workflow_index_open()
         self.assert_workflow_imported(WORKFLOW_NAME)

From 1c0a47a9d2b314cb763904c23e6be9605a2ecdc3 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 27 May 2026 12:49:26 -0400
Subject: [PATCH 009/256] Add gtn_database_refresh_interval so admins can tune
 (or disable, with 0) how often Galaxy re-pulls the GTN search database from
 depot. The periodic celery task that actually does the refresh follows in a
 separate commit.

---
 doc/source/admin/galaxy_options.rst         | 88 ++++++++++++++++++++-
 lib/galaxy/config/sample/galaxy.yml.sample  | 33 ++++++--
 lib/galaxy/config/schemas/config_schema.yml | 13 +++
 3 files changed, 123 insertions(+), 11 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 6b285e7cf4e..e06967bd139 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1305,6 +1305,24 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+``tool_tag_mappings_file``
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Optional YAML file mapping tool ids to curated tag names. Tags
+    drive the `tag:` autocompletion, the favorite-tags grouping in the
+    My Tools panel, and the `tool_tags` Whoosh search field. If unset,
+    Galaxy ships a small example covering the tools used by its own
+    integration tests; admins who want production-grade tag coverage
+    can generate a snapshot for their instance with
+    `scripts/extract_tool_sections_from_api.py`. The file must be a
+    YAML document with a top-level `tool_tags:` mapping from tool id
+    to a list of tag names.
+:Default: ``None``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``biotools_content_directory``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -5663,11 +5681,76 @@
     false }, jupyterlite: { model: gpt-4o } } Set static_responses to
     a YAML file path to replace all LLM calls with deterministic
     responses for testing: inference_services: { static_responses:
-    test/integration/static_agents.yml }
+    test/integration/static_agents.yml } Per-agent or default-block
+    ``structured_output_override: true|false`` beats the model
+    capability table -- see ``agent_model_capabilities_file`` for the
+    table's location and contents.
 :Default: ``None``
 :Type: any
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``agent_model_capabilities_file``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    YAML file with capability hints for agent inference models. Maps
+    fnmatch-style globs against model names to features such as
+    structured-output (tool-calling / JSON-mode) support. Galaxy ships
+    a sample populated with common model families; admins can drop a
+    file named ``agent_model_capabilities.yml`` in ``config_dir`` to
+    override the shipped table for private models.
+    ``inference_services`` ``structured_output_override`` overrides
+    this table for a specific agent or default block.
+    The value of this option will be resolved with respect to
+    <config_dir>.
+:Default: ``agent_model_capabilities.yml``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~
+``gtn_database_path``
+~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Path to the SQLite FTS5 database used by the GTN training agent.
+    Resolves against ``data_dir`` so admins can place it in a
+    mutable-data directory. The file is downloaded automatically on
+    first use from ``gtn_database_url`` if it does not exist.
+    The value of this option will be resolved with respect to
+    <data_dir>.
+:Default: ``gtn/gtn_search.db``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~
+``gtn_database_url``
+~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    URL used to download the GTN search database when the local file
+    at ``gtn_database_path`` is missing.
+:Default: ``https://depot.galaxyproject.org/chatgxy/gtn_search.db``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``gtn_database_refresh_interval``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Time (in seconds) between celery-beat triggered refreshes of the
+    GTN search database from ``gtn_database_url``. The task
+    re-downloads the file and atomically replaces
+    ``gtn_database_path``; live handlers pick up the new copy on their
+    next query since GTNSearchDB opens a read-only connection per
+    call. Set to 0 to disable automatic refresh (admins can still
+    refresh on demand via ``python -m galaxy.agents.gtn --refresh``).
+    Requires celery.
+:Default: ``3600``
+:Type: int
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``enable_tool_recommendations``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -6163,6 +6246,3 @@
     for user defined tools.
 :Default: ``false``
 :Type: bool
-
-
-
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index d8cdb8b7d06..ced13d8d8ca 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1,21 +1,21 @@
 # Galaxy is configured by default to be usable in a single-user development
 # environment.  To tune the application for a multi-user production
 # environment, see the documentation at:
-# 
+#
 #  https://docs.galaxyproject.org/en/master/admin/production.html
-# 
+#
 # Throughout this sample configuration file, except where stated otherwise,
 # uncommented values override the default if left unset, whereas commented
 # values are set to the default value.  Relative paths are relative to the root
 # Galaxy directory.
-# 
+#
 # Examples of many of these options are explained in more detail in the Galaxy
 # Community Hub.
-# 
+#
 #   https://galaxyproject.org/admin/config
-# 
+#
 # Config hackers are encouraged to check there before asking for help.
-# 
+#
 # Configuration for Gravity process manager.
 # ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``).
 gravity:
@@ -1007,6 +1007,17 @@ galaxy:
   # this option will be resolved with respect to <data_dir>.
   #tool_search_index_dir: tool_search_index
 
+  # Optional YAML file mapping tool ids to curated tag names. Tags drive
+  # the `tag:` autocompletion, the favorite-tags grouping in the My
+  # Tools panel, and the `tool_tags` Whoosh search field. If unset,
+  # Galaxy ships a small example covering the tools used by its own
+  # integration tests; admins who want production-grade tag coverage can
+  # generate a snapshot for their instance with
+  # `scripts/extract_tool_sections_from_api.py`. The file must be a YAML
+  # document with a top-level `tool_tags:` mapping from tool id to a
+  # list of tag names.
+  #tool_tag_mappings_file: null
+
   # Point Galaxy at a repository consisting of a copy of the bio.tools
   # database (e.g. https://github.com/bio-tools/content/) to resolve
   # bio.tools data for tool metadata.
@@ -3096,6 +3107,15 @@ galaxy:
   # ``gtn_database_path`` is missing.
   #gtn_database_url: https://depot.galaxyproject.org/chatgxy/gtn_search.db
 
+  # Time (in seconds) between celery-beat triggered refreshes of the GTN
+  # search database from ``gtn_database_url``. The task re-downloads the
+  # file and atomically replaces ``gtn_database_path``; live handlers
+  # pick up the new copy on their next query since GTNSearchDB opens a
+  # read-only connection per call. Set to 0 to disable automatic refresh
+  # (admins can still refresh on demand via ``python -m
+  # galaxy.agents.gtn --refresh``). Requires celery.
+  #gtn_database_refresh_interval: 3600
+
   # Allow the display of tool recommendations in workflow editor and
   # after tool execution. If it is enabled and set to true, please
   # enable 'tool_recommendation_model_path' as well
@@ -3330,4 +3350,3 @@ galaxy:
   # Enable beta tool formats (yaml, cwl, ...) which is a prerequisite
   # for user defined tools.
   #enable_beta_tool_formats: false
-
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index c16bc6901b0..4ab687d8285 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -4243,6 +4243,19 @@ mapping:
           URL used to download the GTN search database when the local file at
           ``gtn_database_path`` is missing.
 
+      gtn_database_refresh_interval:
+        type: int
+        default: 3600
+        required: false
+        desc: |
+          Time (in seconds) between celery-beat triggered refreshes of the GTN
+          search database from ``gtn_database_url``. The task re-downloads the
+          file and atomically replaces ``gtn_database_path``; live handlers
+          pick up the new copy on their next query since GTNSearchDB opens a
+          read-only connection per call. Set to 0 to disable automatic
+          refresh (admins can still refresh on demand via
+          ``python -m galaxy.agents.gtn --refresh``). Requires celery.
+
       enable_tool_recommendations:
         type: bool
         default: false

From 73bd73cdfd4f3184c77d6fdcacdd90ba4b9001c4 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 27 May 2026 12:49:32 -0400
Subject: [PATCH 010/256] Refresh the GTN search database on a celery beat
 schedule. The task re-downloads from depot to a tmp path, validates, and
 atomically renames over the live copy -- handlers pick up the new file on the
 next query since GTNSearchDB opens read-only per call. Registration is gated
 on both the interval being non-zero and a configured gtn_database_path, so
 disabling the GTN agent doesn't leave a dangling periodic task.

---
 lib/galaxy/celery/__init__.py |  3 +++
 lib/galaxy/celery/tasks.py    | 28 ++++++++++++++++++++++++++++
 test/unit/app/test_celery.py  |  4 ++++
 3 files changed, 35 insertions(+)

diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index b580f4340f7..122a44f16a9 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -283,6 +283,9 @@ def setup_periodic_tasks(config, celery_app):
     if config.vault_token_renewal_interval:
         schedule_task("renew_vault_token", config.vault_token_renewal_interval)
 
+    if getattr(config, "gtn_database_refresh_interval", 0) and getattr(config, "gtn_database_path", None):
+        schedule_task("refresh_gtn_database", config.gtn_database_refresh_interval)
+
     if config.celery_user_concurrency_limit:
         # Run cleanup every 5 minutes (300 seconds)
         schedule_task("cleanup_stale_concurrency_slots", 300)
diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py
index 041b8201f49..41f9395f6e7 100644
--- a/lib/galaxy/celery/tasks.py
+++ b/lib/galaxy/celery/tasks.py
@@ -26,6 +26,7 @@ from sqlalchemy import (
 )
 
 from galaxy import model
+from galaxy.agents.gtn import GTNSearchDB
 from galaxy.celery import (
     celery_app,
     galaxy_task,
@@ -829,6 +830,33 @@ def renew_vault_token(vault: Vault):
     renew_vault_token_if_needed(vault)
 
 
+@galaxy_task(action="refreshing GTN training database")
+def refresh_gtn_database(config: GalaxyAppConfiguration):
+    """Re-download the GTN search database from depot, replacing the local copy atomically.
+
+    Handlers open the database read-only per query, so an atomic rename here
+    is picked up by the next ChatGXY request without a restart. Failures are
+    logged and swallowed so a depot outage doesn't kill the periodic queue.
+    """
+    db_path = getattr(config, "gtn_database_path", None)
+    if not db_path:
+        log.debug("refresh_gtn_database: gtn_database_path is unset, skipping")
+        return
+    download_url = getattr(config, "gtn_database_url", None)
+    try:
+        metadata = GTNSearchDB.refresh_database(db_path, download_url)
+    except FileNotFoundError as e:
+        log.warning("refresh_gtn_database: download failed, keeping existing copy: %s", e)
+        return
+    log.info(
+        "refresh_gtn_database: refreshed %s (version=%s, tutorials=%s, faqs=%s)",
+        db_path,
+        metadata["version"],
+        metadata["tutorial_count"],
+        metadata["faq_count"],
+    )
+
+
 @galaxy_task(action="execute workflow completion hook")
 def execute_workflow_completion_hook(
     invocation_id: int,
diff --git a/test/unit/app/test_celery.py b/test/unit/app/test_celery.py
index db16b23b4b8..490d3ac603d 100644
--- a/test/unit/app/test_celery.py
+++ b/test/unit/app/test_celery.py
@@ -26,6 +26,10 @@ def test_default_configuration():
         "task": "galaxy.cleanup_short_term_storage",
         "schedule": galaxy_conf.short_term_storage_cleanup_interval,
     }
+    assert conf.beat_schedule["refresh-gtn-database"] == {
+        "task": "galaxy.refresh_gtn_database",
+        "schedule": galaxy_conf.gtn_database_refresh_interval,
+    }
 
 
 def test_galaxycelery_trim_module_name():

From 8875431e1a6a04b7b3f490f787062c17c08f4f04 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 27 May 2026 13:48:08 -0400
Subject: [PATCH 011/256] Gate the GTN refresh schedule on inference_services
 being configured. Without it, the default config would have every Galaxy
 install pulling from depot on the schedule even though most don't use
 ChatGXY. Same predicate the agent registry already uses to decide whether the
 GTN agent is registered at all.

---
 lib/galaxy/celery/__init__.py | 10 +++++++++-
 test/unit/app/test_celery.py  | 15 +++++++++++++--
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index 122a44f16a9..956d4885eed 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -283,7 +283,15 @@ def setup_periodic_tasks(config, celery_app):
     if config.vault_token_renewal_interval:
         schedule_task("renew_vault_token", config.vault_token_renewal_interval)
 
-    if getattr(config, "gtn_database_refresh_interval", 0) and getattr(config, "gtn_database_path", None):
+    # Only schedule if ChatGXY infrastructure is configured -- the GTN database
+    # serves the gtn_training agent, which only functions when inference_services
+    # is set up. Without this gate every Galaxy install would pull from depot
+    # on the default interval, even ones that don't use the agent.
+    if (
+        getattr(config, "inference_services", None)
+        and config.gtn_database_refresh_interval
+        and config.gtn_database_path
+    ):
         schedule_task("refresh_gtn_database", config.gtn_database_refresh_interval)
 
     if config.celery_user_concurrency_limit:
diff --git a/test/unit/app/test_celery.py b/test/unit/app/test_celery.py
index 490d3ac603d..48dbc02ea6d 100644
--- a/test/unit/app/test_celery.py
+++ b/test/unit/app/test_celery.py
@@ -2,6 +2,7 @@ from galaxy.celery import (
     celery_app,
     DEFAULT_TASK_QUEUE,
     GalaxyCelery,
+    setup_periodic_tasks,
     TASKS_MODULES,
 )
 from galaxy.config import GalaxyAppConfiguration
@@ -26,9 +27,19 @@ def test_default_configuration():
         "task": "galaxy.cleanup_short_term_storage",
         "schedule": galaxy_conf.short_term_storage_cleanup_interval,
     }
-    assert conf.beat_schedule["refresh-gtn-database"] == {
+    # GTN refresh is gated on inference_services being configured; default
+    # config doesn't set it, so the schedule isn't registered here.
+    assert "refresh-gtn-database" not in conf.beat_schedule
+
+
+def test_gtn_refresh_schedules_when_inference_configured():
+    config = GalaxyAppConfiguration(override_tempdir=False)
+    config.inference_services = {"default": {"model": "test"}}
+    app = GalaxyCelery("test-gtn-schedule")
+    setup_periodic_tasks(config, app)
+    assert app.conf.beat_schedule["refresh-gtn-database"] == {
         "task": "galaxy.refresh_gtn_database",
-        "schedule": galaxy_conf.gtn_database_refresh_interval,
+        "schedule": config.gtn_database_refresh_interval,
     }
 
 

From 464a9a0b83d84c276df54c2e1e254980b8dae78c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 27 May 2026 13:49:24 -0400
Subject: [PATCH 012/256] HEAD depot first and only re-download when its
 Last-Modified is newer than the local file. After each successful download
 the local mtime is stamped to depot's Last-Modified so future comparisons are
 exact and survive local clock skew. Raises the default refresh interval to
 once a day -- the dataset updates weekly or so, and the HEAD check keeps
 steady-state cost to a few hundred bytes per tick regardless.

---
 doc/source/admin/galaxy_options.rst         | 17 ++--
 lib/galaxy/agents/gtn/search.py             | 70 ++++++++++++++++
 lib/galaxy/celery/tasks.py                  | 17 ++--
 lib/galaxy/config/sample/galaxy.yml.sample  | 20 +++--
 lib/galaxy/config/schemas/config_schema.yml | 20 +++--
 test/unit/app/test_gtn_search.py            | 90 +++++++++++++++++++++
 6 files changed, 205 insertions(+), 29 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index e06967bd139..4608e85d32b 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -5739,15 +5739,18 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Time (in seconds) between celery-beat triggered refreshes of the
-    GTN search database from ``gtn_database_url``. The task
-    re-downloads the file and atomically replaces
+    Time (in seconds) between celery-beat triggered freshness checks
+    of the GTN search database from ``gtn_database_url``. The task
+    HEADs depot and only re-downloads when its ``Last-Modified`` is
+    newer than the local file -- steady-state cost is a few hundred
+    bytes per tick. When a download does happen it atomically replaces
     ``gtn_database_path``; live handlers pick up the new copy on their
     next query since GTNSearchDB opens a read-only connection per
-    call. Set to 0 to disable automatic refresh (admins can still
-    refresh on demand via ``python -m galaxy.agents.gtn --refresh``).
-    Requires celery.
-:Default: ``3600``
+    call. Only registered when ``inference_services`` is configured
+    (i.e. ChatGXY is in use). Set to 0 to disable automatic refresh --
+    admins can still refresh on demand via ``python -m
+    galaxy.agents.gtn --refresh``. Requires celery.
+:Default: ``86400``
 :Type: int
 
 
diff --git a/lib/galaxy/agents/gtn/search.py b/lib/galaxy/agents/gtn/search.py
index 04da9448130..d4ed28d2386 100644
--- a/lib/galaxy/agents/gtn/search.py
+++ b/lib/galaxy/agents/gtn/search.py
@@ -6,11 +6,18 @@ using SQLite FTS5 full-text search with BM25 ranking.
 """
 
 import logging
+import os
 import re
 import shutil
 import sqlite3
 import urllib.request
 from dataclasses import dataclass
+from datetime import (
+    datetime,
+    timedelta,
+    timezone,
+)
+from email.utils import parsedate_to_datetime
 from pathlib import Path
 from typing import (
     Any,
@@ -24,10 +31,28 @@ GTN_FAQ_BASE_URL = "https://training.galaxyproject.org/training-material/faqs"
 # an agent init forever. Total wall-clock can still exceed this if the
 # remote keeps sending small chunks, which is the trade for stdlib-only.
 GTN_DOWNLOAD_TIMEOUT_SECONDS = 60
+# HEAD is a small request; an unreachable depot during a freshness check
+# shouldn't hold the periodic queue for the full download budget.
+GTN_FRESHNESS_TIMEOUT_SECONDS = 10
+
+_ONE_SECOND = timedelta(seconds=1)
 
 log = logging.getLogger(__name__)
 
 
+def _parse_last_modified(header: Optional[str]) -> Optional[datetime]:
+    """Parse an HTTP Last-Modified header into an aware UTC datetime, or None."""
+    if not header:
+        return None
+    try:
+        parsed = parsedate_to_datetime(header)
+    except (TypeError, ValueError):
+        return None
+    if parsed.tzinfo is None:
+        parsed = parsed.replace(tzinfo=timezone.utc)
+    return parsed
+
+
 def _escape_like(value: str) -> str:
     """Escape SQLite LIKE metacharacters so tool names match literally."""
     return value.replace("\\", "\\\\").replace("%", r"\%").replace("_", r"\_")
@@ -194,6 +219,43 @@ class GTNSearchDB:
         """Download, validate, and atomically replace a GTN database without opening the old copy."""
         return cls._download_database_to_path(Path(db_path), download_url or GTN_DATABASE_URL)
 
+    @classmethod
+    def refresh_database_if_stale(
+        cls, db_path: str | Path, download_url: Optional[str] = None
+    ) -> Optional[dict[str, Any]]:
+        """HEAD the URL and re-download only if its Last-Modified is newer than the local file's mtime.
+
+        Returns the new metadata dict when a refresh happened, ``None`` when the
+        local copy was current. If the local file is missing, or the HEAD fails,
+        falls through to a full download -- safer than skipping silently when we
+        can't tell whether the local copy is current.
+        """
+        target = Path(db_path)
+        url = download_url or GTN_DATABASE_URL
+
+        if target.exists():
+            remote_mtime = cls._remote_last_modified(url)
+            if remote_mtime is not None:
+                local_mtime = datetime.fromtimestamp(target.stat().st_mtime, tz=timezone.utc)
+                # depot's Last-Modified has second resolution; the 1-second slack
+                # absorbs rounding so a successful refresh isn't immediately re-triggered.
+                if remote_mtime <= local_mtime + _ONE_SECOND:
+                    return None
+
+        return cls._download_database_to_path(target, url)
+
+    @staticmethod
+    def _remote_last_modified(url: str) -> Optional[datetime]:
+        """HEAD ``url`` and return its parsed Last-Modified, or None on failure."""
+        try:
+            req = urllib.request.Request(url, method="HEAD")
+            with urllib.request.urlopen(req, timeout=GTN_FRESHNESS_TIMEOUT_SECONDS) as resp:
+                header = resp.headers.get("Last-Modified")
+        except (OSError, ValueError) as e:
+            log.debug(f"GTN freshness HEAD failed for {url}: {e}")
+            return None
+        return _parse_last_modified(header)
+
     @classmethod
     def _download_database_to_path(cls, db_path: Path, download_url: str) -> dict[str, Any]:
         db_path.parent.mkdir(parents=True, exist_ok=True)
@@ -202,9 +264,17 @@ class GTNSearchDB:
         try:
             log.info(f"Downloading GTN database from {download_url} ...")
             with urllib.request.urlopen(download_url, timeout=GTN_DOWNLOAD_TIMEOUT_SECONDS) as response:
+                last_modified_header = response.headers.get("Last-Modified")
                 with open(tmp_path, "wb") as out:
                     shutil.copyfileobj(response, out)
             metadata = cls._validate_database_file(tmp_path)
+            # Stamp the file with depot's Last-Modified so the next stale check
+            # compares against the upstream mtime rather than "right now", which
+            # would also drift with any local clock skew.
+            remote_dt = _parse_last_modified(last_modified_header)
+            if remote_dt is not None:
+                remote_ts = remote_dt.timestamp()
+                os.utime(tmp_path, (remote_ts, remote_ts))
             tmp_path.replace(db_path)
             return metadata
         except (OSError, sqlite3.Error) as e:
diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py
index 41f9395f6e7..44ec4f7db72 100644
--- a/lib/galaxy/celery/tasks.py
+++ b/lib/galaxy/celery/tasks.py
@@ -832,22 +832,27 @@ def renew_vault_token(vault: Vault):
 
 @galaxy_task(action="refreshing GTN training database")
 def refresh_gtn_database(config: GalaxyAppConfiguration):
-    """Re-download the GTN search database from depot, replacing the local copy atomically.
+    """HEAD depot for the GTN search database and re-download only when newer.
 
     Handlers open the database read-only per query, so an atomic rename here
-    is picked up by the next ChatGXY request without a restart. Failures are
-    logged and swallowed so a depot outage doesn't kill the periodic queue.
+    is picked up by the next ChatGXY request without a restart. The HEAD-first
+    pattern keeps the steady-state cost to a few hundred bytes per tick --
+    only when depot has actually been updated do we pull the full ~17MB.
+    Failures are logged and swallowed so a depot outage doesn't kill the
+    periodic queue.
     """
-    db_path = getattr(config, "gtn_database_path", None)
+    db_path = config.gtn_database_path
     if not db_path:
         log.debug("refresh_gtn_database: gtn_database_path is unset, skipping")
         return
-    download_url = getattr(config, "gtn_database_url", None)
     try:
-        metadata = GTNSearchDB.refresh_database(db_path, download_url)
+        metadata = GTNSearchDB.refresh_database_if_stale(db_path, config.gtn_database_url)
     except FileNotFoundError as e:
         log.warning("refresh_gtn_database: download failed, keeping existing copy: %s", e)
         return
+    if metadata is None:
+        log.debug("refresh_gtn_database: %s is current, no download needed", db_path)
+        return
     log.info(
         "refresh_gtn_database: refreshed %s (version=%s, tutorials=%s, faqs=%s)",
         db_path,
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index ced13d8d8ca..dec50bd87a9 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -3107,14 +3107,18 @@ galaxy:
   # ``gtn_database_path`` is missing.
   #gtn_database_url: https://depot.galaxyproject.org/chatgxy/gtn_search.db
 
-  # Time (in seconds) between celery-beat triggered refreshes of the GTN
-  # search database from ``gtn_database_url``. The task re-downloads the
-  # file and atomically replaces ``gtn_database_path``; live handlers
-  # pick up the new copy on their next query since GTNSearchDB opens a
-  # read-only connection per call. Set to 0 to disable automatic refresh
-  # (admins can still refresh on demand via ``python -m
-  # galaxy.agents.gtn --refresh``). Requires celery.
-  #gtn_database_refresh_interval: 3600
+  # Time (in seconds) between celery-beat triggered freshness checks of
+  # the GTN search database from ``gtn_database_url``. The task HEADs
+  # depot and only re-downloads when its ``Last-Modified`` is newer than
+  # the local file -- steady-state cost is a few hundred bytes per tick.
+  # When a download does happen it atomically replaces
+  # ``gtn_database_path``; live handlers pick up the new copy on their
+  # next query since GTNSearchDB opens a read-only connection per call.
+  # Only registered when ``inference_services`` is configured (i.e.
+  # ChatGXY is in use). Set to 0 to disable automatic refresh -- admins
+  # can still refresh on demand via ``python -m galaxy.agents.gtn
+  # --refresh``. Requires celery.
+  #gtn_database_refresh_interval: 86400
 
   # Allow the display of tool recommendations in workflow editor and
   # after tool execution. If it is enabled and set to true, please
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index 4ab687d8285..4b7e493fd35 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -4245,16 +4245,20 @@ mapping:
 
       gtn_database_refresh_interval:
         type: int
-        default: 3600
+        default: 86400
         required: false
         desc: |
-          Time (in seconds) between celery-beat triggered refreshes of the GTN
-          search database from ``gtn_database_url``. The task re-downloads the
-          file and atomically replaces ``gtn_database_path``; live handlers
-          pick up the new copy on their next query since GTNSearchDB opens a
-          read-only connection per call. Set to 0 to disable automatic
-          refresh (admins can still refresh on demand via
-          ``python -m galaxy.agents.gtn --refresh``). Requires celery.
+          Time (in seconds) between celery-beat triggered freshness checks of
+          the GTN search database from ``gtn_database_url``. The task HEADs
+          depot and only re-downloads when its ``Last-Modified`` is newer than
+          the local file -- steady-state cost is a few hundred bytes per tick.
+          When a download does happen it atomically replaces
+          ``gtn_database_path``; live handlers pick up the new copy on their
+          next query since GTNSearchDB opens a read-only connection per call.
+          Only registered when ``inference_services`` is configured (i.e.
+          ChatGXY is in use). Set to 0 to disable automatic refresh -- admins
+          can still refresh on demand via
+          ``python -m galaxy.agents.gtn --refresh``. Requires celery.
 
       enable_tool_recommendations:
         type: bool
diff --git a/test/unit/app/test_gtn_search.py b/test/unit/app/test_gtn_search.py
index d33c458627a..43dd72f1d9b 100644
--- a/test/unit/app/test_gtn_search.py
+++ b/test/unit/app/test_gtn_search.py
@@ -5,7 +5,13 @@ result types against tiny in-memory fixture databases built via
 GTNDatabaseBuilder.
 """
 
+import os
 import sqlite3
+from datetime import (
+    datetime,
+    timedelta,
+    timezone,
+)
 from pathlib import Path
 
 import pytest
@@ -217,3 +223,87 @@ def test_refresh_database_rejects_invalid_payload(tmp_path: Path):
 
     # Target was not replaced with the bogus payload.
     assert target.read_text(errors="replace") != "not a sqlite database"
+
+
+def _build_fixture_db(target: Path, marker_title: str) -> None:
+    """Build a tiny valid GTN DB whose only tutorial title is ``marker_title``."""
+    builder = GTNDatabaseBuilder(gtn_path=target.parent, output_path=target)
+    builder.tutorials = [
+        Tutorial(
+            topic="freshness",
+            tutorial="marker",
+            title=marker_title,
+            description="",
+            url="https://example.invalid",
+            content="content",
+            content_hash="hash",
+        )
+    ]
+    builder.create_database()
+    builder.insert_tutorials()
+    builder.add_metadata()
+
+
+def _tutorial_titles(db_path: Path) -> list[str]:
+    with sqlite3.connect(f"file:{db_path}?mode=ro", uri=True) as conn:
+        return [row[0] for row in conn.execute("SELECT title FROM tutorials")]
+
+
+def test_refresh_database_if_stale_downloads_when_remote_is_newer(tmp_path: Path):
+    remote_path = tmp_path / "remote.db"
+    local_path = tmp_path / "local.db"
+    _build_fixture_db(remote_path, "REMOTE")
+    _build_fixture_db(local_path, "LOCAL")
+
+    # Push local mtime well into the past so remote is unambiguously newer.
+    past = (datetime.now(timezone.utc) - timedelta(days=30)).timestamp()
+    os.utime(local_path, (past, past))
+
+    metadata = GTNSearchDB.refresh_database_if_stale(local_path, remote_path.as_uri())
+
+    assert metadata is not None
+    assert _tutorial_titles(local_path) == ["REMOTE"]
+
+
+def test_refresh_database_if_stale_skips_when_local_is_current(tmp_path: Path):
+    remote_path = tmp_path / "remote.db"
+    local_path = tmp_path / "local.db"
+    _build_fixture_db(remote_path, "REMOTE")
+    _build_fixture_db(local_path, "LOCAL")
+
+    # Push remote into the past so local always looks current.
+    past = (datetime.now(timezone.utc) - timedelta(days=30)).timestamp()
+    os.utime(remote_path, (past, past))
+
+    local_mtime_before = local_path.stat().st_mtime
+    metadata = GTNSearchDB.refresh_database_if_stale(local_path, remote_path.as_uri())
+
+    assert metadata is None
+    assert _tutorial_titles(local_path) == ["LOCAL"]
+    assert local_path.stat().st_mtime == local_mtime_before
+
+
+def test_refresh_database_if_stale_downloads_when_local_is_missing(tmp_path: Path):
+    remote_path = tmp_path / "remote.db"
+    _build_fixture_db(remote_path, "REMOTE")
+    local_path = tmp_path / "cold-start.db"
+
+    metadata = GTNSearchDB.refresh_database_if_stale(local_path, remote_path.as_uri())
+
+    assert metadata is not None
+    assert local_path.exists()
+    assert _tutorial_titles(local_path) == ["REMOTE"]
+
+
+def test_download_stamps_local_mtime_to_remote_last_modified(tmp_path: Path):
+    remote_path = tmp_path / "remote.db"
+    _build_fixture_db(remote_path, "REMOTE")
+    # Pin the remote file's mtime to a known past second so we can assert
+    # the local copy ends up with the same second after download.
+    pinned = (datetime.now(timezone.utc) - timedelta(days=7)).replace(microsecond=0).timestamp()
+    os.utime(remote_path, (pinned, pinned))
+
+    local_path = tmp_path / "local.db"
+    GTNSearchDB.refresh_database(local_path, remote_path.as_uri())
+
+    assert int(local_path.stat().st_mtime) == int(pinned)

From 6cbeadef9e49dda04d30de7f6c84fd58811769ce Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 27 May 2026 16:28:06 -0400
Subject: [PATCH 013/256] Broaden the freshness HEAD catch to include
 http.client.HTTPException. Malformed responses from depot
 (RemoteDisconnected, BadStatusLine) aren't subclasses of OSError so they'd
 escape past the (OSError, ValueError) catch, propagate through
 refresh_database_if_stale to the periodic task, and record a failed run
 instead of falling through to a full download.

---
 lib/galaxy/agents/gtn/search.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/agents/gtn/search.py b/lib/galaxy/agents/gtn/search.py
index d4ed28d2386..77aad0a543d 100644
--- a/lib/galaxy/agents/gtn/search.py
+++ b/lib/galaxy/agents/gtn/search.py
@@ -5,6 +5,7 @@ Provides search over Galaxy Training Network tutorials and FAQs
 using SQLite FTS5 full-text search with BM25 ranking.
 """
 
+import http.client
 import logging
 import os
 import re
@@ -251,7 +252,11 @@ class GTNSearchDB:
             req = urllib.request.Request(url, method="HEAD")
             with urllib.request.urlopen(req, timeout=GTN_FRESHNESS_TIMEOUT_SECONDS) as resp:
                 header = resp.headers.get("Last-Modified")
-        except (OSError, ValueError) as e:
+        except (OSError, ValueError, http.client.HTTPException) as e:
+            # http.client.HTTPException covers malformed responses
+            # (RemoteDisconnected, BadStatusLine) that urllib doesn't wrap
+            # into URLError -- without it the periodic queue would record a
+            # failed run instead of falling through to a full download.
             log.debug(f"GTN freshness HEAD failed for {url}: {e}")
             return None
         return _parse_last_modified(header)

From fdfa892459be7a189ec0b7b55a5136e9a13dde83 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 27 May 2026 17:17:36 -0400
Subject: [PATCH 014/256] Add iwc_manifest_refresh_interval so admins can tune
 (or disable, with 0) how often Galaxy pre-warms the IWC workflow manifest
 cache. Default of 3600 matches the in-process TTL so the cache stays
 continuously warm rather than expiring between user-driven hits. The periodic
 celery task follows in a separate commit.

---
 doc/source/admin/galaxy_options.rst         | 18 ++++++++++++++++++
 lib/galaxy/config/sample/galaxy.yml.sample  | 11 +++++++++++
 lib/galaxy/config/schemas/config_schema.yml | 15 +++++++++++++++
 3 files changed, 44 insertions(+)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 4608e85d32b..d0e3ce3a5ec 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -5754,6 +5754,24 @@
 :Type: int
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``iwc_manifest_refresh_interval``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Time (in seconds) between celery-beat triggered refreshes of the
+    in-process IWC workflow manifest cache used by the agent-ops
+    layer. Default matches the cache's in-process TTL so the cache
+    stays continuously warm rather than expiring between user-driven
+    hits. Failures are logged and the prior cached copy is retained.
+    Only registered when ``inference_services`` is configured (i.e.
+    ChatGXY is in use). Set to 0 to disable automatic refresh --
+    agent-ops callers will then fall back to lazy on-demand fetching
+    with the same hour TTL. Requires celery.
+:Default: ``3600``
+:Type: int
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``enable_tool_recommendations``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index dec50bd87a9..cb3502f35a2 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -3120,6 +3120,17 @@ galaxy:
   # --refresh``. Requires celery.
   #gtn_database_refresh_interval: 86400
 
+  # Time (in seconds) between celery-beat triggered refreshes of the
+  # in-process IWC workflow manifest cache used by the agent-ops layer.
+  # Default matches the cache's in-process TTL so the cache stays
+  # continuously warm rather than expiring between user-driven hits.
+  # Failures are logged and the prior cached copy is retained. Only
+  # registered when ``inference_services`` is configured (i.e. ChatGXY
+  # is in use). Set to 0 to disable automatic refresh -- agent-ops
+  # callers will then fall back to lazy on-demand fetching with the same
+  # hour TTL. Requires celery.
+  #iwc_manifest_refresh_interval: 3600
+
   # Allow the display of tool recommendations in workflow editor and
   # after tool execution. If it is enabled and set to true, please
   # enable 'tool_recommendation_model_path' as well
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index 4b7e493fd35..a365f988fd8 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -4260,6 +4260,21 @@ mapping:
           can still refresh on demand via
           ``python -m galaxy.agents.gtn --refresh``. Requires celery.
 
+      iwc_manifest_refresh_interval:
+        type: int
+        default: 3600
+        required: false
+        desc: |
+          Time (in seconds) between celery-beat triggered refreshes of the
+          in-process IWC workflow manifest cache used by the agent-ops layer.
+          Default matches the cache's in-process TTL so the cache stays
+          continuously warm rather than expiring between user-driven hits.
+          Failures are logged and the prior cached copy is retained. Only
+          registered when ``inference_services`` is configured (i.e. ChatGXY
+          is in use). Set to 0 to disable automatic refresh -- agent-ops
+          callers will then fall back to lazy on-demand fetching with the
+          same hour TTL. Requires celery.
+
       enable_tool_recommendations:
         type: bool
         default: false

From d273c9d6c8d3d8a3a06e86b6902d8519e06cc694 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 27 May 2026 17:17:54 -0400
Subject: [PATCH 015/256] Pre-warm the IWC workflow manifest cache on a celery
 beat schedule. The new refresh_manifest helper in iwc.py is a force-fetch
 sibling of fetch_manifest that holds the cache lock across the network call,
 so concurrent on-demand readers see either the previous value or the new one
 but never an empty cache mid-write. The celery task wraps it with the
 periodic-task error contract (swallow failures, retain prior copy).
 Registration uses the same inference_services gate as the GTN refresh -- IWC
 pre-warm only matters when the agent-ops layer is exposed.

---
 lib/galaxy/agents/iwc.py      | 21 ++++++++++++++++++
 lib/galaxy/celery/__init__.py |  5 +++++
 lib/galaxy/celery/tasks.py    | 23 ++++++++++++++++++++
 test/unit/agents/test_iwc.py  | 41 +++++++++++++++++++++++++++++++++++
 test/unit/app/test_celery.py  | 16 ++++++++++++--
 5 files changed, 104 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/agents/iwc.py b/lib/galaxy/agents/iwc.py
index b65da114178..f3a46016447 100644
--- a/lib/galaxy/agents/iwc.py
+++ b/lib/galaxy/agents/iwc.py
@@ -53,6 +53,27 @@ def fetch_manifest(timeout: float = 30.0) -> list[dict[str, Any]]:
         return manifest
 
 
+def refresh_manifest(timeout: float = 30.0) -> list[dict[str, Any]]:
+    """Force-fetch the manifest and replace the cached entry.
+
+    Used by the celery-beat pre-warm task. The lock is held across the
+    network fetch so a concurrent on-demand call from a request handler
+    sees either the previous value or the new one -- never an empty cache
+    mid-write. Kept as a separate function from ``fetch_manifest`` because
+    the error contracts differ: lazy fetch propagates (caller can't
+    continue without the data); this one is called from a periodic task
+    that has to tolerate transient failure.
+    """
+    with _manifest_cache_lock:
+        response = requests.get(IWC_MANIFEST_URL, timeout=timeout)
+        response.raise_for_status()
+        manifest = response.json()
+        if not isinstance(manifest, list):
+            raise ValueError(f"IWC manifest at {IWC_MANIFEST_URL} did not return a JSON array")
+        _manifest_cache[_CACHE_KEY] = manifest
+        return manifest
+
+
 def all_workflows(manifest: list[dict[str, Any]]) -> list[dict[str, Any]]:
     """Flatten the manifest into a single list of workflow entries."""
     workflows: list[dict[str, Any]] = []
diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index 956d4885eed..5759384c97c 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -294,6 +294,11 @@ def setup_periodic_tasks(config, celery_app):
     ):
         schedule_task("refresh_gtn_database", config.gtn_database_refresh_interval)
 
+    # IWC manifest pre-warm only matters when the agent-ops layer is exposed --
+    # same inference_services gate as the GTN refresh above.
+    if getattr(config, "inference_services", None) and config.iwc_manifest_refresh_interval:
+        schedule_task("refresh_iwc_manifest", config.iwc_manifest_refresh_interval)
+
     if config.celery_user_concurrency_limit:
         # Run cleanup every 5 minutes (300 seconds)
         schedule_task("cleanup_stale_concurrency_slots", 300)
diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py
index 44ec4f7db72..17826ef1d68 100644
--- a/lib/galaxy/celery/tasks.py
+++ b/lib/galaxy/celery/tasks.py
@@ -830,6 +830,29 @@ def renew_vault_token(vault: Vault):
     renew_vault_token_if_needed(vault)
 
 
+@galaxy_task(action="refreshing IWC workflow manifest cache")
+def refresh_iwc_manifest(config: GalaxyAppConfiguration):
+    """Pre-warm the in-process IWC manifest cache.
+
+    The agent-ops layer caches the manifest at module scope with an hour
+    TTL; without this task the first user-driven IWC call after a worker
+    restart pays the full network fetch. Failures are logged and swallowed
+    so an iwc.galaxyproject.org outage doesn't kill the periodic queue --
+    on-demand callers still get the prior cached copy until the TTL lapses.
+    """
+    # Local import keeps the iwc module (and its cachetools / requests
+    # imports) out of celery's startup graph -- they only load on the
+    # workers that actually run this task.
+    from galaxy.agents import iwc
+
+    try:
+        manifest = iwc.refresh_manifest()
+    except Exception as e:  # noqa: BLE001 -- best-effort warm; resilience over precision
+        log.warning("refresh_iwc_manifest: fetch failed, keeping existing cache: %s", e)
+        return
+    log.info("refresh_iwc_manifest: cached %s top-level manifest entries", len(manifest))
+
+
 @galaxy_task(action="refreshing GTN training database")
 def refresh_gtn_database(config: GalaxyAppConfiguration):
     """HEAD depot for the GTN search database and re-download only when newer.
diff --git a/test/unit/agents/test_iwc.py b/test/unit/agents/test_iwc.py
index 337b1cf0e8e..bf716f0f677 100644
--- a/test/unit/agents/test_iwc.py
+++ b/test/unit/agents/test_iwc.py
@@ -48,6 +48,47 @@ def test_fetch_manifest_caches_response():
     assert mock_get.call_count == 1
 
 
+def test_refresh_manifest_replaces_cached_value():
+    with patch("galaxy.agents.iwc.requests.get") as mock_get:
+        mock_get.return_value.json.return_value = SAMPLE_MANIFEST
+        mock_get.return_value.raise_for_status.return_value = None
+
+        first = iwc.refresh_manifest()
+        assert first == SAMPLE_MANIFEST
+
+        new_manifest = [{"workflows": [{"trsID": "#workflow/x/y/main"}]}]
+        mock_get.return_value.json.return_value = new_manifest
+
+        second = iwc.refresh_manifest()
+        assert second == new_manifest
+        # And the next on-demand fetch sees the refreshed value
+        assert iwc.fetch_manifest() == new_manifest
+
+
+def test_refresh_manifest_failure_leaves_prior_cache():
+    with patch("galaxy.agents.iwc.requests.get") as mock_get:
+        mock_get.return_value.json.return_value = SAMPLE_MANIFEST
+        mock_get.return_value.raise_for_status.return_value = None
+        iwc.fetch_manifest()  # prime the cache
+
+        mock_get.side_effect = RuntimeError("boom")
+        with pytest.raises(RuntimeError):
+            iwc.refresh_manifest()
+
+        # fetch_manifest still returns the previously-cached value
+        mock_get.side_effect = None
+        assert iwc.fetch_manifest() == SAMPLE_MANIFEST
+
+
+def test_refresh_manifest_rejects_non_list_payload():
+    with patch("galaxy.agents.iwc.requests.get") as mock_get:
+        mock_get.return_value.json.return_value = {"not": "a list"}
+        mock_get.return_value.raise_for_status.return_value = None
+
+        with pytest.raises(ValueError, match="did not return a JSON array"):
+            iwc.refresh_manifest()
+
+
 def test_clean_readme_summary_strips_headers_and_truncates():
     body = "First line that has plenty of content. Second line continues the thought. "
     readme = "# Heading\n\n" + (body * 10)
diff --git a/test/unit/app/test_celery.py b/test/unit/app/test_celery.py
index 48dbc02ea6d..bf2bcb1d040 100644
--- a/test/unit/app/test_celery.py
+++ b/test/unit/app/test_celery.py
@@ -27,9 +27,10 @@ def test_default_configuration():
         "task": "galaxy.cleanup_short_term_storage",
         "schedule": galaxy_conf.short_term_storage_cleanup_interval,
     }
-    # GTN refresh is gated on inference_services being configured; default
-    # config doesn't set it, so the schedule isn't registered here.
+    # GTN and IWC refreshes are gated on inference_services being configured;
+    # default config doesn't set it, so neither schedule is registered here.
     assert "refresh-gtn-database" not in conf.beat_schedule
+    assert "refresh-iwc-manifest" not in conf.beat_schedule
 
 
 def test_gtn_refresh_schedules_when_inference_configured():
@@ -43,6 +44,17 @@ def test_gtn_refresh_schedules_when_inference_configured():
     }
 
 
+def test_iwc_refresh_schedules_when_inference_configured():
+    config = GalaxyAppConfiguration(override_tempdir=False)
+    config.inference_services = {"default": {"model": "test"}}
+    app = GalaxyCelery("test-iwc-schedule")
+    setup_periodic_tasks(config, app)
+    assert app.conf.beat_schedule["refresh-iwc-manifest"] == {
+        "task": "galaxy.refresh_iwc_manifest",
+        "schedule": config.iwc_manifest_refresh_interval,
+    }
+
+
 def test_galaxycelery_trim_module_name():
     gc = GalaxyCelery()
     assert gc.trim_module_name("notgalaxy.celery.tasks") == "notgalaxy.celery.tasks"

From 1b0d08bd5b4fac803e334138d62c11a87c308cdf Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 29 May 2026 07:33:25 -0400
Subject: [PATCH 016/256] Fetch the IWC manifest outside the cache lock

refresh_manifest held _manifest_cache_lock across the network fetch, so a
slow or hanging iwc.galaxyproject.org would block on-demand fetch_manifest
readers (the agent-ops request handlers) for up to the full timeout even
though a good cached copy was sitting right there. Move the GET and
validation outside the lock and only hold it for the single-assignment
write. A concurrent reader still sees either the previous value or the new
one -- never an empty cache mid-write -- but no longer waits behind the
beat task's network round-trip.
---
 lib/galaxy/agents/iwc.py | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/agents/iwc.py b/lib/galaxy/agents/iwc.py
index f3a46016447..14a1c6e7b12 100644
--- a/lib/galaxy/agents/iwc.py
+++ b/lib/galaxy/agents/iwc.py
@@ -56,22 +56,24 @@ def fetch_manifest(timeout: float = 30.0) -> list[dict[str, Any]]:
 def refresh_manifest(timeout: float = 30.0) -> list[dict[str, Any]]:
     """Force-fetch the manifest and replace the cached entry.
 
-    Used by the celery-beat pre-warm task. The lock is held across the
-    network fetch so a concurrent on-demand call from a request handler
-    sees either the previous value or the new one -- never an empty cache
-    mid-write. Kept as a separate function from ``fetch_manifest`` because
+    Used by the celery-beat pre-warm task. The network fetch runs outside
+    the cache lock so a slow or hanging iwc.galaxyproject.org doesn't block
+    on-demand ``fetch_manifest`` readers -- they keep getting the previous
+    cached copy. Only the single-assignment cache write is locked, so a
+    concurrent reader sees either the previous value or the new one, never
+    an empty cache mid-write. Kept separate from ``fetch_manifest`` because
     the error contracts differ: lazy fetch propagates (caller can't
     continue without the data); this one is called from a periodic task
     that has to tolerate transient failure.
     """
+    response = requests.get(IWC_MANIFEST_URL, timeout=timeout)
+    response.raise_for_status()
+    manifest = response.json()
+    if not isinstance(manifest, list):
+        raise ValueError(f"IWC manifest at {IWC_MANIFEST_URL} did not return a JSON array")
     with _manifest_cache_lock:
-        response = requests.get(IWC_MANIFEST_URL, timeout=timeout)
-        response.raise_for_status()
-        manifest = response.json()
-        if not isinstance(manifest, list):
-            raise ValueError(f"IWC manifest at {IWC_MANIFEST_URL} did not return a JSON array")
         _manifest_cache[_CACHE_KEY] = manifest
-        return manifest
+    return manifest
 
 
 def all_workflows(manifest: list[dict[str, Any]]) -> list[dict[str, Any]]:

From d053bfae0b6c02d2217013af81c11768686586d8 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 29 May 2026 07:41:04 -0400
Subject: [PATCH 017/256] Use the GalaxyAI name in the GTN/IWC refresh config
 and comments

The agent assistant was rebranded from ChatGXY to GalaxyAI, but this
branch's new config descriptions and code comments still said ChatGXY.
Swap them over and regenerate the sample yml + options rst from the
schema. The lowercase depot bucket path in gtn_database_url stays as-is
-- that's a real URL, not a brand reference.
---
 doc/source/admin/galaxy_options.rst         | 6 +++---
 lib/galaxy/celery/__init__.py               | 2 +-
 lib/galaxy/celery/tasks.py                  | 2 +-
 lib/galaxy/config/sample/galaxy.yml.sample  | 4 ++--
 lib/galaxy/config/schemas/config_schema.yml | 4 ++--
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index d0e3ce3a5ec..dbb525bed4b 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -5747,8 +5747,8 @@
     ``gtn_database_path``; live handlers pick up the new copy on their
     next query since GTNSearchDB opens a read-only connection per
     call. Only registered when ``inference_services`` is configured
-    (i.e. ChatGXY is in use). Set to 0 to disable automatic refresh --
-    admins can still refresh on demand via ``python -m
+    (i.e. GalaxyAI is in use). Set to 0 to disable automatic refresh
+    -- admins can still refresh on demand via ``python -m
     galaxy.agents.gtn --refresh``. Requires celery.
 :Default: ``86400``
 :Type: int
@@ -5765,7 +5765,7 @@
     stays continuously warm rather than expiring between user-driven
     hits. Failures are logged and the prior cached copy is retained.
     Only registered when ``inference_services`` is configured (i.e.
-    ChatGXY is in use). Set to 0 to disable automatic refresh --
+    GalaxyAI is in use). Set to 0 to disable automatic refresh --
     agent-ops callers will then fall back to lazy on-demand fetching
     with the same hour TTL. Requires celery.
 :Default: ``3600``
diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index 5759384c97c..d6501248e98 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -283,7 +283,7 @@ def setup_periodic_tasks(config, celery_app):
     if config.vault_token_renewal_interval:
         schedule_task("renew_vault_token", config.vault_token_renewal_interval)
 
-    # Only schedule if ChatGXY infrastructure is configured -- the GTN database
+    # Only schedule if GalaxyAI infrastructure is configured -- the GTN database
     # serves the gtn_training agent, which only functions when inference_services
     # is set up. Without this gate every Galaxy install would pull from depot
     # on the default interval, even ones that don't use the agent.
diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py
index 17826ef1d68..f2be0cd4565 100644
--- a/lib/galaxy/celery/tasks.py
+++ b/lib/galaxy/celery/tasks.py
@@ -858,7 +858,7 @@ def refresh_gtn_database(config: GalaxyAppConfiguration):
     """HEAD depot for the GTN search database and re-download only when newer.
 
     Handlers open the database read-only per query, so an atomic rename here
-    is picked up by the next ChatGXY request without a restart. The HEAD-first
+    is picked up by the next GalaxyAI request without a restart. The HEAD-first
     pattern keeps the steady-state cost to a few hundred bytes per tick --
     only when depot has actually been updated do we pull the full ~17MB.
     Failures are logged and swallowed so a depot outage doesn't kill the
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index cb3502f35a2..c94c2358253 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -3115,7 +3115,7 @@ galaxy:
   # ``gtn_database_path``; live handlers pick up the new copy on their
   # next query since GTNSearchDB opens a read-only connection per call.
   # Only registered when ``inference_services`` is configured (i.e.
-  # ChatGXY is in use). Set to 0 to disable automatic refresh -- admins
+  # GalaxyAI is in use). Set to 0 to disable automatic refresh -- admins
   # can still refresh on demand via ``python -m galaxy.agents.gtn
   # --refresh``. Requires celery.
   #gtn_database_refresh_interval: 86400
@@ -3125,7 +3125,7 @@ galaxy:
   # Default matches the cache's in-process TTL so the cache stays
   # continuously warm rather than expiring between user-driven hits.
   # Failures are logged and the prior cached copy is retained. Only
-  # registered when ``inference_services`` is configured (i.e. ChatGXY
+  # registered when ``inference_services`` is configured (i.e. GalaxyAI
   # is in use). Set to 0 to disable automatic refresh -- agent-ops
   # callers will then fall back to lazy on-demand fetching with the same
   # hour TTL. Requires celery.
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index a365f988fd8..f737f1072c1 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -4256,7 +4256,7 @@ mapping:
           ``gtn_database_path``; live handlers pick up the new copy on their
           next query since GTNSearchDB opens a read-only connection per call.
           Only registered when ``inference_services`` is configured (i.e.
-          ChatGXY is in use). Set to 0 to disable automatic refresh -- admins
+          GalaxyAI is in use). Set to 0 to disable automatic refresh -- admins
           can still refresh on demand via
           ``python -m galaxy.agents.gtn --refresh``. Requires celery.
 
@@ -4270,7 +4270,7 @@ mapping:
           Default matches the cache's in-process TTL so the cache stays
           continuously warm rather than expiring between user-driven hits.
           Failures are logged and the prior cached copy is retained. Only
-          registered when ``inference_services`` is configured (i.e. ChatGXY
+          registered when ``inference_services`` is configured (i.e. GalaxyAI
           is in use). Set to 0 to disable automatic refresh -- agent-ops
           callers will then fall back to lazy on-demand fetching with the
           same hour TTL. Requires celery.

From cb6d67dd370f64cd7907412e077ff8ab6e09abc3 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 31 May 2026 13:50:35 -0400
Subject: [PATCH 018/256] Extract _download_manifest to dedupe the IWC fetch
 block

fetch_manifest and refresh_manifest both had a byte-identical
fetch/raise_for_status/json/isinstance block. Pull it into a private
helper so the two functions differ only in their locking strategy --
which is the actual point refresh_manifest's docstring labors to explain.
---
 lib/galaxy/agents/iwc.py | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/agents/iwc.py b/lib/galaxy/agents/iwc.py
index 14a1c6e7b12..cc5386aa77f 100644
--- a/lib/galaxy/agents/iwc.py
+++ b/lib/galaxy/agents/iwc.py
@@ -33,6 +33,16 @@ def clear_manifest_cache() -> None:
         _manifest_cache.clear()
 
 
+def _download_manifest(timeout: float) -> list[dict[str, Any]]:
+    """Fetch and validate the IWC manifest over the network, bypassing the cache."""
+    response = requests.get(IWC_MANIFEST_URL, timeout=timeout)
+    response.raise_for_status()
+    manifest = response.json()
+    if not isinstance(manifest, list):
+        raise ValueError(f"IWC manifest at {IWC_MANIFEST_URL} did not return a JSON array")
+    return manifest
+
+
 def fetch_manifest(timeout: float = 30.0) -> list[dict[str, Any]]:
     """Fetch the IWC manifest, returning a cached copy when fresh.
 
@@ -44,11 +54,7 @@ def fetch_manifest(timeout: float = 30.0) -> list[dict[str, Any]]:
         if cached is not None:
             return cached
 
-        response = requests.get(IWC_MANIFEST_URL, timeout=timeout)
-        response.raise_for_status()
-        manifest = response.json()
-        if not isinstance(manifest, list):
-            raise ValueError(f"IWC manifest at {IWC_MANIFEST_URL} did not return a JSON array")
+        manifest = _download_manifest(timeout)
         _manifest_cache[_CACHE_KEY] = manifest
         return manifest
 
@@ -66,11 +72,7 @@ def refresh_manifest(timeout: float = 30.0) -> list[dict[str, Any]]:
     continue without the data); this one is called from a periodic task
     that has to tolerate transient failure.
     """
-    response = requests.get(IWC_MANIFEST_URL, timeout=timeout)
-    response.raise_for_status()
-    manifest = response.json()
-    if not isinstance(manifest, list):
-        raise ValueError(f"IWC manifest at {IWC_MANIFEST_URL} did not return a JSON array")
+    manifest = _download_manifest(timeout)
     with _manifest_cache_lock:
         _manifest_cache[_CACHE_KEY] = manifest
     return manifest

From 0064de80cffdf81ccfd0984671c98756a69715b1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 31 May 2026 13:50:37 -0400
Subject: [PATCH 019/256] Hoist the iwc import in refresh_iwc_manifest to
 module top

The local import claimed to keep cachetools/requests out of celery's
startup graph, but cachetools is already pulled in transitively
(NotificationManager -> sse_dispatch) and requests is resident in any
worker that boots galaxy.app. There's no circular-import risk either, and
the sibling refresh_gtn_database imports GTNSearchDB at the top -- so hoist
this one for consistency and drop the comment.
---
 lib/galaxy/celery/tasks.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py
index f2be0cd4565..48e079decd6 100644
--- a/lib/galaxy/celery/tasks.py
+++ b/lib/galaxy/celery/tasks.py
@@ -26,6 +26,7 @@ from sqlalchemy import (
 )
 
 from galaxy import model
+from galaxy.agents import iwc
 from galaxy.agents.gtn import GTNSearchDB
 from galaxy.celery import (
     celery_app,
@@ -840,11 +841,6 @@ def refresh_iwc_manifest(config: GalaxyAppConfiguration):
     so an iwc.galaxyproject.org outage doesn't kill the periodic queue --
     on-demand callers still get the prior cached copy until the TTL lapses.
     """
-    # Local import keeps the iwc module (and its cachetools / requests
-    # imports) out of celery's startup graph -- they only load on the
-    # workers that actually run this task.
-    from galaxy.agents import iwc
-
     try:
         manifest = iwc.refresh_manifest()
     except Exception as e:  # noqa: BLE001 -- best-effort warm; resilience over precision

From dfe8d17bd1a32f08fc5ef57125a93f1b820ea11e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 31 May 2026 17:36:22 -0400
Subject: [PATCH 020/256] Quiet mypy on the inference_services test assignment

inference_services is a schema-loaded config option, so it's not a static
attribute on GalaxyAppConfiguration -- production code reads it via getattr
for the same reason. The two celery schedule tests set it directly, which
trips mypy's attr-defined check, so mark those assignments type: ignore the
way the other config-poking unit tests (test_vault, test_error_reporting) do.
---
 test/unit/app/test_celery.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/unit/app/test_celery.py b/test/unit/app/test_celery.py
index bf2bcb1d040..fb68368560d 100644
--- a/test/unit/app/test_celery.py
+++ b/test/unit/app/test_celery.py
@@ -35,7 +35,7 @@ def test_default_configuration():
 
 def test_gtn_refresh_schedules_when_inference_configured():
     config = GalaxyAppConfiguration(override_tempdir=False)
-    config.inference_services = {"default": {"model": "test"}}
+    config.inference_services = {"default": {"model": "test"}}  # type: ignore[attr-defined]
     app = GalaxyCelery("test-gtn-schedule")
     setup_periodic_tasks(config, app)
     assert app.conf.beat_schedule["refresh-gtn-database"] == {
@@ -46,7 +46,7 @@ def test_gtn_refresh_schedules_when_inference_configured():
 
 def test_iwc_refresh_schedules_when_inference_configured():
     config = GalaxyAppConfiguration(override_tempdir=False)
-    config.inference_services = {"default": {"model": "test"}}
+    config.inference_services = {"default": {"model": "test"}}  # type: ignore[attr-defined]
     app = GalaxyCelery("test-iwc-schedule")
     setup_periodic_tasks(config, app)
     assert app.conf.beat_schedule["refresh-iwc-manifest"] == {

From 884dad89152b78532cc66db3b2f23fbb66f6cf37 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 3 Jun 2026 15:36:06 +0200
Subject: [PATCH 021/256] Use router-link for TRS import navigation

Prevent a full page reload when navigating to the TRS import section.
---
 .../src/components/Workflow/Import/FromFileOrUrl.test.ts  | 8 ++++++--
 client/src/components/Workflow/Import/FromUrl.vue         | 3 ++-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Workflow/Import/FromFileOrUrl.test.ts b/client/src/components/Workflow/Import/FromFileOrUrl.test.ts
index 2bfdaf7f468..b324c6cc148 100644
--- a/client/src/components/Workflow/Import/FromFileOrUrl.test.ts
+++ b/client/src/components/Workflow/Import/FromFileOrUrl.test.ts
@@ -1,6 +1,7 @@
 import { getLocalVue } from "@tests/vitest/helpers";
 import { mount } from "@vue/test-utils";
 import { describe, expect, it, vi } from "vitest";
+import VueRouter from "vue-router";
 
 import FromFile from "./FromFile.vue";
 import FromUrl from "./FromUrl.vue";
@@ -17,6 +18,7 @@ vi.mock("axios", () => ({
 }));
 
 const localVue = getLocalVue(true);
+localVue.use(VueRouter);
 
 const sharedUrl = "http://127.0.0.1:8081/u/admin/w/unnamed-workflow";
 const sharedUrlTrailingSlash = "http://127.0.0.1:8081/u/admin/w/unnamed-workflow/";
@@ -25,7 +27,8 @@ const invalidUrl = "http://127.0.0.1:8081/u/admin/w/unnamed-workflow/additional-
 
 describe("FromUrl", () => {
     it("converts shared urls to json urls", async () => {
-        const wrapper = mount(FromUrl as object, { localVue });
+        const router = new VueRouter();
+        const wrapper = mount(FromUrl as object, { localVue, router });
 
         {
             const input = wrapper.find("#workflow-import-url-input");
@@ -71,7 +74,8 @@ describe("FromUrl", () => {
 
 describe("FromFile", () => {
     it("can mount the component", async () => {
-        const wrapper = mount(FromFile as object, { localVue });
+        const router = new VueRouter();
+        const wrapper = mount(FromFile as object, { localVue, router });
         expect(wrapper.find("form").exists()).toBe(true);
     });
 });
diff --git a/client/src/components/Workflow/Import/FromUrl.vue b/client/src/components/Workflow/Import/FromUrl.vue
index 736842ec3b1..bb53f8507fd 100644
--- a/client/src/components/Workflow/Import/FromUrl.vue
+++ b/client/src/components/Workflow/Import/FromUrl.vue
@@ -2,6 +2,7 @@
 import axios from "axios";
 import { BAlert, BForm, BFormGroup, BFormInput } from "bootstrap-vue";
 import { computed, type Ref, ref, watch } from "vue";
+import { RouterLink } from "vue-router";
 import { useRouter } from "vue-router/composables";
 
 import { getRedirectOnImportPath } from "@/components/Workflow/redirectPath";
@@ -89,7 +90,7 @@ defineExpose({ attemptImport });
                 aria-label="Workflow Import URL"
                 type="url" />
             If your URL is from a workflow repository and doesn't end in <code>.ga</code>, you might need to use the
-            <a href="/workflows/import?trs_url=Enter%20a%20TRS%20URL">TRS import method</a>
+            <RouterLink to="/workflows/import?trs_url=Enter%20a%20TRS%20URL">TRS import method</RouterLink>
             instead.
         </BFormGroup>
 

From 4336259fcb7200a8e82bedde843f2662119a1808 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 3 Jun 2026 15:43:55 +0200
Subject: [PATCH 022/256] Improve code color contrast for accessibility

Overrides the default Bootstrap code color to meet WCAG AA contrast standards.
---
 client/src/style/scss/theme/blue.scss | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/client/src/style/scss/theme/blue.scss b/client/src/style/scss/theme/blue.scss
index 65b5db6f57d..57c2cdf4074 100644
--- a/client/src/style/scss/theme/blue.scss
+++ b/client/src/style/scss/theme/blue.scss
@@ -115,6 +115,9 @@ $h6-font-size: $font-size-base * 0.85; // default 1
 $dropdown-link-hover-color: $brand-light;
 $dropdown-link-hover-bg: $brand-primary;
 
+// Code elements (override Bootstrap default $code-color: $pink which fails WCAG AA contrast)
+$code-color: #c2266e;
+
 // Color of input elements
 $input-color: $text-color;
 $input-color-placeholder: $text-muted;

From ce624514eb04bb66440fdc8b65685a4c5093a9c2 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 26 Mar 2026 09:27:33 +0100
Subject: [PATCH 023/256] Add iRODS file source integration with configuration
 and listing support

---
 lib/galaxy/files/sources/irods.py | 171 ++++++++++++++++++++++++++++++
 1 file changed, 171 insertions(+)
 create mode 100644 lib/galaxy/files/sources/irods.py

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
new file mode 100644
index 00000000000..4e36e0489b9
--- /dev/null
+++ b/lib/galaxy/files/sources/irods.py
@@ -0,0 +1,171 @@
+import ssl
+from fnmatch import fnmatch
+import os
+from typing import (
+    Optional,
+    Union,
+)
+
+import fs
+import fs.errors
+
+from galaxy.files.models import (
+    AnyRemoteEntry,
+    BaseFileSourceConfiguration,
+    BaseFileSourceTemplateConfiguration,
+    FilesSourceRuntimeContext,
+)
+from galaxy.exceptions import (
+    AuthenticationRequired,
+    MessageException,
+)
+from galaxy.util.config_templates import TemplateExpansion
+from ._pyfilesystem2 import PyFilesystem2FilesSource
+
+try:
+    from fs_irods import iRODSFS
+except ImportError:
+    iRODSFS = None
+
+try:
+    from irods.session import iRODSSession
+except ImportError:
+    iRODSSession = None
+
+
+class IrodsFileSourceTemplateConfiguration(BaseFileSourceTemplateConfiguration):
+    host: Union[str, TemplateExpansion]
+    port: Union[int, TemplateExpansion] = 1247
+    username: Union[str, TemplateExpansion]
+    password: Union[str, TemplateExpansion]
+    zone: Union[str, TemplateExpansion]
+    root: Optional[Union[str, TemplateExpansion]] = None
+    timeout: Union[int, TemplateExpansion] = 30
+    refresh_time: Union[int, TemplateExpansion] = 300
+    client_server_negotiation: Optional[Union[str, TemplateExpansion]] = None
+    client_server_policy: Optional[Union[str, TemplateExpansion]] = None
+    encryption_algorithm: Optional[Union[str, TemplateExpansion]] = None
+    encryption_key_size: Optional[Union[int, TemplateExpansion]] = None
+    encryption_num_hash_rounds: Optional[Union[int, TemplateExpansion]] = None
+    encryption_salt_size: Optional[Union[int, TemplateExpansion]] = None
+    ssl_verify_server: Optional[Union[str, TemplateExpansion]] = None
+    ssl_ca_certificate_file: Optional[Union[str, TemplateExpansion]] = None
+    resource: Optional[Union[str, TemplateExpansion]] = None
+
+
+class IrodsFileSourceConfiguration(BaseFileSourceConfiguration):
+    host: str
+    port: int = 1247
+    username: str
+    password: str
+    zone: str
+    root: Optional[str] = None
+    timeout: int = 30
+    refresh_time: int = 300
+    client_server_negotiation: Optional[str] = None
+    client_server_policy: Optional[str] = None
+    encryption_algorithm: Optional[str] = None
+    encryption_key_size: Optional[int] = None
+    encryption_num_hash_rounds: Optional[int] = None
+    encryption_salt_size: Optional[int] = None
+    ssl_verify_server: Optional[str] = None
+    ssl_ca_certificate_file: Optional[str] = None
+    resource: Optional[str] = None
+
+
+class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfiguration, IrodsFileSourceConfiguration]):
+    plugin_type = "irods"
+    required_module = iRODSFS
+    required_package = "fs-irods"
+
+    template_config_class = IrodsFileSourceTemplateConfiguration
+    resolved_config_class = IrodsFileSourceConfiguration
+
+    def _normalize_listdir_name(self, value: str) -> str:
+        # fs-irods currently returns absolute iRODS paths from listdir; convert to simple entry names.
+        return os.path.basename(str(value).rstrip("/"))
+
+    def _list(
+        self,
+        context: FilesSourceRuntimeContext[IrodsFileSourceConfiguration],
+        path="/",
+        recursive=False,
+        write_intent: bool = False,
+        limit: Optional[int] = None,
+        offset: Optional[int] = None,
+        query: Optional[str] = None,
+        sort_by: Optional[str] = None,
+    ) -> tuple[list[AnyRemoteEntry], int]:
+        try:
+            with self._open_fs(context) as h:
+                if recursive:
+                    result: list[AnyRemoteEntry] = []
+                    pending = [path]
+                    while pending:
+                        current_path = pending.pop(0)
+                        for raw_name in h.listdir(current_path):
+                            name = self._normalize_listdir_name(raw_name)
+                            if not name:
+                                continue
+                            entry_path = fs.path.join(current_path, name)
+                            info = h.getinfo(entry_path, namespaces=["details"])
+                            result.append(self._resource_info_to_dict(current_path, info))
+                            if info.is_dir:
+                                pending.append(entry_path)
+                    return result, len(result)
+
+                normalized_query = query.lower() if query else None
+                entries = []
+                for raw_name in h.listdir(path):
+                    name = self._normalize_listdir_name(raw_name)
+                    if not name:
+                        continue
+                    if normalized_query and not fnmatch(name.lower(), f"*{normalized_query}*"):
+                        continue
+                    entry_path = fs.path.join(path, name)
+                    info = h.getinfo(entry_path, namespaces=["details"])
+                    entries.append(self._resource_info_to_dict(path, info))
+
+                count = len(entries)
+                page = self._to_page(limit, offset)
+                if page is not None:
+                    entries = entries[page[0] : page[1]]
+                return entries, count
+        except fs.errors.PermissionDenied as e:
+            raise AuthenticationRequired(
+                f"Permission Denied. Reason: {e}. Please check your credentials in your preferences for {self.label}."
+            ) from e
+        except fs.errors.FSError as e:
+            raise MessageException(f"Problem listing file source path {path}. Reason: {e}") from e
+
+    def _open_fs(self, context: FilesSourceRuntimeContext[IrodsFileSourceConfiguration]):
+        if iRODSFS is None or iRODSSession is None:
+            raise self.required_package_exception
+
+        config = context.config
+        session_kwargs = {
+            "host": config.host,
+            "port": config.port,
+            "user": config.username,
+            "password": config.password,
+            "zone": config.zone,
+            "refresh_time": config.refresh_time,
+            "client_server_negotiation": config.client_server_negotiation,
+            "client_server_policy": config.client_server_policy,
+            "encryption_algorithm": config.encryption_algorithm,
+            "encryption_key_size": config.encryption_key_size,
+            "encryption_num_hash_rounds": config.encryption_num_hash_rounds,
+            "encryption_salt_size": config.encryption_salt_size,
+            "ssl_verify_server": config.ssl_verify_server,
+            "ssl_ca_certificate_file": config.ssl_ca_certificate_file,
+            "ssl_context": ssl.create_default_context(purpose=ssl.Purpose.SERVER_AUTH),
+        }
+        session = iRODSSession(**session_kwargs)
+        session.connection_timeout = config.timeout
+        if config.resource:
+            session.default_resource = config.resource
+
+        return iRODSFS(session=session, root=config.root)
+
+
+__all__ = ("IrodsFilesSource",)

From 995cd8cc1b757a967872f91bf92be4a6815ab648 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 26 Mar 2026 09:32:10 +0100
Subject: [PATCH 024/256] Add iRODS file source configuration and template
 classes

---
 lib/galaxy/files/templates/models.py | 32 ++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/lib/galaxy/files/templates/models.py b/lib/galaxy/files/templates/models.py
index f3e51324ed5..e1e36e80a24 100644
--- a/lib/galaxy/files/templates/models.py
+++ b/lib/galaxy/files/templates/models.py
@@ -38,6 +38,7 @@ FileSourceTemplateType = Literal[
     "s3fs",
     "azure",
     "azureflat",
+    "irods",
     "onedata",
     "webdav",
     "dropbox",
@@ -248,6 +249,34 @@ class AzureFlatFileSourceConfiguration(StrictModel):
     writable: bool = False
 
 
+class IrodsFileSourceTemplateConfiguration(StrictModel):
+    type: Literal["irods"]
+    host: Union[str, TemplateExpansion]
+    port: Union[int, TemplateExpansion] = 1247
+    username: Union[str, TemplateExpansion]
+    password: Union[str, TemplateExpansion]
+    zone: Union[str, TemplateExpansion]
+    root: Optional[Union[str, TemplateExpansion]] = None
+    timeout: Union[int, TemplateExpansion] = 30
+    refresh_time: Union[int, TemplateExpansion] = 300
+    writable: Union[bool, TemplateExpansion] = False
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class IrodsFileSourceConfiguration(StrictModel):
+    type: Literal["irods"]
+    host: str
+    port: int = 1247
+    username: str
+    password: str
+    zone: str
+    root: Optional[str] = None
+    timeout: int = 30
+    refresh_time: int = 300
+    writable: bool = False
+
+
 class OnedataFileSourceTemplateConfiguration(StrictModel):
     type: Literal["onedata"]
     access_token: Union[str, TemplateExpansion]
@@ -438,6 +467,7 @@ FileSourceTemplateConfiguration = Annotated[
         FtpFileSourceTemplateConfiguration,
         AzureFileSourceTemplateConfiguration,
         AzureFlatFileSourceTemplateConfiguration,
+        IrodsFileSourceTemplateConfiguration,
         OnedataFileSourceTemplateConfiguration,
         WebdavFileSourceTemplateConfiguration,
         DropboxFileSourceTemplateConfiguration,
@@ -463,6 +493,7 @@ FileSourceConfiguration = Annotated[
         FtpFileSourceConfiguration,
         AzureFileSourceConfiguration,
         AzureFlatFileSourceConfiguration,
+        IrodsFileSourceConfiguration,
         OnedataFileSourceConfiguration,
         WebdavFileSourceConfiguration,
         DropboxFileSourceConfiguration,
@@ -546,6 +577,7 @@ TypesToConfigurationClasses: dict[FileSourceTemplateType, type[FileSourceConfigu
     "s3fs": S3FSFileSourceConfiguration,
     "azure": AzureFileSourceConfiguration,
     "azureflat": AzureFlatFileSourceConfiguration,
+    "irods": IrodsFileSourceConfiguration,
     "onedata": OnedataFileSourceConfiguration,
     "webdav": WebdavFileSourceConfiguration,
     "dropbox": DropboxFileSourceConfiguration,

From 24f4c07fe4e878e4eb3b1365b395d52cf67c378a Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 26 Mar 2026 09:43:07 +0100
Subject: [PATCH 025/256] Add iRODS template for file source repository
 configuration

---
 lib/galaxy/files/templates/examples/irods.yml | 61 +++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 lib/galaxy/files/templates/examples/irods.yml

diff --git a/lib/galaxy/files/templates/examples/irods.yml b/lib/galaxy/files/templates/examples/irods.yml
new file mode 100644
index 00000000000..22b168a32eb
--- /dev/null
+++ b/lib/galaxy/files/templates/examples/irods.yml
@@ -0,0 +1,61 @@
+- id: irods
+  version: 0
+  name: iRODS
+  description: |
+    Use this template to connect an iRODS collection as a Galaxy file source for
+    importing and exporting datasets.
+
+    You need valid iRODS credentials and the target root collection path.
+  variables:
+    host:
+      label: iRODS host
+      type: string
+      help: Hostname of the iRODS server.
+    port:
+      label: iRODS port
+      type: integer
+      help: Port of the iRODS server.
+      default: 1247
+    username:
+      label: iRODS user
+      type: string
+      help: Username used to authenticate against iRODS.
+    zone:
+      label: iRODS zone
+      type: string
+      help: Zone used for authentication (for example tempZone).
+    root:
+      label: Root collection path
+      type: string
+      help: |
+        Collection path exposed in Galaxy, for example /tempZone/home/rods.
+    timeout:
+      label: Connection timeout (seconds)
+      type: integer
+      help: Timeout in seconds for iRODS connection attempts.
+      default: 30
+    refresh_time:
+      label: Session refresh time (seconds)
+      type: integer
+      help: Seconds between refresh checks for active iRODS sessions.
+      default: 300
+    writable:
+      label: Writable?
+      type: boolean
+      help: Allow writing datasets back to iRODS.
+      default: false
+  secrets:
+    password:
+      label: Password
+      help: Password used to authenticate against iRODS.
+  configuration:
+    type: irods
+    host: "{{ variables.host }}"
+    port: "{{ variables.port }}"
+    username: "{{ variables.username }}"
+    password: "{{ secrets.password }}"
+    zone: "{{ variables.zone }}"
+    root: "{{ variables.root }}"
+    timeout: "{{ variables.timeout }}"
+    refresh_time: "{{ variables.refresh_time }}"
+    writable: "{{ variables.writable }}"
\ No newline at end of file

From 8f2afdf8416a70d17d34d3f473f4131785e5d693 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 26 Mar 2026 17:27:36 +0100
Subject: [PATCH 026/256] Add unit tests for iRODS file source functionality

---
 test/unit/files/test_irods.py | 232 ++++++++++++++++++++++++++++++++++
 1 file changed, 232 insertions(+)
 create mode 100644 test/unit/files/test_irods.py

diff --git a/test/unit/files/test_irods.py b/test/unit/files/test_irods.py
new file mode 100644
index 00000000000..b867088f6d1
--- /dev/null
+++ b/test/unit/files/test_irods.py
@@ -0,0 +1,232 @@
+import os
+import socket
+import pytest
+import yaml
+
+from galaxy.files.models import (
+    FileSourcePluginsConfig,
+    FilesSourceRuntimeContext,
+    UserData,
+)
+from galaxy.files.plugins import FileSourcePluginLoader
+from galaxy.files.sources.irods import IrodsFilesSource
+from ._util import (
+    assert_realizes_contains,
+    configured_file_sources,
+    write_from,
+)
+
+try:
+    from irods.session import iRODSSession
+except ImportError:
+    iRODSSession = None
+
+
+ROUNDTRIP_TEST_FILENAME = "numerical_sort_and_write_back_to_irods_v2.tab"
+
+
+class _FakeSession:
+    init_kwargs = None
+
+    def __init__(self, **kwargs):
+        type(self).init_kwargs = kwargs
+        self.connection_timeout = None
+        self.default_resource = None
+
+
+class _FakeIrodsFs:
+    def __init__(self, session, root=None):
+        self.session = session
+        self.root = root
+
+
+def _get_setting(irods_config: dict, env_name: str, key: str, cast=None):
+    raw = os.environ.get(env_name)
+    if raw is None:
+        raw = irods_config.get(key)
+    if raw is None:
+        pytest.skip(f"Missing iRODS setting '{key}' in file_sources_conf.yml or env {env_name}.")
+    return cast(raw) if cast else raw
+
+
+def _file_sources_config(irods_config: dict) -> dict:
+    return {
+        "host": _get_setting(irods_config, "GALAXY_TEST_IRODS_HOST", "host"),
+        "port": _get_setting(irods_config, "GALAXY_TEST_IRODS_PORT", "port", int),
+        "username": _get_setting(irods_config, "GALAXY_TEST_IRODS_USER", "username"),
+        "password": _get_setting(irods_config, "GALAXY_TEST_IRODS_PASSWORD", "password"),
+        "zone": _get_setting(irods_config, "GALAXY_TEST_IRODS_ZONE", "zone"),
+        "root": _get_setting(irods_config, "GALAXY_TEST_IRODS_ROOT", "root"),
+        "timeout": _get_setting(irods_config, "GALAXY_TEST_IRODS_TIMEOUT", "timeout", int),
+        "refresh_time": _get_setting(irods_config, "GALAXY_TEST_IRODS_REFRESH_TIME", "refresh_time", int),
+    }
+
+
+def _irods_live_settings() -> dict:
+    config_path = os.environ.get(
+        "GALAXY_TEST_FILE_SOURCES_CONFIG",
+        os.path.abspath(
+            os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, "config", "file_sources_conf.yml")
+        ),
+    )
+    if not os.path.exists(config_path):
+        pytest.skip(f"No file sources config at {config_path}; set file_sources_conf.yml to enable iRODS live tests.")
+
+    with open(config_path, "rb") as handle:
+        configs = yaml.safe_load(handle) or []
+
+    irods_id = os.environ.get("GALAXY_TEST_IRODS_SOURCE_ID")
+    irods_configs = [c for c in configs if isinstance(c, dict) and c.get("type") == "irods"]
+    if irods_id:
+        irods_configs = [c for c in irods_configs if c.get("id") == irods_id]
+
+    if not irods_configs:
+        pytest.skip("No iRODS file source found in file_sources_conf.yml; configure one to enable live tests.")
+
+    irods_config = irods_configs[0]
+
+    return _file_sources_config(irods_config)
+
+
+def _skip_if_irods_unreachable(host: str, port: int):
+    try:
+        with socket.create_connection((host, port), timeout=1):
+            return
+    except OSError:
+        pytest.skip(
+            f"No reachable iRODS service at {host}:{port}. "
+            "Start your local iRODS Docker stack or override GALAXY_TEST_IRODS_* settings."
+        )
+
+
+def _live_file_source_config(settings: dict, writable: bool = False) -> list[dict]:
+    return [
+        {
+            "type": "irods",
+            "id": "test1",
+            "label": "iRODS Live Test",
+            "doc": "Live iRODS connectivity smoke test",
+            "host": settings["host"],
+            "port": settings["port"],
+            "username": settings["username"],
+            "password": settings["password"],
+            "zone": settings["zone"],
+            "root": settings["root"],
+            "timeout": settings["timeout"],
+            "refresh_time": settings["refresh_time"],
+            "writable": writable,
+        }
+    ]
+
+
+def _cleanup_live_test_artifacts(settings: dict):
+    root = settings["root"].rstrip("/")
+    logical_path = f"{root}/{ROUNDTRIP_TEST_FILENAME}"
+
+    session = iRODSSession(
+        host=settings["host"],
+        port=settings["port"],
+        user=settings["username"],
+        password=settings["password"],
+        zone=settings["zone"],
+        refresh_time=settings["refresh_time"],
+    )
+    session.connection_timeout = settings["timeout"]
+
+    try:
+        if session.data_objects.exists(logical_path):
+            session.data_objects.unlink(logical_path)
+    finally:
+        session.cleanup()
+
+
+def test_irods_plugin_registered():
+    plugin_loader = FileSourcePluginLoader()
+    plugin_class = plugin_loader.get_plugin_type_class("irods")
+    assert plugin_class is IrodsFilesSource
+
+
+def test_irods_open_fs_builds_session(monkeypatch):
+    monkeypatch.setattr("galaxy.files.sources.irods.iRODSSession", _FakeSession)
+    monkeypatch.setattr("galaxy.files.sources.irods.iRODSFS", _FakeIrodsFs)
+    monkeypatch.setattr(IrodsFilesSource, "required_module", _FakeIrodsFs)
+
+    file_source = IrodsFilesSource(
+        IrodsFilesSource.build_template_config(
+            type="irods",
+            id="test_irods",
+            file_sources_config=FileSourcePluginsConfig(),
+            host="irods.example.org",
+            port=1247,
+            username="rods",
+            password="secret",
+            zone="tempZone",
+            root="/tempZone/home/rods",
+            timeout=42,
+            refresh_time=120,
+            resource="demoResc",
+            writable=True,
+        )
+    )
+
+    resolved_config = file_source._evaluate_template_config(UserData())
+    context = FilesSourceRuntimeContext(user_data=UserData(), config=resolved_config)
+
+    fs = file_source._open_fs(context)
+    init_kwargs = _FakeSession.init_kwargs
+
+    assert isinstance(fs, _FakeIrodsFs)
+    assert fs.root == "/tempZone/home/rods"
+    assert init_kwargs is not None
+    assert init_kwargs["host"] == "irods.example.org"
+    assert init_kwargs["port"] == 1247
+    assert init_kwargs["user"] == "rods"
+    assert init_kwargs["password"] == "secret"
+    assert init_kwargs["zone"] == "tempZone"
+    assert init_kwargs["refresh_time"] == 120
+    assert fs.session.connection_timeout == 42
+    assert fs.session.default_resource == "demoResc"
+
+
+def test_irods_live_touch():
+    settings = _irods_live_settings()
+    _skip_if_irods_unreachable(settings["host"], settings["port"])
+    _cleanup_live_test_artifacts(settings)
+
+    file_sources = configured_file_sources(_live_file_source_config(settings, writable=False))
+    file_source_pair = file_sources.get_file_source_path("gxfiles://test1")
+
+    assert file_source_pair.path == "/"
+    entries, count = file_source_pair.file_source.list("/", recursive=False)
+    assert isinstance(entries, list)
+    assert count >= 0
+    _cleanup_live_test_artifacts(settings)
+
+
+def test_irods_live_recursive_list():
+    settings = _irods_live_settings()
+    _skip_if_irods_unreachable(settings["host"], settings["port"])
+    _cleanup_live_test_artifacts(settings)
+
+    file_sources = configured_file_sources(_live_file_source_config(settings, writable=False))
+    file_source_pair = file_sources.get_file_source_path("gxfiles://test1")
+
+    entries, count = file_source_pair.file_source.list("/", recursive=True)
+    assert isinstance(entries, list)
+    assert count >= 0
+    _cleanup_live_test_artifacts(settings)
+
+
+def test_irods_live_write_and_read_roundtrip():
+    settings = _irods_live_settings()
+    _skip_if_irods_unreachable(settings["host"], settings["port"])
+    _cleanup_live_test_artifacts(settings)
+
+    test_contents = "1\t2\t999\n666\t6\t555\n3\t4\t5\n"
+    target_uri = f"gxfiles://test1/{ROUNDTRIP_TEST_FILENAME}"
+
+    file_sources = configured_file_sources(_live_file_source_config(settings, writable=True))
+    _ = write_from(file_sources, target_uri, test_contents)
+    assert_realizes_contains(file_sources, target_uri, test_contents)
+
+    _cleanup_live_test_artifacts(settings)

From e2a03550dff0cae9fec46a555169c9f8348bb0b3 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Tue, 31 Mar 2026 14:52:43 +0200
Subject: [PATCH 027/256] Refactor iRODS file source listing methods for
 improved maintenance

---
 lib/galaxy/files/sources/irods.py | 78 +++++++++++++++++--------------
 1 file changed, 42 insertions(+), 36 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index 4e36e0489b9..d1e2ed07f19 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -81,9 +81,45 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
     template_config_class = IrodsFileSourceTemplateConfiguration
     resolved_config_class = IrodsFileSourceConfiguration
 
-    def _normalize_listdir_name(self, value: str) -> str:
-        # fs-irods currently returns absolute iRODS paths from listdir; convert to simple entry names.
-        return os.path.basename(str(value).rstrip("/"))
+    def _iter_directory_entries(self, fs_handle, parent_path: str, normalized_query: Optional[str] = None):
+        for raw_name in fs_handle.listdir(parent_path):
+            name = os.path.basename(str(raw_name).rstrip("/"))
+            if not name:
+                continue
+            if normalized_query and not fnmatch(name.lower(), f"*{normalized_query}*"):
+                continue
+            entry_path = fs.path.join(parent_path, name)
+            info = fs_handle.getinfo(entry_path, namespaces=["details"])
+            yield entry_path, info
+
+    def _list_recursive(self, fs_handle, path: str) -> tuple[list[AnyRemoteEntry], int]:
+        result: list[AnyRemoteEntry] = []
+        pending = [path]
+        while pending:
+            current_path = pending.pop(0)
+            for entry_path, info in self._iter_directory_entries(fs_handle, current_path):
+                result.append(self._resource_info_to_dict(current_path, info))
+                if info.is_dir:
+                    pending.append(entry_path)
+        return result, len(result)
+
+    def _list_non_recursive(
+        self,
+        fs_handle,
+        path: str,
+        limit: Optional[int] = None,
+        offset: Optional[int] = None,
+        query: Optional[str] = None,
+    ) -> tuple[list[AnyRemoteEntry], int]:
+        normalized_query = query.lower() if query else None
+        entries = []
+        for _, info in self._iter_directory_entries(fs_handle, path, normalized_query):
+            entries.append(self._resource_info_to_dict(path, info))
+        count = len(entries)
+        page = self._to_page(limit, offset)
+        if page is not None:
+            entries = entries[page[0] : page[1]]
+        return entries, count
 
     def _list(
         self,
@@ -97,40 +133,10 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
         sort_by: Optional[str] = None,
     ) -> tuple[list[AnyRemoteEntry], int]:
         try:
-            with self._open_fs(context) as h:
+            with self._open_fs(context) as fs_handle:
                 if recursive:
-                    result: list[AnyRemoteEntry] = []
-                    pending = [path]
-                    while pending:
-                        current_path = pending.pop(0)
-                        for raw_name in h.listdir(current_path):
-                            name = self._normalize_listdir_name(raw_name)
-                            if not name:
-                                continue
-                            entry_path = fs.path.join(current_path, name)
-                            info = h.getinfo(entry_path, namespaces=["details"])
-                            result.append(self._resource_info_to_dict(current_path, info))
-                            if info.is_dir:
-                                pending.append(entry_path)
-                    return result, len(result)
-
-                normalized_query = query.lower() if query else None
-                entries = []
-                for raw_name in h.listdir(path):
-                    name = self._normalize_listdir_name(raw_name)
-                    if not name:
-                        continue
-                    if normalized_query and not fnmatch(name.lower(), f"*{normalized_query}*"):
-                        continue
-                    entry_path = fs.path.join(path, name)
-                    info = h.getinfo(entry_path, namespaces=["details"])
-                    entries.append(self._resource_info_to_dict(path, info))
-
-                count = len(entries)
-                page = self._to_page(limit, offset)
-                if page is not None:
-                    entries = entries[page[0] : page[1]]
-                return entries, count
+                    return self._list_recursive(fs_handle, path)
+                return self._list_non_recursive(fs_handle, path, limit, offset, query)
         except fs.errors.PermissionDenied as e:
             raise AuthenticationRequired(
                 f"Permission Denied. Reason: {e}. Please check your credentials in your preferences for {self.label}."

From c907c33a919f814e12912693fc08f34dff57d131 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Mon, 18 May 2026 15:19:03 +0200
Subject: [PATCH 028/256] Format by isort and black

---
 lib/galaxy/files/sources/irods.py | 10 +++++-----
 test/unit/files/test_irods.py     |  1 +
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index d1e2ed07f19..86d28427fe0 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -1,6 +1,6 @@
+import os
 import ssl
 from fnmatch import fnmatch
-import os
 from typing import (
     Optional,
     Union,
@@ -9,16 +9,16 @@ from typing import (
 import fs
 import fs.errors
 
+from galaxy.exceptions import (
+    AuthenticationRequired,
+    MessageException,
+)
 from galaxy.files.models import (
     AnyRemoteEntry,
     BaseFileSourceConfiguration,
     BaseFileSourceTemplateConfiguration,
     FilesSourceRuntimeContext,
 )
-from galaxy.exceptions import (
-    AuthenticationRequired,
-    MessageException,
-)
 from galaxy.util.config_templates import TemplateExpansion
 from ._pyfilesystem2 import PyFilesystem2FilesSource
 
diff --git a/test/unit/files/test_irods.py b/test/unit/files/test_irods.py
index b867088f6d1..8a6eac4847a 100644
--- a/test/unit/files/test_irods.py
+++ b/test/unit/files/test_irods.py
@@ -1,5 +1,6 @@
 import os
 import socket
+
 import pytest
 import yaml
 

From 54c688fd8c2bb4b7a00558d1633c65a5b38cd529 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Tue, 19 May 2026 14:27:52 +0200
Subject: [PATCH 029/256] Add iRODS file source configuration to sample YAML

---
 .../config/sample/file_sources_conf.yml.sample   | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index 5b46c69cb07..0cd93f07fef 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -1,3 +1,19 @@
+- type: irods
+  id: irods_local_instance
+  label: Local iRODS
+  doc: iRODS in local Docker stack
+  writable: true
+
+  host: 127.0.0.1
+  port: 1247
+  username: user
+  password: password
+  zone: exampleZone
+  root: /exampleZone/home/user
+
+  timeout: 30
+  refresh_time: 300
+
 - type: dropbox
   id: dropbox1
   label: Dropbox files (configure access in user preferences)

From fccf68f2e29366895eacf1adeb2e98c2e9d43b9a Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Fri, 22 May 2026 10:11:43 +0200
Subject: [PATCH 030/256] Remove the setting from the admin-defined file
 sources sample

---
 .../config/sample/file_sources_conf.yml.sample   | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index 0cd93f07fef..5b46c69cb07 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -1,19 +1,3 @@
-- type: irods
-  id: irods_local_instance
-  label: Local iRODS
-  doc: iRODS in local Docker stack
-  writable: true
-
-  host: 127.0.0.1
-  port: 1247
-  username: user
-  password: password
-  zone: exampleZone
-  root: /exampleZone/home/user
-
-  timeout: 30
-  refresh_time: 300
-
 - type: dropbox
   id: dropbox1
   label: Dropbox files (configure access in user preferences)

From dc0e7b1b1f8f1d650a44d4a282385414c672edd3 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Sun, 24 May 2026 12:01:33 +0200
Subject: [PATCH 031/256] Update the way how conditional dependencies are
 handled

---
 lib/galaxy/files/sources/irods.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index 86d28427fe0..8a28c530216 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -24,12 +24,9 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 try:
     from fs_irods import iRODSFS
-except ImportError:
-    iRODSFS = None
-
-try:
     from irods.session import iRODSSession
 except ImportError:
+    iRODSFS = None
     iRODSSession = None
 
 

From ddd7f8aa12efe0226fa37dbcd04723bde7c1d0b9 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Sun, 24 May 2026 12:04:23 +0200
Subject: [PATCH 032/256] Refactor the iRODS YAML configuration to improve
 optional path handling and remove the connection time setting for the user

---
 lib/galaxy/files/templates/examples/irods.yml | 33 +++++++------------
 1 file changed, 12 insertions(+), 21 deletions(-)

diff --git a/lib/galaxy/files/templates/examples/irods.yml b/lib/galaxy/files/templates/examples/irods.yml
index 22b168a32eb..de088c60dc1 100644
--- a/lib/galaxy/files/templates/examples/irods.yml
+++ b/lib/galaxy/files/templates/examples/irods.yml
@@ -16,32 +16,23 @@
       type: integer
       help: Port of the iRODS server.
       default: 1247
+    zone:
+      label: iRODS zone
+      type: string
+      help: Zone used for authentication (for example teamZone).
     username:
       label: iRODS user
       type: string
       help: Username used to authenticate against iRODS.
-    zone:
-      label: iRODS zone
+    subpath:
+      label: Subfolder path
       type: string
-      help: Zone used for authentication (for example tempZone).
-    root:
-      label: Root collection path
-      type: string
-      help: |
-        Collection path exposed in Galaxy, for example /tempZone/home/rods.
-    timeout:
-      label: Connection timeout (seconds)
-      type: integer
-      help: Timeout in seconds for iRODS connection attempts.
-      default: 30
-    refresh_time:
-      label: Session refresh time (seconds)
-      type: integer
-      help: Seconds between refresh checks for active iRODS sessions.
-      default: 300
+      optional: true
+      help: Optional subfolder under your personal directory (for example projectName).
     writable:
       label: Writable?
       type: boolean
+      optional: true
       help: Allow writing datasets back to iRODS.
       default: false
   secrets:
@@ -55,7 +46,7 @@
     username: "{{ variables.username }}"
     password: "{{ secrets.password }}"
     zone: "{{ variables.zone }}"
-    root: "{{ variables.root }}"
-    timeout: "{{ variables.timeout }}"
-    refresh_time: "{{ variables.refresh_time }}"
+    root: "/{{ variables.zone }}/home/{{ variables.username }}{% if variables.get('subpath') %}/{{ variables.get('subpath') | ensure_path_component }}{% endif %}"
+    timeout: 30
+    refresh_time: 300
     writable: "{{ variables.writable }}"
\ No newline at end of file

From 9c01e04557780e6373f03bd432591c6803c95090 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Mon, 25 May 2026 13:47:14 +0200
Subject: [PATCH 033/256] Make the SSLContext optional and align it with the
 SSL configuration setting in python-irodsclient

---
 lib/galaxy/files/sources/irods.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index 8a28c530216..778479a89bd 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -1,5 +1,4 @@
 import os
-import ssl
 from fnmatch import fnmatch
 from typing import (
     Optional,
@@ -161,8 +160,11 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
             "encryption_salt_size": config.encryption_salt_size,
             "ssl_verify_server": config.ssl_verify_server,
             "ssl_ca_certificate_file": config.ssl_ca_certificate_file,
-            "ssl_context": ssl.create_default_context(purpose=ssl.Purpose.SERVER_AUTH),
         }
+        ssl_context = getattr(config, "ssl_context", None)
+        if ssl_context is not None:
+            session_kwargs["ssl_context"] = ssl_context
+
         session = iRODSSession(**session_kwargs)
         session.connection_timeout = config.timeout
         if config.resource:

From 770913e6435e881e81a9e857d91d3d5eb7ffb69d Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Mon, 25 May 2026 16:24:16 +0200
Subject: [PATCH 034/256] Make recursive requests explicitly unsupported to
 prevent unbounded traversal

---
 lib/galaxy/files/sources/irods.py | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index 778479a89bd..78d649284db 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -88,17 +88,6 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
             info = fs_handle.getinfo(entry_path, namespaces=["details"])
             yield entry_path, info
 
-    def _list_recursive(self, fs_handle, path: str) -> tuple[list[AnyRemoteEntry], int]:
-        result: list[AnyRemoteEntry] = []
-        pending = [path]
-        while pending:
-            current_path = pending.pop(0)
-            for entry_path, info in self._iter_directory_entries(fs_handle, current_path):
-                result.append(self._resource_info_to_dict(current_path, info))
-                if info.is_dir:
-                    pending.append(entry_path)
-        return result, len(result)
-
     def _list_non_recursive(
         self,
         fs_handle,
@@ -131,7 +120,7 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
         try:
             with self._open_fs(context) as fs_handle:
                 if recursive:
-                    return self._list_recursive(fs_handle, path)
+                    raise MessageException("Recursive listing is not supported for iRODS file sources.")
                 return self._list_non_recursive(fs_handle, path, limit, offset, query)
         except fs.errors.PermissionDenied as e:
             raise AuthenticationRequired(

From 02ced4cb21b1c68646a71af4ef0f8f36c664c300 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Tue, 26 May 2026 09:41:49 +0200
Subject: [PATCH 035/256] Remove mock testing and update test to raise
 MessageException on recursive list

---
 test/unit/files/test_irods.py | 63 ++---------------------------------
 1 file changed, 3 insertions(+), 60 deletions(-)

diff --git a/test/unit/files/test_irods.py b/test/unit/files/test_irods.py
index 8a6eac4847a..e7b21e88562 100644
--- a/test/unit/files/test_irods.py
+++ b/test/unit/files/test_irods.py
@@ -4,6 +4,7 @@ import socket
 import pytest
 import yaml
 
+from galaxy.exceptions import MessageException
 from galaxy.files.models import (
     FileSourcePluginsConfig,
     FilesSourceRuntimeContext,
@@ -26,21 +27,6 @@ except ImportError:
 ROUNDTRIP_TEST_FILENAME = "numerical_sort_and_write_back_to_irods_v2.tab"
 
 
-class _FakeSession:
-    init_kwargs = None
-
-    def __init__(self, **kwargs):
-        type(self).init_kwargs = kwargs
-        self.connection_timeout = None
-        self.default_resource = None
-
-
-class _FakeIrodsFs:
-    def __init__(self, session, root=None):
-        self.session = session
-        self.root = root
-
-
 def _get_setting(irods_config: dict, env_name: str, key: str, cast=None):
     raw = os.environ.get(env_name)
     if raw is None:
@@ -147,48 +133,6 @@ def test_irods_plugin_registered():
     assert plugin_class is IrodsFilesSource
 
 
-def test_irods_open_fs_builds_session(monkeypatch):
-    monkeypatch.setattr("galaxy.files.sources.irods.iRODSSession", _FakeSession)
-    monkeypatch.setattr("galaxy.files.sources.irods.iRODSFS", _FakeIrodsFs)
-    monkeypatch.setattr(IrodsFilesSource, "required_module", _FakeIrodsFs)
-
-    file_source = IrodsFilesSource(
-        IrodsFilesSource.build_template_config(
-            type="irods",
-            id="test_irods",
-            file_sources_config=FileSourcePluginsConfig(),
-            host="irods.example.org",
-            port=1247,
-            username="rods",
-            password="secret",
-            zone="tempZone",
-            root="/tempZone/home/rods",
-            timeout=42,
-            refresh_time=120,
-            resource="demoResc",
-            writable=True,
-        )
-    )
-
-    resolved_config = file_source._evaluate_template_config(UserData())
-    context = FilesSourceRuntimeContext(user_data=UserData(), config=resolved_config)
-
-    fs = file_source._open_fs(context)
-    init_kwargs = _FakeSession.init_kwargs
-
-    assert isinstance(fs, _FakeIrodsFs)
-    assert fs.root == "/tempZone/home/rods"
-    assert init_kwargs is not None
-    assert init_kwargs["host"] == "irods.example.org"
-    assert init_kwargs["port"] == 1247
-    assert init_kwargs["user"] == "rods"
-    assert init_kwargs["password"] == "secret"
-    assert init_kwargs["zone"] == "tempZone"
-    assert init_kwargs["refresh_time"] == 120
-    assert fs.session.connection_timeout == 42
-    assert fs.session.default_resource == "demoResc"
-
-
 def test_irods_live_touch():
     settings = _irods_live_settings()
     _skip_if_irods_unreachable(settings["host"], settings["port"])
@@ -212,9 +156,8 @@ def test_irods_live_recursive_list():
     file_sources = configured_file_sources(_live_file_source_config(settings, writable=False))
     file_source_pair = file_sources.get_file_source_path("gxfiles://test1")
 
-    entries, count = file_source_pair.file_source.list("/", recursive=True)
-    assert isinstance(entries, list)
-    assert count >= 0
+    with pytest.raises(MessageException):
+        file_source_pair.file_source.list("/", recursive=True)
     _cleanup_live_test_artifacts(settings)
 
 

From cd3df9012f9e4deac3270b77cdf65c46a8147315 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Tue, 26 May 2026 23:29:28 +0200
Subject: [PATCH 036/256] Fix the OpenAPI linting

---
 client/packages/api-client/src/schema/schema.ts | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index 1ec8b2f8c34..ddc2fb8bb09 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -13044,6 +13044,7 @@ export interface components {
                 | "s3fs"
                 | "azure"
                 | "azureflat"
+                | "irods"
                 | "onedata"
                 | "webdav"
                 | "dropbox"
@@ -25350,6 +25351,7 @@ export interface components {
                 | "s3fs"
                 | "azure"
                 | "azureflat"
+                | "irods"
                 | "onedata"
                 | "webdav"
                 | "dropbox"

From a4c25be83f1cba4d29f8de961e7cef5f6cb21249 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 28 May 2026 14:03:48 +0200
Subject: [PATCH 037/256] Add check for iRODS file source and update
 conditional requirements

---
 lib/galaxy/dependencies/__init__.py                  | 3 +++
 lib/galaxy/dependencies/conditional-requirements.txt | 1 +
 test/unit/app/dependencies/test_deps.py              | 2 ++
 3 files changed, 6 insertions(+)

diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 7153f44105f..b28bf8af973 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -291,6 +291,9 @@ class ConditionalDependencies:
     def check_rspace_client(self):
         return "rspace" in self.file_sources
 
+    def check_fs_irods(self):
+        return "irods" in self.file_sources
+
     def check_watchdog(self):
         install_set = {"auto", "True", "true", "polling", True}
         return self.config["watch_tools"] in install_set or self.config["watch_tool_data_dir"] in install_set
diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index 8d84205bfd2..2c45fb5ba80 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -35,6 +35,7 @@ adlfs
 huggingface_hub
 omero-py #type: omero
 iiif-fsspec # type: iiif
+fs-irods # type: irods, depends on python-irodsclient
 
 # Vault backend
 hvac
diff --git a/test/unit/app/dependencies/test_deps.py b/test/unit/app/dependencies/test_deps.py
index 7e2f8efa03a..f36e1b929f0 100644
--- a/test/unit/app/dependencies/test_deps.py
+++ b/test/unit/app/dependencies/test_deps.py
@@ -25,6 +25,7 @@ FILES_SOURCES_CONFIG = """
 - type: webdav
 - type: dropbox
 - type: googledrive
+- type: irods
 """
 JOB_CONF_YAML = """
 runners:
@@ -95,6 +96,7 @@ def test_fs_configured():
         assert cds.check_gdrive_fsspec()
         assert cds.check_dropboxdrivefs()
         assert cds.check_webdav4()
+        assert cds.check_fs_irods()
 
 
 def test_yaml_jobconf_runners():

From 8eccf2577a4b0bd39bcf4d97d04cea616e432dae Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 28 May 2026 14:10:41 +0200
Subject: [PATCH 038/256] Remove unused imports from test_irods.py

---
 test/unit/files/test_irods.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/test/unit/files/test_irods.py b/test/unit/files/test_irods.py
index e7b21e88562..8396dc108e0 100644
--- a/test/unit/files/test_irods.py
+++ b/test/unit/files/test_irods.py
@@ -5,11 +5,6 @@ import pytest
 import yaml
 
 from galaxy.exceptions import MessageException
-from galaxy.files.models import (
-    FileSourcePluginsConfig,
-    FilesSourceRuntimeContext,
-    UserData,
-)
 from galaxy.files.plugins import FileSourcePluginLoader
 from galaxy.files.sources.irods import IrodsFilesSource
 from ._util import (

From 1fd2a3fad48d8a3fa91560c8d38488110670beb1 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 28 May 2026 16:12:13 +0200
Subject: [PATCH 039/256] Add iRODS file source type to templateTypes

---
 client/src/api/fileSources.ts | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/client/src/api/fileSources.ts b/client/src/api/fileSources.ts
index e7121c3a270..008775f999b 100644
--- a/client/src/api/fileSources.ts
+++ b/client/src/api/fileSources.ts
@@ -91,6 +91,10 @@ export const templateTypes: FileSourceTypesDetail = {
         icon: faNetworkWired,
         message: "This is a file repository plugin that connects with a remote server over SSH.",
     },
+    irods: {
+        icon: faNetworkWired,
+        message: "This is a file repository plugin that connects with an iRODS server.",
+    },
 };
 
 export const FileSourcesValidFilters = {

From 8a6f311c6bdcdcf88638d7a2333019298c0b079b Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Fri, 5 Jun 2026 04:42:52 +0200
Subject: [PATCH 040/256] try to optimize the purge_historyless_hdas case

---
 scripts/cleanup_datasets/pgcleanup.py | 42 ++++++++++++++++-----------
 1 file changed, 25 insertions(+), 17 deletions(-)

diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index c88a44e9c32..6921911ac03 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -215,35 +215,38 @@ class Action:
             args["days"] = self._days
         return args
 
-    def _collect_row_results(self, row, results, primary_key):
-        primary_key = row._fields[0]
-        primary = getattr(row, primary_key)
-        if primary not in results:
-            results[primary] = [set() for x in range(len(self.causals))]
+    def _collect_row_results(self, row, results):
         rowgetter = partial(getattr, row)
         for i, causal in enumerate(self.causals):
             vals = tuple(map(rowgetter, causal))
             if any(vals[1:]):
-                results[primary][i].add(vals)
+                results[i].add(vals)
 
-    def _log_results(self, results, primary_key):
-        for primary in sorted(results.keys()):
-            self.log.info(f"{primary_key}: {primary}")
-            for causal, s in zip(self.causals, results[primary]):
-                for r in sorted(s):
-                    secondaries = ", ".join(f"{x[0]}: {x[1]}" for x in zip(causal[1:], r[1:]))
-                    self.log.info(f"{causal[0]} {r[0]} caused {secondaries}")
+    def _log_results(self, primary, results, primary_key):
+        self.log.info(f"{primary_key}: {primary}")
+        for causal, s in zip(self.causals, results):
+            for r in sorted(s):
+                secondaries = ", ".join(f"{x[0]}: {x[1]}" for x in zip(causal[1:], r[1:]))
+                self.log.info(f"{causal[0]} {r[0]} caused {secondaries}")
 
     def handle_results(self, cur):
-        results = {}
         primary_key = self.primary_key
+        primary = None
+        results = None
         for row in cur:
             if primary_key is None:
                 primary_key = row._fields[0]
-            self._collect_row_results(row, results, primary_key)
+            row_primary = getattr(row, primary_key)
+            if results is None or row_primary != primary:
+                if results is not None:
+                    self._log_results(primary, results, primary_key)
+                primary = row_primary
+                results = [set() for x in range(len(self.causals))]
+            self._collect_row_results(row, results)
             for method in self.__row_methods:
                 method(row)
-        self._log_results(results, primary_key)
+        if results is not None:
+            self._log_results(primary, results, primary_key)
         for method in self.__post_methods:
             method()
 
@@ -261,6 +264,7 @@ class RemovesObjects:
     """Base class for mixins that remove objects from object stores."""
 
     requires_objectstore = True
+    object_removal_batch_size = 1000
 
     def _init(self):
         super()._init()
@@ -276,10 +280,13 @@ class RemovesObjects:
             object_uuid = str(uuid.UUID(object_uuid))
         if object_id:
             self.objects_to_remove.add(self.object_class(object_id, row.object_store_id, object_uuid))
+            if len(self.objects_to_remove) >= self.object_removal_batch_size:
+                self.remove_objects()
 
     def remove_objects(self):
         for object_to_remove in sorted(self.objects_to_remove):
             self.remove_object(object_to_remove)
+        self.objects_to_remove.clear()
 
     def remove_from_object_store(self, object_to_remove, object_store_kwargs, entire_dir=False, check_exists=False):
         # only remove the "object store path" - if it's at an external_filename, that file will be untouched anyway
@@ -905,7 +912,8 @@ class PurgeHistorylessHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRe
           AS (     UPDATE history_dataset_association
                       SET purged = true, deleted = true{update_time_sql}
                      FROM dataset
-                    WHERE history_id IS NULL{force_retry_sql}{object_store_id_sql}
+                    WHERE history_dataset_association.dataset_id = dataset.id
+                          AND history_id IS NULL{force_retry_sql}{object_store_id_sql}
                           AND history_dataset_association.update_time < (NOW() AT TIME ZONE 'utc' - (:days * interval '1 day'))
                 RETURNING history_dataset_association.id as id,
                           history_dataset_association.history_id as history_id),

From d83c8e102e93f3df1e5e9dd84c23b92d58836cda Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 6 Jun 2026 13:23:11 +0200
Subject: [PATCH 041/256] Drop overly defensive getattre

---
 lib/galaxy/celery/__init__.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index d6501248e98..a251ebadd22 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -287,16 +287,12 @@ def setup_periodic_tasks(config, celery_app):
     # serves the gtn_training agent, which only functions when inference_services
     # is set up. Without this gate every Galaxy install would pull from depot
     # on the default interval, even ones that don't use the agent.
-    if (
-        getattr(config, "inference_services", None)
-        and config.gtn_database_refresh_interval
-        and config.gtn_database_path
-    ):
+    if config.inference_services and config.gtn_database_refresh_interval and config.gtn_database_path:
         schedule_task("refresh_gtn_database", config.gtn_database_refresh_interval)
 
     # IWC manifest pre-warm only matters when the agent-ops layer is exposed --
     # same inference_services gate as the GTN refresh above.
-    if getattr(config, "inference_services", None) and config.iwc_manifest_refresh_interval:
+    if config.inference_services and config.iwc_manifest_refresh_interval:
         schedule_task("refresh_iwc_manifest", config.iwc_manifest_refresh_interval)
 
     if config.celery_user_concurrency_limit:

From 310c7795fd3c76b81a38fddcc974c15354563d48 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 6 Jun 2026 16:09:42 +0200
Subject: [PATCH 042/256] implement batch-size

---
 scripts/cleanup_datasets/pgcleanup.py | 29 +++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index 6921911ac03..5a140aacfa4 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -118,6 +118,7 @@ class Action:
             self._object_store_id_sql = ""
         self._epoch_time = str(int(time.time()))
         self._days = app.args.days
+        self._batch_size = app.args.batch_size
         self._config = app.config
         self._update = app._update
         self.__log = None
@@ -213,6 +214,7 @@ class Action:
         args = self._action_sql_args.copy()
         if "days" not in args:
             args["days"] = self._days
+        args["batch_size"] = self._batch_size
         return args
 
     def _collect_row_results(self, row, results):
@@ -287,6 +289,7 @@ class RemovesObjects:
         for object_to_remove in sorted(self.objects_to_remove):
             self.remove_object(object_to_remove)
         self.objects_to_remove.clear()
+        self.objects_to_remove.clear()
 
     def remove_from_object_store(self, object_to_remove, object_store_kwargs, entire_dir=False, check_exists=False):
         # only remove the "object store path" - if it's at an external_filename, that file will be untouched anyway
@@ -412,6 +415,7 @@ class RequiresDiskUsageRecalculation:
                 self._update(sql, args, add_event=False)
 
             self.log.info("recalculate_disk_usage user_id %i", user_id)
+        self.__recalculate_disk_usage_user_ids.clear()
 
 
 class RemovesMetadataFiles(RemovesObjects):
@@ -471,13 +475,19 @@ class UpdateHDAPurgedFlag(Action):
 
     # update_time is intentionally left unmodified.
     _action_sql = """
-        WITH purged_hda_ids
+        WITH batch_ids
+          AS (SELECT history_dataset_association.id
+                FROM history_dataset_association
+                JOIN dataset ON history_dataset_association.dataset_id = dataset.id
+               WHERE dataset.purged
+                     AND NOT history_dataset_association.purged
+               ORDER BY history_dataset_association.id
+               LIMIT :batch_size),
+              purged_hda_ids
           AS (     UPDATE history_dataset_association
                       SET purged = true, deleted = true
-                     FROM dataset
-                        WHERE history_dataset_association.dataset_id = dataset.id
-                          AND dataset.purged
-                          AND NOT history_dataset_association.purged
+                    FROM batch_ids
+                   WHERE history_dataset_association.id = batch_ids.id
                 RETURNING history_dataset_association.id),
              hda_events
           AS (INSERT INTO cleanup_event_hda_association
@@ -486,7 +496,6 @@ class UpdateHDAPurgedFlag(Action):
                      FROM purged_hda_ids)
       SELECT id AS purged_hda_id
         FROM purged_hda_ids
-    ORDER BY id;
     """
 
 
@@ -1264,6 +1273,14 @@ class Cleanup:
         parser.add_argument(
             "-w", "--work-mem", dest="work_mem", default=None, help="Set PostgreSQL work_mem for this connection"
         )
+        parser.add_argument(
+            "-b",
+            "--batch-size",
+            dest="batch_size",
+            type=int,
+            default=5000,
+            help="Process rows in batches of the given size (default: 5000)",
+        )
         parser.add_argument("-l", "--log-dir", default=DEFAULT_LOG_DIR, help="Log file directory")
         parser.add_argument("-g", "--log-file", default=None, help="Log file name")
         parser.add_argument(

From 7be9e24e1738f07cdeb3df461c62c855f72c47d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 10 Jun 2026 03:04:38 +0200
Subject: [PATCH 043/256] Remove duplicate clear call in remove_objects method

Removed redundant call to clear objects_to_remove.
---
 scripts/cleanup_datasets/pgcleanup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index 5a140aacfa4..3b32cbd2404 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -289,7 +289,6 @@ class RemovesObjects:
         for object_to_remove in sorted(self.objects_to_remove):
             self.remove_object(object_to_remove)
         self.objects_to_remove.clear()
-        self.objects_to_remove.clear()
 
     def remove_from_object_store(self, object_to_remove, object_store_kwargs, entire_dir=False, check_exists=False):
         # only remove the "object store path" - if it's at an external_filename, that file will be untouched anyway

From 356ceabc1a703a2a58916a7d24e7c991aa0387ee Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 10 Jun 2026 14:29:35 +0200
Subject: [PATCH 044/256] Update tiffviewer to v0.0.5

---
 client/visualizations.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/visualizations.yml b/client/visualizations.yml
index 41a072c891e..82ce07ba1e8 100644
--- a/client/visualizations.yml
+++ b/client/visualizations.yml
@@ -110,7 +110,7 @@ tabulator:
     version: 0.0.9
 tiffviewer:
     package: "@galaxyproject/tiffviewer"
-    version: 0.0.4
+    version: 0.0.5
 ts_visjs:
     package: "@galaxyproject/ts_visjs"
     version: 0.0.6

From b022bda4157161c31df429deaa82d3ed6b414081 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 9 Jun 2026 16:01:36 -0400
Subject: [PATCH 045/256] Handle existing rows in tool_source during db
 migration

---
 ...91307a5_persist_validated_job_internal_tool_.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/566b691307a5_persist_validated_job_internal_tool_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/566b691307a5_persist_validated_job_internal_tool_.py
index 05fed8a427a..c5f9956b4eb 100644
--- a/lib/galaxy/model/migrations/alembic/versions_gxy/566b691307a5_persist_validated_job_internal_tool_.py
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/566b691307a5_persist_validated_job_internal_tool_.py
@@ -6,6 +6,7 @@ Create Date: 2025-09-30 04:48:19.727414
 
 """
 
+from alembic import op
 from sqlalchemy import (
     Column,
     Integer,
@@ -55,7 +56,18 @@ def upgrade():
         # Add tool_source.source_class as a new NOT NULL string column
         add_column(
             tool_source_table_name,
-            Column(tool_source_source_class_column, String(255), nullable=False),
+            Column(tool_source_source_class_column, String(255)),
+        )
+
+        # Set tool_source.source_class on existing rows
+        op.execute("UPDATE tool_source SET source_class = 'YamlToolSource' WHERE source_class IS NULL")
+
+        # Set nullable on tool_source.source_class
+        alter_column(
+            tool_source_table_name,
+            tool_source_source_class_column,
+            existing_type=String(255),
+            nullable=False,
         )
 
 

From 5c47d4235efd0ebfa6570036dbc70423236e5dd0 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 3 Jun 2026 17:23:06 -0500
Subject: [PATCH 046/256] associate history_id automatically with page on
 invocation report creation

---
 client/src/components/PageDisplay/PageForm.vue | 2 ++
 lib/galaxy/managers/pages.py                   | 5 +++++
 2 files changed, 7 insertions(+)

diff --git a/client/src/components/PageDisplay/PageForm.vue b/client/src/components/PageDisplay/PageForm.vue
index 400c4e83403..427a2bd3c22 100644
--- a/client/src/components/PageDisplay/PageForm.vue
+++ b/client/src/components/PageDisplay/PageForm.vue
@@ -114,6 +114,8 @@ async function onSubmit() {
         });
         if (error) {
             errorMessage.value = error.err_msg;
+        } else if (data.history_id) {
+            router.push(`/histories/${data.history_id}/pages/${data.id}`);
         } else {
             router.push(`/pages/editor?id=${data.id}`);
         }
diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index a65d136ff9c..b74ac813d1b 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -272,6 +272,11 @@ class PageManager(sharable.SharableModelManager[model.Page], UsesAnnotations):
         user = trans.get_user()
         history_id = getattr(payload, "history_id", None)
 
+        # When creating from an invocation, automatically attach to its history
+        if payload.invocation_id and not history_id:
+            invocation = self.workflow_manager.get_invocation(trans, payload.invocation_id)
+            history_id = invocation.history_id
+
         # Slug validation: required for non-history pages
         if history_id:
             # Verify user owns the history

From 4a543797ca36b49692e94fd0d0519261263475ff Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 9 Jun 2026 16:48:48 -0500
Subject: [PATCH 047/256] only check for accessibility, not ownership when
 creating history page

Fixes https://github.com/galaxyproject/galaxy/issues/22859
---
 lib/galaxy/managers/pages.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index b74ac813d1b..a961188a6e6 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -274,17 +274,19 @@ class PageManager(sharable.SharableModelManager[model.Page], UsesAnnotations):
 
         # When creating from an invocation, automatically attach to its history
         if payload.invocation_id and not history_id:
-            invocation = self.workflow_manager.get_invocation(trans, payload.invocation_id)
+            invocation = self.workflow_manager.get_invocation(
+                trans, payload.invocation_id, check_ownership=False, check_accessible=True
+            )
             history_id = invocation.history_id
 
         # Slug validation: required for non-history pages
         if history_id:
-            # Verify user owns the history
+            # Get the accessible history
             history = trans.sa_session.get(model.History, history_id)
             if not history:
                 raise exceptions.ObjectNotFound("History not found")
-            if history.user != user:
-                raise exceptions.ItemOwnershipException("Cannot create page on history you do not own")
+            base.security_check(trans, history, check_ownership=False, check_accessible=True)
+
             # History-attached pages don't need a slug
             content_format = payload.content_format or "markdown"
             content = payload.content or ""

From c19929fdbc79aacb0b674360364e99f8349547df Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Tue, 9 Jun 2026 16:51:03 -0500
Subject: [PATCH 048/256] add tests for accessible-not-owned history and
 invocation page creation

---
 .../api/test_pages_history_attached.py        | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/lib/galaxy_test/api/test_pages_history_attached.py b/lib/galaxy_test/api/test_pages_history_attached.py
index 981a58f17da..062e8401646 100644
--- a/lib/galaxy_test/api/test_pages_history_attached.py
+++ b/lib/galaxy_test/api/test_pages_history_attached.py
@@ -3,6 +3,7 @@
 from galaxy_test.base.populators import (
     DatasetPopulator,
     skip_without_agents,
+    skip_without_tool,
 )
 from .test_pages import BasePagesApiTestCase
 
@@ -274,6 +275,50 @@ class TestHistoryPagesApi(BasePagesApiTestCase):
             )
             self._assert_status_code_is(update_response, 403)
 
+    def test_history_page_accessible_history_create(self):
+        # Published (accessible but not owned) history — user should be able to create a page on it.
+        history_id = self.dataset_populator.new_history()
+        self._put(f"histories/{history_id}/publish", json=True)
+        with self._different_user():
+            payload = {"history_id": history_id, "content": "# Shared page", "content_format": "markdown"}
+            create_response = self._post("pages", payload, json=True)
+            self._assert_status_code_is(create_response, 200)
+            assert create_response.json()["history_id"] == history_id
+
+    @skip_without_tool("cat")
+    def test_accessible_invocation_create_page(self):
+        # Invocation whose history is published — another user can create a page via invocation_id.
+        test_data = """
+input_1:
+  value: 1.bed
+  type: File
+"""
+        with self.dataset_populator.test_history() as history_id:
+            summary = self.workflow_populator.run_workflow(
+                """
+class: GalaxyWorkflow
+inputs:
+  input_1: data
+outputs:
+  output_1:
+    outputSource: first_cat/out_file1
+steps:
+  first_cat:
+    tool_id: cat
+    in:
+      input1: input_1
+""",
+                test_data=test_data,
+                history_id=history_id,
+            )
+            invocation_id = summary.invocation_id
+            self._put(f"histories/{history_id}/publish", json=True)
+            with self._different_user():
+                payload = {"invocation_id": invocation_id, "title": "Shared Invocation Page"}
+                create_response = self._post("pages", payload, json=True)
+                self._assert_status_code_is(create_response, 200)
+                assert create_response.json()["history_id"] == history_id
+
     # --- A5: Cross-Type Validation ---
 
     def test_history_page_ignores_slug(self):

From a3b59371c8be7b71b62f77efe1147d99f643e322 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 17:30:38 -0500
Subject: [PATCH 049/256] add notebook context detection to useActiveContext

Adds a `notebook` variant to the `ActiveContext` union type, detected from the
`/histories/:historyId/pages/:pageId` route. Both `pageId` and `historyId` are
exposed so downstream consumers can scope chat and proposals to the right page
without additional lookups.

GalaxyAI.vue gains the `faBook` icon branch for notebook context so the context
indicator already renders correctly when the user is editing a history notebook.

Covers the new branch with vitest cases for both detection and labeling.

Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: John Chilton <jmchilton@gmail.com>
---
 client/src/components/GalaxyAI.vue            |  4 ++-
 .../src/composables/useActiveContext.test.ts  | 27 +++++++++++++++++++
 client/src/composables/useActiveContext.ts    | 13 ++++++++-
 3 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index 1ecfda352a2..66fe69b5250 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faFile, faMagic, faSitemap, faTimes, faTrash, faWrench } from "@fortawesome/free-solid-svg-icons";
+import { faBook, faFile, faMagic, faSitemap, faTimes, faTrash, faWrench } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BSkeleton } from "bootstrap-vue";
 import { computed, nextTick, onMounted, ref, watch } from "vue";
@@ -68,6 +68,8 @@ const contextIcon = computed(() => {
         case "workflow_editor":
         case "workflow_run":
             return faSitemap;
+        case "notebook":
+            return faBook;
         default:
             return faMagic;
     }
diff --git a/client/src/composables/useActiveContext.test.ts b/client/src/composables/useActiveContext.test.ts
index 7d16ddefc21..c39ff8b321e 100644
--- a/client/src/composables/useActiveContext.test.ts
+++ b/client/src/composables/useActiveContext.test.ts
@@ -118,6 +118,24 @@ describe("useActiveContext", () => {
                 jobId: "job-7",
             });
         });
+
+        it("detects notebook context from page editor route", () => {
+            const { activeContext } = withRoute(
+                "/histories/test-history-id/pages/test-page-id",
+                {},
+                { historyId: "test-history-id", pageId: "test-page-id" },
+            );
+            expect(activeContext.value).toEqual({
+                contextType: "notebook",
+                pageId: "test-page-id",
+                historyId: "test-history-id",
+            });
+        });
+
+        it("returns null for page editor route without id", () => {
+            const { activeContext } = withRoute("/pages/editor");
+            expect(activeContext.value).toBeNull();
+        });
     });
 
     describe("contextLabel", () => {
@@ -160,5 +178,14 @@ describe("useActiveContext", () => {
             const { contextLabel } = withRoute("/jobs/j-5", {}, { jobId: "j-5" });
             expect(contextLabel.value).toBe("Job: j-5");
         });
+
+        it("labels notebook context", () => {
+            const { contextLabel } = withRoute(
+                "/histories/test-history-id/pages/test-page-id",
+                {},
+                { historyId: "test-history-id", pageId: "test-page-id" },
+            );
+            expect(contextLabel.value).toBe("History Notebook: test-page-id");
+        });
     });
 });
diff --git a/client/src/composables/useActiveContext.ts b/client/src/composables/useActiveContext.ts
index e931702a100..c67ed329527 100644
--- a/client/src/composables/useActiveContext.ts
+++ b/client/src/composables/useActiveContext.ts
@@ -8,7 +8,8 @@ export type ActiveContext =
     | { contextType: "dataset"; datasetId: string }
     | { contextType: "workflow_editor"; workflowId: string }
     | { contextType: "workflow_run"; workflowId: string }
-    | { contextType: "job"; jobId: string; toolId?: string };
+    | { contextType: "job"; jobId: string; toolId?: string }
+    | { contextType: "notebook"; pageId: string; historyId: string };
 
 export function useActiveContext() {
     const route = useRoute();
@@ -67,6 +68,14 @@ export function useActiveContext() {
             };
         }
 
+        if (path.startsWith("/histories/") && params.historyId && params.pageId) {
+            return {
+                contextType: "notebook",
+                pageId: String(params.pageId),
+                historyId: String(params.historyId),
+            };
+        }
+
         return null;
     });
 
@@ -86,6 +95,8 @@ export function useActiveContext() {
                 return `Running workflow: ${ctx.workflowId}`;
             case "job":
                 return `Job: ${ctx.jobId}`;
+            case "notebook":
+                return `History Notebook: ${ctx.pageId}`;
             default:
                 return null;
         }

From f12e17aea797449e4edca1d80a033a5aad9f9dcf Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 18:10:09 -0500
Subject: [PATCH 050/256] accept notebook context in chat API via
 interface_context

The POST /api/chat endpoint now recognises `{"contextType": "notebook", "pageId": "..."}` in the JSON `context` field as an alternative to the legacy `payload.page_id` field. When detected, the encoded page ID is decoded and the existing page access-check and content-injection path is reused unchanged, keeping the two surfaces in sync without any new persistence logic.

The legacy `payload.page_id` path is left intact for one-release backward compatibility.

Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: John Chilton <jmchilton@gmail.com>
---
 lib/galaxy/webapps/galaxy/api/chat.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/lib/galaxy/webapps/galaxy/api/chat.py b/lib/galaxy/webapps/galaxy/api/chat.py
index f6070914e3b..a530f368c59 100644
--- a/lib/galaxy/webapps/galaxy/api/chat.py
+++ b/lib/galaxy/webapps/galaxy/api/chat.py
@@ -197,6 +197,26 @@ class ChatAPI:
             # being masked as 500.
             page_obj = self.chat_manager.get_accessible_page(trans, page_id)
 
+        # New unified format: notebook context via interface_context JSON.
+        # Accepts {"contextType": "notebook", "pageId": "<encoded-id>", "historyId": "<encoded-id>"}
+        # sent by GalaxyAI when the user is on the page editor route.  We decode the
+        # ID here so the rest of the handler can reuse the existing page_id path unchanged.
+        # Backward-compatible: legacy payload.page_id still works.
+        if page_id is None:
+            interface_context = query_context.get("interface_context") if isinstance(query_context, dict) else None
+            if (
+                isinstance(interface_context, dict)
+                and interface_context.get("contextType") == "notebook"
+                and interface_context.get("pageId")
+            ):
+                try:
+                    page_id = trans.security.decode_id(interface_context["pageId"])
+                    page_obj = self.chat_manager.get_accessible_page(trans, page_id)
+                except Exception:
+                    log.warning(
+                        "Ignoring invalid notebook pageId in interface_context: %s", interface_context.get("pageId")
+                    )
+
         try:
             if HAS_AGENTS:
                 full_context: dict[str, Any] = query_context.copy() if query_context else {}

From 57d154cf691d2d72020771791af29073337c2580 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 18:40:57 -0500
Subject: [PATCH 051/256] enforce `agent_type = "page_assistant"` when a
 `page_id` is in context

---
 lib/galaxy/webapps/galaxy/api/chat.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/lib/galaxy/webapps/galaxy/api/chat.py b/lib/galaxy/webapps/galaxy/api/chat.py
index a530f368c59..cd86cd3251e 100644
--- a/lib/galaxy/webapps/galaxy/api/chat.py
+++ b/lib/galaxy/webapps/galaxy/api/chat.py
@@ -259,6 +259,11 @@ class ChatAPI:
                 if payload and payload.entity_context:
                     full_context["entities"] = payload.entity_context.model_dump(exclude_none=True)
 
+                # When we already know this is a notebook chat, bypass the router
+                # and go straight to page_assistant — no need for an LLM to decide.
+                if page_id and agent_type == "auto":
+                    agent_type = "page_assistant"
+
                 agent_response = await self._get_agent_response_full(
                     query_text, agent_type, trans, user, job, full_context
                 )

From adec3e9dd5018f3b23dd4c4b3302eb9e781c33ef Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 20:18:51 -0500
Subject: [PATCH 052/256] use notebook context to conditionally fetch chats for
 a page id in main panel

---
 .../packages/api-client/src/schema/schema.ts  |  2 ++
 .../components/GalaxyAI/ChatHistoryPanel.vue  | 19 +++++++++++++++++--
 client/src/stores/chatStore.ts                |  4 ++--
 lib/galaxy/managers/chat.py                   |  8 +++++++-
 lib/galaxy/webapps/galaxy/api/chat.py         | 10 ++++++++--
 5 files changed, 36 insertions(+), 7 deletions(-)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index ddc2fb8bb09..2341a92935c 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -31485,6 +31485,8 @@ export interface operations {
             query?: {
                 /** @description Maximum number of chats to return */
                 limit?: number;
+                /** @description When provided, include chats for this page alongside general chats. */
+                page_id?: string | null;
             };
             header?: {
                 /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
diff --git a/client/src/components/GalaxyAI/ChatHistoryPanel.vue b/client/src/components/GalaxyAI/ChatHistoryPanel.vue
index d9110bca74f..ea41961b73b 100644
--- a/client/src/components/GalaxyAI/ChatHistoryPanel.vue
+++ b/client/src/components/GalaxyAI/ChatHistoryPanel.vue
@@ -3,11 +3,12 @@ import { faCheckSquare, faSquare } from "@fortawesome/free-regular-svg-icons";
 import { faClock, faPlus, faTimes, faTrash } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { storeToRefs } from "pinia";
-import { computed, onMounted } from "vue";
+import { computed, onMounted, watch } from "vue";
 import { useRoute, useRouter } from "vue-router/composables";
 
 import { useConfirmDialog } from "@/composables/confirmDialog";
 import { useToast } from "@/composables/toast";
+import { useActiveContext } from "@/composables/useActiveContext";
 import { useSidebarSelection } from "@/composables/useSidebarSelection";
 import { useChatStore } from "@/stores/chatStore";
 import { errorMessageAsString } from "@/utils/simple-error";
@@ -26,6 +27,12 @@ const Toast = useToast();
 const route = useRoute();
 const router = useRouter();
 const chatStore = useChatStore();
+const { activeContext } = useActiveContext();
+
+const notebookPageId = computed(() => {
+    const ctx = activeContext.value;
+    return ctx?.contextType === "notebook" ? ctx.pageId : undefined;
+});
 
 const { chatHistory, loading } = storeToRefs(chatStore);
 
@@ -49,7 +56,15 @@ const currentExchangeId = computed(() => {
 
 onMounted(async () => {
     try {
-        await chatStore.loadHistory();
+        await chatStore.loadHistory(notebookPageId.value);
+    } catch (e) {
+        Toast.error(errorMessageAsString(e), "Failed to load chat history");
+    }
+});
+
+watch(notebookPageId, async (pageId) => {
+    try {
+        await chatStore.loadHistory(pageId);
     } catch (e) {
         Toast.error(errorMessageAsString(e), "Failed to load chat history");
     }
diff --git a/client/src/stores/chatStore.ts b/client/src/stores/chatStore.ts
index 9847e132aa6..f83e0c24bfd 100644
--- a/client/src/stores/chatStore.ts
+++ b/client/src/stores/chatStore.ts
@@ -71,10 +71,10 @@ export const useChatStore = defineStore("chatStore", () => {
         }
     }
 
-    async function loadHistory() {
+    async function loadHistory(pageId?: string) {
         loading.value = true;
         const { data, error } = await GalaxyApi().GET("/api/chat/history", {
-            params: { query: { limit: 50 } },
+            params: { query: { limit: 50, ...(pageId ? { page_id: pageId } : {}) } },
         });
 
         loading.value = false;
diff --git a/lib/galaxy/managers/chat.py b/lib/galaxy/managers/chat.py
index a8cc60b5cff..763baa606e3 100644
--- a/lib/galaxy/managers/chat.py
+++ b/lib/galaxy/managers/chat.py
@@ -14,6 +14,7 @@ from pydantic_ai.messages import (
 )
 from sqlalchemy import (
     and_,
+    or_,
     select,
 )
 from sqlalchemy.exc import (
@@ -372,6 +373,7 @@ class ChatManager:
         limit: int = 50,
         include_job_chats: bool = False,
         include_page_chats: bool = False,
+        page_id: Optional[int] = None,
     ) -> list[ChatExchange]:
         """
         Get all chat exchanges for a user.
@@ -379,6 +381,7 @@ class ChatManager:
         :param limit: Maximum number of exchanges to return
         :param include_job_chats: Whether to include job-related chats
         :param include_page_chats: Whether to include page-scoped chats
+        :param page_id: When given, include chats for this specific page alongside general chats
         :returns: List of ChatExchange objects
         """
         try:
@@ -387,7 +390,10 @@ class ChatManager:
             if not include_job_chats:
                 stmt = stmt.where(ChatExchange.job_id.is_(None))
 
-            if not include_page_chats:
+            if page_id is not None:
+                # General chats (no page) plus chats for this specific page
+                stmt = stmt.where(or_(ChatExchange.page_id.is_(None), ChatExchange.page_id == page_id))
+            elif not include_page_chats:
                 stmt = stmt.where(ChatExchange.page_id.is_(None))
 
             stmt = stmt.order_by(ChatExchange.id.desc()).limit(limit)
diff --git a/lib/galaxy/webapps/galaxy/api/chat.py b/lib/galaxy/webapps/galaxy/api/chat.py
index cd86cd3251e..5d817360dc8 100644
--- a/lib/galaxy/webapps/galaxy/api/chat.py
+++ b/lib/galaxy/webapps/galaxy/api/chat.py
@@ -331,11 +331,17 @@ class ChatAPI:
     def get_chat_history(
         self,
         limit: int = Query(default=50, description="Maximum number of chats to return"),
+        page_id: Optional[DecodedDatabaseIdField] = Query(
+            default=None,
+            description="When provided, include chats for this page alongside general chats.",
+        ),
         trans: ProvidesUserContext = DependsOnTrans,
         user: User = DependsOnUser,
     ) -> list[ChatHistoryItemResponse]:
-        """Get user's chat history."""
-        exchanges = self.chat_manager.get_user_chat_history(trans, limit=limit, include_job_chats=False)
+        """Get user's chat history, optionally including chats for a specific page."""
+        exchanges = self.chat_manager.get_user_chat_history(
+            trans, limit=limit, include_job_chats=False, page_id=page_id
+        )
         return self._format_exchange_history(exchanges)
 
     @router.get("/api/chat/page/{page_id}/history", unstable=True)

From 3c4acca453c19b70375e8ad6b88247cc17a7086b Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 20:57:54 -0500
Subject: [PATCH 053/256] open docked GalaxyAI when on notebook route

---
 client/src/components/ActivityBar/ActivityBar.vue | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/client/src/components/ActivityBar/ActivityBar.vue b/client/src/components/ActivityBar/ActivityBar.vue
index 43a5926b73a..80dffbc594d 100644
--- a/client/src/components/ActivityBar/ActivityBar.vue
+++ b/client/src/components/ActivityBar/ActivityBar.vue
@@ -8,6 +8,7 @@ import { useRoute, useRouter } from "vue-router/composables";
 import draggable from "vuedraggable";
 
 import { useConfig } from "@/composables/config";
+import { useActiveContext } from "@/composables/useActiveContext";
 import { convertDropData } from "@/stores/activitySetup";
 import { useActivityStore } from "@/stores/activityStore";
 import type { Activity } from "@/stores/activityStoreTypes";
@@ -82,6 +83,7 @@ const route = useRoute();
 const router = useRouter();
 const userStore = useUserStore();
 const chatStore = useChatStore();
+const { activeContext } = useActiveContext();
 
 const eventStore = useEventStore();
 const activityStore = useActivityStore(props.activityBarId);
@@ -239,6 +241,18 @@ function toggleSidebar(toggle: string = "", to: string | null = null) {
 }
 
 function onChatGxyClick() {
+    // On notebook routes, always use the right panel — never navigate to center.
+    if (activeContext.value?.contextType === "notebook") {
+        if (chatStore.isCenterMode) {
+            chatStore.setLocation("right");
+        }
+        chatStore.toggleChat();
+        if (isActiveSideBar("galaxyai")) {
+            toggleSidebar("galaxyai");
+        }
+        return;
+    }
+
     if (chatStore.isCenterMode) {
         toggleSidebar("galaxyai");
         if (!route.path.startsWith("/galaxyai")) {

From a39ea8d82c528824aa5bead9359a8c80d28cea61 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 22:45:56 -0500
Subject: [PATCH 054/256] sync `currentChatExchangeId` for notebook chats in
 GalaxyAI component

Since we're using the global GalaxyAI component for history notebooks, we sync the `currentChatExchangeId` from `pageEditorStore` in that central component when on a notebook (route).
---
 client/src/components/GalaxyAI.vue | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index 66fe69b5250..f5ec0c2df54 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -13,6 +13,7 @@ import { useToast } from "@/composables/toast";
 import { useActiveContext } from "@/composables/useActiveContext";
 import { buildEntityContext, parseMentions, resolveMentions } from "@/composables/useEntityMentions";
 import { useChatStore } from "@/stores/chatStore";
+import { usePageEditorStore } from "@/stores/pageEditorStore";
 import { errorMessageAsString } from "@/utils/simple-error";
 
 import { getAgentIcon } from "./GalaxyAI/agentTypes";
@@ -46,6 +47,7 @@ const chatStore = useChatStore();
 const Toast = useToast();
 
 const { activeContext, contextLabel } = useActiveContext();
+const pageEditorStore = usePageEditorStore();
 const contextDismissed = ref(false);
 
 watch(activeContext, () => {
@@ -94,7 +96,19 @@ onMounted(async () => {
     if (props.exchangeId && props.exchangeId !== "new") {
         await fetchConversation(props.exchangeId);
     } else if (props.docked || props.panel || props.exchangeId === "new") {
-        startNewChat();
+        // In panel/docked mode with notebook context: restore the cached exchange
+        // for this page if one exists and no chat is already active.
+        const ctx = activeContext.value;
+        if (ctx?.contextType === "notebook" && !chatStore.activeChatId) {
+            const cachedId = pageEditorStore.getCurrentChatExchangeId(ctx.pageId);
+            if (cachedId) {
+                await fetchConversation(cachedId);
+            } else {
+                startNewChat();
+            }
+        } else {
+            startNewChat();
+        }
     } else {
         await loadLatestChat();
     }
@@ -391,6 +405,12 @@ function dockTo(location: "right" | "bottom") {
 watch(currentChatId, async (newId) => {
     if (props.docked || props.panel) {
         chatStore.setActiveChatId(newId);
+
+        // Keep the per-page cache in sync so reopening the panel restores this exchange.
+        const ctx = activeContext.value;
+        if (ctx?.contextType === "notebook") {
+            pageEditorStore.setCurrentChatExchangeId(ctx.pageId, newId);
+        }
     }
 
     if (newId && !chatStore.chatHistory.some((item) => item.id === newId)) {

From 6b37452e402bab141bf09556de519f59e0c61f17 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 22:47:32 -0500
Subject: [PATCH 055/256] show dock operation buttons on docked chats as well

---
 .../src/components/GalaxyAI/ChatActions.vue   | 24 ++++++++++++-------
 client/src/components/GalaxyAI/ChatPanel.vue  | 13 +++++++++-
 2 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/client/src/components/GalaxyAI/ChatActions.vue b/client/src/components/GalaxyAI/ChatActions.vue
index 4a27b07871d..5bb475819be 100644
--- a/client/src/components/GalaxyAI/ChatActions.vue
+++ b/client/src/components/GalaxyAI/ChatActions.vue
@@ -117,14 +117,22 @@ function onDockTo(location: "right" | "bottom") {
             @click="maximize">
             <FontAwesomeIcon :icon="faExpand" fixed-width />
         </GButton>
-        <template v-if="props.source === 'center'">
-            <GButton size="small" transparent title="Dock to side panel" @click="onDockTo('right')">
-                <FontAwesomeIcon :icon="faColumns" fixed-width />
-            </GButton>
-            <GButton size="small" transparent title="Dock to bottom panel" @click="onDockTo('bottom')">
-                <FontAwesomeIcon :icon="faAngleDoubleDown" fixed-width />
-            </GButton>
-        </template>
+        <GButton
+            v-if="props.source !== 'docked'"
+            size="small"
+            transparent
+            title="Dock to side panel"
+            @click="onDockTo('right')">
+            <FontAwesomeIcon :icon="faColumns" fixed-width />
+        </GButton>
+        <GButton
+            v-if="props.source !== 'panel'"
+            size="small"
+            transparent
+            title="Dock to bottom panel"
+            @click="onDockTo('bottom')">
+            <FontAwesomeIcon :icon="faAngleDoubleDown" fixed-width />
+        </GButton>
         <GButton size="small" transparent title="Open in floating window" @click="popOut">
             <FontAwesomeIcon :icon="faExternalLinkAlt" fixed-width />
         </GButton>
diff --git a/client/src/components/GalaxyAI/ChatPanel.vue b/client/src/components/GalaxyAI/ChatPanel.vue
index 70faa669f85..1377ccae561 100644
--- a/client/src/components/GalaxyAI/ChatPanel.vue
+++ b/client/src/components/GalaxyAI/ChatPanel.vue
@@ -1,6 +1,7 @@
 <script setup lang="ts">
 import { storeToRefs } from "pinia";
 import { ref } from "vue";
+import { useRoute, useRouter } from "vue-router/composables";
 
 import { useChatStore } from "@/stores/chatStore";
 
@@ -10,14 +11,24 @@ import GalaxyAI from "@/components/GalaxyAI.vue";
 const chatStore = useChatStore();
 const { activeChatId } = storeToRefs(chatStore);
 
+const route = useRoute();
+const router = useRouter();
+
 const collapsed = ref(false);
+
+function dockTo(location: "right" | "bottom") {
+    chatStore.dockChat(location, activeChatId.value);
+    if (route.path.startsWith("/galaxyai")) {
+        router.push("/");
+    }
+}
 </script>
 
 <template>
     <div class="chat-panel" :class="collapsed ? 'collapsed' : 'expanded'">
         <div class="chat-panel-header">
             <span class="chat-panel-title">GalaxyAI</span>
-            <ChatActions source="panel" :collapsed.sync="collapsed" />
+            <ChatActions source="panel" :collapsed.sync="collapsed" @dock-to="dockTo" />
         </div>
         <div v-show="!collapsed" class="chat-panel-body">
             <GalaxyAI :exchange-id="activeChatId || undefined" panel />

From b19d89fba52ab2cab34c81da4e858ef40b7643a8 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 23:01:03 -0500
Subject: [PATCH 056/256] include `page_id` in `ChatHistoryItemResponse`

This way we can highlight chats related to the currently opened notebook.
---
 client/packages/api-client/src/schema/schema.ts     |  5 +++++
 client/src/components/GalaxyAI/ChatHistoryPanel.vue | 13 ++++++++++++-
 client/src/components/GalaxyAI/chatTypes.ts         |  1 +
 lib/galaxy/schema/schema.py                         |  5 +++++
 lib/galaxy/webapps/galaxy/api/chat.py               |  1 +
 5 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index 2341a92935c..23e6c9423ff 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -8561,6 +8561,11 @@ export interface components {
              * @description Total number of messages in this exchange.
              */
             message_count: number;
+            /**
+             * Page ID
+             * @description Encoded page ID if this exchange is scoped to a page.
+             */
+            page_id?: string | null;
             /**
              * Query
              * @description The user's query that started or continued this exchange.
diff --git a/client/src/components/GalaxyAI/ChatHistoryPanel.vue b/client/src/components/GalaxyAI/ChatHistoryPanel.vue
index ea41961b73b..a30641dd38f 100644
--- a/client/src/components/GalaxyAI/ChatHistoryPanel.vue
+++ b/client/src/components/GalaxyAI/ChatHistoryPanel.vue
@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { faCheckSquare, faSquare } from "@fortawesome/free-regular-svg-icons";
-import { faClock, faPlus, faTimes, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { faBook, faClock, faPlus, faTimes, faTrash } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { storeToRefs } from "pinia";
 import { computed, onMounted, watch } from "vue";
@@ -184,6 +184,12 @@ async function deleteSelected() {
                             <span class="history-agent">
                                 <FontAwesomeIcon :icon="getAgentIcon(item.agent_type)" fixed-width />
                             </span>
+                            <span
+                                v-if="notebookPageId && item.page_id === notebookPageId"
+                                class="history-notebook-badge"
+                                title="This chat is linked to the current notebook">
+                                <FontAwesomeIcon :icon="faBook" fixed-width />
+                            </span>
                             <span class="history-time">
                                 <FontAwesomeIcon :icon="faClock" class="mr-1" />
                                 <UtcDate :date="item.timestamp" mode="elapsed" />
@@ -264,6 +270,11 @@ async function deleteSelected() {
         color: $brand-primary;
     }
 
+    .history-notebook-badge {
+        color: $brand-primary;
+        opacity: 0.7;
+    }
+
     .history-time {
         display: flex;
         align-items: center;
diff --git a/client/src/components/GalaxyAI/chatTypes.ts b/client/src/components/GalaxyAI/chatTypes.ts
index 87e06c3ab9c..1d0ba1a84ec 100644
--- a/client/src/components/GalaxyAI/chatTypes.ts
+++ b/client/src/components/GalaxyAI/chatTypes.ts
@@ -22,4 +22,5 @@ export interface ChatHistoryItem {
     timestamp: string;
     feedback?: number | null;
     message_count?: number;
+    page_id?: string | null;
 }
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 3e4d498e8d2..d23c14cfc7e 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -4095,6 +4095,11 @@ class ChatHistoryItemResponse(BaseModel):
         title="Message Count",
         description="Total number of messages in this exchange.",
     )
+    page_id: Optional[EncodedDatabaseIdField] = Field(
+        default=None,
+        title="Page ID",
+        description="Encoded page ID if this exchange is scoped to a page.",
+    )
 
 
 class ChatExchangeBatchDeletePayload(Model):
diff --git a/lib/galaxy/webapps/galaxy/api/chat.py b/lib/galaxy/webapps/galaxy/api/chat.py
index 5d817360dc8..8d4d64bdb76 100644
--- a/lib/galaxy/webapps/galaxy/api/chat.py
+++ b/lib/galaxy/webapps/galaxy/api/chat.py
@@ -556,6 +556,7 @@ class ChatAPI:
                         timestamp=message.create_time.isoformat() if message.create_time else None,
                         feedback=message.feedback,
                         message_count=len(exchange.messages),
+                        page_id=exchange.page_id,
                     )
                 )
             except (json.JSONDecodeError, AttributeError):

From f75863c277ef30c263126db132d988b34794170b Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 23:57:32 -0500
Subject: [PATCH 057/256] simplify notebook chat history: use separate endpoint
 and hide center mode button

- Replace the page_id query param on GET /api/chat/history with a dedicated
  /api/chat/page/{page_id}/history call when in notebook context. Removes page_id
  from ChatHistoryItemResponse, ChatHistoryItem, and the general history endpoint.
- chatStore.loadHistory(pageId?) routes to the correct endpoint based on context.
- ChatHistoryPanel consolidates onMounted + watch into a single immediate watcher
  and removes the notebook badge and toggle that are no longer needed.
- ChatModeSelector hides the "Full View" (center mode) button in notebook context.

Co-Authored-By: Claude <noreply@anthropic.com>
---
 .../packages/api-client/src/schema/schema.ts  |  7 ----
 client/src/components/GalaxyAI.vue            |  3 +-
 .../components/GalaxyAI/ChatHistoryPanel.vue  | 41 ++++++-------------
 .../components/GalaxyAI/ChatModeSelector.vue  | 13 +++++-
 client/src/components/GalaxyAI/chatTypes.ts   |  1 -
 client/src/stores/chatStore.ts                | 11 +++--
 lib/galaxy/managers/chat.py                   |  8 +---
 lib/galaxy/schema/schema.py                   |  5 ---
 lib/galaxy/webapps/galaxy/api/chat.py         | 11 +----
 9 files changed, 38 insertions(+), 62 deletions(-)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index 23e6c9423ff..ddc2fb8bb09 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -8561,11 +8561,6 @@ export interface components {
              * @description Total number of messages in this exchange.
              */
             message_count: number;
-            /**
-             * Page ID
-             * @description Encoded page ID if this exchange is scoped to a page.
-             */
-            page_id?: string | null;
             /**
              * Query
              * @description The user's query that started or continued this exchange.
@@ -31490,8 +31485,6 @@ export interface operations {
             query?: {
                 /** @description Maximum number of chats to return */
                 limit?: number;
-                /** @description When provided, include chats for this page alongside general chats. */
-                page_id?: string | null;
             };
             header?: {
                 /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index f5ec0c2df54..ae7908e716a 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -414,8 +414,9 @@ watch(currentChatId, async (newId) => {
     }
 
     if (newId && !chatStore.chatHistory.some((item) => item.id === newId)) {
+        const pageId = activeContext.value?.contextType === "notebook" ? activeContext.value.pageId : undefined;
         try {
-            await chatStore.loadHistory();
+            await chatStore.loadHistory(pageId);
         } catch (e) {
             Toast.error(errorMessageAsString(e), "Failed to load chat history");
         }
diff --git a/client/src/components/GalaxyAI/ChatHistoryPanel.vue b/client/src/components/GalaxyAI/ChatHistoryPanel.vue
index a30641dd38f..3fb92fa1805 100644
--- a/client/src/components/GalaxyAI/ChatHistoryPanel.vue
+++ b/client/src/components/GalaxyAI/ChatHistoryPanel.vue
@@ -1,9 +1,9 @@
 <script setup lang="ts">
 import { faCheckSquare, faSquare } from "@fortawesome/free-regular-svg-icons";
-import { faBook, faClock, faPlus, faTimes, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { faClock, faPlus, faTimes, faTrash } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { storeToRefs } from "pinia";
-import { computed, onMounted, watch } from "vue";
+import { computed, watch } from "vue";
 import { useRoute, useRouter } from "vue-router/composables";
 
 import { useConfirmDialog } from "@/composables/confirmDialog";
@@ -54,21 +54,17 @@ const currentExchangeId = computed(() => {
     }
 });
 
-onMounted(async () => {
-    try {
-        await chatStore.loadHistory(notebookPageId.value);
-    } catch (e) {
-        Toast.error(errorMessageAsString(e), "Failed to load chat history");
-    }
-});
-
-watch(notebookPageId, async (pageId) => {
-    try {
-        await chatStore.loadHistory(pageId);
-    } catch (e) {
-        Toast.error(errorMessageAsString(e), "Failed to load chat history");
-    }
-});
+watch(
+    notebookPageId,
+    async (pageId) => {
+        try {
+            await chatStore.loadHistory(pageId);
+        } catch (e) {
+            Toast.error(errorMessageAsString(e), "Failed to load chat history");
+        }
+    },
+    { immediate: true },
+);
 
 function handleItemClick(item: ChatHistoryItem, index: number, event: MouseEvent) {
     if (handleSelectionClick(item, index, event)) {
@@ -184,12 +180,6 @@ async function deleteSelected() {
                             <span class="history-agent">
                                 <FontAwesomeIcon :icon="getAgentIcon(item.agent_type)" fixed-width />
                             </span>
-                            <span
-                                v-if="notebookPageId && item.page_id === notebookPageId"
-                                class="history-notebook-badge"
-                                title="This chat is linked to the current notebook">
-                                <FontAwesomeIcon :icon="faBook" fixed-width />
-                            </span>
                             <span class="history-time">
                                 <FontAwesomeIcon :icon="faClock" class="mr-1" />
                                 <UtcDate :date="item.timestamp" mode="elapsed" />
@@ -270,11 +260,6 @@ async function deleteSelected() {
         color: $brand-primary;
     }
 
-    .history-notebook-badge {
-        color: $brand-primary;
-        opacity: 0.7;
-    }
-
     .history-time {
         display: flex;
         align-items: center;
diff --git a/client/src/components/GalaxyAI/ChatModeSelector.vue b/client/src/components/GalaxyAI/ChatModeSelector.vue
index 63f7e6d9274..c02348803de 100644
--- a/client/src/components/GalaxyAI/ChatModeSelector.vue
+++ b/client/src/components/GalaxyAI/ChatModeSelector.vue
@@ -5,6 +5,7 @@ import { storeToRefs } from "pinia";
 import { computed } from "vue";
 import { useRoute, useRouter } from "vue-router/composables";
 
+import { useActiveContext } from "@/composables/useActiveContext";
 import { useChatStore } from "@/stores/chatStore.js";
 
 import GButton from "../BaseComponents/GButton.vue";
@@ -14,6 +15,9 @@ const route = useRoute();
 const router = useRouter();
 
 const chatStore = useChatStore();
+const { activeContext } = useActiveContext();
+
+const isNotebookContext = computed(() => activeContext.value?.contextType === "notebook");
 
 const { activeChatId, isBottomPanelOpen, isCenterMode, isRightPanelOpen } = storeToRefs(chatStore);
 
@@ -45,7 +49,14 @@ function openDockedChat(location: "right" | "bottom") {
 
 <template>
     <GButtonGroup class="chat-mode-selector" size="small">
-        <GButton color="blue" outline :pressed="isOnCenter" title="Enable Full View" tooltip @click="openCenterChat">
+        <GButton
+            v-if="!isNotebookContext"
+            color="blue"
+            outline
+            :pressed="isOnCenter"
+            title="Enable Full View"
+            tooltip
+            @click="openCenterChat">
             <FontAwesomeIcon :icon="faExpand" />
         </GButton>
         <GButton
diff --git a/client/src/components/GalaxyAI/chatTypes.ts b/client/src/components/GalaxyAI/chatTypes.ts
index 1d0ba1a84ec..87e06c3ab9c 100644
--- a/client/src/components/GalaxyAI/chatTypes.ts
+++ b/client/src/components/GalaxyAI/chatTypes.ts
@@ -22,5 +22,4 @@ export interface ChatHistoryItem {
     timestamp: string;
     feedback?: number | null;
     message_count?: number;
-    page_id?: string | null;
 }
diff --git a/client/src/stores/chatStore.ts b/client/src/stores/chatStore.ts
index f83e0c24bfd..fec7beeeafe 100644
--- a/client/src/stores/chatStore.ts
+++ b/client/src/stores/chatStore.ts
@@ -73,9 +73,14 @@ export const useChatStore = defineStore("chatStore", () => {
 
     async function loadHistory(pageId?: string) {
         loading.value = true;
-        const { data, error } = await GalaxyApi().GET("/api/chat/history", {
-            params: { query: { limit: 50, ...(pageId ? { page_id: pageId } : {}) } },
-        });
+
+        const { data, error } = pageId
+            ? await GalaxyApi().GET("/api/chat/page/{page_id}/history", {
+                  params: { path: { page_id: pageId }, query: { limit: 50 } },
+              })
+            : await GalaxyApi().GET("/api/chat/history", {
+                  params: { query: { limit: 50 } },
+              });
 
         loading.value = false;
 
diff --git a/lib/galaxy/managers/chat.py b/lib/galaxy/managers/chat.py
index 763baa606e3..a8cc60b5cff 100644
--- a/lib/galaxy/managers/chat.py
+++ b/lib/galaxy/managers/chat.py
@@ -14,7 +14,6 @@ from pydantic_ai.messages import (
 )
 from sqlalchemy import (
     and_,
-    or_,
     select,
 )
 from sqlalchemy.exc import (
@@ -373,7 +372,6 @@ class ChatManager:
         limit: int = 50,
         include_job_chats: bool = False,
         include_page_chats: bool = False,
-        page_id: Optional[int] = None,
     ) -> list[ChatExchange]:
         """
         Get all chat exchanges for a user.
@@ -381,7 +379,6 @@ class ChatManager:
         :param limit: Maximum number of exchanges to return
         :param include_job_chats: Whether to include job-related chats
         :param include_page_chats: Whether to include page-scoped chats
-        :param page_id: When given, include chats for this specific page alongside general chats
         :returns: List of ChatExchange objects
         """
         try:
@@ -390,10 +387,7 @@ class ChatManager:
             if not include_job_chats:
                 stmt = stmt.where(ChatExchange.job_id.is_(None))
 
-            if page_id is not None:
-                # General chats (no page) plus chats for this specific page
-                stmt = stmt.where(or_(ChatExchange.page_id.is_(None), ChatExchange.page_id == page_id))
-            elif not include_page_chats:
+            if not include_page_chats:
                 stmt = stmt.where(ChatExchange.page_id.is_(None))
 
             stmt = stmt.order_by(ChatExchange.id.desc()).limit(limit)
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index d23c14cfc7e..3e4d498e8d2 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -4095,11 +4095,6 @@ class ChatHistoryItemResponse(BaseModel):
         title="Message Count",
         description="Total number of messages in this exchange.",
     )
-    page_id: Optional[EncodedDatabaseIdField] = Field(
-        default=None,
-        title="Page ID",
-        description="Encoded page ID if this exchange is scoped to a page.",
-    )
 
 
 class ChatExchangeBatchDeletePayload(Model):
diff --git a/lib/galaxy/webapps/galaxy/api/chat.py b/lib/galaxy/webapps/galaxy/api/chat.py
index 8d4d64bdb76..cd86cd3251e 100644
--- a/lib/galaxy/webapps/galaxy/api/chat.py
+++ b/lib/galaxy/webapps/galaxy/api/chat.py
@@ -331,17 +331,11 @@ class ChatAPI:
     def get_chat_history(
         self,
         limit: int = Query(default=50, description="Maximum number of chats to return"),
-        page_id: Optional[DecodedDatabaseIdField] = Query(
-            default=None,
-            description="When provided, include chats for this page alongside general chats.",
-        ),
         trans: ProvidesUserContext = DependsOnTrans,
         user: User = DependsOnUser,
     ) -> list[ChatHistoryItemResponse]:
-        """Get user's chat history, optionally including chats for a specific page."""
-        exchanges = self.chat_manager.get_user_chat_history(
-            trans, limit=limit, include_job_chats=False, page_id=page_id
-        )
+        """Get user's chat history."""
+        exchanges = self.chat_manager.get_user_chat_history(trans, limit=limit, include_job_chats=False)
         return self._format_exchange_history(exchanges)
 
     @router.get("/api/chat/page/{page_id}/history", unstable=True)
@@ -556,7 +550,6 @@ class ChatAPI:
                         timestamp=message.create_time.isoformat() if message.create_time else None,
                         feedback=message.feedback,
                         message_count=len(exchange.messages),
-                        page_id=exchange.page_id,
                     )
                 )
             except (json.JSONDecodeError, AttributeError):

From 8e478574c0c67950e8422c2eeb7fef542792388c Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 23:58:06 -0500
Subject: [PATCH 058/256] clear `activeChatId` when navigating away from a
 notebook

---
 client/src/components/GalaxyAI.vue | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index ae7908e716a..559e7dcceb1 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -50,8 +50,18 @@ const { activeContext, contextLabel } = useActiveContext();
 const pageEditorStore = usePageEditorStore();
 const contextDismissed = ref(false);
 
-watch(activeContext, () => {
+watch(activeContext, (newCtx, oldCtx) => {
     contextDismissed.value = false;
+
+    // When navigating away from a notebook, clear activeChatId if it belongs to that
+    // page (i.e. was loaded from the page-scoped history) so the panel doesn't keep
+    // showing a notebook-specific conversation in a non-notebook context.
+    if (oldCtx?.contextType === "notebook" && newCtx?.contextType !== "notebook") {
+        const currentId = chatStore.activeChatId;
+        if (currentId && chatStore.chatHistory.some((item) => item.id === currentId)) {
+            chatStore.setActiveChatId(null);
+        }
+    }
 });
 
 const effectiveContext = computed(() => {

From 4e24a0f5e5e2b6768be01043386d3e39c38cf6b6 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 Jun 2026 23:59:10 -0500
Subject: [PATCH 059/256] enforce docked mode for GalaxyAI in history notebooks

ActivityBar forces chatLocation to "right" whenever activeContext transitions to notebook, so center mode is never retained on a notebook page.
---
 client/src/components/ActivityBar/ActivityBar.vue | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/client/src/components/ActivityBar/ActivityBar.vue b/client/src/components/ActivityBar/ActivityBar.vue
index 80dffbc594d..deecff3d8c9 100644
--- a/client/src/components/ActivityBar/ActivityBar.vue
+++ b/client/src/components/ActivityBar/ActivityBar.vue
@@ -3,7 +3,7 @@ import type { IconDefinition } from "@fortawesome/fontawesome-svg-core";
 import { faBell, faEllipsisH, faUserCog } from "@fortawesome/free-solid-svg-icons";
 import { watchImmediate } from "@vueuse/core";
 import { storeToRefs } from "pinia";
-import { computed, type Ref, ref } from "vue";
+import { computed, type Ref, ref, watch } from "vue";
 import { useRoute, useRouter } from "vue-router/composables";
 import draggable from "vuedraggable";
 
@@ -85,6 +85,14 @@ const userStore = useUserStore();
 const chatStore = useChatStore();
 const { activeContext } = useActiveContext();
 
+// Notebook context must never use center mode — the chat panel floats alongside
+// the page editor, so force right-panel whenever we enter a notebook context.
+watch(activeContext, (ctx) => {
+    if (ctx?.contextType === "notebook" && chatStore.isCenterMode) {
+        chatStore.setLocation("right");
+    }
+});
+
 const eventStore = useEventStore();
 const activityStore = useActivityStore(props.activityBarId);
 

From 50231deb02681f7c156f69f48db996fa7add380d Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 2 Jun 2026 21:17:16 -0500
Subject: [PATCH 060/256] integrate page_assistant proposal rendering into
 GalaxyAI panel

Adds ProposalDiffView / SectionPatchView to GalaxyAI.vue via a new
usePageProposals composable. Proposal state (dismissed set, page content,
apply/dismiss actions) is scoped to notebook context and guarded explicitly
in isProposalVisible.

Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: John Chilton <jmchilton@gmail.com>
---
 client/src/components/GalaxyAI.vue         |  43 ++++++-
 client/src/composables/usePageProposals.ts | 138 +++++++++++++++++++++
 2 files changed, 180 insertions(+), 1 deletion(-)
 create mode 100644 client/src/composables/usePageProposals.ts

diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index 559e7dcceb1..82fc3540f52 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -12,6 +12,7 @@ import { useMarkdown } from "@/composables/markdown";
 import { useToast } from "@/composables/toast";
 import { useActiveContext } from "@/composables/useActiveContext";
 import { buildEntityContext, parseMentions, resolveMentions } from "@/composables/useEntityMentions";
+import { usePageProposals } from "@/composables/usePageProposals";
 import { useChatStore } from "@/stores/chatStore";
 import { usePageEditorStore } from "@/stores/pageEditorStore";
 import { errorMessageAsString } from "@/utils/simple-error";
@@ -23,6 +24,8 @@ import { generateId, scrollToBottom } from "./GalaxyAI/chatUtils";
 import ChatActions from "./GalaxyAI/ChatActions.vue";
 import ChatInput from "./GalaxyAI/ChatInput.vue";
 import ChatMessageCell from "./GalaxyAI/ChatMessageCell.vue";
+import ProposalDiffView from "./PageEditor/ProposalDiffView.vue";
+import SectionPatchView from "./PageEditor/SectionPatchView.vue";
 import Heading from "@/components/Common/Heading.vue";
 
 const props = withDefaults(
@@ -61,6 +64,7 @@ watch(activeContext, (newCtx, oldCtx) => {
         if (currentId && chatStore.chatHistory.some((item) => item.id === currentId)) {
             chatStore.setActiveChatId(null);
         }
+        clearProposals();
     }
 });
 
@@ -102,6 +106,20 @@ const hasLoadedInitialChat = ref(false);
 const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true, removeNewlinesAfterList: true });
 const { processingAction, handleAction } = useAgentActions();
 
+// Proposal rendering (notebook / page_assistant context)
+const {
+    pageContent,
+    loadForPage: loadProposalsForPage,
+    clear: clearProposals,
+    getEditProposal,
+    isProposalStale,
+    isProposalVisible,
+    buildProposedContent,
+    applyFullReplacement,
+    applySectionPatched,
+    dismissProposal,
+} = usePageProposals(activeContext);
+
 onMounted(async () => {
     if (props.exchangeId && props.exchangeId !== "new") {
         await fetchConversation(props.exchangeId);
@@ -342,6 +360,11 @@ async function fetchConversation(exchangeId: string) {
     currentChatId.value = exchangeId;
     nextTick(() => scrollToBottom(chatContainer.value));
 
+    const ctx = activeContext.value;
+    if (ctx?.contextType === "notebook") {
+        loadProposalsForPage(ctx.pageId);
+    }
+
     hasLoadedInitialChat.value = true;
 }
 
@@ -376,6 +399,7 @@ function startNewChat() {
     ];
     currentChatId.value = null;
     query.value = "";
+    clearProposals();
     if (props.docked || props.panel) {
         chatStore.setActiveChatId(null);
     }
@@ -479,7 +503,24 @@ watch(currentChatId, async (newId) => {
                 :processing-action="processingAction"
                 @feedback="sendFeedback"
                 @handle-action="handleAction"
-                @select-clarification-option="selectClarificationOption" />
+                @select-clarification-option="selectClarificationOption">
+                <template v-if="isProposalVisible(message)" v-slot:after-content>
+                    <ProposalDiffView
+                        v-if="getEditProposal(message)?.mode === 'full_replacement'"
+                        :original="pageContent"
+                        :proposed="buildProposedContent(message)"
+                        :stale="isProposalStale(message)"
+                        @accept="applyFullReplacement(message)"
+                        @reject="dismissProposal(message)" />
+                    <SectionPatchView
+                        v-else-if="getEditProposal(message)?.mode === 'section_patch'"
+                        :original="pageContent"
+                        :proposed="buildProposedContent(message)"
+                        :stale="isProposalStale(message)"
+                        @accept="applySectionPatched($event, message)"
+                        @reject="dismissProposal(message)" />
+                </template>
+            </ChatMessageCell>
 
             <!-- Loading state -->
             <div v-if="busy" class="loading-entry">
diff --git a/client/src/composables/usePageProposals.ts b/client/src/composables/usePageProposals.ts
new file mode 100644
index 00000000000..fd666127d9c
--- /dev/null
+++ b/client/src/composables/usePageProposals.ts
@@ -0,0 +1,138 @@
+import { computed, type Ref, ref } from "vue";
+
+import type { ChatMessage } from "@/components/GalaxyAI/chatTypes";
+import { applySectionEdit } from "@/components/PageEditor/sectionDiffUtils";
+import type { EditProposal } from "@/composables/agentActions";
+import type { ActiveContext } from "@/composables/useActiveContext";
+import { usePageEditorStore } from "@/stores/pageEditorStore";
+
+/**
+ * Encapsulates proposal rendering state and actions for the GalaxyAI panel
+ * when operating in notebook (page_assistant) context.
+ *
+ * Owns the `dismissedProposals` set and all helpers needed to render
+ * ProposalDiffView / SectionPatchView inside ChatMessageCell.
+ */
+export function usePageProposals(activeContext: Readonly<Ref<ActiveContext | null>>) {
+    const pageEditorStore = usePageEditorStore();
+
+    /** Live page content — empty when not in notebook context. */
+    const pageContent = computed(() =>
+        activeContext.value?.contextType === "notebook" ? pageEditorStore.currentContent : "",
+    );
+
+    /** Message IDs whose proposals have been dismissed or already applied. */
+    const dismissedProposals = ref(new Set<string>());
+
+    /** Load the persisted dismissed set for a page after fetching a conversation. */
+    function loadForPage(pageId: string) {
+        dismissedProposals.value = new Set(pageEditorStore.getDismissedProposals(pageId));
+    }
+
+    /** Clear the dismissed set (new chat or leaving notebook context). */
+    function clear() {
+        dismissedProposals.value = new Set();
+    }
+
+    function djb2Hash(s: string): string {
+        let h = 5381;
+        for (let i = 0; i < s.length; i++) {
+            h = (h * 33 + s.charCodeAt(i)) >>> 0;
+        }
+        return h.toString(16).padStart(8, "0");
+    }
+
+    function getEditProposal(msg: ChatMessage): EditProposal | null {
+        const meta = msg.agentResponse?.metadata;
+        const editMode = meta?.edit_mode as EditProposal["mode"] | undefined;
+        if (!editMode) {
+            return null;
+        }
+        return {
+            mode: editMode,
+            content: (meta?.content as string) || (meta?.new_section_content as string) || "",
+            target_section_heading: meta?.target_section_heading as string | undefined,
+            new_section_content: meta?.new_section_content as string | undefined,
+        };
+    }
+
+    function isProposalStale(msg: ChatMessage): boolean {
+        const originalHash = msg.agentResponse?.metadata?.original_content_hash as string | undefined;
+        return !!originalHash && originalHash !== djb2Hash(pageContent.value);
+    }
+
+    function isProposalVisible(msg: ChatMessage): boolean {
+        if (activeContext.value?.contextType !== "notebook") {
+            return false;
+        }
+        if (dismissedProposals.value.has(msg.id)) {
+            return false;
+        }
+        const proposal = getEditProposal(msg);
+        if (!proposal) {
+            return false;
+        }
+        if (proposal.mode === "full_replacement" && proposal.content === pageContent.value) {
+            return false;
+        }
+        return true;
+    }
+
+    function buildProposedContent(msg: ChatMessage): string {
+        const proposal = getEditProposal(msg);
+        if (!proposal) {
+            return pageContent.value;
+        }
+        if (proposal.mode === "full_replacement") {
+            return proposal.content;
+        }
+        return applySectionEdit(
+            pageContent.value,
+            proposal.target_section_heading || "",
+            proposal.new_section_content || proposal.content,
+        );
+    }
+
+    async function applyFullReplacement(msg: ChatMessage) {
+        const proposal = getEditProposal(msg);
+        if (!proposal) {
+            return;
+        }
+        pageEditorStore.updateContent(proposal.content);
+        await pageEditorStore.savePage("agent");
+        dismissedProposals.value.add(msg.id);
+        if (activeContext.value?.contextType === "notebook") {
+            pageEditorStore.addDismissedProposal(activeContext.value.pageId, msg.id);
+        }
+    }
+
+    async function applySectionPatched(patchedContent: string, msg: ChatMessage) {
+        pageEditorStore.updateContent(patchedContent);
+        await pageEditorStore.savePage("agent");
+        dismissedProposals.value.add(msg.id);
+        if (activeContext.value?.contextType === "notebook") {
+            pageEditorStore.addDismissedProposal(activeContext.value.pageId, msg.id);
+        }
+    }
+
+    function dismissProposal(msg: ChatMessage) {
+        dismissedProposals.value.add(msg.id);
+        if (activeContext.value?.contextType === "notebook") {
+            pageEditorStore.addDismissedProposal(activeContext.value.pageId, msg.id);
+        }
+    }
+
+    return {
+        pageContent,
+        dismissedProposals,
+        loadForPage,
+        clear,
+        getEditProposal,
+        isProposalStale,
+        isProposalVisible,
+        buildProposedContent,
+        applyFullReplacement,
+        applySectionPatched,
+        dismissProposal,
+    };
+}

From 513bac4d4341f4fbb02d3ce3d97502ba390f3b71 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 2 Jun 2026 22:27:32 -0500
Subject: [PATCH 061/256] add usePageProposals composable with tests

Co-Authored-By: Claude <noreply@anthropic.com>
---
 .../components/PageEditor/sectionDiffUtils.ts |   8 +
 .../src/composables/usePageProposals.test.ts  | 297 ++++++++++++++++++
 client/src/composables/usePageProposals.ts    |  10 +-
 3 files changed, 306 insertions(+), 9 deletions(-)
 create mode 100644 client/src/composables/usePageProposals.test.ts

diff --git a/client/src/components/PageEditor/sectionDiffUtils.ts b/client/src/components/PageEditor/sectionDiffUtils.ts
index 5b2d5ce5b2f..b3d56579aad 100644
--- a/client/src/components/PageEditor/sectionDiffUtils.ts
+++ b/client/src/components/PageEditor/sectionDiffUtils.ts
@@ -215,3 +215,11 @@ export function diffStats(changes: Change[]): DiffStats {
     }
     return { additions, deletions };
 }
+
+export function djb2Hash(s: string): string {
+    let h = 5381;
+    for (let i = 0; i < s.length; i++) {
+        h = (h * 33 + s.charCodeAt(i)) >>> 0;
+    }
+    return h.toString(16).padStart(8, "0");
+}
diff --git a/client/src/composables/usePageProposals.test.ts b/client/src/composables/usePageProposals.test.ts
new file mode 100644
index 00000000000..2fb8a1256fc
--- /dev/null
+++ b/client/src/composables/usePageProposals.test.ts
@@ -0,0 +1,297 @@
+import { createTestingPinia } from "@pinia/testing";
+import flushPromises from "flush-promises";
+import { setActivePinia } from "pinia";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+import { ref } from "vue";
+
+import { djb2Hash } from "@/components/PageEditor/sectionDiffUtils";
+import type { ActiveContext } from "@/composables/useActiveContext";
+import { usePageEditorStore } from "@/stores/pageEditorStore";
+
+import { usePageProposals } from "./usePageProposals";
+
+const PAGE_ID = "page-abc";
+const PAGE_CONTENT = "# Intro\nSome intro text\n# Methods\nSome methods text";
+
+const PAGE_CONTENT_HASH = djb2Hash(PAGE_CONTENT);
+
+function makeNotebookContext(pageId = PAGE_ID): ActiveContext {
+    return { contextType: "notebook", pageId, historyId: "hist-1" };
+}
+
+function makeMsg(overrides: Record<string, unknown> = {}) {
+    return {
+        id: "msg-1",
+        role: "assistant" as const,
+        content: "Here is my suggestion.",
+        timestamp: new Date(),
+        feedback: null,
+        ...overrides,
+    };
+}
+
+function makeProposalMsg(
+    mode: "full_replacement" | "section_patch",
+    content: string,
+    extras: Record<string, unknown> = {},
+) {
+    return makeMsg({
+        agentResponse: {
+            agent_type: "page_assistant",
+            confidence: "high",
+            suggestions: [],
+            metadata: {
+                edit_mode: mode,
+                content,
+                original_content_hash: PAGE_CONTENT_HASH,
+                ...extras,
+            },
+        },
+    });
+}
+
+describe("usePageProposals", () => {
+    beforeEach(() => {
+        setActivePinia(createTestingPinia({ createSpy: vi.fn }));
+    });
+
+    afterEach(() => {
+        vi.restoreAllMocks();
+    });
+
+    function setup(initialContext: ActiveContext | null = makeNotebookContext()) {
+        const activeContext = ref<ActiveContext | null>(initialContext);
+        const store = usePageEditorStore();
+        store.currentContent = PAGE_CONTENT;
+        vi.mocked(store.savePage).mockResolvedValue(undefined);
+        const composable = usePageProposals(activeContext);
+        return { activeContext, store, ...composable };
+    }
+
+    describe("pageContent", () => {
+        it("returns store content when in notebook context", () => {
+            const { pageContent } = setup();
+            expect(pageContent.value).toBe(PAGE_CONTENT);
+        });
+
+        it("returns empty string when context is null", () => {
+            const { pageContent } = setup(null);
+            expect(pageContent.value).toBe("");
+        });
+
+        it("returns empty string for non-notebook context types", () => {
+            const { pageContent } = setup({ contextType: "tool", toolId: "bwa" });
+            expect(pageContent.value).toBe("");
+        });
+    });
+
+    describe("loadForPage / clear", () => {
+        it("loads dismissed proposals from store for a page", () => {
+            const { store, loadForPage, dismissedProposals } = setup();
+            vi.mocked(store.getDismissedProposals).mockReturnValue(["msg-1", "msg-2"]);
+
+            loadForPage(PAGE_ID);
+
+            expect(store.getDismissedProposals).toHaveBeenCalledWith(PAGE_ID);
+            expect(dismissedProposals.value.has("msg-1")).toBe(true);
+            expect(dismissedProposals.value.has("msg-2")).toBe(true);
+        });
+
+        it("clear resets the dismissed set", () => {
+            const { store, loadForPage, clear, dismissedProposals } = setup();
+            vi.mocked(store.getDismissedProposals).mockReturnValue(["msg-1"]);
+            loadForPage(PAGE_ID);
+            expect(dismissedProposals.value.size).toBe(1);
+
+            clear();
+            expect(dismissedProposals.value.size).toBe(0);
+        });
+    });
+
+    describe("getEditProposal", () => {
+        it("returns null for messages without agentResponse", () => {
+            const { getEditProposal } = setup();
+            expect(getEditProposal(makeMsg())).toBeNull();
+        });
+
+        it("returns null when edit_mode is absent", () => {
+            const { getEditProposal } = setup();
+            const msg = makeMsg({ agentResponse: { metadata: {} } });
+            expect(getEditProposal(msg)).toBeNull();
+        });
+
+        it("returns full_replacement proposal", () => {
+            const { getEditProposal } = setup();
+            const msg = makeProposalMsg("full_replacement", "new content");
+            const proposal = getEditProposal(msg);
+            expect(proposal?.mode).toBe("full_replacement");
+            expect(proposal?.content).toBe("new content");
+        });
+
+        it("returns section_patch proposal with target heading", () => {
+            const { getEditProposal } = setup();
+            const msg = makeProposalMsg("section_patch", "", {
+                target_section_heading: "Methods",
+                new_section_content: "## Methods\nNew methods text",
+            });
+            const proposal = getEditProposal(msg);
+            expect(proposal?.mode).toBe("section_patch");
+            expect(proposal?.target_section_heading).toBe("Methods");
+        });
+    });
+
+    describe("isProposalStale", () => {
+        it("returns false when no original_content_hash in metadata", () => {
+            const { isProposalStale } = setup();
+            const msg = makeMsg({
+                agentResponse: { metadata: { edit_mode: "full_replacement", content: "x" } },
+            });
+            expect(isProposalStale(msg)).toBe(false);
+        });
+
+        it("returns false when hash matches current content", () => {
+            const { isProposalStale } = setup();
+            const msg = makeProposalMsg("full_replacement", "x");
+            expect(isProposalStale(msg)).toBe(false);
+        });
+
+        it("returns true when hash does not match current content", () => {
+            const { store, isProposalStale } = setup();
+            store.currentContent = "# Changed content";
+            const msg = makeProposalMsg("full_replacement", "x"); // hash is for original PAGE_CONTENT
+            expect(isProposalStale(msg)).toBe(true);
+        });
+    });
+
+    describe("isProposalVisible", () => {
+        it("returns false when not in notebook context", () => {
+            const { isProposalVisible } = setup(null);
+            const msg = makeProposalMsg("full_replacement", "new");
+            expect(isProposalVisible(msg)).toBe(false);
+        });
+
+        it("returns false when message is dismissed", () => {
+            const { isProposalVisible, dismissProposal } = setup();
+            const msg = makeProposalMsg("full_replacement", "new");
+            dismissProposal(msg);
+            expect(isProposalVisible(msg)).toBe(false);
+        });
+
+        it("returns false when message has no proposal", () => {
+            const { isProposalVisible } = setup();
+            expect(isProposalVisible(makeMsg())).toBe(false);
+        });
+
+        it("returns false for full_replacement when content already matches page", () => {
+            const { isProposalVisible } = setup();
+            const msg = makeProposalMsg("full_replacement", PAGE_CONTENT);
+            expect(isProposalVisible(msg)).toBe(false);
+        });
+
+        it("returns true for a fresh full_replacement proposal", () => {
+            const { isProposalVisible } = setup();
+            const msg = makeProposalMsg("full_replacement", "brand new content");
+            expect(isProposalVisible(msg)).toBe(true);
+        });
+
+        it("returns true for a section_patch proposal", () => {
+            const { isProposalVisible } = setup();
+            const msg = makeProposalMsg("section_patch", "", {
+                target_section_heading: "Methods",
+                new_section_content: "## Methods\nUpdated",
+            });
+            expect(isProposalVisible(msg)).toBe(true);
+        });
+    });
+
+    describe("buildProposedContent", () => {
+        it("returns pageContent when no proposal", () => {
+            const { buildProposedContent } = setup();
+            expect(buildProposedContent(makeMsg())).toBe(PAGE_CONTENT);
+        });
+
+        it("returns proposal content directly for full_replacement", () => {
+            const { buildProposedContent } = setup();
+            const msg = makeProposalMsg("full_replacement", "completely new doc");
+            expect(buildProposedContent(msg)).toBe("completely new doc");
+        });
+
+        it("applies section patch to produce full document", () => {
+            const { buildProposedContent } = setup();
+            const msg = makeProposalMsg("section_patch", "", {
+                target_section_heading: "Methods",
+                new_section_content: "# Methods\nReplaced methods",
+            });
+            const result = buildProposedContent(msg);
+            expect(result).toContain("Replaced methods");
+            expect(result).toContain("Intro");
+        });
+    });
+
+    describe("dismissProposal", () => {
+        it("adds message ID to dismissed set", () => {
+            const { dismissedProposals, dismissProposal } = setup();
+            const msg = makeProposalMsg("full_replacement", "x");
+            dismissProposal(msg);
+            expect(dismissedProposals.value.has(msg.id)).toBe(true);
+        });
+
+        it("persists dismissed ID to the store", () => {
+            const { store, dismissProposal } = setup();
+            const msg = makeProposalMsg("full_replacement", "x");
+            dismissProposal(msg);
+            expect(store.addDismissedProposal).toHaveBeenCalledWith(PAGE_ID, msg.id);
+        });
+
+        it("does not call store when not in notebook context", () => {
+            const { activeContext, store, dismissProposal } = setup();
+            activeContext.value = null;
+            dismissProposal(makeProposalMsg("full_replacement", "x"));
+            expect(store.addDismissedProposal).not.toHaveBeenCalled();
+        });
+    });
+
+    describe("applyFullReplacement", () => {
+        it("updates store content and saves", async () => {
+            const { store, applyFullReplacement } = setup();
+            const msg = makeProposalMsg("full_replacement", "new page content");
+            await applyFullReplacement(msg);
+            await flushPromises();
+
+            expect(store.updateContent).toHaveBeenCalledWith("new page content");
+            expect(store.savePage).toHaveBeenCalledWith("agent");
+        });
+
+        it("marks message as dismissed after applying", async () => {
+            const { dismissedProposals, applyFullReplacement } = setup();
+            const msg = makeProposalMsg("full_replacement", "new page content");
+            await applyFullReplacement(msg);
+            expect(dismissedProposals.value.has(msg.id)).toBe(true);
+        });
+
+        it("does nothing when message has no proposal", async () => {
+            const { store, applyFullReplacement } = setup();
+            await applyFullReplacement(makeMsg());
+            expect(store.updateContent).not.toHaveBeenCalled();
+        });
+    });
+
+    describe("applySectionPatched", () => {
+        it("updates store with patched content and saves", async () => {
+            const { store, applySectionPatched } = setup();
+            const msg = makeProposalMsg("section_patch", "");
+            await applySectionPatched("# Patched doc", msg);
+            await flushPromises();
+
+            expect(store.updateContent).toHaveBeenCalledWith("# Patched doc");
+            expect(store.savePage).toHaveBeenCalledWith("agent");
+        });
+
+        it("marks message as dismissed after applying", async () => {
+            const { dismissedProposals, applySectionPatched } = setup();
+            const msg = makeMsg();
+            await applySectionPatched("patched", msg);
+            expect(dismissedProposals.value.has(msg.id)).toBe(true);
+        });
+    });
+});
diff --git a/client/src/composables/usePageProposals.ts b/client/src/composables/usePageProposals.ts
index fd666127d9c..1b6b5101af4 100644
--- a/client/src/composables/usePageProposals.ts
+++ b/client/src/composables/usePageProposals.ts
@@ -1,7 +1,7 @@
 import { computed, type Ref, ref } from "vue";
 
 import type { ChatMessage } from "@/components/GalaxyAI/chatTypes";
-import { applySectionEdit } from "@/components/PageEditor/sectionDiffUtils";
+import { applySectionEdit, djb2Hash } from "@/components/PageEditor/sectionDiffUtils";
 import type { EditProposal } from "@/composables/agentActions";
 import type { ActiveContext } from "@/composables/useActiveContext";
 import { usePageEditorStore } from "@/stores/pageEditorStore";
@@ -34,14 +34,6 @@ export function usePageProposals(activeContext: Readonly<Ref<ActiveContext | nul
         dismissedProposals.value = new Set();
     }
 
-    function djb2Hash(s: string): string {
-        let h = 5381;
-        for (let i = 0; i < s.length; i++) {
-            h = (h * 33 + s.charCodeAt(i)) >>> 0;
-        }
-        return h.toString(16).padStart(8, "0");
-    }
-
     function getEditProposal(msg: ChatMessage): EditProposal | null {
         const meta = msg.agentResponse?.metadata;
         const editMode = meta?.edit_mode as EditProposal["mode"] | undefined;

From 4ac60b7875973885221acac64e593549b6ee34ae Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 2 Jun 2026 22:53:42 -0500
Subject: [PATCH 062/256] make sure to `clearCurrentChatExchangeId`

---
 client/src/components/GalaxyAI.vue | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index 82fc3540f52..efc7e1999e7 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -131,6 +131,12 @@ onMounted(async () => {
             const cachedId = pageEditorStore.getCurrentChatExchangeId(ctx.pageId);
             if (cachedId) {
                 await fetchConversation(cachedId);
+                // If the cached exchange was deleted or returned no messages, drop the stale ID
+                // so the next open doesn't try it again.
+                if (messages.value.length === 0) {
+                    pageEditorStore.clearCurrentChatExchangeId(ctx.pageId);
+                    startNewChat();
+                }
             } else {
                 startNewChat();
             }

From e0a82b1b21c0458be04a293bd0c69175dcfe79b3 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 2 Jun 2026 23:16:23 -0500
Subject: [PATCH 063/256] remove PageChatPanel and other dead code now
 superseded by unified GalaxyAI panel
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Delete PageChatPanel.vue, SplitView.vue, and their test files — all functionality has been absorbed into the unified GalaxyAI panel and the new usePageProposals composable
- Clean up dead state from pageEditorStore (dismissed proposals, chat history, loadPageChatHistory, toggleChatHistory, etc.)
- Fix usePageProposals to persist dismissed proposals via useUserLocalStorage directly instead of the now-removed store methods; update tests accordingly

Co-Authored-By: Claude <noreply@anthropic.com>
---
 .../src/components/Common/SplitView.test.ts   |  41 --
 client/src/components/Common/SplitView.vue    |  92 ---
 .../PageEditor/PageChatPanel.test.ts          | 385 ------------
 .../components/PageEditor/PageChatPanel.vue   | 570 ------------------
 .../PageEditor/PageEditorView.test.ts         | 107 ----
 .../components/PageEditor/PageEditorView.vue  |  76 +--
 .../src/composables/usePageProposals.test.ts  |  32 +-
 client/src/composables/usePageProposals.ts    |  35 +-
 client/src/stores/pageEditorStore.ts          | 109 ----
 9 files changed, 62 insertions(+), 1385 deletions(-)
 delete mode 100644 client/src/components/Common/SplitView.test.ts
 delete mode 100644 client/src/components/Common/SplitView.vue
 delete mode 100644 client/src/components/PageEditor/PageChatPanel.test.ts
 delete mode 100644 client/src/components/PageEditor/PageChatPanel.vue

diff --git a/client/src/components/Common/SplitView.test.ts b/client/src/components/Common/SplitView.test.ts
deleted file mode 100644
index 96c756344d0..00000000000
--- a/client/src/components/Common/SplitView.test.ts
+++ /dev/null
@@ -1,41 +0,0 @@
-import { getLocalVue } from "@tests/vitest/helpers";
-import { shallowMount } from "@vue/test-utils";
-import { describe, expect, it } from "vitest";
-
-import SplitView from "./SplitView.vue";
-import DraggableSeparator from "@/components/Common/DraggableSeparator.vue";
-
-const localVue = getLocalVue();
-
-function mountComponent(propsData = {}) {
-    return shallowMount(SplitView as object, {
-        localVue,
-        propsData,
-        slots: {
-            left: '<div class="test-left">Left</div>',
-            right: '<div class="test-right">Right</div>',
-        },
-    });
-}
-
-describe("SplitView", () => {
-    it("renders split view container", () => {
-        const wrapper = mountComponent();
-        expect(wrapper.find('[data-description="split view"]').exists()).toBe(true);
-    });
-
-    it("renders left slot", () => {
-        const wrapper = mountComponent();
-        expect(wrapper.find(".test-left").exists()).toBe(true);
-    });
-
-    it("renders right slot", () => {
-        const wrapper = mountComponent();
-        expect(wrapper.find(".test-right").exists()).toBe(true);
-    });
-
-    it("delegates the divider to DraggableSeparator", () => {
-        const wrapper = mountComponent();
-        expect(wrapper.findComponent(DraggableSeparator).exists()).toBe(true);
-    });
-});
diff --git a/client/src/components/Common/SplitView.vue b/client/src/components/Common/SplitView.vue
deleted file mode 100644
index 2e4b368ca3e..00000000000
--- a/client/src/components/Common/SplitView.vue
+++ /dev/null
@@ -1,92 +0,0 @@
-<script setup lang="ts">
-/**
- * Two-pane split layout with a draggable resize handle.
- *
- * Composes ``DraggableSeparator`` for the divider, inheriting its
- * keyboard accessibility, hover-delay, and animation-frame throttling.
- * Caller supplies the pane content via ``left``/``right`` slots.
- */
-import { useElementBounding } from "@vueuse/core";
-import { computed, ref, watch } from "vue";
-
-import DraggableSeparator from "@/components/Common/DraggableSeparator.vue";
-
-const props = withDefaults(
-    defineProps<{
-        /** Starting size of the left pane, as a percent of the container. */
-        initialSplit?: number;
-        /** Smallest left-pane size, as a percent of the container. */
-        minPercent?: number;
-        /** Largest left-pane size, as a percent of the container. */
-        maxPercent?: number;
-    }>(),
-    {
-        initialSplit: 60,
-        minPercent: 20,
-        maxPercent: 80,
-    },
-);
-
-const containerRef = ref<HTMLElement>();
-const { width: containerWidth } = useElementBounding(containerRef);
-
-// Position is the left-pane width in pixels; ``DraggableSeparator`` works in
-// pixels so this is the natural shape and avoids percent<->px drift.
-const leftWidthPx = ref(0);
-let initialized = false;
-
-watch(
-    containerWidth,
-    (w) => {
-        if (!w) {
-            return;
-        }
-        if (!initialized) {
-            leftWidthPx.value = (props.initialSplit / 100) * w;
-            initialized = true;
-        } else {
-            const minPx = (props.minPercent / 100) * w;
-            const maxPx = (props.maxPercent / 100) * w;
-            leftWidthPx.value = Math.min(Math.max(leftWidthPx.value, minPx), maxPx);
-        }
-    },
-    { immediate: true },
-);
-
-const minPx = computed(() => (containerWidth.value * props.minPercent) / 100);
-const maxPx = computed(() => (containerWidth.value * props.maxPercent) / 100);
-const rightWidthPx = computed(() => Math.max(containerWidth.value - leftWidthPx.value, 0));
-</script>
-
-<template>
-    <div ref="containerRef" class="split-view" data-description="split view">
-        <div class="split-pane" :style="{ flexBasis: `${leftWidthPx}px` }">
-            <slot name="left" />
-        </div>
-        <DraggableSeparator
-            :position="leftWidthPx"
-            side="left"
-            :inner="true"
-            :min="minPx"
-            :max="maxPx"
-            @positionChanged="(v) => (leftWidthPx = v)" />
-        <div class="split-pane" :style="{ flexBasis: `${rightWidthPx}px` }">
-            <slot name="right" />
-        </div>
-    </div>
-</template>
-
-<style scoped>
-.split-view {
-    display: flex;
-    flex: 1;
-    overflow: hidden;
-    min-height: 0;
-    position: relative;
-}
-
-.split-pane {
-    overflow: auto;
-    min-width: 0;
-}
-</style>
diff --git a/client/src/components/PageEditor/PageChatPanel.test.ts b/client/src/components/PageEditor/PageChatPanel.test.ts
deleted file mode 100644
index aba3de33d10..00000000000
--- a/client/src/components/PageEditor/PageChatPanel.test.ts
+++ /dev/null
@@ -1,385 +0,0 @@
-import { createTestingPinia } from "@pinia/testing";
-import { getLocalVue } from "@tests/vitest/helpers";
-import { mount } from "@vue/test-utils";
-import flushPromises from "flush-promises";
-import type { Pinia } from "pinia";
-import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
-
-import { usePageEditorStore } from "@/stores/pageEditorStore";
-
-import PageChatPanel from "./PageChatPanel.vue";
-import ChatInput from "@/components/GalaxyAI/ChatInput.vue";
-import ChatMessageCell from "@/components/GalaxyAI/ChatMessageCell.vue";
-
-// Mock GalaxyApi
-const mockPOST = vi.fn();
-const mockGET = vi.fn();
-const mockPUT = vi.fn();
-
-vi.mock("@/api", () => ({
-    GalaxyApi: () => ({
-        POST: mockPOST,
-        GET: mockGET,
-        PUT: mockPUT,
-    }),
-}));
-
-vi.mock("vue-router/composables", () => ({
-    useRouter: vi.fn(() => ({ push: vi.fn() })),
-    useRoute: vi.fn(() => ({ params: {} })),
-}));
-
-const localVue = getLocalVue();
-
-const HISTORY_ID = "history-1";
-const PAGE_ID = "page-1";
-const PAGE_CONTENT = "# Intro\nSome intro text\n# Methods\nSome methods text";
-
-let pinia: Pinia;
-
-function mountComponent(
-    propsData: { historyId?: string; pageId: string; pageContent: string } = {
-        historyId: HISTORY_ID,
-        pageId: PAGE_ID,
-        pageContent: PAGE_CONTENT,
-    },
-) {
-    return mount(PageChatPanel as any, {
-        localVue,
-        propsData,
-        pinia,
-        stubs: {
-            FontAwesomeIcon: true,
-            BSkeleton: true,
-            LoadingSpan: true,
-            ChatMessageCell: true,
-            ProposalDiffView: true,
-            SectionPatchView: true,
-        },
-    });
-}
-
-describe("PageChatPanel", () => {
-    beforeEach(() => {
-        pinia = createTestingPinia({ createSpy: vi.fn });
-        vi.clearAllMocks();
-        // Default: no page chat history
-        mockGET.mockResolvedValue({ data: [], error: null });
-    });
-
-    afterEach(() => {
-        vi.restoreAllMocks();
-    });
-
-    describe("Initial render", () => {
-        it("renders chat panel container", async () => {
-            const wrapper = mountComponent();
-            await flushPromises();
-            expect(wrapper.find('[data-description="page chat panel"]').exists()).toBe(true);
-        });
-
-        it("renders header with Markdown Assistant title", async () => {
-            const wrapper = mountComponent();
-            await flushPromises();
-            expect(wrapper.find(".chat-panel-header").text()).toContain("Markdown Assistant");
-        });
-
-        it("renders ChatInput component", async () => {
-            const wrapper = mountComponent();
-            await flushPromises();
-            expect(wrapper.findComponent(ChatInput).exists()).toBe(true);
-        });
-
-        it("shows welcome message when no history", async () => {
-            const wrapper = mountComponent();
-            await flushPromises();
-            const cells = wrapper.findAllComponents(ChatMessageCell);
-            expect(cells.length).toBe(1);
-        });
-
-        it("renders new conversation button", async () => {
-            const wrapper = mountComponent();
-            await flushPromises();
-            expect(wrapper.find('[data-description="new conversation button"]').exists()).toBe(true);
-        });
-    });
-
-    describe("Message submission", () => {
-        it("sends query to API on submit", async () => {
-            mockPOST.mockResolvedValue({
-                data: {
-                    response: "I can help with that.",
-                    exchange_id: 42,
-                    agent_response: {
-                        agent_type: "page_assistant",
-                        confidence: "high",
-                        suggestions: [],
-                        metadata: {},
-                    },
-                },
-                error: null,
-            });
-
-            const wrapper = mountComponent();
-            await flushPromises();
-
-            // Use ChatInput's v-model: set value via the textarea + trigger submit
-            const textarea = wrapper.find("textarea");
-            await textarea.setValue("Rewrite the intro section");
-            await wrapper.find(".send-button").trigger("click");
-            await flushPromises();
-
-            expect(mockPOST).toHaveBeenCalledWith(
-                "/api/chat",
-                expect.objectContaining({
-                    params: { query: { agent_type: "page_assistant" } },
-                }),
-            );
-        });
-
-        it("adds user and assistant messages after submit", async () => {
-            mockPOST.mockResolvedValue({
-                data: {
-                    response: "Here is a rewrite.",
-                    exchange_id: 42,
-                    agent_response: {
-                        agent_type: "page_assistant",
-                        confidence: "high",
-                        suggestions: [],
-                        metadata: {},
-                    },
-                },
-                error: null,
-            });
-
-            const wrapper = mountComponent();
-            await flushPromises();
-
-            const textarea = wrapper.find("textarea");
-            await textarea.setValue("Rewrite intro");
-            await wrapper.find(".send-button").trigger("click");
-            await flushPromises();
-
-            const cells = wrapper.findAllComponents(ChatMessageCell);
-            // Welcome + user + assistant = 3
-            expect(cells.length).toBe(3);
-        });
-
-        it("shows error message on API failure", async () => {
-            mockPOST.mockResolvedValue({
-                data: null,
-                error: { err_msg: "Server error" },
-            });
-
-            const wrapper = mountComponent();
-            await flushPromises();
-
-            const textarea = wrapper.find("textarea");
-            await textarea.setValue("test query");
-            await wrapper.find(".send-button").trigger("click");
-            await flushPromises();
-
-            const cells = wrapper.findAllComponents(ChatMessageCell);
-            const lastCell = cells.at(cells.length - 1);
-            expect(lastCell.props("message").content).toContain("Error");
-        });
-
-        it("sets exchange_id from response for follow-up queries", async () => {
-            mockPOST.mockResolvedValue({
-                data: { response: "Done.", exchange_id: 99, agent_response: null },
-                error: null,
-            });
-
-            const wrapper = mountComponent();
-            await flushPromises();
-
-            const textarea = wrapper.find("textarea");
-            await textarea.setValue("hello");
-            await wrapper.find(".send-button").trigger("click");
-            await flushPromises();
-
-            // Subsequent request should include the exchange_id
-            mockPOST.mockResolvedValue({
-                data: { response: "Follow up.", exchange_id: 99, agent_response: null },
-                error: null,
-            });
-
-            await textarea.setValue("follow up");
-            await wrapper.find(".send-button").trigger("click");
-            await flushPromises();
-
-            const lastCall = mockPOST.mock.calls[mockPOST.mock.calls.length - 1]!;
-            expect(lastCall[1].body.exchange_id).toBe(99);
-        });
-    });
-
-    describe("New conversation", () => {
-        it("resets messages on new conversation click", async () => {
-            mockPOST.mockResolvedValue({
-                data: { response: "Test", exchange_id: 1, agent_response: null },
-                error: null,
-            });
-
-            const wrapper = mountComponent();
-            await flushPromises();
-
-            const textarea = wrapper.find("textarea");
-            await textarea.setValue("hello");
-            await wrapper.find(".send-button").trigger("click");
-            await flushPromises();
-
-            // Click new conversation
-            await wrapper.find('[data-description="new conversation button"]').trigger("click");
-            await flushPromises();
-
-            const cells = wrapper.findAllComponents(ChatMessageCell);
-            expect(cells.length).toBe(1);
-        });
-    });
-
-    describe("Loading state", () => {
-        it("shows loading indicator when busy", async () => {
-            // Make POST never resolve to keep busy=true
-            mockPOST.mockReturnValue(new Promise(() => {}));
-
-            const wrapper = mountComponent();
-            await flushPromises();
-
-            const textarea = wrapper.find("textarea");
-            await textarea.setValue("hello");
-            await wrapper.find(".send-button").trigger("click");
-            await wrapper.vm.$nextTick();
-
-            expect(wrapper.find('[data-description="chat loading indicator"]').exists()).toBe(true);
-        });
-    });
-
-    describe("Store integration", () => {
-        it("does not call store methods on mount", async () => {
-            const store = usePageEditorStore();
-            mountComponent();
-            await flushPromises();
-
-            expect(store.updateContent).not.toHaveBeenCalled();
-            expect(store.savePage).not.toHaveBeenCalled();
-        });
-    });
-
-    describe("Chat persistence", () => {
-        it("stores exchange ID in store after first submit", async () => {
-            mockPOST.mockResolvedValue({
-                data: { response: "Done.", exchange_id: 77, agent_response: null },
-                error: null,
-            });
-            const wrapper = mountComponent();
-            await flushPromises();
-            const store = usePageEditorStore();
-
-            const textarea = wrapper.find("textarea");
-            await textarea.setValue("hello");
-            await wrapper.find(".send-button").trigger("click");
-            await flushPromises();
-
-            expect(store.setCurrentChatExchangeId).toHaveBeenCalledWith(PAGE_ID, 77);
-        });
-
-        it("clears stored exchange ID on new conversation", async () => {
-            const wrapper = mountComponent();
-            await flushPromises();
-            const store = usePageEditorStore();
-
-            await wrapper.find('[data-description="new conversation button"]').trigger("click");
-            await flushPromises();
-
-            expect(store.setCurrentChatExchangeId).toHaveBeenCalledWith(PAGE_ID, null);
-        });
-
-        it("checks store for cached exchange ID on mount", async () => {
-            const store = usePageEditorStore();
-            vi.mocked(store.getCurrentChatExchangeId).mockReturnValue("abc55");
-            // Mock the exchange messages load
-            mockGET.mockResolvedValue({
-                data: [
-                    { role: "user", content: "hello", timestamp: null },
-                    { role: "assistant", content: "hi", agent_type: "page_assistant", timestamp: null },
-                ],
-                error: null,
-            });
-
-            const wrapper = mountComponent();
-            await flushPromises();
-
-            expect(store.getCurrentChatExchangeId).toHaveBeenCalledWith(PAGE_ID);
-            // Should have loaded 2 messages from the cached conversation
-            const cells = wrapper.findAllComponents(ChatMessageCell);
-            expect(cells.length).toBe(2);
-        });
-
-        it("falls back to API when stored exchange ID returns empty messages", async () => {
-            const store = usePageEditorStore();
-            vi.mocked(store.getCurrentChatExchangeId).mockReturnValue("abc999");
-            // All GET calls return empty — stored exchange has no messages, no page history
-            mockGET.mockResolvedValue({ data: [], error: null });
-
-            const wrapper = mountComponent();
-            await flushPromises();
-
-            // Stored ID yielded nothing, API fallback yielded nothing — welcome message shown
-            const cells = wrapper.findAllComponents(ChatMessageCell);
-            expect(cells.length).toBe(1);
-        });
-    });
-
-    describe("Standalone page mode (no historyId)", () => {
-        function mountStandalone() {
-            return mountComponent({ pageId: PAGE_ID, pageContent: PAGE_CONTENT });
-        }
-
-        it("renders header with Markdown Assistant title", async () => {
-            const wrapper = mountStandalone();
-            await flushPromises();
-            expect(wrapper.find(".chat-panel-header").text()).toContain("Markdown Assistant");
-        });
-
-        it("shows Markdown Assistant welcome message", async () => {
-            const wrapper = mountStandalone();
-            await flushPromises();
-            const cells = wrapper.findAllComponents(ChatMessageCell);
-            expect(cells.length).toBe(1);
-            // The welcome message should mention "Markdown Assistant"
-            expect(cells.at(0).props("message").content).toContain("Markdown Assistant");
-        });
-
-        it("sends query to API without historyId", async () => {
-            mockPOST.mockResolvedValue({
-                data: {
-                    response: "I can help with that.",
-                    exchange_id: 42,
-                    agent_response: null,
-                },
-                error: null,
-            });
-
-            const wrapper = mountStandalone();
-            await flushPromises();
-
-            const textarea = wrapper.find("textarea");
-            await textarea.setValue("Rewrite the intro");
-            await wrapper.find(".send-button").trigger("click");
-            await flushPromises();
-
-            expect(mockPOST).toHaveBeenCalledWith(
-                "/api/chat",
-                expect.objectContaining({
-                    params: { query: { agent_type: "page_assistant" } },
-                }),
-            );
-        });
-
-        it("renders Markdown Assistant header when historyId is provided", async () => {
-            const wrapper = mountComponent();
-            await flushPromises();
-            expect(wrapper.find(".chat-panel-header").text()).toContain("Markdown Assistant");
-        });
-    });
-});
diff --git a/client/src/components/PageEditor/PageChatPanel.vue b/client/src/components/PageEditor/PageChatPanel.vue
deleted file mode 100644
index 04a3fc5317d..00000000000
--- a/client/src/components/PageEditor/PageChatPanel.vue
+++ /dev/null
@@ -1,570 +0,0 @@
-<script setup lang="ts">
-/**
- * Page-specific chat panel.
- * Talks to the page_assistant agent, shows diff views for edit proposals,
- * and applies accepted edits to the page via the store.
- */
-import { faBook, faHistory, faTrash } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton, BSkeleton } from "bootstrap-vue";
-import { computed, nextTick, onMounted, ref, watch } from "vue";
-
-import { GalaxyApi } from "@/api";
-import type { ChatMessage } from "@/components/GalaxyAI/chatTypes";
-import { generateId, scrollToBottom } from "@/components/GalaxyAI/chatUtils";
-import { PAGE_LABELS } from "@/components/Page/constants";
-import { type AgentResponse, type EditProposal, useAgentActions } from "@/composables/agentActions";
-import { useMarkdown } from "@/composables/markdown";
-import { type PageEditorMode, usePageEditorStore } from "@/stores/pageEditorStore";
-import { errorMessageAsString } from "@/utils/simple-error";
-
-import { applySectionEdit } from "./sectionDiffUtils";
-
-import PageChatHistoryList from "./PageChatHistoryList.vue";
-import ProposalDiffView from "./ProposalDiffView.vue";
-import SectionPatchView from "./SectionPatchView.vue";
-import ChatInput from "@/components/GalaxyAI/ChatInput.vue";
-import ChatMessageCell from "@/components/GalaxyAI/ChatMessageCell.vue";
-import LoadingSpan from "@/components/LoadingSpan.vue";
-
-const props = withDefaults(
-    defineProps<{
-        historyId?: string;
-        pageId: string;
-        pageContent: string;
-    }>(),
-    { historyId: "" },
-);
-
-const isHistoryAttached = computed(() => !!props.historyId);
-const chatMode = computed<PageEditorMode>(() => (isHistoryAttached.value ? "history" : "standalone"));
-const chatLabels = computed(() => PAGE_LABELS[chatMode.value]);
-const assistantName = computed(() => chatLabels.value.assistantName);
-
-const AGENT_TYPE = "page_assistant";
-
-const store = usePageEditorStore();
-const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true, removeNewlinesAfterList: true });
-const { processingAction, handleAction } = useAgentActions();
-
-const query = ref("");
-const messages = ref<ChatMessage[]>([]);
-const busy = ref(false);
-const chatContainer = ref<HTMLElement>();
-const currentChatId = ref<string | null>(null);
-const dismissedProposals = ref(new Set<string>());
-
-onMounted(async () => {
-    await loadPageChat();
-
-    if (messages.value.length === 0) {
-        messages.value.push({
-            id: generateId(),
-            role: "assistant",
-            content: chatLabels.value.assistantWelcome,
-            timestamp: new Date(),
-            agentType: AGENT_TYPE,
-            confidence: "high",
-            feedback: null,
-            isSystemMessage: true,
-        });
-    }
-});
-
-async function loadPageChat() {
-    store.chatError = null;
-
-    // Try store-cached exchange ID first (avoids API round-trip on panel reopen)
-    const storedExchangeId = store.getCurrentChatExchangeId(props.pageId);
-    if (storedExchangeId !== null) {
-        try {
-            await loadConversation(storedExchangeId);
-            if (messages.value.length > 0) {
-                return;
-            }
-        } catch (e) {
-            console.warn("Failed to load cached chat exchange:", e);
-            store.clearCurrentChatExchangeId(props.pageId);
-        }
-    }
-
-    // Fall back to API
-    try {
-        const { data, error } = await GalaxyApi().GET("/api/chat/page/{page_id}/history", {
-            params: { path: { page_id: props.pageId }, query: { limit: 1 } },
-        });
-
-        if (data && !error && data.length > 0) {
-            await loadConversation(data[0]!.id);
-        }
-    } catch (e) {
-        console.warn("Failed to load page chat history:", e);
-        store.chatError = errorMessageAsString(e);
-    }
-}
-
-async function loadConversation(exchangeId: string) {
-    const { data } = await GalaxyApi().GET("/api/chat/exchange/{exchange_id}/messages", {
-        params: { path: { exchange_id: exchangeId } },
-    });
-
-    if (data && data.length > 0) {
-        messages.value = data.map((msg: any, index: number) => {
-            const m: ChatMessage = {
-                id: `hist-${msg.role}-${exchangeId}-${index}`,
-                role: msg.role,
-                content: msg.content,
-                timestamp: msg.timestamp ? new Date(msg.timestamp) : new Date(),
-                feedback: null,
-            };
-
-            if (msg.role === "assistant") {
-                m.agentType = msg.agent_type || AGENT_TYPE;
-                m.confidence = msg.agent_response?.confidence || "medium";
-                m.feedback = msg.feedback === 1 ? "up" : msg.feedback === 0 ? "down" : null;
-                if (msg.agent_response) {
-                    m.agentResponse = msg.agent_response;
-                    m.suggestions = msg.agent_response.suggestions || [];
-                }
-            }
-
-            return m;
-        });
-        currentChatId.value = exchangeId;
-        store.setCurrentChatExchangeId(props.pageId, exchangeId);
-        dismissedProposals.value = new Set(store.getDismissedProposals(props.pageId));
-    }
-}
-
-async function submitQuery() {
-    if (!query.value.trim()) {
-        return;
-    }
-
-    const userMessage: ChatMessage = {
-        id: generateId(),
-        role: "user",
-        content: query.value,
-        timestamp: new Date(),
-        feedback: null,
-    };
-
-    messages.value.push(userMessage);
-    const currentQuery = query.value;
-    query.value = "";
-
-    await nextTick();
-    scrollToBottom(chatContainer.value);
-
-    busy.value = true;
-
-    const wasNewExchange = currentChatId.value === null;
-
-    try {
-        const { data, error } = await GalaxyApi().POST("/api/chat", {
-            params: { query: { agent_type: AGENT_TYPE } },
-            body: {
-                query: currentQuery,
-                context: null,
-                exchange_id: currentChatId.value,
-                page_id: props.pageId,
-            },
-        });
-
-        if (error) {
-            const errStr = errorMessageAsString(error, "Failed to get response.");
-            messages.value.push({
-                id: generateId(),
-                role: "assistant",
-                content: `Error: ${errStr}`,
-                timestamp: new Date(),
-                agentType: AGENT_TYPE,
-                confidence: "low",
-                feedback: null,
-            });
-        } else if (data) {
-            if (data.exchange_id) {
-                currentChatId.value = data.exchange_id;
-                store.setCurrentChatExchangeId(props.pageId, data.exchange_id);
-            }
-
-            if (wasNewExchange) {
-                store.loadPageChatHistory(props.pageId);
-            }
-
-            const agentResponse = data.agent_response as AgentResponse | undefined;
-
-            messages.value.push({
-                id: generateId(),
-                role: "assistant",
-                content: data.response || "No response received",
-                timestamp: new Date(),
-                agentType: agentResponse?.agent_type || AGENT_TYPE,
-                confidence: agentResponse?.confidence || "medium",
-                feedback: null,
-                agentResponse: agentResponse,
-                suggestions: agentResponse?.suggestions || [],
-            });
-        }
-    } catch (e) {
-        messages.value.push({
-            id: generateId(),
-            role: "assistant",
-            content: "Unexpected error occurred. Please try again.",
-            timestamp: new Date(),
-            agentType: AGENT_TYPE,
-            confidence: "low",
-            feedback: null,
-        });
-    } finally {
-        busy.value = false;
-        await nextTick();
-        scrollToBottom(chatContainer.value);
-    }
-}
-
-watch(busy, (isBusy) => {
-    if (isBusy) {
-        nextTick(() => scrollToBottom(chatContainer.value));
-    }
-});
-
-async function sendFeedback(messageId: string, value: "up" | "down") {
-    const message = messages.value.find((m) => m.id === messageId);
-    if (!message || !currentChatId.value) {
-        return;
-    }
-    message.feedback = value;
-    try {
-        const feedbackValue = value === "up" ? 1 : 0;
-        const { error } = await GalaxyApi().PUT("/api/chat/exchange/{exchange_id}/feedback", {
-            params: { path: { exchange_id: currentChatId.value } },
-            body: feedbackValue,
-        });
-        if (error) {
-            message.feedback = null;
-        }
-    } catch {
-        message.feedback = null;
-    }
-}
-
-function djb2Hash(s: string): string {
-    let h = 5381;
-    for (let i = 0; i < s.length; i++) {
-        h = (h * 33 + s.charCodeAt(i)) >>> 0;
-    }
-    return h.toString(16).padStart(8, "0");
-}
-
-function isProposalStale(msg: ChatMessage): boolean {
-    const meta = msg.agentResponse?.metadata;
-    const originalHash = meta?.original_content_hash as string | undefined;
-    if (!originalHash) {
-        return false;
-    }
-    return originalHash !== djb2Hash(props.pageContent);
-}
-
-function getEditProposal(msg: ChatMessage): EditProposal | null {
-    const meta = msg.agentResponse?.metadata;
-    const editMode = meta?.edit_mode as EditProposal["mode"] | undefined;
-    if (!editMode) {
-        return null;
-    }
-    return {
-        mode: editMode,
-        content: (meta?.content as string) || (meta?.new_section_content as string) || "",
-        target_section_heading: meta?.target_section_heading as string | undefined,
-        new_section_content: meta?.new_section_content as string | undefined,
-    };
-}
-
-function isProposalVisible(msg: ChatMessage): boolean {
-    if (dismissedProposals.value.has(msg.id)) {
-        return false;
-    }
-    const proposal = getEditProposal(msg);
-    if (!proposal) {
-        return false;
-    }
-    // Content-based: if full_replacement content matches current doc, already applied
-    if (proposal.mode === "full_replacement" && proposal.content === props.pageContent) {
-        return false;
-    }
-    return true;
-}
-
-function getProposalMode(msg: ChatMessage): string {
-    return getEditProposal(msg)?.mode || "";
-}
-
-function buildProposedContent(msg: ChatMessage): string {
-    const proposal = getEditProposal(msg);
-    if (!proposal) {
-        return props.pageContent;
-    }
-    if (proposal.mode === "full_replacement") {
-        return proposal.content;
-    }
-    // section_patch: reconstruct full doc by replacing the target section
-    return applySectionEdit(
-        props.pageContent,
-        proposal.target_section_heading || "",
-        proposal.new_section_content || proposal.content,
-    );
-}
-
-async function applyFullReplacement(msg: ChatMessage) {
-    const proposal = getEditProposal(msg);
-    if (!proposal) {
-        return;
-    }
-    store.updateContent(proposal.content);
-    await store.savePage("agent");
-    dismissedProposals.value.add(msg.id);
-    store.addDismissedProposal(props.pageId, msg.id);
-}
-
-async function applySectionPatched(patchedContent: string, msg: ChatMessage) {
-    store.updateContent(patchedContent);
-    await store.savePage("agent");
-    dismissedProposals.value.add(msg.id);
-    store.addDismissedProposal(props.pageId, msg.id);
-}
-
-function dismissProposal(msg: ChatMessage) {
-    dismissedProposals.value.add(msg.id);
-    store.addDismissedProposal(props.pageId, msg.id);
-}
-
-function toggleHistory() {
-    store.toggleChatHistory();
-    if (store.showChatHistory) {
-        store.loadPageChatHistory(props.pageId);
-    }
-}
-
-async function handleHistorySelect(item: { id: string }) {
-    try {
-        await loadConversation(item.id);
-        store.showChatHistory = false;
-        await nextTick();
-        scrollToBottom(chatContainer.value);
-    } catch (e) {
-        store.chatHistoryError = errorMessageAsString(e);
-    }
-}
-
-function resetToNewChat() {
-    messages.value = [
-        {
-            id: generateId(),
-            role: "assistant",
-            content: chatLabels.value.newConversation,
-            timestamp: new Date(),
-            agentType: AGENT_TYPE,
-            confidence: "high",
-            feedback: null,
-            isSystemMessage: true,
-        },
-    ];
-    currentChatId.value = null;
-    store.setCurrentChatExchangeId(props.pageId, null);
-    query.value = "";
-    dismissedProposals.value = new Set();
-    store.clearDismissedProposals(props.pageId);
-}
-
-async function handleHistoryDelete(ids: string[]) {
-    try {
-        await store.deletePageChatExchanges(props.pageId, ids);
-        if (currentChatId.value && ids.includes(currentChatId.value)) {
-            resetToNewChat();
-        }
-    } catch (e) {
-        store.chatHistoryError = errorMessageAsString(e);
-    }
-}
-
-async function deleteCurrentExchange() {
-    if (!currentChatId.value) {
-        return;
-    }
-    try {
-        await store.deletePageChatExchanges(props.pageId, [currentChatId.value]);
-        resetToNewChat();
-    } catch (e) {
-        store.chatError = errorMessageAsString(e);
-    }
-}
-
-function startNewConversation() {
-    resetToNewChat();
-}
-</script>
-
-<template>
-    <div class="page-chat-panel d-flex flex-column h-100" data-description="page chat panel">
-        <div class="chat-panel-header d-flex align-items-center justify-content-between p-2 border-bottom">
-            <span class="d-flex align-items-center gap-2">
-                <FontAwesomeIcon :icon="faBook" fixed-width />
-                <strong>{{ assistantName }}</strong>
-            </span>
-            <span class="d-flex align-items-center gap-1">
-                <BButton
-                    variant="outline-secondary"
-                    size="sm"
-                    :pressed="store.showChatHistory"
-                    data-description="chat history button"
-                    @click="toggleHistory">
-                    <FontAwesomeIcon :icon="faHistory" fixed-width />
-                </BButton>
-                <BButton
-                    v-if="currentChatId"
-                    variant="outline-danger"
-                    size="sm"
-                    title="Delete current conversation"
-                    data-description="delete conversation button"
-                    @click="deleteCurrentExchange">
-                    <FontAwesomeIcon :icon="faTrash" fixed-width />
-                </BButton>
-                <BButton
-                    variant="outline-primary"
-                    size="sm"
-                    data-description="new conversation button"
-                    @click="startNewConversation">
-                    New Chat
-                </BButton>
-            </span>
-        </div>
-
-        <div class="chat-body d-flex flex-grow-1" style="min-height: 0">
-            <div ref="chatContainer" class="chat-panel-messages flex-grow-1 overflow-auto">
-                <BAlert
-                    v-if="store.chatError"
-                    variant="danger"
-                    dismissible
-                    show
-                    data-description="chat error alert"
-                    @dismissed="store.chatError = null">
-                    {{ store.chatError }}
-                </BAlert>
-
-                <ChatMessageCell
-                    v-for="msg in messages"
-                    :key="msg.id"
-                    :message="msg"
-                    :render-markdown="renderMarkdown"
-                    :processing-action="processingAction"
-                    @feedback="sendFeedback"
-                    @handle-action="handleAction">
-                    <template v-if="isProposalVisible(msg)" v-slot:after-content>
-                        <ProposalDiffView
-                            v-if="getProposalMode(msg) === 'full_replacement'"
-                            :original="pageContent"
-                            :proposed="buildProposedContent(msg)"
-                            :stale="isProposalStale(msg)"
-                            @accept="applyFullReplacement(msg)"
-                            @reject="dismissProposal(msg)" />
-                        <SectionPatchView
-                            v-else-if="getProposalMode(msg) === 'section_patch'"
-                            :original="pageContent"
-                            :proposed="buildProposedContent(msg)"
-                            :stale="isProposalStale(msg)"
-                            @accept="applySectionPatched($event, msg)"
-                            @reject="dismissProposal(msg)" />
-                    </template>
-                </ChatMessageCell>
-
-                <div v-if="busy" class="loading-cell" data-description="chat loading indicator">
-                    <div class="cell-label">
-                        <FontAwesomeIcon :icon="faBook" fixed-width />
-                        <span>{{ assistantName }}</span>
-                    </div>
-                    <div class="cell-content">
-                        <BSkeleton animation="wave" width="85%" />
-                        <BSkeleton animation="wave" width="55%" />
-                        <BSkeleton animation="wave" width="70%" />
-                    </div>
-                </div>
-
-                <div v-if="!busy && messages.length === 0" class="text-muted text-center p-4">
-                    <LoadingSpan message="Loading conversation..." />
-                </div>
-            </div>
-
-            <PageChatHistoryList
-                v-if="store.showChatHistory"
-                class="chat-history-sidebar border-left"
-                :items="store.pageChatHistory"
-                :is-loading="store.isLoadingChatHistory"
-                :error="store.chatHistoryError"
-                :active-exchange-id="currentChatId"
-                data-description="chat history sidebar"
-                @select="handleHistorySelect"
-                @delete="handleHistoryDelete"
-                @dismiss-error="store.chatHistoryError = null" />
-        </div>
-
-        <div class="chat-panel-footer p-2 border-top">
-            <ChatInput v-model="query" :busy="busy" :placeholder="chatLabels.chatPlaceholder" @submit="submitQuery" />
-        </div>
-    </div>
-</template>
-
-<style scoped>
-.page-chat-panel {
-    background: var(--body-bg, #fff);
-    min-width: 0;
-}
-
-.chat-panel-header {
-    background: var(--panel-header-bg, #f8f9fa);
-    font-size: 0.85rem;
-}
-
-.chat-panel-header .gap-2 {
-    gap: 0.5rem;
-}
-
-.chat-panel-messages {
-    padding: 0.75rem;
-    min-width: 0;
-}
-
-.chat-history-sidebar {
-    width: 220px;
-    flex-shrink: 0;
-    overflow-y: auto;
-}
-
-.chat-panel-footer {
-    background: var(--panel-header-bg, #f8f9fa);
-}
-
-.loading-cell {
-    margin-bottom: 1rem;
-    opacity: 0.7;
-}
-
-.loading-cell .cell-label {
-    display: flex;
-    align-items: center;
-    gap: 0.5rem;
-    font-size: 0.75rem;
-    font-weight: 600;
-    text-transform: uppercase;
-    letter-spacing: 0.025em;
-    margin-bottom: 0.375rem;
-    padding-left: 0.25rem;
-    color: var(--text-muted, #6c757d);
-}
-
-.loading-cell .cell-content {
-    border-left: 3px solid var(--brand-secondary, #6c757d);
-    background: var(--panel-bg-color, #f8f9fa);
-    padding: 0.75rem 1rem;
-    border-radius: 4px;
-}
-</style>
diff --git a/client/src/components/PageEditor/PageEditorView.test.ts b/client/src/components/PageEditor/PageEditorView.test.ts
index 40389c2f711..1ff36e8f84a 100644
--- a/client/src/components/PageEditor/PageEditorView.test.ts
+++ b/client/src/components/PageEditor/PageEditorView.test.ts
@@ -10,12 +10,10 @@ import { ref } from "vue";
 import type { HistoryPageDetails, PageRevisionDetails, PageRevisionSummary } from "@/api/pages";
 import { usePageEditorStore } from "@/stores/pageEditorStore";
 
-import PageChatPanel from "./PageChatPanel.vue";
 import PageEditorView from "./PageEditorView.vue";
 import PageRevisionList from "./PageRevisionList.vue";
 import PageRevisionView from "./PageRevisionView.vue";
 import ClickToEdit from "@/components/ClickToEdit.vue";
-import SplitView from "@/components/Common/SplitView.vue";
 import Markdown from "@/components/Markdown/Markdown.vue";
 import MarkdownEditor from "@/components/Markdown/MarkdownEditor.vue";
 
@@ -67,7 +65,6 @@ const SELECTORS = {
     UNSAVED_INDICATOR: "[data-description='page unsaved indicator']",
     REVISIONS_BUTTON: "[data-description='page revisions button']",
     REVISION_PANEL: ".page-revision-panel",
-    CHAT_BUTTON: "[data-description='page chat button']",
     PREVIEW_BUTTON: "[data-description='page preview button']",
     PERMISSIONS_BUTTON: "[data-description='page permissions button']",
     SAVE_VIEW_BUTTON: "[data-description='page save-view button']",
@@ -531,110 +528,6 @@ describe("PageEditorView", () => {
         });
     });
 
-    describe("Chat Panel", () => {
-        it("shows Chat button in toolbar", async () => {
-            setupLoadedPage(HISTORY_ID);
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            const chatBtn = wrapper.find(SELECTORS.CHAT_BUTTON);
-            expect(chatBtn.exists()).toBe(true);
-            expect(chatBtn.text()).toContain("Chat");
-        });
-
-        it("clicking Chat button calls store.toggleChatPanel", async () => {
-            const store = setupLoadedPage(HISTORY_ID);
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            const chatBtn = wrapper.find(SELECTORS.CHAT_BUTTON);
-            await chatBtn.trigger("click");
-            await flushPromises();
-
-            expect(store.toggleChatPanel).toHaveBeenCalled();
-        });
-
-        it("renders split view when store.showChatPanel is true", async () => {
-            const store = setupLoadedPage(HISTORY_ID);
-            store.showChatPanel = true;
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            expect(wrapper.findComponent(SplitView).exists()).toBe(true);
-            expect(wrapper.findComponent(PageChatPanel).exists()).toBe(true);
-        });
-
-        it("hides split view when store.showChatPanel is false", async () => {
-            const store = setupLoadedPage(HISTORY_ID);
-            store.showChatPanel = false;
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            expect(wrapper.findComponent(SplitView).exists()).toBe(false);
-        });
-
-        it("hides Chat button when llm_api_configured is false", async () => {
-            setupLoadedPage(HISTORY_ID);
-            mockConfig.value = { llm_api_configured: false };
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            expect(wrapper.find(SELECTORS.CHAT_BUTTON).exists()).toBe(false);
-        });
-
-        it("shows Chat button when llm_api_configured is true", async () => {
-            setupLoadedPage(HISTORY_ID);
-            mockConfig.value = { llm_api_configured: true };
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            expect(wrapper.find(SELECTORS.CHAT_BUTTON).exists()).toBe(true);
-        });
-
-        it("hides Chat button when config is null (not yet loaded)", async () => {
-            setupLoadedPage(HISTORY_ID);
-            mockConfig.value = null;
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            expect(wrapper.find(SELECTORS.CHAT_BUTTON).exists()).toBe(false);
-        });
-
-        it("passes hideToolbox=true to MarkdownEditor when chat is open", async () => {
-            const store = setupLoadedPage(HISTORY_ID);
-            store.showChatPanel = true;
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            const editor = wrapper.findComponent(MarkdownEditor);
-            expect(editor.exists()).toBe(true);
-            expect(editor.props("hideToolbox")).toBe(true);
-        });
-
-        it("does not set hideToolbox when chat is closed", async () => {
-            const store = setupLoadedPage(HISTORY_ID);
-            store.showChatPanel = false;
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            const editor = wrapper.findComponent(MarkdownEditor);
-            expect(editor.exists()).toBe(true);
-            expect(editor.props("hideToolbox")).toBeFalsy();
-        });
-
-        it("passes props to PageChatPanel", async () => {
-            const store = setupLoadedPage(HISTORY_ID);
-            store.showChatPanel = true;
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            const panel = wrapper.findComponent(PageChatPanel);
-            expect(panel.props("historyId")).toBe(HISTORY_ID);
-            expect(panel.props("pageId")).toBe(PAGE_ID);
-            expect(panel.props("pageContent")).toBe("# Hello");
-        });
-    });
-
     describe("Lifecycle", () => {
         it("calls store.loadPage on mount", async () => {
             const store = usePageEditorStore();
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 73d4c29ce47..923b0211d98 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -1,14 +1,5 @@
 <script setup lang="ts">
-import {
-    faArrowLeft,
-    faComments,
-    faEdit,
-    faEye,
-    faHistory,
-    faSave,
-    faSpinner,
-    faUsers,
-} from "@fortawesome/free-solid-svg-icons";
+import { faArrowLeft, faEdit, faEye, faHistory, faSave, faSpinner, faUsers } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert, BBadge, BButton } from "bootstrap-vue";
 import { computed, onMounted, onUnmounted, ref, watch } from "vue";
@@ -16,18 +7,15 @@ import { useRouter } from "vue-router/composables";
 
 import { getGalaxyInstance } from "@/app";
 import type { RouterPushOptions } from "@/components/History/Content/router-push-options";
-import { PAGE_LABELS, PERMISSIONS_LABELS } from "@/components/Page/constants";
-import { useConfig } from "@/composables/config";
+import { PAGE_LABELS } from "@/components/Page/constants";
 import { useWindowAwareNavigation } from "@/composables/windowAwareNavigation";
 import { useHistoryStore } from "@/stores/historyStore";
 import { type PageEditorMode, usePageEditorStore } from "@/stores/pageEditorStore";
 
 import ObjectPermissionsModal from "./ObjectPermissionsModal.vue";
-import PageChatPanel from "./PageChatPanel.vue";
 import PageRevisionList from "./PageRevisionList.vue";
 import PageRevisionView from "./PageRevisionView.vue";
 import ClickToEdit from "@/components/ClickToEdit.vue";
-import SplitView from "@/components/Common/SplitView.vue";
 import Markdown from "@/components/Markdown/Markdown.vue";
 import MarkdownEditor from "@/components/Markdown/MarkdownEditor.vue";
 
@@ -41,9 +29,6 @@ const router = useRouter();
 const { pushToFrameOrPage } = useWindowAwareNavigation();
 const store = usePageEditorStore();
 const historyStore = useHistoryStore();
-const { config } = useConfig();
-
-const agentsAvailable = computed(() => !!config.value?.llm_api_configured);
 
 const editorMode = computed<PageEditorMode>(() => (props.historyId ? "history" : "standalone"));
 const isStandalone = computed(() => editorMode.value === "standalone");
@@ -265,16 +250,6 @@ function handleRevisionRestore(revisionId: string) {
                     <FontAwesomeIcon :icon="faEye" />
                     Preview
                 </BButton>
-                <BButton
-                    v-if="agentsAvailable"
-                    :variant="store.showChatPanel ? 'primary' : 'outline-primary'"
-                    size="sm"
-                    class="mr-2"
-                    data-description="page chat button"
-                    @click="store.toggleChatPanel">
-                    <FontAwesomeIcon :icon="faComments" />
-                    Chat
-                </BButton>
                 <template v-if="isStandalone">
                     <ObjectPermissionsModal
                         id="object-permissions-modal"
@@ -316,38 +291,21 @@ function handleRevisionRestore(revisionId: string) {
             </div>
 
             <div class="page-body d-flex flex-grow-1 overflow-hidden">
-                <SplitView v-if="store.showChatPanel">
-                    <template v-slot:left>
-                        <div class="page-editor-pane">
-                            <MarkdownEditor
-                                :markdown-text="store.currentContent"
-                                :mode="markdownEditorMode"
-                                :title="editorTitle"
-                                :hide-toolbox="true"
-                                @update="handleContentUpdate" />
-                        </div>
-                    </template>
-                    <template v-slot:right>
-                        <PageChatPanel :history-id="historyId" :page-id="pageId" :page-content="store.currentContent" />
-                    </template>
-                </SplitView>
-                <template v-else>
-                    <div class="page-content flex-grow-1 overflow-auto">
-                        <MarkdownEditor
-                            :markdown-text="store.currentContent"
-                            :mode="markdownEditorMode"
-                            :title="editorTitle"
-                            @update="handleContentUpdate" />
-                    </div>
-                    <div v-if="store.showRevisions" class="page-revision-panel border-left">
-                        <PageRevisionList
-                            :revisions="store.revisions"
-                            :is-loading="store.isLoadingRevisions"
-                            :is-reverting="store.isReverting"
-                            @select="handleRevisionSelect"
-                            @restore="handleRevisionRestore" />
-                    </div>
-                </template>
+                <div class="page-content flex-grow-1 overflow-auto">
+                    <MarkdownEditor
+                        :markdown-text="store.currentContent"
+                        :mode="markdownEditorMode"
+                        :title="editorTitle"
+                        @update="handleContentUpdate" />
+                </div>
+                <div v-if="store.showRevisions" class="page-revision-panel border-left">
+                    <PageRevisionList
+                        :revisions="store.revisions"
+                        :is-loading="store.isLoadingRevisions"
+                        :is-reverting="store.isReverting"
+                        @select="handleRevisionSelect"
+                        @restore="handleRevisionRestore" />
+                </div>
             </div>
         </template>
     </div>
diff --git a/client/src/composables/usePageProposals.test.ts b/client/src/composables/usePageProposals.test.ts
index 2fb8a1256fc..bf9d6a95801 100644
--- a/client/src/composables/usePageProposals.test.ts
+++ b/client/src/composables/usePageProposals.test.ts
@@ -10,6 +10,12 @@ import { usePageEditorStore } from "@/stores/pageEditorStore";
 
 import { usePageProposals } from "./usePageProposals";
 
+// Mock useUserLocalStorage so localStorage isn't touched in tests.
+const mockPersistedDismissed = ref<Record<string, string[]>>({});
+vi.mock("@/composables/userLocalStorage", () => ({
+    useUserLocalStorage: () => mockPersistedDismissed,
+}));
+
 const PAGE_ID = "page-abc";
 const PAGE_CONTENT = "# Intro\nSome intro text\n# Methods\nSome methods text";
 
@@ -53,6 +59,7 @@ function makeProposalMsg(
 describe("usePageProposals", () => {
     beforeEach(() => {
         setActivePinia(createTestingPinia({ createSpy: vi.fn }));
+        mockPersistedDismissed.value = {};
     });
 
     afterEach(() => {
@@ -86,20 +93,19 @@ describe("usePageProposals", () => {
     });
 
     describe("loadForPage / clear", () => {
-        it("loads dismissed proposals from store for a page", () => {
-            const { store, loadForPage, dismissedProposals } = setup();
-            vi.mocked(store.getDismissedProposals).mockReturnValue(["msg-1", "msg-2"]);
+        it("loads dismissed proposals from localStorage for a page", () => {
+            mockPersistedDismissed.value[PAGE_ID] = ["msg-1", "msg-2"];
+            const { loadForPage, dismissedProposals } = setup();
 
             loadForPage(PAGE_ID);
 
-            expect(store.getDismissedProposals).toHaveBeenCalledWith(PAGE_ID);
             expect(dismissedProposals.value.has("msg-1")).toBe(true);
             expect(dismissedProposals.value.has("msg-2")).toBe(true);
         });
 
-        it("clear resets the dismissed set", () => {
-            const { store, loadForPage, clear, dismissedProposals } = setup();
-            vi.mocked(store.getDismissedProposals).mockReturnValue(["msg-1"]);
+        it("clear resets the in-memory set", () => {
+            mockPersistedDismissed.value[PAGE_ID] = ["msg-1"];
+            const { loadForPage, clear, dismissedProposals } = setup();
             loadForPage(PAGE_ID);
             expect(dismissedProposals.value.size).toBe(1);
 
@@ -236,18 +242,18 @@ describe("usePageProposals", () => {
             expect(dismissedProposals.value.has(msg.id)).toBe(true);
         });
 
-        it("persists dismissed ID to the store", () => {
-            const { store, dismissProposal } = setup();
+        it("persists dismissed ID to localStorage", () => {
+            const { dismissProposal } = setup();
             const msg = makeProposalMsg("full_replacement", "x");
             dismissProposal(msg);
-            expect(store.addDismissedProposal).toHaveBeenCalledWith(PAGE_ID, msg.id);
+            expect(mockPersistedDismissed.value[PAGE_ID]).toContain(msg.id);
         });
 
-        it("does not call store when not in notebook context", () => {
-            const { activeContext, store, dismissProposal } = setup();
+        it("does not persist to localStorage when not in notebook context", () => {
+            const { activeContext, dismissProposal } = setup();
             activeContext.value = null;
             dismissProposal(makeProposalMsg("full_replacement", "x"));
-            expect(store.addDismissedProposal).not.toHaveBeenCalled();
+            expect(mockPersistedDismissed.value[PAGE_ID]).toBeUndefined();
         });
     });
 
diff --git a/client/src/composables/usePageProposals.ts b/client/src/composables/usePageProposals.ts
index 1b6b5101af4..abdd9270d4b 100644
--- a/client/src/composables/usePageProposals.ts
+++ b/client/src/composables/usePageProposals.ts
@@ -4,6 +4,7 @@ import type { ChatMessage } from "@/components/GalaxyAI/chatTypes";
 import { applySectionEdit, djb2Hash } from "@/components/PageEditor/sectionDiffUtils";
 import type { EditProposal } from "@/composables/agentActions";
 import type { ActiveContext } from "@/composables/useActiveContext";
+import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import { usePageEditorStore } from "@/stores/pageEditorStore";
 
 /**
@@ -12,28 +13,41 @@ import { usePageEditorStore } from "@/stores/pageEditorStore";
  *
  * Owns the `dismissedProposals` set and all helpers needed to render
  * ProposalDiffView / SectionPatchView inside ChatMessageCell.
+ *
+ * Dismissed proposal IDs are persisted in localStorage keyed by pageId so they
+ * survive page reloads for the same conversation.
  */
 export function usePageProposals(activeContext: Readonly<Ref<ActiveContext | null>>) {
     const pageEditorStore = usePageEditorStore();
 
+    /** Persisted map of pageId → dismissed message ID list. */
+    const persistedDismissed = useUserLocalStorage<Record<string, string[]>>("page-chat-dismissed-proposals", {});
+
     /** Live page content — empty when not in notebook context. */
     const pageContent = computed(() =>
         activeContext.value?.contextType === "notebook" ? pageEditorStore.currentContent : "",
     );
 
-    /** Message IDs whose proposals have been dismissed or already applied. */
+    /** In-memory working set for the current conversation. */
     const dismissedProposals = ref(new Set<string>());
 
     /** Load the persisted dismissed set for a page after fetching a conversation. */
     function loadForPage(pageId: string) {
-        dismissedProposals.value = new Set(pageEditorStore.getDismissedProposals(pageId));
+        dismissedProposals.value = new Set(persistedDismissed.value[pageId] ?? []);
     }
 
-    /** Clear the dismissed set (new chat or leaving notebook context). */
+    /** Clear the in-memory set (new chat or leaving notebook context). */
     function clear() {
         dismissedProposals.value = new Set();
     }
 
+    function persistDismiss(pageId: string, messageId: string) {
+        const current = persistedDismissed.value[pageId] ?? [];
+        if (!current.includes(messageId)) {
+            persistedDismissed.value = { ...persistedDismissed.value, [pageId]: [...current, messageId] };
+        }
+    }
+
     function getEditProposal(msg: ChatMessage): EditProposal | null {
         const meta = msg.agentResponse?.metadata;
         const editMode = meta?.edit_mode as EditProposal["mode"] | undefined;
@@ -93,8 +107,9 @@ export function usePageProposals(activeContext: Readonly<Ref<ActiveContext | nul
         pageEditorStore.updateContent(proposal.content);
         await pageEditorStore.savePage("agent");
         dismissedProposals.value.add(msg.id);
-        if (activeContext.value?.contextType === "notebook") {
-            pageEditorStore.addDismissedProposal(activeContext.value.pageId, msg.id);
+        const ctx = activeContext.value;
+        if (ctx?.contextType === "notebook") {
+            persistDismiss(ctx.pageId, msg.id);
         }
     }
 
@@ -102,15 +117,17 @@ export function usePageProposals(activeContext: Readonly<Ref<ActiveContext | nul
         pageEditorStore.updateContent(patchedContent);
         await pageEditorStore.savePage("agent");
         dismissedProposals.value.add(msg.id);
-        if (activeContext.value?.contextType === "notebook") {
-            pageEditorStore.addDismissedProposal(activeContext.value.pageId, msg.id);
+        const ctx = activeContext.value;
+        if (ctx?.contextType === "notebook") {
+            persistDismiss(ctx.pageId, msg.id);
         }
     }
 
     function dismissProposal(msg: ChatMessage) {
         dismissedProposals.value.add(msg.id);
-        if (activeContext.value?.contextType === "notebook") {
-            pageEditorStore.addDismissedProposal(activeContext.value.pageId, msg.id);
+        const ctx = activeContext.value;
+        if (ctx?.contextType === "notebook") {
+            persistDismiss(ctx.pageId, msg.id);
         }
     }
 
diff --git a/client/src/stores/pageEditorStore.ts b/client/src/stores/pageEditorStore.ts
index 3ca76082603..60b56c1adc2 100644
--- a/client/src/stores/pageEditorStore.ts
+++ b/client/src/stores/pageEditorStore.ts
@@ -1,7 +1,6 @@
 import { defineStore } from "pinia";
 import { computed, ref } from "vue";
 
-import { type components, GalaxyApi } from "@/api";
 import {
     createHistoryPage,
     type CreateHistoryPagePayload,
@@ -22,8 +21,6 @@ import { ERROR_MESSAGES } from "@/components/Page/constants";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-type ChatHistoryItem = components["schemas"]["ChatHistoryItemResponse"];
-
 export type PageEditorMode = "history" | "standalone";
 
 export const usePageEditorStore = defineStore("pageEditor", () => {
@@ -47,12 +44,6 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
     // Per-page chat exchange ID persisted across panel close/reopen
     const currentChatExchangeIds = useUserLocalStorage<Record<string, string | null>>("history-page-chat-exchange", {});
 
-    // Per-page dismissed proposal message IDs
-    const dismissedChatProposals = useUserLocalStorage<Record<string, string[]>>(
-        "history-page-dismissed-proposals",
-        {},
-    );
-
     // Revision state
     const revisions = ref<PageRevisionSummary[]>([]);
     const selectedRevision = ref<PageRevisionDetails | null>(null);
@@ -62,13 +53,6 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
     const previousRevisionContent = ref<string | null>(null);
     const revisionViewMode = ref<"preview" | "changes_current" | "changes_previous">("preview");
     const showRevisions = ref(false);
-    const showChatPanel = ref(false);
-
-    // Chat history sidebar state
-    const pageChatHistory = ref<ChatHistoryItem[]>([]);
-    const isLoadingChatHistory = ref(false);
-    const showChatHistory = ref(false);
-    const chatHistoryError = ref<string | null>(null);
 
     const hasPages = computed(() => pages.value.length > 0);
     const hasCurrentPage = computed(() => currentPage.value !== null);
@@ -208,7 +192,6 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
             await deleteHistoryPage(deletedId);
             clearCurrentPageId(historyId.value);
             clearCurrentChatExchangeId(deletedId);
-            clearDismissedProposals(deletedId);
             currentPage.value = null;
             originalContent.value = "";
             currentContent.value = "";
@@ -240,11 +223,7 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
         currentContent.value = "";
         originalTitle.value = "";
         currentTitle.value = "";
-        showChatPanel.value = false;
         chatError.value = null;
-        pageChatHistory.value = [];
-        showChatHistory.value = false;
-        chatHistoryError.value = null;
         clearRevisionState();
     }
 
@@ -278,66 +257,6 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
         currentChatExchangeIds.value = rest;
     }
 
-    // --- Dismissed proposals persistence ---
-
-    function getDismissedProposals(pageId: string): string[] {
-        return dismissedChatProposals.value[pageId] ?? [];
-    }
-
-    function addDismissedProposal(pageId: string, messageId: string) {
-        const current = dismissedChatProposals.value[pageId] ?? [];
-        if (!current.includes(messageId)) {
-            dismissedChatProposals.value = {
-                ...dismissedChatProposals.value,
-                [pageId]: [...current, messageId],
-            };
-        }
-    }
-
-    function clearDismissedProposals(pageId: string) {
-        const { [pageId]: _removed, ...rest } = dismissedChatProposals.value;
-        dismissedChatProposals.value = rest;
-    }
-
-    // --- Chat history actions ---
-
-    async function loadPageChatHistory(pageId: string) {
-        isLoadingChatHistory.value = true;
-        chatHistoryError.value = null;
-        try {
-            const { data, error } = await GalaxyApi().GET("/api/chat/page/{page_id}/history", {
-                params: { path: { page_id: pageId }, query: { limit: 50 } },
-            });
-            if (error) {
-                chatHistoryError.value = errorMessageAsString(error);
-            } else {
-                pageChatHistory.value = data ?? [];
-            }
-        } catch (e) {
-            chatHistoryError.value = errorMessageAsString(e);
-        } finally {
-            isLoadingChatHistory.value = false;
-        }
-    }
-
-    async function deletePageChatExchanges(pageId: string, ids: string[]) {
-        const { error } = await GalaxyApi().PUT("/api/chat/exchanges/batch/delete", {
-            body: { ids },
-        });
-        if (error) {
-            throw Error(errorMessageAsString(error));
-        }
-        pageChatHistory.value = pageChatHistory.value.filter((item) => !ids.includes(item.id));
-        const activeId = currentChatExchangeIds.value[pageId];
-        if (activeId && ids.includes(activeId)) {
-            setCurrentChatExchangeId(pageId, null);
-        }
-    }
-
-    function toggleChatHistory() {
-        showChatHistory.value = !showChatHistory.value;
-    }
-
     async function resolveCurrentPage(forHistoryId: string): Promise<string> {
         // Always populate the list so callers can look up titles
         await loadPages(forHistoryId);
@@ -433,21 +352,12 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
     function toggleRevisions() {
         showRevisions.value = !showRevisions.value;
         if (showRevisions.value) {
-            showChatPanel.value = false;
             loadRevisions();
         } else {
             selectedRevision.value = null;
         }
     }
 
-    function toggleChatPanel() {
-        showChatPanel.value = !showChatPanel.value;
-        if (showChatPanel.value && showRevisions.value) {
-            showRevisions.value = false;
-            selectedRevision.value = null;
-        }
-    }
-
     function clearSelectedRevision() {
         selectedRevision.value = null;
         previousRevisionContent.value = null;
@@ -480,11 +390,6 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
         error.value = null;
         chatError.value = null;
         historyId.value = null;
-        showChatPanel.value = false;
-        pageChatHistory.value = [];
-        isLoadingChatHistory.value = false;
-        showChatHistory.value = false;
-        chatHistoryError.value = null;
         clearRevisionState();
     }
 
@@ -525,18 +430,6 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
         getCurrentChatExchangeId,
         setCurrentChatExchangeId,
         clearCurrentChatExchangeId,
-        // Dismissed proposals persistence
-        getDismissedProposals,
-        addDismissedProposal,
-        clearDismissedProposals,
-        // Chat history state
-        pageChatHistory,
-        isLoadingChatHistory,
-        showChatHistory,
-        chatHistoryError,
-        loadPageChatHistory,
-        deletePageChatExchanges,
-        toggleChatHistory,
         // Revision state
         revisionViewMode,
         revisions,
@@ -548,7 +441,6 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
         isLoadingRevision,
         isReverting,
         showRevisions,
-        showChatPanel,
         revisionCount,
         hasRevisions,
         // Revision actions
@@ -556,7 +448,6 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
         loadRevision,
         restoreRevision,
         toggleRevisions,
-        toggleChatPanel,
         clearSelectedRevision,
         $reset,
     };

From 1ff16fa411923f372372a4cb22b37f3008a7ddea Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 2 Jun 2026 23:49:53 -0500
Subject: [PATCH 064/256] remove PageChatHistoryList and test; remove chat from
 pageEditorStore test

---
 .../PageEditor/PageChatHistoryList.test.ts    | 231 -----------
 .../PageEditor/PageChatHistoryList.vue        | 234 -----------
 client/src/stores/pageEditorStore.test.ts     | 381 ------------------
 3 files changed, 846 deletions(-)
 delete mode 100644 client/src/components/PageEditor/PageChatHistoryList.test.ts
 delete mode 100644 client/src/components/PageEditor/PageChatHistoryList.vue

diff --git a/client/src/components/PageEditor/PageChatHistoryList.test.ts b/client/src/components/PageEditor/PageChatHistoryList.test.ts
deleted file mode 100644
index 8aa4bab4487..00000000000
--- a/client/src/components/PageEditor/PageChatHistoryList.test.ts
+++ /dev/null
@@ -1,231 +0,0 @@
-import { createTestingPinia } from "@pinia/testing";
-import { mount } from "@vue/test-utils";
-import { beforeEach, describe, expect, it, vi } from "vitest";
-
-import PageChatHistoryList from "./PageChatHistoryList.vue";
-
-const MOCK_ITEMS = [
-    {
-        id: "enc1",
-        query: "First question",
-        response: "First answer",
-        agent_type: "page_assistant",
-        timestamp: "2025-06-15T10:00:00Z",
-        feedback: null,
-        message_count: 2,
-    },
-    {
-        id: "enc2",
-        query: "Second question",
-        response: "Second answer",
-        agent_type: "page_assistant",
-        timestamp: "2025-06-14T09:00:00Z",
-        feedback: 1,
-        message_count: 4,
-    },
-    {
-        id: "enc3",
-        query: "Third question",
-        response: "Third answer",
-        agent_type: "page_assistant",
-        timestamp: "2025-06-13T08:00:00Z",
-        feedback: null,
-        message_count: 2,
-    },
-];
-
-function mountList(props: Record<string, unknown> = {}) {
-    return mount(PageChatHistoryList as any, {
-        propsData: {
-            items: MOCK_ITEMS,
-            isLoading: false,
-            error: null,
-            activeExchangeId: null,
-            ...props,
-        },
-        stubs: {
-            FontAwesomeIcon: true,
-            UtcDate: true,
-            BAlert: true,
-        },
-    });
-}
-
-describe("PageChatHistoryList", () => {
-    // Vue 2.7 emits prop warnings for `string | null` TS types; suppress them
-    beforeEach(() => {
-        vi.spyOn(console, "error").mockImplementation(() => {});
-        createTestingPinia({ createSpy: vi.fn, stubActions: false });
-    });
-    describe("rendering", () => {
-        it("renders items", () => {
-            const wrapper = mountList();
-            const items = wrapper.findAll('[data-description="sidebar item"]');
-            expect(items.length).toBe(3);
-        });
-
-        it("shows query text for each item", () => {
-            const wrapper = mountList();
-            expect(wrapper.text()).toContain("First question");
-            expect(wrapper.text()).toContain("Second question");
-            expect(wrapper.text()).toContain("Third question");
-        });
-
-        it("shows empty message when no items", () => {
-            const wrapper = mountList({ items: [] });
-            expect(wrapper.text()).toContain("No conversations yet.");
-        });
-
-        it("shows loading message when loading", () => {
-            const wrapper = mountList({ isLoading: true });
-            expect(wrapper.text()).toContain("Loading history...");
-        });
-    });
-
-    describe("selection mode toggle", () => {
-        it("trash button toggles selection mode on", async () => {
-            const wrapper = mountList();
-            expect(wrapper.find(".selection-toolbar").exists()).toBe(false);
-
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            expect(wrapper.find(".selection-toolbar").exists()).toBe(true);
-        });
-
-        it("cancel button toggles selection mode off", async () => {
-            const wrapper = mountList();
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-            expect(wrapper.find(".selection-toolbar").exists()).toBe(true);
-
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            expect(wrapper.find(".selection-toolbar").exists()).toBe(false);
-        });
-
-        it("checkboxes visible in selection mode", async () => {
-            const wrapper = mountList();
-            expect(wrapper.find(".history-checkbox").exists()).toBe(false);
-
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            expect(wrapper.findAll(".history-checkbox").length).toBe(3);
-        });
-    });
-
-    describe("item clicks", () => {
-        it("emits select when clicking item outside selection mode", async () => {
-            const wrapper = mountList();
-            await wrapper.findAll('[data-description="sidebar item"]').at(0)!.trigger("click");
-
-            const emitted = wrapper.emitted("select");
-            expect(emitted).toBeTruthy();
-            expect(emitted![0]![0]).toEqual(MOCK_ITEMS[0]);
-        });
-
-        it("does NOT emit select when clicking item in selection mode", async () => {
-            const wrapper = mountList();
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            await wrapper.findAll('[data-description="sidebar item"]').at(0)!.trigger("click");
-
-            expect(wrapper.emitted("select")).toBeFalsy();
-        });
-
-        it("toggles item selection when clicking in selection mode", async () => {
-            const wrapper = mountList();
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            await wrapper.findAll('[data-description="sidebar item"]').at(1)!.trigger("click");
-
-            // Delete button should show count
-            const deleteBtn = wrapper.find('[data-description="delete selected button"]');
-            expect(deleteBtn.text()).toContain("1");
-        });
-    });
-
-    describe("select all / deselect all", () => {
-        it("select all selects all items", async () => {
-            const wrapper = mountList();
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            await wrapper.find(".select-all-toggle").trigger("click");
-
-            const deleteBtn = wrapper.find('[data-description="delete selected button"]');
-            expect(deleteBtn.text()).toContain("3");
-        });
-
-        it("deselect all clears selection", async () => {
-            const wrapper = mountList();
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-            // Select all
-            await wrapper.find(".select-all-toggle").trigger("click");
-            // Deselect all
-            await wrapper.find(".select-all-toggle").trigger("click");
-
-            const deleteBtn = wrapper.find('[data-description="delete selected button"]');
-            expect((deleteBtn.element as HTMLButtonElement).disabled).toBe(true);
-        });
-    });
-
-    describe("delete", () => {
-        it("delete button disabled when nothing selected", async () => {
-            const wrapper = mountList();
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            const deleteBtn = wrapper.find('[data-description="delete selected button"]');
-            expect((deleteBtn.element as HTMLButtonElement).disabled).toBe(true);
-        });
-
-        it("delete button emits delete with selected IDs", async () => {
-            const wrapper = mountList();
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            // Click first and third items
-            const items = wrapper.findAll('[data-description="sidebar item"]');
-            await items.at(0)!.trigger("click");
-            await items.at(2)!.trigger("click");
-
-            await wrapper.find('[data-description="delete selected button"]').trigger("click");
-
-            const emitted = wrapper.emitted("delete");
-            expect(emitted).toBeTruthy();
-            const ids = emitted![0]![0] as string[];
-            expect(ids).toHaveLength(2);
-            expect(ids).toContain("enc1");
-            expect(ids).toContain("enc3");
-        });
-    });
-
-    describe("shift-click range selection", () => {
-        it("selects range with shift-click", async () => {
-            const wrapper = mountList();
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            const items = wrapper.findAll('[data-description="sidebar item"]');
-            // Click first item normally
-            await items.at(0)!.trigger("click");
-            // Shift-click third item
-            await items.at(2)!.trigger("click", { shiftKey: true });
-
-            // All 3 should be selected
-            const deleteBtn = wrapper.find('[data-description="delete selected button"]');
-            expect(deleteBtn.text()).toContain("3");
-        });
-    });
-
-    describe("active exchange highlight", () => {
-        it("applies active class to matching item when not in selection mode", () => {
-            const wrapper = mountList({ activeExchangeId: "enc2" });
-            const items = wrapper.findAll('[data-description="sidebar item"]');
-            expect(items.at(1)!.classes()).toContain("active");
-        });
-
-        it("does not apply active class in selection mode", async () => {
-            const wrapper = mountList({ activeExchangeId: "enc2" });
-            await wrapper.find('[data-description="toggle selection button"]').trigger("click");
-
-            const items = wrapper.findAll('[data-description="sidebar item"]');
-            expect(items.at(1)!.classes()).not.toContain("active");
-        });
-    });
-});
diff --git a/client/src/components/PageEditor/PageChatHistoryList.vue b/client/src/components/PageEditor/PageChatHistoryList.vue
deleted file mode 100644
index 7c20470fe90..00000000000
--- a/client/src/components/PageEditor/PageChatHistoryList.vue
+++ /dev/null
@@ -1,234 +0,0 @@
-<script setup lang="ts">
-import { faCheckSquare, faSquare } from "@fortawesome/free-regular-svg-icons";
-import { faClock, faComments, faTimes, faTrash } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert } from "bootstrap-vue";
-import { computed, watch } from "vue";
-
-import type { components } from "@/api";
-import { useSidebarSelection } from "@/composables/useSidebarSelection";
-
-import SidebarList from "@/components/Common/SidebarList.vue";
-import UtcDate from "@/components/UtcDate.vue";
-
-type ChatHistoryItem = components["schemas"]["ChatHistoryItemResponse"];
-
-const props = defineProps<{
-    items: ChatHistoryItem[];
-    isLoading: boolean;
-    error: string | null;
-    activeExchangeId: string | null;
-}>();
-
-const emit = defineEmits<{
-    (e: "select", item: ChatHistoryItem): void;
-    (e: "delete", ids: string[]): void;
-    (e: "dismiss-error"): void;
-}>();
-
-const itemsRef = computed(() => props.items);
-
-const {
-    selectionMode,
-    selectedIds,
-    allSelected,
-    toggleSelectionMode,
-    toggleSelectAll,
-    handleSelectionClick,
-    pruneAfterDelete,
-} = useSidebarSelection(itemsRef, (item) => item.id);
-
-function itemKey(item: ChatHistoryItem): string {
-    return item.id;
-}
-
-function itemClass(item: ChatHistoryItem): Record<string, boolean> {
-    return {
-        active: !selectionMode.value && item.id === props.activeExchangeId,
-        selected: selectedIds.value.has(item.id),
-    };
-}
-
-function onSelect(item: ChatHistoryItem, index: number, event: MouseEvent) {
-    if (handleSelectionClick(item, index, event)) {
-        return;
-    }
-    emit("select", item);
-}
-
-function deleteSelected() {
-    if (selectedIds.value.size === 0) {
-        return;
-    }
-    emit("delete", Array.from(selectedIds.value));
-}
-
-// Items are owned by the parent (store) and removed asynchronously after
-// the "delete" emit. Prune stale selections once the prop actually updates.
-watch(itemsRef, () => {
-    if (selectionMode.value) {
-        pruneAfterDelete();
-    }
-});
-
-defineExpose({ selectionMode, toggleSelectionMode });
-</script>
-
-<template>
-    <div class="page-chat-history-list" data-description="page chat history list">
-        <div class="history-toolbar d-flex align-items-center justify-content-between px-2 py-1 border-bottom">
-            <span class="toolbar-label">History</span>
-            <button
-                class="btn btn-sm"
-                :class="selectionMode ? 'btn-outline-secondary' : 'btn-outline-danger'"
-                :title="selectionMode ? 'Cancel selection' : 'Select chats to delete'"
-                data-description="toggle selection button"
-                @click="toggleSelectionMode">
-                <FontAwesomeIcon :icon="selectionMode ? faTimes : faTrash" fixed-width />
-            </button>
-        </div>
-
-        <div v-if="selectionMode && items.length > 0" class="selection-toolbar">
-            <!-- eslint-disable-next-line vuejs-accessibility/click-events-have-key-events vuejs-accessibility/no-static-element-interactions -->
-            <span class="select-all-toggle" @click="toggleSelectAll">
-                <FontAwesomeIcon :icon="allSelected ? faCheckSquare : faSquare" fixed-width />
-                {{ allSelected ? "Deselect all" : "Select all" }}
-            </span>
-            <button
-                class="btn btn-sm btn-danger"
-                :disabled="selectedIds.size === 0"
-                data-description="delete selected button"
-                @click="deleteSelected">
-                Delete {{ selectedIds.size > 0 ? selectedIds.size : "" }}
-            </button>
-        </div>
-
-        <BAlert
-            v-if="props.error"
-            variant="danger"
-            dismissible
-            show
-            class="m-2 mb-0"
-            data-description="chat history error"
-            @dismissed="emit('dismiss-error')">
-            {{ props.error }}
-        </BAlert>
-
-        <SidebarList
-            :items="items"
-            :is-loading="isLoading"
-            loading-message="Loading history..."
-            empty-message="No conversations yet."
-            :item-key="itemKey"
-            :item-class="itemClass"
-            @select="onSelect">
-            <template v-slot:item="{ item }">
-                <span v-if="selectionMode" class="history-checkbox">
-                    <FontAwesomeIcon :icon="selectedIds.has(item.id) ? faCheckSquare : faSquare" fixed-width />
-                </span>
-                <div class="history-content">
-                    <div class="history-query">{{ item.query }}</div>
-                    <div class="history-meta">
-                        <span v-if="item.message_count" class="history-messages">
-                            <FontAwesomeIcon :icon="faComments" fixed-width />
-                            {{ item.message_count }}
-                        </span>
-                        <span v-if="item.timestamp" class="history-time">
-                            <FontAwesomeIcon :icon="faClock" fixed-width />
-                            <UtcDate :date="item.timestamp" mode="elapsed" />
-                        </span>
-                    </div>
-                </div>
-            </template>
-        </SidebarList>
-    </div>
-</template>
-
-<style scoped>
-.page-chat-history-list {
-    max-height: 100%;
-    overflow-y: auto;
-}
-
-.history-toolbar {
-    font-size: 0.75rem;
-    font-weight: 600;
-}
-
-.toolbar-label {
-    text-transform: uppercase;
-    letter-spacing: 0.025em;
-    color: var(--text-muted, #6c757d);
-}
-
-.selection-toolbar {
-    display: flex;
-    align-items: center;
-    justify-content: space-between;
-    padding: 0.375rem 0.5rem;
-    border-bottom: 1px solid var(--border-color, #dee2e6);
-    font-size: 0.75rem;
-}
-
-.select-all-toggle {
-    cursor: pointer;
-    color: var(--text-muted, #6c757d);
-    display: flex;
-    align-items: center;
-    gap: 0.25rem;
-}
-
-.select-all-toggle:hover {
-    color: var(--text-color, #212529);
-}
-
-:deep(.sidebar-item.active) {
-    background: rgba(var(--brand-primary-rgb, 0, 123, 255), 0.08);
-    border-left: 3px solid var(--brand-primary, #007bff);
-    padding-left: calc(0.5rem - 3px);
-}
-
-:deep(.sidebar-item.selected) {
-    background: rgba(var(--brand-primary-rgb, 0, 123, 255), 0.06);
-}
-
-.history-checkbox {
-    flex-shrink: 0;
-    color: var(--text-muted, #6c757d);
-    padding-top: 0.1rem;
-}
-
-.history-content {
-    flex: 1;
-    min-width: 0;
-}
-
-.history-query {
-    font-size: 0.8rem;
-    color: var(--text-color, #212529);
-    overflow: hidden;
-    text-overflow: ellipsis;
-    white-space: nowrap;
-    margin-bottom: 0.2rem;
-}
-
-.history-meta {
-    display: flex;
-    justify-content: space-between;
-    align-items: center;
-    font-size: 0.7rem;
-    color: var(--text-muted, #6c757d);
-}
-
-.history-messages {
-    display: flex;
-    align-items: center;
-    gap: 0.2rem;
-}
-
-.history-time {
-    display: flex;
-    align-items: center;
-    gap: 0.2rem;
-}
-</style>
diff --git a/client/src/stores/pageEditorStore.test.ts b/client/src/stores/pageEditorStore.test.ts
index 175c554695b..06c59ba8f92 100644
--- a/client/src/stores/pageEditorStore.test.ts
+++ b/client/src/stores/pageEditorStore.test.ts
@@ -637,295 +637,6 @@ describe("usePageEditorStore", () => {
         });
     });
 
-    describe("panel toggle mutual exclusion", () => {
-        it("toggleChatPanel opens and closes chat", () => {
-            const store = usePageEditorStore();
-            expect(store.showChatPanel).toBe(false);
-
-            store.toggleChatPanel();
-            expect(store.showChatPanel).toBe(true);
-
-            store.toggleChatPanel();
-            expect(store.showChatPanel).toBe(false);
-        });
-
-        it("toggleChatPanel closes revisions and clears selectedRevision when opening chat", () => {
-            const store = usePageEditorStore();
-            store.$patch({ showRevisions: true });
-            store.selectedRevision = {
-                id: "rev-1",
-                page_id: TEST_PAGE_ID,
-                content: "# Old",
-                content_format: "markdown",
-                edit_source: "user",
-                create_time: "2024-01-01T00:00:00",
-                update_time: "2024-01-01T00:00:00",
-            } as any;
-
-            store.toggleChatPanel();
-
-            expect(store.showChatPanel).toBe(true);
-            expect(store.showRevisions).toBe(false);
-            expect(store.selectedRevision).toBeNull();
-        });
-
-        it("toggleChatPanel does not touch revisions when closing chat", () => {
-            const store = usePageEditorStore();
-            store.$patch({ showChatPanel: true, showRevisions: false });
-
-            store.toggleChatPanel();
-
-            expect(store.showChatPanel).toBe(false);
-            expect(store.showRevisions).toBe(false);
-        });
-
-        it("toggleRevisions closes chat when opening revisions", () => {
-            useDefaultHandlers();
-            const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID, showChatPanel: true });
-            store.currentPage = TEST_PAGE_DETAILS;
-
-            store.toggleRevisions();
-
-            expect(store.showRevisions).toBe(true);
-            expect(store.showChatPanel).toBe(false);
-        });
-
-        it("toggleRevisions does not touch chat when closing revisions", () => {
-            const store = usePageEditorStore();
-            store.$patch({ showRevisions: true, showChatPanel: false });
-
-            store.toggleRevisions();
-
-            expect(store.showRevisions).toBe(false);
-            expect(store.showChatPanel).toBe(false);
-        });
-
-        it("$reset clears showChatPanel", () => {
-            const store = usePageEditorStore();
-            store.$patch({ showChatPanel: true });
-
-            store.$reset();
-
-            expect(store.showChatPanel).toBe(false);
-        });
-
-        it("clearCurrentPage clears showChatPanel", () => {
-            const store = usePageEditorStore();
-            store.$patch({ showChatPanel: true });
-
-            store.clearCurrentPage();
-
-            expect(store.showChatPanel).toBe(false);
-        });
-    });
-
-    describe("chat exchange persistence", () => {
-        it("get/set/clear exchange ID", () => {
-            const store = usePageEditorStore();
-
-            expect(store.getCurrentChatExchangeId("p-1")).toBeNull();
-
-            store.setCurrentChatExchangeId("p-1", "42");
-            expect(store.getCurrentChatExchangeId("p-1")).toBe("42");
-
-            store.setCurrentChatExchangeId("p-2", "99");
-            expect(store.getCurrentChatExchangeId("p-2")).toBe("99");
-
-            store.clearCurrentChatExchangeId("p-1");
-            expect(store.getCurrentChatExchangeId("p-1")).toBeNull();
-            expect(store.getCurrentChatExchangeId("p-2")).toBe("99");
-        });
-
-        it("setCurrentChatExchangeId with null stores null", () => {
-            const store = usePageEditorStore();
-            store.setCurrentChatExchangeId("p-1", "42");
-            store.setCurrentChatExchangeId("p-1", null);
-            expect(store.getCurrentChatExchangeId("p-1")).toBeNull();
-        });
-
-        it("clearCurrentPage preserves chat exchange ID", async () => {
-            useDefaultHandlers();
-            const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
-            await store.loadPageById(TEST_PAGE_ID);
-            store.setCurrentChatExchangeId(TEST_PAGE_ID, "abc123exchangeid");
-
-            store.clearCurrentPage();
-
-            expect(store.getCurrentChatExchangeId(TEST_PAGE_ID)).toBe("abc123exchangeid");
-        });
-
-        it("deleteCurrentPage clears chat exchange ID", async () => {
-            server.use(
-                http.get("/api/pages/{id}", ({ response }: any) => {
-                    return response(200).json(TEST_PAGE_DETAILS);
-                }) as any,
-                http.get("/api/pages", ({ response }: any) => {
-                    return response(200).json([]);
-                }) as any,
-                http.delete("/api/pages/{id}", ({ response }: any) => {
-                    return response(204).empty();
-                }) as any,
-            );
-            const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
-            await store.loadPageById(TEST_PAGE_ID);
-            store.setCurrentChatExchangeId(TEST_PAGE_ID, "77");
-
-            await store.deleteCurrentPage();
-
-            expect(store.getCurrentChatExchangeId(TEST_PAGE_ID)).toBeNull();
-        });
-    });
-
-    describe("chatError", () => {
-        it("is null initially", () => {
-            const store = usePageEditorStore();
-            expect(store.chatError).toBeNull();
-        });
-
-        it("can be set directly", () => {
-            const store = usePageEditorStore();
-            store.chatError = "Failed to load chat";
-            expect(store.chatError).toBe("Failed to load chat");
-        });
-
-        it("is cleared by clearCurrentPage", () => {
-            const store = usePageEditorStore();
-            store.chatError = "some error";
-
-            store.clearCurrentPage();
-
-            expect(store.chatError).toBeNull();
-        });
-
-        it("is cleared by $reset", () => {
-            const store = usePageEditorStore();
-            store.chatError = "some error";
-
-            store.$reset();
-
-            expect(store.chatError).toBeNull();
-        });
-    });
-
-    describe("chat history state", () => {
-        const MOCK_HISTORY = [
-            {
-                id: "enc1",
-                query: "What is this?",
-                response: "It is a page.",
-                agent_type: "page_assistant",
-                timestamp: "2025-06-15T10:00:00Z",
-                feedback: null,
-                message_count: 2,
-            },
-            {
-                id: "enc2",
-                query: "Summarize",
-                response: "Summary here.",
-                agent_type: "page_assistant",
-                timestamp: "2025-06-14T09:00:00Z",
-                feedback: 1,
-                message_count: 4,
-            },
-        ];
-
-        it("initial state is empty / not loading / no error", () => {
-            const store = usePageEditorStore();
-            expect(store.pageChatHistory).toEqual([]);
-            expect(store.isLoadingChatHistory).toBe(false);
-            expect(store.showChatHistory).toBe(false);
-            expect(store.chatHistoryError).toBeNull();
-        });
-
-        it("loadPageChatHistory populates pageChatHistory on success", async () => {
-            server.use(
-                http.get("/api/chat/page/{page_id}/history", ({ response }: any) => {
-                    return response(200).json(MOCK_HISTORY);
-                }) as any,
-            );
-            const store = usePageEditorStore();
-
-            await store.loadPageChatHistory(TEST_PAGE_ID);
-
-            expect(store.pageChatHistory).toEqual(MOCK_HISTORY);
-            expect(store.isLoadingChatHistory).toBe(false);
-            expect(store.chatHistoryError).toBeNull();
-        });
-
-        it("loadPageChatHistory sets chatHistoryError on failure", async () => {
-            server.use(
-                http.get("/api/chat/page/{page_id}/history", ({ response }: any) => {
-                    return response("5XX").json({ err_msg: "DB down", err_code: 500 }, { status: 500 });
-                }) as any,
-            );
-            const store = usePageEditorStore();
-
-            await store.loadPageChatHistory(TEST_PAGE_ID);
-
-            expect(store.pageChatHistory).toEqual([]);
-            expect(store.chatHistoryError).toBeTruthy();
-            expect(store.isLoadingChatHistory).toBe(false);
-        });
-
-        it("loadPageChatHistory clears previous error on retry", async () => {
-            server.use(
-                http.get("/api/chat/page/{page_id}/history", ({ response }: any) => {
-                    return response(200).json(MOCK_HISTORY);
-                }) as any,
-            );
-            const store = usePageEditorStore();
-            store.$patch({ chatHistoryError: "old error" });
-
-            await store.loadPageChatHistory(TEST_PAGE_ID);
-
-            expect(store.chatHistoryError).toBeNull();
-        });
-
-        it("toggleChatHistory toggles showChatHistory", () => {
-            const store = usePageEditorStore();
-            expect(store.showChatHistory).toBe(false);
-
-            store.toggleChatHistory();
-            expect(store.showChatHistory).toBe(true);
-
-            store.toggleChatHistory();
-            expect(store.showChatHistory).toBe(false);
-        });
-
-        it("clearCurrentPage resets chat history state", () => {
-            const store = usePageEditorStore();
-            store.$patch({
-                pageChatHistory: MOCK_HISTORY as any,
-                showChatHistory: true,
-                chatHistoryError: "some error",
-            });
-
-            store.clearCurrentPage();
-
-            expect(store.pageChatHistory).toEqual([]);
-            expect(store.showChatHistory).toBe(false);
-            expect(store.chatHistoryError).toBeNull();
-        });
-
-        it("$reset clears chat history state", () => {
-            const store = usePageEditorStore();
-            store.$patch({
-                pageChatHistory: MOCK_HISTORY as any,
-                showChatHistory: true,
-                chatHistoryError: "some error",
-            });
-
-            store.$reset();
-
-            expect(store.pageChatHistory).toEqual([]);
-            expect(store.showChatHistory).toBe(false);
-            expect(store.chatHistoryError).toBeNull();
-        });
-    });
-
     describe("synchronous actions", () => {
         it("updateContent updates currentContent", () => {
             const store = usePageEditorStore();
@@ -1254,98 +965,6 @@ describe("usePageEditorStore", () => {
         });
     });
 
-    describe("deletePageChatExchanges", () => {
-        const MOCK_HISTORY = [
-            {
-                id: "enc1",
-                query: "First question",
-                response: "First answer",
-                agent_type: "page_assistant",
-                timestamp: "2025-06-15T10:00:00Z",
-                feedback: null,
-                message_count: 2,
-            },
-            {
-                id: "enc2",
-                query: "Second question",
-                response: "Second answer",
-                agent_type: "page_assistant",
-                timestamp: "2025-06-14T09:00:00Z",
-                feedback: 1,
-                message_count: 4,
-            },
-            {
-                id: "enc3",
-                query: "Third question",
-                response: "Third answer",
-                agent_type: "page_assistant",
-                timestamp: "2025-06-13T08:00:00Z",
-                feedback: null,
-                message_count: 2,
-            },
-        ];
-
-        it("removes deleted items from pageChatHistory", async () => {
-            server.use(
-                http.put("/api/chat/exchanges/batch/delete", ({ response }: any) => {
-                    return response(200).json({});
-                }) as any,
-            );
-            const store = usePageEditorStore();
-            store.$patch({ pageChatHistory: MOCK_HISTORY as any });
-
-            await store.deletePageChatExchanges(TEST_PAGE_ID, ["enc1", "enc3"]);
-
-            expect(store.pageChatHistory).toHaveLength(1);
-            expect(store.pageChatHistory[0]!.id).toBe("enc2");
-        });
-
-        it("clears active exchange when it is in the delete set", async () => {
-            server.use(
-                http.put("/api/chat/exchanges/batch/delete", ({ response }: any) => {
-                    return response(200).json({});
-                }) as any,
-            );
-            const store = usePageEditorStore();
-            store.$patch({ pageChatHistory: MOCK_HISTORY as any });
-            store.setCurrentChatExchangeId(TEST_PAGE_ID, "enc2");
-
-            await store.deletePageChatExchanges(TEST_PAGE_ID, ["enc2"]);
-
-            expect(store.getCurrentChatExchangeId(TEST_PAGE_ID)).toBeNull();
-        });
-
-        it("preserves active exchange when it is NOT in the delete set", async () => {
-            server.use(
-                http.put("/api/chat/exchanges/batch/delete", ({ response }: any) => {
-                    return response(200).json({});
-                }) as any,
-            );
-            const store = usePageEditorStore();
-            store.$patch({ pageChatHistory: MOCK_HISTORY as any });
-            store.setCurrentChatExchangeId(TEST_PAGE_ID, "enc2");
-
-            await store.deletePageChatExchanges(TEST_PAGE_ID, ["enc1"]);
-
-            expect(store.getCurrentChatExchangeId(TEST_PAGE_ID)).toBe("enc2");
-            expect(store.pageChatHistory).toHaveLength(2);
-        });
-
-        it("throws and leaves pageChatHistory unchanged on API error", async () => {
-            server.use(
-                http.put("/api/chat/exchanges/batch/delete", ({ response }: any) => {
-                    return response("5XX").json({ err_msg: "Server error", err_code: 500 }, { status: 500 });
-                }) as any,
-            );
-            const store = usePageEditorStore();
-            store.$patch({ pageChatHistory: MOCK_HISTORY as any });
-
-            await expect(store.deletePageChatExchanges(TEST_PAGE_ID, ["enc1"])).rejects.toThrow();
-
-            expect(store.pageChatHistory).toHaveLength(3);
-        });
-    });
-
     describe("standalone mode", () => {
         const STANDALONE_PAGE: HistoryPageDetails = {
             ...TEST_PAGE_DETAILS,

From 1c1ff67597ab37d8466dfbf997b578f5608e0704 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 2 Jun 2026 23:53:00 -0500
Subject: [PATCH 065/256] remove assistant variables from PAGE_LABELS

---
 client/src/components/Page/constants.ts | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/client/src/components/Page/constants.ts b/client/src/components/Page/constants.ts
index b365c75af00..6068907f17f 100644
--- a/client/src/components/Page/constants.ts
+++ b/client/src/components/Page/constants.ts
@@ -24,8 +24,6 @@ export const PAGE_LABELS: Record<
         viewButton: string;
         createButton: string;
         historyCounterTooltip: string;
-        assistantName: string;
-        assistantWelcome: string;
         chatPlaceholder: string;
         newConversation: string;
     }
@@ -42,10 +40,6 @@ export const PAGE_LABELS: Record<
         viewButton: "View notebook",
         createButton: "Create Notebook",
         historyCounterTooltip: "Galaxy Notebooks",
-        assistantName: "Markdown Assistant",
-        assistantWelcome:
-            "I'm the Markdown Assistant. I can help you edit this notebook — " +
-            "ask me to rewrite sections, add content, fix formatting, or analyze your history datasets.",
         chatPlaceholder: "Ask about your history or request notebook edits...",
         newConversation: "Starting a new conversation. How can I help with this notebook?",
     },
@@ -60,11 +54,6 @@ export const PAGE_LABELS: Record<
         viewButton: "View report",
         createButton: "Create Report",
         historyCounterTooltip: "",
-        assistantName: "Markdown Assistant",
-        assistantWelcome:
-            "I'm the Markdown Assistant. I can help you edit this report — " +
-            "ask me to rewrite sections, add content, fix formatting, " +
-            "or browse your current history's datasets.",
         chatPlaceholder: "Ask about your history or request report edits...",
         newConversation: "Starting a new conversation. How can I help with this report?",
     },

From 0d083085bd2ac932494f8d230a1b8f65e3262112 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 2 Jun 2026 23:55:12 -0500
Subject: [PATCH 066/256] remove selectors and seleniums for removed notebook
 centric chat

---
 client/src/utils/navigation/navigation.yml    |  20 ----
 lib/galaxy/selenium/navigates_galaxy.py       |  26 -----
 .../selenium/test_history_pages.py            | 103 ------------------
 3 files changed, 149 deletions(-)

diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 46273128abf..9c6f7e584ed 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -710,26 +710,6 @@ pages:
       save_view_button:
         type: data-description
         selector: 'page save-view button'
-      chat_button:
-        type: data-description
-        selector: 'page chat button'
-      chat_panel:
-        type: data-description
-        selector: 'page chat panel'
-      chat_input: '.page-chat-panel #chat-input'
-      chat_send_button: '.page-chat-panel .send-button'
-      chat_loading: '.page-chat-panel [data-description="chat loading indicator"]'
-      chat_query_cell: '.page-chat-panel .entry-query .query-text'
-      chat_response_content: '.page-chat-panel .entry-response .response-content'
-      chat_new_conversation:
-        type: data-description
-        selector: 'new conversation button'
-      chat_history_button:
-        type: data-description
-        selector: 'chat history button'
-      chat_history_sidebar:
-        type: data-description
-        selector: 'page chat history list'
       revision_compare_current_button:
         type: data-description
         selector: 'revision compare current button'
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index d4cb02d2f03..5b0419676d1 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -2339,32 +2339,6 @@ class NavigatesGalaxy(HasDriverProxy[WaitType]):
         self.send_enter(title_input)
         self.sleep_for(self.wait_types.UX_RENDER)
 
-    def history_page_open_chat(self):
-        """Click chat button in page toolbar, wait for chat panel visible."""
-        self.components.pages.history.chat_button.wait_for_and_click()
-        self.components.pages.history.chat_panel.wait_for_visible()
-
-    def history_page_chat_send_message(self, text):
-        """Type into chat input, click send, wait for response."""
-        chat = self.components.pages.history
-        chat.chat_input.wait_for_and_send_keys(text)
-        chat.chat_send_button.wait_for_and_click()
-        chat.chat_loading.wait_for_absent_or_hidden()
-        chat.chat_response_content.wait_for_visible()
-
-    def history_page_chat_ensure_new(self):
-        """Click new conversation button if messages exist."""
-        chat = self.components.pages.history
-        if len(chat.chat_query_cell.all()) > 0 or len(chat.chat_response_content.all()) > 0:
-            chat.chat_new_conversation.wait_for_and_click()
-        self._history_page_chat_assert_empty()
-
-    @retry_during_transitions
-    def _history_page_chat_assert_empty(self):
-        chat = self.components.pages.history
-        assert len(chat.chat_query_cell.all()) == 0
-        assert len(chat.chat_response_content.all()) == 0
-
     @retry_during_transitions
     def click_history_options(self):
         component = self.components.history_panel.options_button_icon
diff --git a/lib/galaxy_test/selenium/test_history_pages.py b/lib/galaxy_test/selenium/test_history_pages.py
index 55756101916..ea4adfd6f6c 100644
--- a/lib/galaxy_test/selenium/test_history_pages.py
+++ b/lib/galaxy_test/selenium/test_history_pages.py
@@ -1,4 +1,3 @@
-from galaxy_test.base.populators import skip_without_agents
 from .framework import (
     managed_history,
     retry_assertion_during_transitions,
@@ -565,105 +564,3 @@ class TestHistoryPages(SeleniumTestCase):
         assert "This History's Notebooks" in back_text
         assert "Back to Reports" not in back_text
         self.screenshot("history_toolbar_controls")
-
-    # --- Page Chat Panel Tests ---
-
-    @skip_without_agents
-    @selenium_test
-    @managed_history
-    def test_chat_panel_toggle(self):
-        """Open page, click chat button, verify panel visible; click again, verify hidden."""
-        history_id = self.current_history_id()
-        self.dataset_populator.new_history_page(history_id, title="Chat Toggle", content="# Test")
-
-        self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
-        self.components.pages.history.editor.wait_for_visible()
-
-        # Open chat panel
-        self.history_page_open_chat()
-        self.screenshot("history_page_chat_open")
-
-        # Close chat panel
-        self.components.pages.history.chat_button.wait_for_and_click()
-        self.components.pages.history.chat_panel.assert_absent_or_hidden()
-        self.screenshot("history_page_chat_closed")
-
-    @skip_without_agents
-    @selenium_test
-    @managed_history
-    def test_page_chat_greeting_flow(self):
-        """Send greeting, verify query cell and response content."""
-        history_id = self.current_history_id()
-        self.dataset_populator.new_history_page(history_id, title="Chat Greeting", content="# Test")
-
-        self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
-        self.components.pages.history.editor.wait_for_visible()
-
-        self.history_page_open_chat()
-        self.history_page_chat_ensure_new()
-        self.history_page_chat_send_message("Hello!")
-
-        chat = self.components.pages.history
-        assert chat.chat_query_cell.wait_for_text() == "Hello!"
-
-        @retry_assertion_during_transitions
-        def assert_response():
-            text = chat.chat_response_content.wait_for_text()
-            assert len(text) > 0
-
-        assert_response()
-        self.screenshot("history_page_chat_greeting")
-
-    @skip_without_agents
-    @selenium_test
-    @managed_history
-    def test_page_chat_multi_turn(self):
-        """Send two messages, assert 2 query cells and 2 response cells."""
-        history_id = self.current_history_id()
-        self.dataset_populator.new_history_page(history_id, title="Chat Multi", content="# Test")
-
-        self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
-        self.components.pages.history.editor.wait_for_visible()
-
-        self.history_page_open_chat()
-        self.history_page_chat_ensure_new()
-        self.history_page_chat_send_message("Hello!")
-        self.history_page_chat_send_message("Summarize this history")
-
-        chat = self.components.pages.history
-
-        @retry_assertion_during_transitions
-        def assert_two_exchanges():
-            assert len(chat.chat_query_cell.all()) == 2
-            assert len(chat.chat_response_content.all()) >= 2
-
-        assert_two_exchanges()
-        self.screenshot("history_page_chat_multi_turn")
-
-    @skip_without_agents
-    @selenium_test
-    @managed_history
-    def test_page_chat_new_conversation(self):
-        """Send message, click new conversation, assert chat is empty."""
-        history_id = self.current_history_id()
-        self.dataset_populator.new_history_page(history_id, title="Chat New Conv", content="# Test")
-
-        self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
-        self.components.pages.history.editor.wait_for_visible()
-
-        self.history_page_open_chat()
-        self.history_page_chat_ensure_new()
-        self.history_page_chat_send_message("Hello!")
-
-        # Verify message exists
-        chat = self.components.pages.history
-        assert len(chat.chat_query_cell.all()) >= 1
-
-        # New conversation
-        chat.chat_new_conversation.wait_for_and_click()
-        self._history_page_chat_assert_empty()
-        self.screenshot("history_page_chat_new_conversation")

From ab23f1d512eba60b2cca17d7bdec312354835aca Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 3 Jun 2026 00:08:50 -0500
Subject: [PATCH 067/256] fix ChatModeSelector tests broken by useActiveContext
 addition

The test's mockRoute was missing a `query` field, causing useActiveContext to throw when accessing route.query.tool_id. Added query: {} to all mockRoute fixtures and added two new tests covering the notebook context behaviour (full view button hidden when contextType is "notebook").

Co-Authored-By: Claude <noreply@anthropic.com>
---
 .../GalaxyAI/ChatModeSelector.test.ts         | 44 +++++++++++++++----
 1 file changed, 35 insertions(+), 9 deletions(-)

diff --git a/client/src/components/GalaxyAI/ChatModeSelector.test.ts b/client/src/components/GalaxyAI/ChatModeSelector.test.ts
index 629a8e05a9f..1c1811db519 100644
--- a/client/src/components/GalaxyAI/ChatModeSelector.test.ts
+++ b/client/src/components/GalaxyAI/ChatModeSelector.test.ts
@@ -13,7 +13,11 @@ import ChatModeSelector from "./ChatModeSelector.vue";
 import GButton from "@/components/BaseComponents/GButton.vue";
 
 const mockPush = vi.fn();
-let mockRoute: { path: string; params: Record<string, string> } = { path: "/", params: {} };
+let mockRoute: { path: string; params: Record<string, string>; query: Record<string, string> } = {
+    path: "/",
+    params: {},
+    query: {},
+};
 
 vi.mock("vue-router/composables", () => ({
     useRouter: () => ({ push: mockPush }),
@@ -41,7 +45,7 @@ function getButtons(wrapper: Wrapper<Vue>) {
 
 describe("ChatModeSelector", () => {
     beforeEach(() => {
-        mockRoute = { path: "/", params: {} };
+        mockRoute = { path: "/", params: {}, query: {} };
         vi.clearAllMocks();
     });
 
@@ -53,7 +57,7 @@ describe("ChatModeSelector", () => {
 
     describe("button active states", () => {
         it("full view button is pressed when in center mode on /galaxyai route", async () => {
-            mockRoute = { path: "/galaxyai/chat-1", params: { exchangeId: "chat-1" } };
+            mockRoute = { path: "/galaxyai/chat-1", params: { exchangeId: "chat-1" }, query: {} };
             const { wrapper, store } = mountComponent();
             store.chatLocation = "center";
             await nextTick();
@@ -100,6 +104,28 @@ describe("ChatModeSelector", () => {
         });
     });
 
+    // ── notebook context ──────────────────────────────────────────────────────
+
+    describe("notebook context", () => {
+        it("hides full view button when in notebook context", async () => {
+            mockRoute = {
+                path: "/histories/hist-1/page/page-1",
+                params: { historyId: "hist-1", pageId: "page-1" },
+                query: {},
+            };
+            const { wrapper } = mountComponent();
+            await nextTick();
+            // Only 2 buttons should be rendered (side panel + bottom panel)
+            expect(getButtons(wrapper).length).toBe(2);
+        });
+
+        it("shows full view button when not in notebook context", async () => {
+            const { wrapper } = mountComponent();
+            await nextTick();
+            expect(getButtons(wrapper).length).toBe(3);
+        });
+    });
+
     // ── openCenterChat ─────────────────────────────────────────────────────────
 
     describe("openCenterChat", () => {
@@ -134,21 +160,21 @@ describe("ChatModeSelector", () => {
 
     describe("openDockedChat — navigation", () => {
         it("pushes '/' when on /galaxyai root route", async () => {
-            mockRoute = { path: "/galaxyai", params: {} };
+            mockRoute = { path: "/galaxyai", params: {}, query: {} };
             const { wrapper } = mountComponent();
             await getButtons(wrapper).at(1).trigger("click");
             expect(mockPush).toHaveBeenCalledWith("/");
         });
 
         it("pushes '/' when on /galaxyai/:id route", async () => {
-            mockRoute = { path: "/galaxyai/chat-1", params: { exchangeId: "chat-1" } };
+            mockRoute = { path: "/galaxyai/chat-1", params: { exchangeId: "chat-1" }, query: {} };
             const { wrapper } = mountComponent();
             await getButtons(wrapper).at(1).trigger("click");
             expect(mockPush).toHaveBeenCalledWith("/");
         });
 
         it("does not navigate when on an unrelated route", async () => {
-            mockRoute = { path: "/histories", params: {} };
+            mockRoute = { path: "/histories", params: {}, query: {} };
             const { wrapper } = mountComponent();
             await getButtons(wrapper).at(1).trigger("click");
             expect(mockPush).not.toHaveBeenCalled();
@@ -173,7 +199,7 @@ describe("ChatModeSelector", () => {
         });
 
         it("uses routedChatId when coming from center mode with exchangeId in route", async () => {
-            mockRoute = { path: "/galaxyai/routed-chat", params: { exchangeId: "routed-chat" } };
+            mockRoute = { path: "/galaxyai/routed-chat", params: { exchangeId: "routed-chat" }, query: {} };
             const { wrapper, store } = mountComponent();
             store.chatLocation = "center";
             await getButtons(wrapper).at(1).trigger("click");
@@ -181,7 +207,7 @@ describe("ChatModeSelector", () => {
         });
 
         it("uses activeChatId fallback when in center mode but no exchangeId in route", async () => {
-            mockRoute = { path: "/galaxyai", params: {} };
+            mockRoute = { path: "/galaxyai", params: {}, query: {} };
             const { wrapper, store } = mountComponent();
             store.chatLocation = "center";
             store.activeChatId = "active-chat";
@@ -222,7 +248,7 @@ describe("ChatModeSelector", () => {
         });
 
         it("does NOT use routedChatId when not in center mode even with exchangeId in route", async () => {
-            mockRoute = { path: "/galaxyai/some-chat", params: { exchangeId: "some-chat" } };
+            mockRoute = { path: "/galaxyai/some-chat", params: { exchangeId: "some-chat" }, query: {} };
             const { wrapper, store } = mountComponent();
             store.chatLocation = "right";
             store.activeChatId = "active-chat";

From 3b0965868a2c6c2b405f140abf1223b57fd98971 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 3 Jun 2026 17:21:08 -0500
Subject: [PATCH 068/256] add non-notebook page editor to `activeContext` as
 well

---
 client/src/components/GalaxyAI.vue              | 13 +++++++++++--
 client/src/composables/useActiveContext.test.ts | 10 +++++++++-
 client/src/composables/useActiveContext.ts      | 11 +++++++++--
 3 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index efc7e1999e7..20479292a5b 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -1,5 +1,14 @@
 <script setup lang="ts">
-import { faBook, faFile, faMagic, faSitemap, faTimes, faTrash, faWrench } from "@fortawesome/free-solid-svg-icons";
+import {
+    faBook,
+    faFile,
+    faFileContract,
+    faMagic,
+    faSitemap,
+    faTimes,
+    faTrash,
+    faWrench,
+} from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BSkeleton } from "bootstrap-vue";
 import { computed, nextTick, onMounted, ref, watch } from "vue";
@@ -85,7 +94,7 @@ const contextIcon = computed(() => {
         case "workflow_run":
             return faSitemap;
         case "notebook":
-            return faBook;
+            return effectiveContext.value?.historyId ? faBook : faFileContract;
         default:
             return faMagic;
     }
diff --git a/client/src/composables/useActiveContext.test.ts b/client/src/composables/useActiveContext.test.ts
index c39ff8b321e..75d8f20599c 100644
--- a/client/src/composables/useActiveContext.test.ts
+++ b/client/src/composables/useActiveContext.test.ts
@@ -119,7 +119,7 @@ describe("useActiveContext", () => {
             });
         });
 
-        it("detects notebook context from page editor route", () => {
+        it("detects notebook context from notebook editor route", () => {
             const { activeContext } = withRoute(
                 "/histories/test-history-id/pages/test-page-id",
                 {},
@@ -132,6 +132,14 @@ describe("useActiveContext", () => {
             });
         });
 
+        it("detects notebook context from page editor route", () => {
+            const { activeContext } = withRoute("/pages/editor", { id: "test-page-id" }, {});
+            expect(activeContext.value).toEqual({
+                contextType: "notebook",
+                pageId: "test-page-id",
+            });
+        });
+
         it("returns null for page editor route without id", () => {
             const { activeContext } = withRoute("/pages/editor");
             expect(activeContext.value).toBeNull();
diff --git a/client/src/composables/useActiveContext.ts b/client/src/composables/useActiveContext.ts
index c67ed329527..b5aff5bb1b0 100644
--- a/client/src/composables/useActiveContext.ts
+++ b/client/src/composables/useActiveContext.ts
@@ -9,7 +9,7 @@ export type ActiveContext =
     | { contextType: "workflow_editor"; workflowId: string }
     | { contextType: "workflow_run"; workflowId: string }
     | { contextType: "job"; jobId: string; toolId?: string }
-    | { contextType: "notebook"; pageId: string; historyId: string };
+    | { contextType: "notebook"; pageId: string; historyId?: string };
 
 export function useActiveContext() {
     const route = useRoute();
@@ -76,6 +76,13 @@ export function useActiveContext() {
             };
         }
 
+        if (path === "/pages/editor" && query.id) {
+            return {
+                contextType: "notebook",
+                pageId: String(query.id),
+            };
+        }
+
         return null;
     });
 
@@ -96,7 +103,7 @@ export function useActiveContext() {
             case "job":
                 return `Job: ${ctx.jobId}`;
             case "notebook":
-                return `History Notebook: ${ctx.pageId}`;
+                return ctx.historyId ? `History Notebook: ${ctx.pageId}` : `Page: ${ctx.pageId}`;
             default:
                 return null;
         }

From c74c111064aa803f18c59d81264682b14aecec27 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 3 Jun 2026 17:22:42 -0500
Subject: [PATCH 069/256] fix padding and height of page editor

---
 client/src/components/Page/PageView.vue             | 2 +-
 client/src/components/PageEditor/PageEditorView.vue | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Page/PageView.vue b/client/src/components/Page/PageView.vue
index 937a3ac1541..e4f7796ea8e 100644
--- a/client/src/components/Page/PageView.vue
+++ b/client/src/components/Page/PageView.vue
@@ -125,7 +125,7 @@ function stsUrl(config: any) {
                     {{ page.title || page.name }}
                 </Heading>
 
-                <div class="page-content">
+                <div class="page-content h-100">
                     <Markdown
                         v-if="page.content_format === 'markdown'"
                         :markdown-config="page"
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 923b0211d98..e7df7887416 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -293,6 +293,7 @@ function handleRevisionRestore(revisionId: string) {
             <div class="page-body d-flex flex-grow-1 overflow-hidden">
                 <div class="page-content flex-grow-1 overflow-auto">
                     <MarkdownEditor
+                        class="h-100"
                         :markdown-text="store.currentContent"
                         :mode="markdownEditorMode"
                         :title="editorTitle"
@@ -319,9 +320,6 @@ function handleRevisionRestore(revisionId: string) {
 .page-display-toolbar {
     background: var(--panel-header-bg);
 }
-.page-content {
-    padding: 1rem;
-}
 .page-revision-panel {
     width: 300px;
     min-width: 300px;

From 868dc90bd10d0620f6384f00d61debe666f99c71 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sat, 6 Jun 2026 13:10:24 -0500
Subject: [PATCH 070/256] mock `useRoute` fully in `ActivityBar` vitest

---
 client/src/components/ActivityBar/ActivityBar.test.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/ActivityBar/ActivityBar.test.js b/client/src/components/ActivityBar/ActivityBar.test.js
index be4088d80e0..4d48bc3e387 100644
--- a/client/src/components/ActivityBar/ActivityBar.test.js
+++ b/client/src/components/ActivityBar/ActivityBar.test.js
@@ -21,7 +21,7 @@ vi.mock("@/composables/config", () => ({
 }));
 
 vi.mock("vue-router/composables", () => ({
-    useRoute: vi.fn(() => ({})),
+    useRoute: vi.fn(() => ({ path: "/", params: {}, query: {} })),
     useRouter: vi.fn(() => ({ push: vi.fn() })),
 }));
 

From 1df63698954b53738b488e7113296304ba531dd8 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 7 Jun 2026 21:35:02 -0500
Subject: [PATCH 071/256] expand collapsed panel if a chat is selected from the
 sidebar

---
 client/src/components/GalaxyAI/ChatPanel.vue | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/client/src/components/GalaxyAI/ChatPanel.vue b/client/src/components/GalaxyAI/ChatPanel.vue
index 1377ccae561..ab9909842a4 100644
--- a/client/src/components/GalaxyAI/ChatPanel.vue
+++ b/client/src/components/GalaxyAI/ChatPanel.vue
@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { storeToRefs } from "pinia";
-import { ref } from "vue";
+import { ref, watch } from "vue";
 import { useRoute, useRouter } from "vue-router/composables";
 
 import { useChatStore } from "@/stores/chatStore";
@@ -22,6 +22,17 @@ function dockTo(location: "right" | "bottom") {
         router.push("/");
     }
 }
+
+// Expand collapsed panel if a chat is selected from the sidebar
+watch(
+    activeChatId,
+    (chatId) => {
+        if (chatId && collapsed.value) {
+            collapsed.value = false;
+        }
+    },
+    { immediate: true },
+);
 </script>
 
 <template>

From 930a75b5a1c4c1897a13856fa64d3347ac4f44bc Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 7 Jun 2026 22:37:39 -0500
Subject: [PATCH 072/256] persist activeChatId across page refreshes in
 docked/panel chat
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

activeChatId is stored in localStorage via useUserLocalStorage, which syncs asynchronously — the value is only available after the user API resolves. Because onMounted ran before that, the component always saw null for activeChatId and started a new chat instead of restoring the previous one.

activeChatId in chatStore is now backed by useUserLocalStorage directly, so the persisted value is automatically restored once the store initializes and the composable resolves.

Two related bugs fixed alongside this:
- exchangeId="new" was incorrectly falling into the docked/panel restoration branch, causing a stale activeChatId to be loaded and flipping the center-mode route back to the old chat when the user explicitly navigated to a new one
- watch(props.exchangeId) now skips when the incoming ID already matches currentChatId, preventing a redundant fetchConversation triggered by the store-update chain that could reorder messages in the view
- onMounted restructured to separate concerns: explicit exchange → fetch it, "new" → start fresh, docked/panel → restore from context, center → load latest

Co-Authored-By: Claude <noreply@anthropic.com>
---
 client/src/components/GalaxyAI.test.ts | 282 +++++++++++++++++++++++++
 client/src/components/GalaxyAI.vue     |  31 +--
 client/src/stores/chatStore.ts         |  13 +-
 3 files changed, 310 insertions(+), 16 deletions(-)
 create mode 100644 client/src/components/GalaxyAI.test.ts

diff --git a/client/src/components/GalaxyAI.test.ts b/client/src/components/GalaxyAI.test.ts
new file mode 100644
index 00000000000..841838dbe05
--- /dev/null
+++ b/client/src/components/GalaxyAI.test.ts
@@ -0,0 +1,282 @@
+import { createTestingPinia } from "@pinia/testing";
+import { getLocalVue } from "@tests/vitest/helpers";
+import { shallowMount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { setActivePinia } from "pinia";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+import { ref } from "vue";
+
+import type { ActiveContext } from "@/composables/useActiveContext";
+import { useChatStore } from "@/stores/chatStore";
+import { usePageEditorStore } from "@/stores/pageEditorStore";
+
+import GalaxyAI from "./GalaxyAI.vue";
+
+// ── API mock ─────────────────────────────────────────────────────────────────
+const mockGetMessages = vi.fn();
+const mockGetHistory = vi.fn();
+
+vi.mock("@/api", () => ({
+    GalaxyApi: () => ({
+        GET: (path: string, _opts: unknown) => {
+            if (path.includes("messages")) {
+                return mockGetMessages();
+            }
+            if (path.includes("history")) {
+                return mockGetHistory();
+            }
+            return { data: null, error: null };
+        },
+    }),
+}));
+
+// ── Composable stubs ──────────────────────────────────────────────────────────
+const mockActiveContext = ref<ActiveContext | null>(null);
+
+vi.mock("@/composables/useActiveContext", () => ({
+    useActiveContext: () => ({ activeContext: mockActiveContext, contextLabel: ref("") }),
+}));
+
+vi.mock("@/composables/userLocalStorage", () => ({
+    useUserLocalStorage: (_key: string, initial: unknown) => ref(initial),
+}));
+
+vi.mock("@/composables/markdown", () => ({
+    useMarkdown: () => ({ renderMarkdown: (s: string) => s }),
+}));
+
+vi.mock("@/composables/agentActions", () => ({
+    useAgentActions: () => ({ processingAction: ref(false), handleAction: vi.fn() }),
+}));
+
+vi.mock("@/composables/confirmDialog", () => ({
+    useConfirmDialog: () => ({ confirm: vi.fn() }),
+}));
+
+vi.mock("@/composables/toast", () => ({
+    useToast: () => ({ error: vi.fn(), success: vi.fn() }),
+}));
+
+vi.mock("@/composables/useEntityMentions", () => ({
+    parseMentions: (s: string) => s,
+    resolveMentions: (s: string) => s,
+    buildEntityContext: () => null,
+}));
+
+vi.mock("@/composables/usePageProposals", () => ({
+    usePageProposals: () => ({
+        pageContent: ref(""),
+        loadForPage: vi.fn(),
+        clear: vi.fn(),
+        getEditProposal: vi.fn(),
+        isProposalStale: vi.fn(),
+        isProposalVisible: vi.fn(() => false),
+        buildProposedContent: vi.fn(),
+        applyFullReplacement: vi.fn(),
+        applySectionPatched: vi.fn(),
+        dismissProposal: vi.fn(),
+    }),
+}));
+
+vi.mock("vue-router/composables", () => ({
+    useRoute: () => ({ path: "/", params: {}, query: {} }),
+    useRouter: () => ({ push: vi.fn(), replace: vi.fn() }),
+}));
+
+// ── Helpers ───────────────────────────────────────────────────────────────────
+const localVue = getLocalVue();
+
+const EXCHANGE_ID = "exchange-abc";
+const MESSAGES_RESPONSE = [
+    { role: "user", content: "Hello", timestamp: null },
+    { role: "assistant", content: "Hi", timestamp: null, agent_type: "router", agent_response: null, feedback: null },
+];
+
+function makeSuccessfulFetch(messages = MESSAGES_RESPONSE) {
+    mockGetMessages.mockResolvedValue({ data: messages, error: null });
+}
+
+function makeEmptyFetch() {
+    mockGetMessages.mockResolvedValue({ data: [], error: null });
+}
+
+function makeHistoryFetch(items = [{ id: "latest-chat" }]) {
+    mockGetHistory.mockResolvedValue({ data: items, error: null });
+}
+
+interface MountOptions {
+    props?: Record<string, unknown>;
+    activeChatId?: string | null;
+    cachedExchangeId?: string | null;
+    pageId?: string;
+}
+
+function mountGalaxyAI({
+    props = {},
+    activeChatId = null,
+    cachedExchangeId = null,
+    pageId = "page-1",
+}: MountOptions = {}) {
+    const pinia = createTestingPinia({ createSpy: vi.fn, stubActions: false });
+    setActivePinia(pinia);
+
+    const chatStore = useChatStore();
+    chatStore.activeChatId = activeChatId as any;
+
+    const pageEditorStore = usePageEditorStore();
+    if (cachedExchangeId) {
+        pageEditorStore.setCurrentChatExchangeId(pageId, cachedExchangeId);
+    }
+
+    const wrapper = shallowMount(GalaxyAI as object, {
+        localVue,
+        pinia,
+        propsData: props,
+        stubs: {
+            FontAwesomeIcon: true,
+            ChatActions: true,
+            ChatInput: true,
+            ChatMessageCell: true,
+            ProposalDiffView: true,
+            SectionPatchView: true,
+            Heading: true,
+            BSkeleton: true,
+        },
+    });
+
+    return { wrapper, chatStore, pageEditorStore };
+}
+
+// ── Tests ─────────────────────────────────────────────────────────────────────
+describe("GalaxyAI fetch operations on mount", () => {
+    beforeEach(() => {
+        mockActiveContext.value = null;
+        vi.clearAllMocks();
+        // Default: empty history so loadLatestChat doesn't cascade into fetchConversation
+        makeHistoryFetch([]);
+    });
+
+    afterEach(() => {
+        vi.restoreAllMocks();
+    });
+
+    // Branch 1: explicit exchangeId prop (not "new")
+    describe("when exchangeId prop is provided and not 'new'", () => {
+        it("fetches the specified exchange on mount", async () => {
+            makeSuccessfulFetch();
+            mountGalaxyAI({ props: { exchangeId: EXCHANGE_ID } });
+            await flushPromises();
+            expect(mockGetMessages).toHaveBeenCalledOnce();
+        });
+
+        it("does not call loadLatestChat", async () => {
+            makeSuccessfulFetch();
+            mountGalaxyAI({ props: { exchangeId: EXCHANGE_ID } });
+            await flushPromises();
+            expect(mockGetHistory).not.toHaveBeenCalled();
+        });
+    });
+
+    // Branch 2: exchangeId === "new"
+    describe("when exchangeId prop is 'new'", () => {
+        it("starts a new chat without fetching messages", async () => {
+            mountGalaxyAI({ props: { exchangeId: "new" } });
+            await flushPromises();
+            expect(mockGetMessages).not.toHaveBeenCalled();
+        });
+
+        it("does not restore from activeChatId even when one is set", async () => {
+            // Regression: exchangeId='new' previously fell into the docked/panel restore branch
+            // and would fetch activeChatId, causing the route to flip back to the old chat.
+            mountGalaxyAI({ props: { exchangeId: "new" }, activeChatId: EXCHANGE_ID });
+            await flushPromises();
+            expect(mockGetMessages).not.toHaveBeenCalled();
+        });
+    });
+
+    // Branch 3: docked/panel — notebook context with a cached exchange ID and no activeChatId
+    describe("docked/panel — notebook context with cached exchange ID", () => {
+        it("fetches the cached exchange when activeChatId is null", async () => {
+            makeSuccessfulFetch();
+            mockActiveContext.value = { contextType: "notebook", pageId: "page-1", historyId: "hist-1" };
+            mountGalaxyAI({ props: { docked: true }, activeChatId: null, cachedExchangeId: EXCHANGE_ID });
+            await flushPromises();
+            expect(mockGetMessages).toHaveBeenCalledOnce();
+        });
+
+        it("clears stale cached ID when fetch returns no messages", async () => {
+            makeEmptyFetch();
+            mockActiveContext.value = { contextType: "notebook", pageId: "page-1", historyId: "hist-1" };
+            const { pageEditorStore } = mountGalaxyAI({
+                props: { docked: true },
+                activeChatId: null,
+                cachedExchangeId: EXCHANGE_ID,
+            });
+            await flushPromises();
+            expect(pageEditorStore.getCurrentChatExchangeId("page-1")).toBeNull();
+        });
+    });
+
+    // Branch 4: docked/panel — notebook context, no cached exchange but activeChatId set
+    describe("docked/panel — notebook context, no cached ID but activeChatId present", () => {
+        it("fetches from activeChatId", async () => {
+            makeSuccessfulFetch();
+            mockActiveContext.value = { contextType: "notebook", pageId: "page-1", historyId: "hist-1" };
+            mountGalaxyAI({ props: { panel: true }, activeChatId: EXCHANGE_ID });
+            await flushPromises();
+            expect(mockGetMessages).toHaveBeenCalledOnce();
+        });
+    });
+
+    // Branch 5: docked/panel — notebook context, no cached exchange, no activeChatId
+    describe("docked/panel — notebook context, no cached ID and no activeChatId", () => {
+        it("starts a new chat without fetching", async () => {
+            mockActiveContext.value = { contextType: "notebook", pageId: "page-1", historyId: "hist-1" };
+            mountGalaxyAI({ props: { docked: true }, activeChatId: null });
+            await flushPromises();
+            expect(mockGetMessages).not.toHaveBeenCalled();
+        });
+    });
+
+    // Branch 6: docked/panel — non-notebook context with activeChatId set
+    describe("docked/panel — non-notebook context with activeChatId", () => {
+        it("fetches the active chat exchange", async () => {
+            makeSuccessfulFetch();
+            mountGalaxyAI({ props: { panel: true }, activeChatId: EXCHANGE_ID });
+            await flushPromises();
+            expect(mockGetMessages).toHaveBeenCalledOnce();
+        });
+    });
+
+    // Branch 7: docked/panel — non-notebook context, no activeChatId
+    describe("docked/panel — non-notebook context, no activeChatId", () => {
+        it("starts a new chat without fetching", async () => {
+            mountGalaxyAI({ props: { docked: true }, activeChatId: null });
+            await flushPromises();
+            expect(mockGetMessages).not.toHaveBeenCalled();
+        });
+    });
+
+    // Branch 8: center mode (no exchangeId, not docked/panel)
+    describe("center mode (no exchangeId, not docked/panel)", () => {
+        it("calls loadLatestChat to fetch most recent history", async () => {
+            mountGalaxyAI({});
+            await flushPromises();
+            expect(mockGetHistory).toHaveBeenCalledOnce();
+        });
+
+        it("does not fetch exchange messages when history is empty", async () => {
+            mountGalaxyAI({});
+            await flushPromises();
+            expect(mockGetMessages).not.toHaveBeenCalled();
+        });
+
+        it("fetches the latest exchange when history has items", async () => {
+            makeHistoryFetch([{ id: "latest-chat" }]);
+            makeSuccessfulFetch();
+            mountGalaxyAI({});
+            await flushPromises();
+            expect(mockGetMessages).toHaveBeenCalledOnce();
+        });
+    });
+});
diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index 20479292a5b..1e247b69c26 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -132,21 +132,22 @@ const {
 onMounted(async () => {
     if (props.exchangeId && props.exchangeId !== "new") {
         await fetchConversation(props.exchangeId);
-    } else if (props.docked || props.panel || props.exchangeId === "new") {
-        // In panel/docked mode with notebook context: restore the cached exchange
-        // for this page if one exists and no chat is already active.
+    } else if (props.exchangeId === "new") {
+        startNewChat();
+    } else if (props.docked || props.panel) {
         const ctx = activeContext.value;
-        if (ctx?.contextType === "notebook" && !chatStore.activeChatId) {
-            const cachedId = pageEditorStore.getCurrentChatExchangeId(ctx.pageId);
-            if (cachedId) {
-                await fetchConversation(cachedId);
-                // If the cached exchange was deleted or returned no messages, drop the stale ID
-                // so the next open doesn't try it again.
-                if (messages.value.length === 0) {
-                    pageEditorStore.clearCurrentChatExchangeId(ctx.pageId);
-                    startNewChat();
-                }
-            } else {
+        // For notebook pages, prefer the per-page cached exchange over the global activeChatId.
+        const notebookPageId = ctx?.contextType === "notebook" ? ctx.pageId : null;
+        const cachedId = notebookPageId && !chatStore.activeChatId
+            ? pageEditorStore.getCurrentChatExchangeId(notebookPageId)
+            : null;
+        const chatId = cachedId || chatStore.activeChatId || null;
+
+        if (chatId) {
+            await fetchConversation(chatId);
+            // If the cached notebook exchange was deleted/empty, drop the stale ID.
+            if (cachedId && messages.value.length === 0) {
+                pageEditorStore.clearCurrentChatExchangeId(notebookPageId!);
                 startNewChat();
             }
         } else {
@@ -164,7 +165,7 @@ onMounted(async () => {
 watch(
     () => props.exchangeId,
     async (newId, oldId) => {
-        if (newId === oldId) {
+        if (newId === oldId || newId === currentChatId.value) {
             return;
         }
         if (newId && newId !== "new") {
diff --git a/client/src/stores/chatStore.ts b/client/src/stores/chatStore.ts
index fec7beeeafe..02b3c57c6f2 100644
--- a/client/src/stores/chatStore.ts
+++ b/client/src/stores/chatStore.ts
@@ -11,7 +11,7 @@ export type ChatLocation = "center" | "right" | "bottom";
 export const useChatStore = defineStore("chatStore", () => {
     const chatLocation = useUserLocalStorage<ChatLocation>("chat-location", "center");
     const chatVisible = useUserLocalStorage("chat-visible", false);
-    const activeChatId = ref<string | null>(null);
+    const cachedActiveChatId = useUserLocalStorage<string>("active-chat-id", "");
     const chatHistory = ref<ChatHistoryItem[]>([]);
     const loading = ref(false);
 
@@ -19,6 +19,17 @@ export const useChatStore = defineStore("chatStore", () => {
     const isBottomPanelOpen = computed(() => chatLocation.value === "bottom" && chatVisible.value);
     const isCenterMode = computed(() => chatLocation.value === "center");
 
+    const activeChatId = computed({
+        get: () => cachedActiveChatId.value || null,
+        set: (id: string | null) => {
+            if (id) {
+                cachedActiveChatId.value = id;
+            } else {
+                cachedActiveChatId.value = "";
+            }
+        },
+    });
+
     function deleteChats(ids: Set<string>) {
         chatHistory.value = chatHistory.value.filter((item) => !ids.has(item.id));
         // If the chat currently in view was deleted, drop the reference so we don't

From ed712c1b669b15d8b209aa3e00f7b612c00fea7f Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 7 Jun 2026 23:35:45 -0500
Subject: [PATCH 073/256] restore context-appropriate chat when switching
 between views in docked/panel mode
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Previously the context watcher only handled notebook → non-notebook (clearing activeChatId). This caused two problems: navigating into a notebook (or between notebooks) left the panel showing whatever chat was last open in the non-notebook context, and the per-page notebook chat cache was ignored whenever a global activeChatId happened to be set.

The context watcher now handles all transitions for docked/panel mode:
- any → notebook (including notebook A → notebook B): restores the per-page cached exchange, falls back to the most recent chat in that page's history, then starts fresh if none exists
- notebook → non-notebook: clears proposals and starts a new chat so the panel doesn't keep showing a notebook-specific conversation

onMounted is updated to match the same logic: notebook context always looks up the per-page cache first, then falls back to page history rather than falling through to the global activeChatId (which may belong to a completely unrelated context).

Test updates:
- wrapper.destroy() added to afterEach to prevent stale watcher callbacks from leaking across tests and polluting the shared mock call counters
- Branch 4 updated: notebook context with no cached exchange now correctly falls back to page history, not activeChatId; chatHistoryItems option added to mountGalaxyAI to pre-populate history and stub loadHistory (chatStore imports @/api/client which is not mocked globally)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 client/src/components/GalaxyAI.test.ts | 32 ++++++++--
 client/src/components/GalaxyAI.vue     | 84 ++++++++++++++++++++------
 2 files changed, 90 insertions(+), 26 deletions(-)

diff --git a/client/src/components/GalaxyAI.test.ts b/client/src/components/GalaxyAI.test.ts
index 841838dbe05..32ebea643b7 100644
--- a/client/src/components/GalaxyAI.test.ts
+++ b/client/src/components/GalaxyAI.test.ts
@@ -85,6 +85,7 @@ vi.mock("vue-router/composables", () => ({
 
 // ── Helpers ───────────────────────────────────────────────────────────────────
 const localVue = getLocalVue();
+let lastWrapper: ReturnType<typeof shallowMount> | null = null;
 
 const EXCHANGE_ID = "exchange-abc";
 const MESSAGES_RESPONSE = [
@@ -109,6 +110,8 @@ interface MountOptions {
     activeChatId?: string | null;
     cachedExchangeId?: string | null;
     pageId?: string;
+    /** Pre-populate chatStore.chatHistory and stub loadHistory as a no-op so no real HTTP call is made. */
+    chatHistoryItems?: { id: string }[];
 }
 
 function mountGalaxyAI({
@@ -116,6 +119,7 @@ function mountGalaxyAI({
     activeChatId = null,
     cachedExchangeId = null,
     pageId = "page-1",
+    chatHistoryItems,
 }: MountOptions = {}) {
     const pinia = createTestingPinia({ createSpy: vi.fn, stubActions: false });
     setActivePinia(pinia);
@@ -123,6 +127,13 @@ function mountGalaxyAI({
     const chatStore = useChatStore();
     chatStore.activeChatId = activeChatId as any;
 
+    if (chatHistoryItems !== undefined) {
+        chatStore.chatHistory = chatHistoryItems as any;
+        // Stub loadHistory so it doesn't make real HTTP calls (chatStore imports @/api/client
+        // which is not mocked); keep chatHistory as pre-populated.
+        vi.spyOn(chatStore, "loadHistory").mockResolvedValue(undefined);
+    }
+
     const pageEditorStore = usePageEditorStore();
     if (cachedExchangeId) {
         pageEditorStore.setCurrentChatExchangeId(pageId, cachedExchangeId);
@@ -144,6 +155,7 @@ function mountGalaxyAI({
         },
     });
 
+    lastWrapper = wrapper;
     return { wrapper, chatStore, pageEditorStore };
 }
 
@@ -157,6 +169,8 @@ describe("GalaxyAI fetch operations on mount", () => {
     });
 
     afterEach(() => {
+        lastWrapper?.destroy();
+        lastWrapper = null;
         vi.restoreAllMocks();
     });
 
@@ -217,20 +231,26 @@ describe("GalaxyAI fetch operations on mount", () => {
         });
     });
 
-    // Branch 4: docked/panel — notebook context, no cached exchange but activeChatId set
-    describe("docked/panel — notebook context, no cached ID but activeChatId present", () => {
-        it("fetches from activeChatId", async () => {
+    // Branch 4: docked/panel — notebook context, no cached exchange but page has history
+    describe("docked/panel — notebook context, no cached ID but page has history", () => {
+        it("fetches the most recent chat from page history (ignores global activeChatId)", async () => {
+            // activeChatId is set but belongs to a different context — must not be used for notebook.
             makeSuccessfulFetch();
             mockActiveContext.value = { contextType: "notebook", pageId: "page-1", historyId: "hist-1" };
-            mountGalaxyAI({ props: { panel: true }, activeChatId: EXCHANGE_ID });
+            mountGalaxyAI({
+                props: { panel: true },
+                activeChatId: "some-other-chat",
+                chatHistoryItems: [{ id: EXCHANGE_ID }],
+            });
             await flushPromises();
             expect(mockGetMessages).toHaveBeenCalledOnce();
         });
     });
 
-    // Branch 5: docked/panel — notebook context, no cached exchange, no activeChatId
-    describe("docked/panel — notebook context, no cached ID and no activeChatId", () => {
+    // Branch 5: docked/panel — notebook context, no cached exchange, empty history
+    describe("docked/panel — notebook context, no cached ID and empty history", () => {
         it("starts a new chat without fetching", async () => {
+            // beforeEach already mocks history as empty
             mockActiveContext.value = { contextType: "notebook", pageId: "page-1", historyId: "hist-1" };
             mountGalaxyAI({ props: { docked: true }, activeChatId: null });
             await flushPromises();
diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index 1e247b69c26..62992541d32 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -62,18 +62,44 @@ const { activeContext, contextLabel } = useActiveContext();
 const pageEditorStore = usePageEditorStore();
 const contextDismissed = ref(false);
 
-watch(activeContext, (newCtx, oldCtx) => {
+watch(activeContext, async (newCtx, oldCtx) => {
     contextDismissed.value = false;
 
-    // When navigating away from a notebook, clear activeChatId if it belongs to that
-    // page (i.e. was loaded from the page-scoped history) so the panel doesn't keep
-    // showing a notebook-specific conversation in a non-notebook context.
-    if (oldCtx?.contextType === "notebook" && newCtx?.contextType !== "notebook") {
-        const currentId = chatStore.activeChatId;
-        if (currentId && chatStore.chatHistory.some((item) => item.id === currentId)) {
-            chatStore.setActiveChatId(null);
+    if (!props.docked && !props.panel) {
+        return;
+    }
+
+    const switchingToNotebook =
+        newCtx?.contextType === "notebook" && (oldCtx?.contextType !== "notebook" || oldCtx.pageId !== newCtx.pageId);
+
+    if (switchingToNotebook) {
+        // Switched to a notebook page (or to a different notebook page): restore this page's
+        // cached exchange, or fall back to the most recent chat in this page's history.
+        const pageId = newCtx.pageId;
+        const cachedId = pageEditorStore.getCurrentChatExchangeId(pageId);
+        if (cachedId) {
+            await fetchConversation(cachedId);
+            if (messages.value.length === 0) {
+                pageEditorStore.clearCurrentChatExchangeId(pageId);
+                startNewChat();
+            }
+        } else {
+            try {
+                await chatStore.loadHistory(pageId);
+            } catch (e) {
+                Toast.error(errorMessageAsString(e), "Failed to load chat history");
+            }
+            const latestChat = chatStore.chatHistory[0];
+            if (latestChat) {
+                await fetchConversation(latestChat.id);
+            } else {
+                startNewChat();
+            }
         }
+    } else if (oldCtx?.contextType === "notebook" && newCtx?.contextType !== "notebook") {
+        // Switched away from notebook: drop notebook-specific state and start fresh.
         clearProposals();
+        startNewChat();
     }
 });
 
@@ -136,22 +162,40 @@ onMounted(async () => {
         startNewChat();
     } else if (props.docked || props.panel) {
         const ctx = activeContext.value;
-        // For notebook pages, prefer the per-page cached exchange over the global activeChatId.
+        // For notebook pages, always prefer the per-page cached exchange over the global
+        // activeChatId — the global one may belong to a completely unrelated normal chat.
         const notebookPageId = ctx?.contextType === "notebook" ? ctx.pageId : null;
-        const cachedId = notebookPageId && !chatStore.activeChatId
-            ? pageEditorStore.getCurrentChatExchangeId(notebookPageId)
-            : null;
-        const chatId = cachedId || chatStore.activeChatId || null;
 
-        if (chatId) {
-            await fetchConversation(chatId);
-            // If the cached notebook exchange was deleted/empty, drop the stale ID.
-            if (cachedId && messages.value.length === 0) {
-                pageEditorStore.clearCurrentChatExchangeId(notebookPageId!);
-                startNewChat();
+        if (notebookPageId) {
+            // Notebook context: prefer per-page cached exchange, fall back to page history.
+            const cachedId = pageEditorStore.getCurrentChatExchangeId(notebookPageId);
+            if (cachedId) {
+                await fetchConversation(cachedId);
+                if (messages.value.length === 0) {
+                    pageEditorStore.clearCurrentChatExchangeId(notebookPageId);
+                    startNewChat();
+                }
+            } else {
+                try {
+                    await chatStore.loadHistory(notebookPageId);
+                } catch (e) {
+                    Toast.error(errorMessageAsString(e), "Failed to load chat history");
+                }
+                const latestChat = chatStore.chatHistory[0];
+                if (latestChat) {
+                    await fetchConversation(latestChat.id);
+                } else {
+                    startNewChat();
+                }
             }
         } else {
-            startNewChat();
+            // Non-notebook context: use global activeChatId if available.
+            const chatId = chatStore.activeChatId;
+            if (chatId) {
+                await fetchConversation(chatId);
+            } else {
+                startNewChat();
+            }
         }
     } else {
         await loadLatestChat();

From 85b6e92b16a77962e75595e855284d5dfbda577d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 10 Jun 2026 18:15:21 +0200
Subject: [PATCH 074/256] Match tpv in conditional dependency requirement to
 pinned version

---
 lib/galaxy/dependencies/conditional-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index 2c45fb5ba80..122ceca4836 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -14,7 +14,7 @@ ldap3==2.9.1
 python-pam
 galaxycloudrunner
 pkce
-total-perspective-vortex>=3.1.2,<4
+total-perspective-vortex>=3.2.1,<4
 openai
 fastmcp>=2.13.0
 # upper version constraint because of https://github.com/galaxyproject/galaxy/issues/20600

From 21a1c98ad851695decb85ff9fbc5fdf8d3d7e69e Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 10 Jun 2026 12:22:19 -0500
Subject: [PATCH 075/256] ensure workflow is accessible as well

---
 lib/galaxy_test/api/test_pages_history_attached.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy_test/api/test_pages_history_attached.py b/lib/galaxy_test/api/test_pages_history_attached.py
index 062e8401646..56777c68fc6 100644
--- a/lib/galaxy_test/api/test_pages_history_attached.py
+++ b/lib/galaxy_test/api/test_pages_history_attached.py
@@ -313,6 +313,7 @@ steps:
             )
             invocation_id = summary.invocation_id
             self._put(f"histories/{history_id}/publish", json=True)
+            self._put(f"workflows/{summary.workflow_id}/publish", json=True)
             with self._different_user():
                 payload = {"invocation_id": invocation_id, "title": "Shared Invocation Page"}
                 create_response = self._post("pages", payload, json=True)

From 70f22bcaf6dc5024895dca3ad37abcce2f859796 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 10 Jun 2026 14:35:26 +0200
Subject: [PATCH 076/256] Fix syncServerAttributes clobbering conditional case
 options for shared param names
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

When a conditional has multiple cases that all define a parameter with the
same name (e.g. `feature` in every `when` branch of `Extract features from
GFF`), the previous flat-key approach in `syncServerAttributes` would store
only the last case's server node under that key. Every case then received the
last case's options, causing `FormSelect.setInitialValue()` to auto-select the
first option of the wrong case — e.g. `"0"` from the Frame column — as the
value for a different active case. The client then submitted that invalid value
to `POST /api/jobs`, which passed lenient Pydantic validation at request time
(dynamic selects accept any `StrictStr`) but failed with
`RequestParameterInvalidException` when the Celery worker validated the value
against the real dataset options.

Replace the flat-dict + `visitAllInputs` approach with a structural recursive
`syncInputsStructural`/`syncNodeAttributes` pair that matches each conditional
case's inputs to the corresponding server case by index. Also align
`_buildLevel`'s conditional case selection in `utilities.js` to use the
actual value from `formData` rather than the potentially-stale
`node.test_param.value` from `formConfig.inputs`.

Fixes #22864
---
 .../Form/composables/useFormState.test.js     | 53 ++++++++++++++++
 .../Form/composables/useFormState.ts          | 63 ++++++++++++++-----
 client/src/components/Form/utilities.js       |  5 +-
 3 files changed, 105 insertions(+), 16 deletions(-)

diff --git a/client/src/components/Form/composables/useFormState.test.js b/client/src/components/Form/composables/useFormState.test.js
index 7618b129784..c74e329236b 100644
--- a/client/src/components/Form/composables/useFormState.test.js
+++ b/client/src/components/Form/composables/useFormState.test.js
@@ -153,6 +153,59 @@ describe("useFormState", () => {
         expect(caseBInput.attributes.options).toEqual([["col1", "col1"]]);
     });
 
+    it("should not overwrite earlier case attributes when multiple conditional cases share a parameter name", () => {
+        const { cloneInputs, formInputs, syncServerAttributes } = useFormState();
+
+        // All cases have a "feature" parameter — same name, different options per case
+        cloneInputs([
+            {
+                name: "col_choice",
+                type: "conditional",
+                test_param: { name: "col", type: "select", value: "0" },
+                cases: [
+                    { value: "0", inputs: [{ name: "feature", type: "select", value: null }] },
+                    { value: "2", inputs: [{ name: "feature", type: "select", value: null }] },
+                ],
+            },
+        ]);
+
+        // Server returns distinct options for each case
+        syncServerAttributes([
+            {
+                name: "col_choice",
+                type: "conditional",
+                test_param: { name: "col", type: "select" },
+                cases: [
+                    { value: "0", inputs: [{ name: "feature", type: "select", options: [["seqA", "seqA"]] }] },
+                    {
+                        value: "2",
+                        inputs: [
+                            {
+                                name: "feature",
+                                type: "select",
+                                options: [
+                                    ["mRNA", "mRNA"],
+                                    ["exon", "exon"],
+                                ],
+                            },
+                        ],
+                    },
+                ],
+            },
+        ]);
+
+        const cond = formInputs.value[0];
+        const case0Feature = cond.cases[0].inputs[0];
+        const case2Feature = cond.cases[1].inputs[0];
+
+        // Each case must keep its OWN options, not inherit the last case's options
+        expect(case0Feature.attributes.options).toEqual([["seqA", "seqA"]]);
+        expect(case2Feature.attributes.options).toEqual([
+            ["mRNA", "mRNA"],
+            ["exon", "exon"],
+        ]);
+    });
+
     it("should update formIndex and formData on conditional switch", () => {
         const { cloneInputs, formInputs, rebuildIndex, buildFormData, formIndex, formData } = useFormState();
         cloneInputs(makeConditionalInputs());
diff --git a/client/src/components/Form/composables/useFormState.ts b/client/src/components/Form/composables/useFormState.ts
index 58ef1c7ab22..034406864b7 100644
--- a/client/src/components/Form/composables/useFormState.ts
+++ b/client/src/components/Form/composables/useFormState.ts
@@ -122,28 +122,63 @@ export function useFormState(options: UseFormStateOptions = {}): UseFormStateRet
      * Only copies server-owned fields; value, error, and warning are excluded
      * to maintain the separation between server state (attributes) and client
      * state (the clone's own properties).
+     *
+     * Uses a structural recursive approach so that conditional cases with the
+     * same parameter name (e.g. "feature" in every `when` branch) are each
+     * synced from their corresponding server case rather than from the last
+     * case (which is what a flat-key dict would produce).
      */
     function syncServerAttributes(newInputs: FormInputNode[]): void {
-        const newAttributes: Record<string, FormInputNode> = {};
-        visitAllInputs(newInputs, (input: FormInputNode, name: string) => {
-            newAttributes[name] = input;
-        });
-        visitAllInputs(formInputs.value, (input: FormInputNode, name: string) => {
-            const serverNode = newAttributes[name];
-            if (serverNode != undefined) {
-                const attrs: Record<string, unknown> = {};
-                const raw = serverNode as unknown as Record<string, unknown>;
-                for (const key in raw) {
-                    if (!CLIENT_OWNED_FIELDS.has(key)) {
-                        attrs[key] = raw[key];
+        syncInputsStructural(formInputs.value, newInputs);
+    }
+
+    function syncInputsStructural(cloneInputs: FormInputNode[], serverInputs: FormInputNode[]): void {
+        const serverByName = new Map(serverInputs.map((n) => [String(n.name ?? ""), n]));
+        cloneInputs.forEach((cloneNode) => {
+            const serverNode = serverByName.get(String(cloneNode.name ?? ""));
+            if (!serverNode) {
+                return;
+            }
+            if (cloneNode.type === "conditional" && cloneNode.cases && serverNode.cases) {
+                syncNodeAttributes(cloneNode.test_param, serverNode.test_param);
+                cloneNode.cases.forEach((cloneCase, i) => {
+                    const serverCase = serverNode.cases![i];
+                    if (serverCase) {
+                        syncInputsStructural(cloneCase.inputs, serverCase.inputs);
                     }
+                });
+            } else if (cloneNode.type === "section" && cloneNode.inputs && serverNode.inputs) {
+                syncInputsStructural(cloneNode.inputs, serverNode.inputs);
+            } else if (cloneNode.type === "repeat") {
+                if (cloneNode.cache && serverNode.cache) {
+                    cloneNode.cache.forEach((instance, i) => {
+                        const serverInstance = serverNode.cache![i];
+                        if (serverInstance) {
+                            syncInputsStructural(instance, serverInstance);
+                        }
+                    });
                 }
-                // set() required: attributes is a genuinely new property on clone nodes.
-                set(input, "attributes", attrs);
+            } else {
+                syncNodeAttributes(cloneNode, serverNode);
             }
         });
     }
 
+    function syncNodeAttributes(cloneNode: FormInputNode | undefined, serverNode: FormInputNode | undefined): void {
+        if (!cloneNode || !serverNode) {
+            return;
+        }
+        const attrs: Record<string, unknown> = {};
+        const raw = serverNode as unknown as Record<string, unknown>;
+        for (const key in raw) {
+            if (!CLIENT_OWNED_FIELDS.has(key)) {
+                attrs[key] = raw[key];
+            }
+        }
+        // set() required: attributes is a genuinely new property on clone nodes.
+        set(cloneNode, "attributes", attrs);
+    }
+
     function applyErrors(errors: FormMessages | null): void {
         resetErrors();
         if (errors) {
diff --git a/client/src/components/Form/utilities.js b/client/src/components/Form/utilities.js
index d4831b389af..99b2e2de474 100644
--- a/client/src/components/Form/utilities.js
+++ b/client/src/components/Form/utilities.js
@@ -190,8 +190,9 @@ function _buildLevel(inputs, formData, prefix) {
                 const condResult = {};
                 if (node.test_param) {
                     const testKey = `${flatKey}|${node.test_param.name}`;
-                    condResult[node.test_param.name] = _convertValue(node.test_param, formData[testKey]);
-                    const selectedCase = matchCase(node, node.test_param.value);
+                    const testValue = _convertValue(node.test_param, formData[testKey]);
+                    condResult[node.test_param.name] = testValue;
+                    const selectedCase = matchCase(node, testValue ?? node.test_param.value);
                     if (selectedCase !== -1) {
                         Object.assign(condResult, _buildLevel(node.cases[selectedCase].inputs, formData, flatKey));
                     }

From c3bcb5185e920ea0e7ed513ad06f7dcc7852f7f0 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 10 Jun 2026 14:50:38 -0500
Subject: [PATCH 077/256] [26.1] Add missing `confirm` prop to `GModal` in
 `RefactorConfirmationModal`

---
 .../components/Workflow/Editor/RefactorConfirmationModal.vue    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Editor/RefactorConfirmationModal.vue b/client/src/components/Workflow/Editor/RefactorConfirmationModal.vue
index 2b0015f5b0f..a96b4aa9b32 100644
--- a/client/src/components/Workflow/Editor/RefactorConfirmationModal.vue
+++ b/client/src/components/Workflow/Editor/RefactorConfirmationModal.vue
@@ -118,7 +118,7 @@ async function executeRefactoring() {
 </script>
 
 <template>
-    <GModal :show.sync="show" :title="title" fixed-height ok-text="Save" @ok="executeRefactoring">
+    <GModal confirm :show.sync="show" :title="title" fixed-height ok-text="Save" @ok="executeRefactoring">
         <div class="workflow-refactor-modal">
             {{ message }}
             <ul>

From 3cfa2e09f09584c085798d58423447921efcc062 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 10 Jun 2026 15:56:51 -0400
Subject: [PATCH 078/256] Fix convert_memory_to_mib decimal MB/GB conversions
 (were off by 1000x)

---
 .../jobs/runners/util/gcp_batch/helpers.py    | 20 ++++++++++++++-----
 test/unit/app/jobs/test_gcp_batch_runner.py   | 13 ++++++++++++
 2 files changed, 28 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/jobs/runners/util/gcp_batch/helpers.py b/lib/galaxy/jobs/runners/util/gcp_batch/helpers.py
index ee67b99d80d..09ec9a553ed 100644
--- a/lib/galaxy/jobs/runners/util/gcp_batch/helpers.py
+++ b/lib/galaxy/jobs/runners/util/gcp_batch/helpers.py
@@ -12,6 +12,16 @@ DEFAULT_NFS_MOUNT_PATH = "/mnt/nfs"
 DEFAULT_NFS_PATH = "/"
 DEFAULT_MEMORY_MIB = 2048
 DEFAULT_CPU_MILLI = 1000
+
+# Memory-unit conversion factors to MiB (1 MiB = 1024 * 1024 bytes). Decimal units
+# (KB/MB/GB) scale by powers of 1000; binary units (KiB/GiB) by powers of 1024.
+# Precomputed so the constant arithmetic isn't re-evaluated on every conversion.
+BYTES_PER_MIB = 1024 * 1024
+KIB_TO_MIB = 1 / 1024
+GIB_TO_MIB = 1024
+KB_TO_MIB = 1000 / BYTES_PER_MIB
+MB_TO_MIB = 1000 * 1000 / BYTES_PER_MIB
+GB_TO_MIB = 1000 * 1000 * 1000 / BYTES_PER_MIB
 DEFAULT_CVMFS_DOCKER_VOLUME = (
     '-v "/cvmfs/data.galaxyproject.org:/cvmfs/data.galaxyproject.org:ro" '
     '-v "/cvmfs/cloud.galaxyproject.org:/cvmfs/cloud.galaxyproject.org:ro"'
@@ -166,15 +176,15 @@ def convert_memory_to_mib(memory_str):
     if unit in ["", "mib", "mi"]:
         return int(value)
     elif unit in ["gib", "gi"]:
-        return int(value * 1024)  # GiB to MiB
+        return int(value * GIB_TO_MIB)  # GiB to MiB
     elif unit in ["mb", "m"]:
-        return int(value * 1000 / 1024)  # MB to MiB (decimal to binary)
+        return int(value * MB_TO_MIB)  # MB to MiB (decimal to binary)
     elif unit in ["gb", "g"]:
-        return int(value * 1000 * 1000 / 1024 / 1024)  # GB to MiB
+        return int(value * GB_TO_MIB)  # GB to MiB (decimal to binary)
     elif unit in ["kib", "ki"]:
-        return int(value / 1024)  # KiB to MiB
+        return int(value * KIB_TO_MIB)  # KiB to MiB
     elif unit in ["kb", "k"]:
-        return int(value * 1000 / 1024 / 1024)  # KB to MiB
+        return int(value * KB_TO_MIB)  # KB to MiB (decimal to binary)
     else:
         log.warning("Unknown memory unit: %s, treating as MiB", unit)
         return int(value)
diff --git a/test/unit/app/jobs/test_gcp_batch_runner.py b/test/unit/app/jobs/test_gcp_batch_runner.py
index 22e65225e0d..57c05b2c9ac 100644
--- a/test/unit/app/jobs/test_gcp_batch_runner.py
+++ b/test/unit/app/jobs/test_gcp_batch_runner.py
@@ -81,6 +81,19 @@ class TestConvertMemoryToMib:
             ("1.5Gi", 1536),  # decimal GiB
             ("256Mi", 256),  # small MiB value
             ("4Gi", 4096),  # larger GiB value
+            # Decimal units (KB/MB/GB use powers of 1000, converted to MiB)
+            ("1gb", 953),  # 1 GB -> MiB (10^9 / 1024^2)
+            ("4gb", 3814),  # larger GB value
+            ("2g", 1907),  # GB short form
+            ("1000mb", 953),  # 1000 MB == 1 GB == 953 MiB (consistency check)
+            ("1024mb", 976),  # MB -> MiB
+            ("1000m", 953),  # MB short form
+            ("1048576kb", 1000),  # KB -> MiB
+            # Binary KiB
+            ("1024kib", 1),  # KiB -> MiB (value / 1024)
+            ("2048ki", 2),  # KiB short form
+            # Unknown unit falls back to treating the value as MiB
+            ("5xyz", 5),
         ],
     )
     def test_convert_memory_to_mib(self, input_value, expected):

From f1dbe409cbd1cdc71e147d7678a8a9b0e010fdbf Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 10 Jun 2026 15:33:35 -0500
Subject: [PATCH 079/256] add vitest for testing save in
 `RefactorConfirmationModal`

---
 .../Editor/RefactorConfirmationModal.test.ts   | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Workflow/Editor/RefactorConfirmationModal.test.ts b/client/src/components/Workflow/Editor/RefactorConfirmationModal.test.ts
index 8e79dffe650..bd613e504cc 100644
--- a/client/src/components/Workflow/Editor/RefactorConfirmationModal.test.ts
+++ b/client/src/components/Workflow/Editor/RefactorConfirmationModal.test.ts
@@ -1,5 +1,5 @@
 import { getLocalVue } from "@tests/vitest/helpers";
-import { shallowMount, type Wrapper } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { beforeEach, describe, expect, it, vi } from "vitest";
 
@@ -29,7 +29,7 @@ describe("RefactorConfirmationModal.vue", () => {
     beforeEach(() => {
         vi.clearAllMocks();
         mockConfirm.mockReset();
-        wrapper = shallowMount(RefactorConfirmationModal as object, {
+        wrapper = mount(RefactorConfirmationModal as object, {
             propsData: {
                 refactorActions: [],
                 workflowId: TEST_WORKFLOW_ID,
@@ -87,7 +87,7 @@ describe("RefactorConfirmationModal.vue", () => {
         expect(wrapper.emitted().onRefactor!.length).toBe(1);
     });
 
-    it("should show confirmation dialog if there are messages from the server", async () => {
+    it("should show confirmation modal if there are messages from the server", async () => {
         vi.mocked(refactor).mockReturnValue(
             new Promise((then) => {
                 then({
@@ -121,7 +121,19 @@ describe("RefactorConfirmationModal.vue", () => {
         // but didn't follow up with executing the action because we need to confirm
         expect(vi.mocked(refactor).mock.calls.length).toBe(1);
 
+        // Modal should now be shown with the message from the server
         expect(wrapper.findComponent(GModal).props().show).toBeTruthy();
+        expect(wrapper.find(".workflow-refactor-modal").text()).toContain(
+            "hey, a connection was dropped - better respond",
+        );
+
+        // Simulate confirming the modal
+        const saveButton = wrapper.findComponent(GModal).find(".g-modal-confirm-buttons .g-button.g-blue");
+        await saveButton.trigger("click");
+
+        // On save, refactor should be called again to execute the action (not a dry run this time)
+        expect(vi.mocked(refactor).mock.calls[1]![0]).toEqual(TEST_WORKFLOW_ID);
+        expect(vi.mocked(refactor).mock.calls[1]![3]).toBeFalsy();
     });
 
     it("should show confirm dialog when refactoring a non-latest version", async () => {

From 26081fb75dd442e084911942e8ee43e525472359 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 10 Jun 2026 16:11:43 -0400
Subject: [PATCH 080/256] Honor polling_interval in GCP Batch runner via
 monitor_sleep_time

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/jobs/runners/gcp_batch.py        | 12 +++++++
 test/unit/app/jobs/test_gcp_batch_runner.py | 37 +++++++++++++++++++++
 2 files changed, 49 insertions(+)

diff --git a/lib/galaxy/jobs/runners/gcp_batch.py b/lib/galaxy/jobs/runners/gcp_batch.py
index 3f916cc1f69..f3f792f97f2 100644
--- a/lib/galaxy/jobs/runners/gcp_batch.py
+++ b/lib/galaxy/jobs/runners/gcp_batch.py
@@ -136,6 +136,18 @@ class GoogleCloudBatchJobRunner(AsynchronousJobRunner):
 
         log.info("Google Cloud Batch client initialized successfully")
 
+    @property
+    def monitor_sleep_time(self):
+        """Throttle the monitor loop so it polls the GCP Batch API no more often
+        than the configured ``polling_interval``.
+
+        The base ``AsynchronousJobRunner.monitor()`` loop sleeps this long between
+        sweeps; each runner has its own monitor thread, so this only affects the
+        GCP Batch runner. Item access (not ``.get()``) is used so the spec default
+        of 30 resolves through ``ParamsWithSpecs.__missing__``.
+        """
+        return max(self.app.config.job_runner_monitor_sleep, int(self.runner_params["polling_interval"]))
+
     def queue_job(self, job_wrapper):
         """Queue a job for execution on Google Cloud Batch."""
         log.debug("Starting queue_job for Galaxy job %s", job_wrapper.get_id_tag())
diff --git a/test/unit/app/jobs/test_gcp_batch_runner.py b/test/unit/app/jobs/test_gcp_batch_runner.py
index 57c05b2c9ac..6d9b019ac3d 100644
--- a/test/unit/app/jobs/test_gcp_batch_runner.py
+++ b/test/unit/app/jobs/test_gcp_batch_runner.py
@@ -1,7 +1,15 @@
 """Unit tests for Google Cloud Batch job runner utility methods."""
 
+from types import SimpleNamespace
+from typing import (
+    Any,
+    cast,
+)
+
 import pytest
 
+from galaxy.jobs.runners import RunnerParams
+from galaxy.jobs.runners.gcp_batch import GoogleCloudBatchJobRunner
 from galaxy.jobs.runners.util.gcp_batch import (
     convert_cpu_to_milli,
     convert_duration_to_seconds,
@@ -320,3 +328,32 @@ class TestResolveMaxRunDuration:
             resource_params={"walltime": ""},
         )
         assert result == "7200s"
+
+
+def _sleep_runner(runner_params, job_runner_monitor_sleep=1.0):
+    """A runner instance with __init__ skipped, for exercising monitor_sleep_time."""
+    runner = object.__new__(GoogleCloudBatchJobRunner)
+    runner.runner_params = runner_params
+    config = SimpleNamespace(job_runner_monitor_sleep=job_runner_monitor_sleep)
+    runner.app = cast(Any, SimpleNamespace(config=config))
+    return runner
+
+
+class TestMonitorSleepTime:
+    """The runner throttles its monitor loop to the configured polling_interval so
+    the base loop does not poll the GCP Batch API more often than necessary."""
+
+    def test_uses_polling_interval_over_default_monitor_sleep(self):
+        runner = _sleep_runner({"polling_interval": 30}, job_runner_monitor_sleep=1.0)
+        assert runner.monitor_sleep_time == 30
+
+    def test_respects_larger_monitor_sleep(self):
+        # max(global, polling_interval): a larger global sleep wins.
+        runner = _sleep_runner({"polling_interval": 30}, job_runner_monitor_sleep=60)
+        assert runner.monitor_sleep_time == 60
+
+    def test_interval_default_resolves_via_spec(self):
+        # polling_interval unset -> must fall back to the spec default (30) through
+        # ParamsWithSpecs.__missing__; .get() would yield None and raise in max().
+        runner = _sleep_runner(RunnerParams(specs={"polling_interval": dict(map=int, default=30)}, params={}))
+        assert runner.monitor_sleep_time == 30

From 5f7fc94d6a443958bb1dfaff97719f4827bb0d2e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 11 Jun 2026 10:22:26 +0200
Subject: [PATCH 081/256] Bump up gravity to 1.2.3

---
 lib/galaxy/dependencies/pinned-requirements.txt | 2 +-
 packages/config/setup.cfg                       | 2 +-
 pyproject.toml                                  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index c57c9125ea7..471c31e7b27 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -98,7 +98,7 @@ google-auth==2.53.0
 google-cloud-batch==0.21.0
 google-genai==2.3.0
 googleapis-common-protos==1.75.0
-gravity==1.2.2
+gravity==1.2.3
 greenlet==3.5.0 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
 griffelib==2.0.2
 groq==1.2.0
diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg
index 37f23f6f266..44d5724a467 100644
--- a/packages/config/setup.cfg
+++ b/packages/config/setup.cfg
@@ -27,7 +27,7 @@ python_requires = >=3.10
 [options.extras_require]
 test = 
     pytest
-    gravity>=1.2.0
+    gravity>=1.2.3
 
 [options.packages.find]
 where = src
diff --git a/pyproject.toml b/pyproject.toml
index 51eee63d95d..58136807761 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,7 +41,7 @@ dependencies = [
     "fissix",
     "fs",
     "future>=1.0.0",  # Python 3.12 support
-    "gravity>=1.2.0",  # Python 3.14 support
+    "gravity>=1.2.3",  # Graceful restart on galaxy >= 26.1
     "gunicorn!=25.1.0",  # https://github.com/benoitc/gunicorn/discussions/3509
     "gxformat2>=0.27.0",
     "h5grove>=1.2.1",

From 9526dc7d79304561253c03d5e0d9abd9ebc6d646 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 11 Jun 2026 07:48:39 -0400
Subject: [PATCH 082/256] Fix GTN FTS5 sanitizer choking on URL-ish search
 terms

The model sometimes builds searches with site: prefixes and dotted
hostnames, and the sanitizer wasn't stripping . : or / -- so those tokens
reached FTS5 as syntax and the whole search errored out as no results.
Strip them along with the other operators so the search just ignores the
noise.
---
 lib/galaxy/agents/gtn/search.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/agents/gtn/search.py b/lib/galaxy/agents/gtn/search.py
index 77aad0a543d..3da6515bcdf 100644
--- a/lib/galaxy/agents/gtn/search.py
+++ b/lib/galaxy/agents/gtn/search.py
@@ -80,6 +80,8 @@ def sanitize_fts5_query(query: str, preserve_phrases: bool = True) -> str:
     'find "exact phrase" in data'
     >>> sanitize_fts5_query('find "exact phrase" in data', preserve_phrases=False)
     'find exact phrase in data'
+    >>> sanitize_fts5_query("color deconvolution site:example.org/path")
+    'color deconvolution site example org path'
     """
     if not query or not query.strip():
         return ""
@@ -88,7 +90,11 @@ def sanitize_fts5_query(query: str, preserve_phrases: bool = True) -> str:
     # word individually rather than treating the hyphenated form as one token.
     sanitized = query.replace("-", " ")
 
-    for char in ",():+?!;[]":
+    # Models sometimes paste URL- or operator-flavored tokens (site:, dotted
+    # hostnames, slashes, column-filter colons). Left in, ".", ":" and "/" reach
+    # FTS5 as syntax and the whole search errors out as no-results -- so strip
+    # them along with the other FTS5 operators.
+    for char in ",.:/()+?!;[]^=~@<>{}|&":
         sanitized = sanitized.replace(char, " ")
 
     # Phrase preservation only works with a balanced pair of quotes. An odd

From 187a9af9d76d40e1e7bed5964835d4bade08ef19 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 11 Jun 2026 07:48:39 -0400
Subject: [PATCH 083/256] Cap the GTN agent's search loop to stop the token
 blowup

The GTN agent was firing ~18 searches for a single question, and since
every round re-sends the whole growing transcript that came to ~90k tokens
for one query. Add a small budget -- after a few data-gathering tool calls
the search/content tools return a "you have enough, answer now" message
instead of more results, so the model synthesizes from what it already has.
Brings a representative query from ~88k down to ~21k tokens with the same
tutorial picks.

Also bump the structured-output retries to 3, since gpt-oss occasionally
emits prose instead of a valid GTNSearchResponse and the single default
retry turned that into a hard error.
---
 lib/galaxy/agents/gtn_training.py | 47 +++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/lib/galaxy/agents/gtn_training.py b/lib/galaxy/agents/gtn_training.py
index b0d4abd032c..50229ef8586 100644
--- a/lib/galaxy/agents/gtn_training.py
+++ b/lib/galaxy/agents/gtn_training.py
@@ -52,9 +52,30 @@ class GTNTrainingAgent(BaseGalaxyAgent):
 
     agent_type = AgentType.GTN_TRAINING
 
+    # The model tends to keep re-searching long after it has enough material,
+    # and every extra round re-sends the whole growing transcript -- a single
+    # query was costing ~18 search rounds / ~90k tokens. Cap the number of
+    # data-gathering tool calls and, once spent, return a terminal instruction
+    # so the model synthesizes from what it already has instead of looping.
+    MAX_TOOL_CALLS = 3
+    # Note: name the search tools explicitly rather than saying "don't call any
+    # tools" -- the structured response is itself delivered via an output tool
+    # call, so a blanket "no tools" instruction makes the model emit prose that
+    # fails structured-output validation.
+    _TOOL_BUDGET_MESSAGE = (
+        "SEARCH BUDGET REACHED. You already have enough material to answer. "
+        "Do NOT call search_gtn_tutorials, search_gtn_faqs, "
+        "search_tutorials_by_tools, or get_tutorial_content again. Produce your "
+        "final structured answer now from the results and tutorial content "
+        "already returned above. If none is a strong match, say so and point to "
+        "the relevant GTN topic page."
+    )
+
     def __init__(self, deps: GalaxyAgentDependencies):
         super().__init__(deps)
 
+        self._tool_calls = 0
+
         db_path = getattr(deps.config, "gtn_database_path", None)
         download_url = getattr(deps.config, "gtn_database_url", None)
 
@@ -66,6 +87,14 @@ class GTNTrainingAgent(BaseGalaxyAgent):
             log.warning(f"GTN database not available: {e}")
             self.gtn_db = None
 
+    def _charge_tool_budget(self) -> Optional[str]:
+        """Count a data-gathering tool call; once over budget return a stop
+        message instead of more data so the model answers from what it has."""
+        self._tool_calls += 1
+        if self._tool_calls > self.MAX_TOOL_CALLS:
+            return self._TOOL_BUDGET_MESSAGE
+        return None
+
     def _create_agent(self) -> Agent[GalaxyAgentDependencies, Any]:
         if not self._supports_structured_output():
             return Agent(
@@ -79,6 +108,10 @@ class GTNTrainingAgent(BaseGalaxyAgent):
             deps_type=GalaxyAgentDependencies,
             output_type=GTNSearchResponse,
             system_prompt=self.get_system_prompt(),
+            # gpt-oss occasionally emits prose instead of a valid GTNSearchResponse;
+            # the pydantic-ai default of 1 output retry turns that into a hard error.
+            # Allow a couple more attempts so an occasional malformed output recovers.
+            retries=3,
         )
 
         @agent.tool
@@ -91,6 +124,9 @@ class GTNTrainingAgent(BaseGalaxyAgent):
             limit: int = 5,
         ) -> str:
             """Search GTN tutorials using full-text search over titles, descriptions, and content."""
+            over_budget = self._charge_tool_budget()
+            if over_budget:
+                return over_budget
             if not self.gtn_db:
                 return json.dumps({"error": "GTN database not available"})
             try:
@@ -119,6 +155,9 @@ class GTNTrainingAgent(BaseGalaxyAgent):
             max_length: int = 1500,
         ) -> str:
             """Get the full content of a specific tutorial by topic and name."""
+            over_budget = self._charge_tool_budget()
+            if over_budget:
+                return over_budget
             if not self.gtn_db:
                 return "GTN database not available"
             try:
@@ -154,6 +193,9 @@ class GTNTrainingAgent(BaseGalaxyAgent):
             over ``search_gtn_tutorials`` for queries shorter than about
             eight words or phrased as ``what is X`` / ``how do I X``.
             """
+            over_budget = self._charge_tool_budget()
+            if over_budget:
+                return over_budget
             if not self.gtn_db:
                 return json.dumps({"error": "GTN database not available"})
             try:
@@ -175,6 +217,9 @@ class GTNTrainingAgent(BaseGalaxyAgent):
             limit: int = 5,
         ) -> str:
             """Find tutorials that use specific Galaxy tools."""
+            over_budget = self._charge_tool_budget()
+            if over_budget:
+                return over_budget
             if not self.gtn_db:
                 return json.dumps({"error": "GTN database not available"})
             try:
@@ -201,6 +246,8 @@ class GTNTrainingAgent(BaseGalaxyAgent):
         if validation_error:
             return self._validation_error_response(validation_error)
 
+        self._tool_calls = 0
+
         if not self.gtn_db:
             return self._build_response(
                 content="GTN database is not available. Please ensure it's properly initialized.",

From 329e36bf3377ec351db65577592315867c30e5d4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 10 Jun 2026 19:34:05 +0200
Subject: [PATCH 084/256] Add namespace stripping to
 CachedExplicitSingularityContainerResolver

Add an optional `namespace` config parameter that strips
`docker://quay.io/{namespace}/` from image identifiers when constructing
the local cache path, producing flat filenames compatible with
CVMFS-hosted biocontainer caches (e.g. /cvmfs/singularity.galaxyproject.org/all/).

Mirrors the same stripping already done in pull_mulled_singularity_command.
---
 doc/source/admin/container_resolvers.rst      | 15 +++++
 .../sample/container_resolvers.yml.sample     | 14 +++++
 .../deps/container_resolvers/explicit.py      | 52 +++++++++++++++--
 .../deps/container_resolvers/mulled.py        |  2 +
 test/integration/test_container_resolvers.py  | 58 +++++++++++++++++++
 5 files changed, 136 insertions(+), 5 deletions(-)

diff --git a/doc/source/admin/container_resolvers.rst b/doc/source/admin/container_resolvers.rst
index 153c5053c60..4743bfa25b0 100644
--- a/doc/source/admin/container_resolvers.rst
+++ b/doc/source/admin/container_resolvers.rst
@@ -238,6 +238,21 @@ return a container description that points to the image file in the
    yield the path (even if non existent, i.e. before the 1st tool run or the
    caching was triggered).
 
+The optional ``namespace`` parameter strips ``docker://quay.io/NAMESPACE/``
+from the image identifier when constructing the local cache path. This yields a
+flat filename (e.g. ``bwa:0.7.17--h7132678_9``) instead of a nested path, which
+is required when pointing ``cache_directory`` at a pre-populated flat cache such
+as ``/cvmfs/singularity.galaxyproject.org/all/``:
+
+.. code-block:: yaml
+
+   - type: cached_explicit_singularity
+     cache_directory: /cvmfs/singularity.galaxyproject.org/all
+     namespace: biocontainers
+
+Images whose identifier does not start with ``docker://quay.io/NAMESPACE/``
+(e.g. ``shub://`` URIs) are not affected by this setting.
+
 2. Mulled resolvers
 """""""""""""""""""
 
diff --git a/lib/galaxy/config/sample/container_resolvers.yml.sample b/lib/galaxy/config/sample/container_resolvers.yml.sample
index dc68dcdce10..9d253efc55b 100644
--- a/lib/galaxy/config/sample/container_resolvers.yml.sample
+++ b/lib/galaxy/config/sample/container_resolvers.yml.sample
@@ -19,6 +19,20 @@
 #- type: cached_explicit_singularity
   # set the cache directory for storing images
   #cache_directory: database/container_cache/singularity/explicit
+  #
+  # When namespace is set, the prefix docker://quay.io/NAMESPACE/ is stripped
+  # from the image identifier before constructing the cache path, yielding a
+  # flat filename (e.g. "bwa:0.7.17--h7132678_9") instead of a nested path.
+  # This is useful when pointing cache_directory at a pre-populated flat cache
+  # such as /cvmfs/singularity.galaxyproject.org/all/.
+  #namespace: biocontainers
+  #
+  # Caching strategy for the directory listing used when namespace is set.
+  # "uncached" (default) re-reads the directory on every resolve.
+  # "dir_mtime" caches the full directory listing and only re-reads it when
+  # the directory mtime changes; recommended for large network-mounted caches
+  # such as CVMFS where repeated directory scans are expensive.
+  #cache_directory_cacher_type: uncached
 
 # Mulled container resolvers
 # ==========================
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/explicit.py b/lib/galaxy/tool_util/deps/container_resolvers/explicit.py
index f8e4d4d8205..c1690e1124e 100644
--- a/lib/galaxy/tool_util/deps/container_resolvers/explicit.py
+++ b/lib/galaxy/tool_util/deps/container_resolvers/explicit.py
@@ -11,7 +11,13 @@ from typing import (
 
 from galaxy.util.commands import shell
 from . import ContainerResolver
-from .mulled import CliContainerResolver
+from .mulled import (
+    CacheDirectory,
+    CachedMulledImageSingleTarget,
+    CliContainerResolver,
+    get_cache_directory_cacher,
+    identifier_to_cached_target,
+)
 from ..container_classes import SingularityContainer
 from ..requirements import ContainerDescription
 
@@ -85,6 +91,10 @@ class CachedExplicitSingularityContainerResolver(CliContainerResolver):
             assert self.app_info.container_image_cache_path
             cache_directory_path = os.path.join(self.app_info.container_image_cache_path, "singularity", "explicit")
         self.cache_directory_path = cache_directory_path
+        self.namespace = kwargs.get("namespace")
+        cache_directory_cacher_type = kwargs.get("cache_directory_cacher_type")
+        cacher_class = get_cache_directory_cacher(cache_directory_cacher_type)
+        self.cache_directory: CacheDirectory = cacher_class(self.cache_directory_path)
         os.makedirs(self.cache_directory_path, exist_ok=True)
 
     def resolve(
@@ -103,11 +113,37 @@ class CachedExplicitSingularityContainerResolver(CliContainerResolver):
                 container_description.identifier = f"docker://{container_description.identifier}"
             if not self._container_type_enabled(container_description, enabled_container_types):
                 return None
-            if not self.cli_available:
-                return container_description
             image_id = container_description.identifier
-            cache_path = os.path.normpath(os.path.join(self.cache_directory_path, image_id))
+            if self.namespace:
+                prefix = f"docker://quay.io/{self.namespace}/"
+                if image_id.startswith(prefix):
+                    image_id = image_id[len(prefix) :]
+                parsed = identifier_to_cached_target(image_id, "v2")
+                if parsed and isinstance(parsed, CachedMulledImageSingleTarget):
+                    cached_images = self.cache_directory.list_cached_mulled_images_from_path()
+                    for cached in cached_images:
+                        if (
+                            isinstance(cached, CachedMulledImageSingleTarget)
+                            and cached.package_name == parsed.package_name
+                            and cached.version == parsed.version
+                        ):
+                            container_description.identifier = os.path.join(
+                                self.cache_directory_path, cached.image_identifier
+                            )
+                            return container_description
+                    if not install:
+                        return None
+                else:
+                    if not install and not os.path.exists(os.path.join(self.cache_directory_path, image_id)):
+                        return None
+                cache_path = os.path.join(self.cache_directory_path, image_id)
+            else:
+                if not self.cli_available:
+                    return container_description
+                cache_path = os.path.normpath(os.path.join(self.cache_directory_path, image_id))
             if install and not os.path.exists(cache_path):
+                if not self.cli_available:
+                    return None
                 destination_info = {}
                 destination_for_container_type = kwds.get("destination_for_container_type")
                 if destination_for_container_type:
@@ -122,6 +158,7 @@ class CachedExplicitSingularityContainerResolver(CliContainerResolver):
                 )
                 command = container.build_singularity_pull_command(cache_path=cache_path)
                 shell(command)
+                self.cache_directory.invalidate_cache()
             # Point to container in the cache in stead.
             container_description.identifier = cache_path
             return container_description
@@ -129,7 +166,12 @@ class CachedExplicitSingularityContainerResolver(CliContainerResolver):
             return None
 
     def __str__(self):
-        return f"CachedExplicitSingularityContainerResolver[cache_directory={self.cache_directory_path}]"
+        return (
+            f"CachedExplicitSingularityContainerResolver["
+            f"cache_directory={self.cache_directory_path},"
+            f"namespace={self.namespace},"
+            f"cache_directory_cacher_type={self.cache_directory.cacher_type}]"
+        )
 
 
 class BaseAdminConfiguredContainerResolver(ContainerResolver):
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
index 5f9165b867d..d907abd8851 100644
--- a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
+++ b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
@@ -106,6 +106,8 @@ CachedTarget = Union[CachedMulledImageSingleTarget, CachedV1MulledImageMultiTarg
 
 
 class CacheDirectory(metaclass=ABCMeta):
+    cacher_type: str
+
     def __init__(self, path: str, hash_func: Literal["v1", "v2"] = "v2") -> None:
         self.path = path
         self.hash_func = hash_func
diff --git a/test/integration/test_container_resolvers.py b/test/integration/test_container_resolvers.py
index 4e3fdcfb4ca..0e75b1feaa6 100644
--- a/test/integration/test_container_resolvers.py
+++ b/test/integration/test_container_resolvers.py
@@ -1217,3 +1217,61 @@ class TestCachedExplicitSingularityContainerResolverWithSingularityRequirement(
     def handle_galaxy_config_kwds(cls, config) -> None:
         super().handle_galaxy_config_kwds(config)
         config["container_resolvers"] = cls.container_resolvers_config
+
+
+class TestCachedExplicitSingularityContainerResolverWithNamespace(
+    SingularityContainerResolverTestCase, ContainerResolverTestCases, ExplicitTestCase
+):
+    """
+    test cached_explicit_singularity container resolver with namespace stripping
+
+    when namespace="biocontainers" is configured, the resolver strips
+    docker://quay.io/biocontainers/ from the image identifier so that the
+    cached image is stored as a flat filename (e.g. bwa:0.7.17--h7132678_9)
+    compatible with CVMFS-hosted biocontainer caches.
+    """
+
+    _image_name = ExplicitTestCase.mulled_hash.rsplit("/", 1)[-1]
+
+    container_resolvers_config: list[dict[str, Any]] = [
+        {"type": "cached_explicit_singularity", "namespace": "biocontainers"},
+    ]
+    assumptions: dict[str, Any] = {
+        "run": {
+            "output": [
+                "Program: bwa (alignment via Burrows-Wheeler transformation)",
+                "Version: 0.7.17-r1188",
+            ],
+            "cached": True,
+            "resolver_type": "cached_explicit_singularity",
+            "cache_name": _image_name,
+            "cache_namespace": "biocontainers",
+        },
+        # With namespace set the resolver returns None when the image is not yet
+        # cached, so listing resolves to NullDependency before any install.
+        "list": [
+            {"unresolved": True},
+            {"unresolved": True},
+        ],
+        "build": [
+            {
+                "resolver_type": "cached_explicit_singularity",
+                "identifier": f"/tmp/.*/singularity/explicit/{_image_name}",
+                "cached": True,
+                "cache_name": _image_name,
+                "cache_namespace": "biocontainers",
+            },
+            {
+                "resolver_type": "cached_explicit_singularity",
+                "identifier": f"/tmp/.*/singularity/explicit/{_image_name}",
+                "cached": True,
+                "cache_name": _image_name,
+                "cache_namespace": "biocontainers",
+            },
+        ],
+    }
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config) -> None:
+        super().handle_galaxy_config_kwds(config)
+        config["container_resolvers"] = cls.container_resolvers_config

From 5953703358b046b7838e0d39ca6bae60c838851d Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 10 Jun 2026 15:55:31 +0300
Subject: [PATCH 085/256] Use pydantic_extra_types_color for color input
 validation

---
 lib/galaxy/dependencies/pinned-requirements.txt |  1 +
 lib/galaxy/tool_util_models/parameters.py       | 16 ++++++----------
 packages/tool_util_models/setup.cfg             |  1 +
 pyproject.toml                                  |  1 +
 test/unit/tool_util/parameter_specification.yml |  2 +-
 5 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index c57c9125ea7..a830cccc0f9 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -207,6 +207,7 @@ pydantic-ai==1.99.0
 pydantic-ai-slim==1.99.0
 pydantic-core==2.46.4
 pydantic-evals==1.99.0
+pydantic-extra-types==2.11.1
 pydantic-graph==1.99.0
 pydantic-handlebars==0.1.0
 pydantic-settings==2.14.1
diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index 4aa956fc41d..3922cf39b70 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -41,6 +41,7 @@ from pydantic import (
     TypeAdapter,
 )
 from pydantic.json_schema import SkipJsonSchema
+from pydantic_extra_types.color import Color
 from typing_extensions import (
     Annotated,
     Literal,
@@ -1540,15 +1541,10 @@ def ensure_color_valid(value: Optional[Any]):
         return
     if not isinstance(value, str):
         raise ValueError(f"Invalid color value type {value.__class__} encountered.")
-    value_str: str = value
-    message = f"Invalid color value string format {value_str} encountered."
-    if len(value_str) != 7:
-        raise ValueError(message + "0")
-    if value_str[0] != "#":
-        raise ValueError(message + "1")
-    for byte_str in value_str[1:]:
-        if byte_str not in "0123456789abcdef":
-            raise ValueError(message + "2")
+    try:
+        Color(value)
+    except Exception as e:
+        raise ValueError(f"Invalid color value {value!r}: {e}")
 
 
 class ColorParameterModel(BaseGalaxyToolParameterModelDefinition):
@@ -1558,7 +1554,7 @@ class ColorParameterModel(BaseGalaxyToolParameterModelDefinition):
 
     def field_kwargs(self) -> Dict[str, Any]:
         kwargs = super().field_kwargs()
-        kwargs["json_schema_extra"]["pattern"] = "^#[0-9a-f]{6}$"
+        kwargs["json_schema_extra"]["format"] = "color"
         return kwargs
 
     @property
diff --git a/packages/tool_util_models/setup.cfg b/packages/tool_util_models/setup.cfg
index 7b39184dd28..ad7ded316f0 100644
--- a/packages/tool_util_models/setup.cfg
+++ b/packages/tool_util_models/setup.cfg
@@ -15,6 +15,7 @@ version = 26.1.dev0
 include_package_data = True
 install_requires =
     pydantic>=2.7.4
+    pydantic-extra-types
     typing-extensions
 package_dir =
     =src
diff --git a/pyproject.toml b/pyproject.toml
index 51eee63d95d..6451f5f675d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -76,6 +76,7 @@ dependencies = [
     "pycryptodome",
     "pydantic[email]>=2.7.4",  # https://github.com/pydantic/pydantic/pull/9639
     "pydantic-ai>=1.56.0",  # https://github.com/pydantic/pydantic-ai/security/advisories/GHSA-2jrp-274c-jhv3
+    "pydantic-extra-types",
     "pydicom; python_version >= '3.10'",
     "PyJWT",
     "pykwalify",
diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
index dc34e7061ce..486ddf07de8 100644
--- a/test/unit/tool_util/parameter_specification.yml
+++ b/test/unit/tool_util/parameter_specification.yml
@@ -1233,10 +1233,10 @@ gx_color:
   request_valid:
    - parameter: '#aabbcc'
    - parameter: '#000000'
+   - parameter: '#abcd'
   request_invalid:
    - parameter: null
    - parameter: {}
-   - parameter: '#abcd'
   workflow_step_valid:
    - parameter: '#aabbcc'
    - parameter: '#000000'

From 8e83c16080e8df1a614423b9081fee38eed3d12f Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 10 Jun 2026 10:16:58 -0400
Subject: [PATCH 086/256] Use a proper default value for job_id_prefix if not
 defined in the job_conf.yml

---
 lib/galaxy/jobs/runners/gcp_batch.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/runners/gcp_batch.py b/lib/galaxy/jobs/runners/gcp_batch.py
index f3f792f97f2..7ec82364320 100644
--- a/lib/galaxy/jobs/runners/gcp_batch.py
+++ b/lib/galaxy/jobs/runners/gcp_batch.py
@@ -213,7 +213,7 @@ class GoogleCloudBatchJobRunner(AsynchronousJobRunner):
         params = self._get_job_params(job_destination)
 
         # Generate unique job name
-        prefix = params.get("job_id_prefix", "galaxy-job")
+        prefix = params.get("job_id_prefix") or "galaxy-job"
         job_name = f"{prefix}-{int(time.time())}-{os.urandom(4).hex()}-{job_wrapper.get_id_tag()}"
 
         # Create the batch job specification

From ad8d8497184827e3fe0628554cf49de421410d72 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 10 Jun 2026 11:43:47 -0400
Subject: [PATCH 087/256] Fix _get_job_params to fall back to
 runner_param_specs defaults via subscript access

---
 lib/galaxy/jobs/runners/gcp_batch.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/runners/gcp_batch.py b/lib/galaxy/jobs/runners/gcp_batch.py
index 7ec82364320..438c6572aaa 100644
--- a/lib/galaxy/jobs/runners/gcp_batch.py
+++ b/lib/galaxy/jobs/runners/gcp_batch.py
@@ -269,7 +269,10 @@ class GoogleCloudBatchJobRunner(AsynchronousJobRunner):
             "service_account_email",
             "job_id_prefix",
         ]:
-            params[key] = job_destination.params.get(key, self.runner_params.get(key))
+            # Subscript access on runner_params (a defaultdict) so unset keys fall
+            # back to the spec defaults defined in runner_param_specs; .get() would
+            # bypass __missing__ and yield None instead of the configured default.
+            params[key] = job_destination.params.get(key, self.runner_params[key])
 
         log.debug("Finished _get_job_params")
         return params

From 16e08d3dc9e0c202b98731cfeebc10f2d41ece27 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 10 Jun 2026 15:42:37 -0400
Subject: [PATCH 088/256] Add pointer drag/resize tests for WindowManagerWindow

These demonstrate galaxyproject/galaxy#22875: dragging or resizing the
floating window has to capture the pointer, otherwise the interaction
dies as soon as the cursor crosses an iframe (the center frame, or the
window's own iframe body). The tests drive the header drag and corner
resize through pointer events and assert the handle captures the
pointer; they fail before the fix since the component only listens for
mouse events.
---
 .../WindowManager/WindowManagerWindow.test.ts | 149 ++++++++++++++++++
 1 file changed, 149 insertions(+)
 create mode 100644 client/src/components/WindowManager/WindowManagerWindow.test.ts

diff --git a/client/src/components/WindowManager/WindowManagerWindow.test.ts b/client/src/components/WindowManager/WindowManagerWindow.test.ts
new file mode 100644
index 00000000000..6aff6ba8d58
--- /dev/null
+++ b/client/src/components/WindowManager/WindowManagerWindow.test.ts
@@ -0,0 +1,149 @@
+import { createTestingPinia } from "@pinia/testing";
+import { getLocalVue } from "@tests/vitest/helpers";
+import { mount } from "@vue/test-utils";
+import { setActivePinia } from "pinia";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+import { useWindowManagerStore } from "@/stores/windowManagerStore";
+
+import WindowManagerWindow from "./WindowManagerWindow.vue";
+
+const localVue = getLocalVue();
+
+// happy-dom does not implement pointer capture, so stub it. Capturing the
+// pointer is what keeps drag/resize alive when the cursor crosses an iframe
+// (the center frame or the window's own body), so we assert on these calls.
+const setPointerCapture = vi.fn();
+
+function pointerEvent(type: string, options: PointerEventInit = {}) {
+    return new PointerEvent(type, { bubbles: true, cancelable: true, button: 0, pointerId: 7, ...options });
+}
+
+function mountWindow() {
+    const pinia = createTestingPinia({ createSpy: vi.fn, stubActions: false });
+    setActivePinia(pinia);
+    const store = useWindowManagerStore();
+    store.add({ title: "GalaxyAI", url: "/galaxyai", x: 50, y: 60, width: 400, height: 300 });
+    const win = store.windows[0]!;
+    const wrapper = mount(WindowManagerWindow as object, {
+        localVue,
+        pinia,
+        propsData: { window: win },
+    });
+    return { wrapper, win };
+}
+
+describe("WindowManagerWindow", () => {
+    beforeEach(() => {
+        (HTMLElement.prototype as any).setPointerCapture = setPointerCapture;
+    });
+
+    afterEach(() => {
+        vi.clearAllMocks();
+        delete (HTMLElement.prototype as any).setPointerCapture;
+    });
+
+    it("resizes with the pointer and captures it on the handle", () => {
+        const { wrapper, win } = mountWindow();
+        const handle = wrapper.find(".window-manager-resize-handle");
+
+        handle.element.dispatchEvent(pointerEvent("pointerdown", { clientX: 450, clientY: 360 }));
+        expect(setPointerCapture).toHaveBeenCalledWith(7);
+
+        document.dispatchEvent(pointerEvent("pointermove", { clientX: 550, clientY: 410 }));
+        expect(win.width).toBe(500);
+        expect(win.height).toBe(350);
+
+        document.dispatchEvent(pointerEvent("pointerup", { clientX: 550, clientY: 410 }));
+        document.dispatchEvent(pointerEvent("pointermove", { clientX: 650, clientY: 460 }));
+        expect(win.width).toBe(500);
+        expect(win.height).toBe(350);
+    });
+
+    it("drags with the pointer and captures it on the header", () => {
+        const { wrapper, win } = mountWindow();
+        const header = wrapper.find(".window-manager-window-header");
+
+        header.element.dispatchEvent(pointerEvent("pointerdown", { clientX: 200, clientY: 80 }));
+        expect(setPointerCapture).toHaveBeenCalledWith(7);
+
+        document.dispatchEvent(pointerEvent("pointermove", { clientX: 230, clientY: 120 }));
+        expect(win.x).toBe(80);
+        expect(win.y).toBe(100);
+
+        document.dispatchEvent(pointerEvent("pointerup", { clientX: 230, clientY: 120 }));
+        document.dispatchEvent(pointerEvent("pointermove", { clientX: 300, clientY: 200 }));
+        expect(win.x).toBe(80);
+        expect(win.y).toBe(100);
+    });
+
+    it("stops resizing when the pointer is cancelled", () => {
+        const { wrapper, win } = mountWindow();
+        const handle = wrapper.find(".window-manager-resize-handle");
+
+        handle.element.dispatchEvent(pointerEvent("pointerdown", { clientX: 450, clientY: 360 }));
+        document.dispatchEvent(pointerEvent("pointermove", { clientX: 550, clientY: 410 }));
+        expect(win.width).toBe(500);
+
+        document.dispatchEvent(pointerEvent("pointercancel", { clientX: 550, clientY: 410 }));
+        document.dispatchEvent(pointerEvent("pointermove", { clientX: 650, clientY: 460 }));
+        expect(win.width).toBe(500);
+        expect(win.height).toBe(350);
+    });
+
+    it("does not start a drag from the window controls", () => {
+        const { wrapper, win } = mountWindow();
+        const controls = wrapper.find(".window-manager-window-controls");
+
+        controls.element.dispatchEvent(pointerEvent("pointerdown", { clientX: 420, clientY: 70 }));
+        document.dispatchEvent(pointerEvent("pointermove", { clientX: 500, clientY: 200 }));
+        expect(win.x).toBe(50);
+        expect(win.y).toBe(60);
+    });
+
+    it("ignores a second pointer while dragging", () => {
+        const { wrapper, win } = mountWindow();
+        const header = wrapper.find(".window-manager-window-header");
+
+        header.element.dispatchEvent(pointerEvent("pointerdown", { clientX: 200, clientY: 80 }));
+        header.element.dispatchEvent(pointerEvent("pointerdown", { pointerId: 9, clientX: 300, clientY: 200 }));
+
+        document.dispatchEvent(pointerEvent("pointermove", { pointerId: 9, clientX: 400, clientY: 300 }));
+        expect(win.x).toBe(50);
+        expect(win.y).toBe(60);
+
+        document.dispatchEvent(pointerEvent("pointermove", { clientX: 230, clientY: 120 }));
+        expect(win.x).toBe(80);
+        expect(win.y).toBe(100);
+
+        document.dispatchEvent(pointerEvent("pointerup", { clientX: 230, clientY: 120 }));
+    });
+
+    it("does not steal focus when clicking the controls of an unfocused window", () => {
+        const pinia = createTestingPinia({ createSpy: vi.fn, stubActions: false });
+        setActivePinia(pinia);
+        const store = useWindowManagerStore();
+        store.add({ title: "First", url: "/a", x: 50, y: 60, width: 400, height: 300 });
+        store.add({ title: "Second", url: "/b" });
+        const first = store.windows[0]!;
+        const second = store.windows[1]!;
+        const wrapper = mount(WindowManagerWindow as object, {
+            localVue,
+            pinia,
+            propsData: { window: first },
+        });
+        expect(store.focusedId).toBe(second.id);
+
+        // a real click delivers pointerdown plus a compatibility mousedown;
+        // neither may bubble to the root focus handler from the controls
+        const controls = wrapper.find(".window-manager-window-controls");
+        controls.element.dispatchEvent(pointerEvent("pointerdown", { clientX: 420, clientY: 70 }));
+        controls.element.dispatchEvent(new MouseEvent("mousedown", { bubbles: true, cancelable: true, button: 0 }));
+        expect(store.focusedId).toBe(second.id);
+
+        const header = wrapper.find(".window-manager-window-header");
+        header.element.dispatchEvent(pointerEvent("pointerdown", { clientX: 200, clientY: 80 }));
+        expect(store.focusedId).toBe(first.id);
+        document.dispatchEvent(pointerEvent("pointerup", { clientX: 200, clientY: 80 }));
+    });
+});

From a8218f172e40ff1ed2ec800cea64b84ad2399046 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 10 Jun 2026 15:42:57 -0400
Subject: [PATCH 089/256] Capture the pointer for window manager drag and
 resize

Fixes galaxyproject/galaxy#22875. The floating window's drag and resize
listened for mouse events on the document, but mouse events stop
reaching the parent document the moment the cursor moves over an iframe
-- and with the center frame loaded, most of the screen is iframe. The
resize would freeze mid-drag, and a mouseup over an iframe was never
seen, leaving the window glued to the cursor.

Switching to pointer events and calling setPointerCapture on the header
and resize handle keeps every move/up/cancel event flowing to the
parent document for the duration of the drag, no matter what the
pointer is over. Same bug class FlexPanel hit in #20349; that fix used
an interaction overlay because vueuse's useDraggable can't capture, but
these hand-rolled handlers can do it natively. Pointer events also make
touch real, so the handlers now track the active pointerId and the drag
surfaces get touch-action: none.
---
 .../WindowManager/WindowManagerWindow.vue     | 76 +++++++++++++------
 1 file changed, 53 insertions(+), 23 deletions(-)

diff --git a/client/src/components/WindowManager/WindowManagerWindow.vue b/client/src/components/WindowManager/WindowManagerWindow.vue
index 714e67f16e9..13e7956fdb3 100644
--- a/client/src/components/WindowManager/WindowManagerWindow.vue
+++ b/client/src/components/WindowManager/WindowManagerWindow.vue
@@ -56,23 +56,31 @@ const windowStyle = computed(() => {
 const iframeSrc = computed(() => store.buildUrl(props.window.url));
 
 // --- Drag ---
+let dragPointerId = -1;
 let dragStartMouseX = 0;
 let dragStartMouseY = 0;
 let dragStartX = 0;
 let dragStartY = 0;
 
-function onDragStart(e: MouseEvent) {
-    if (props.window.maximized || props.window.minimized) {
+function onDragStart(e: PointerEvent) {
+    // ignore further pointers while a drag is active (first pointer wins)
+    if (props.window.maximized || props.window.minimized || dragPointerId !== -1) {
         return;
     }
     e.preventDefault();
     store.focus(props.window.id);
+    dragPointerId = e.pointerId;
     dragStartMouseX = e.clientX;
     dragStartMouseY = e.clientY;
     dragStartX = props.window.x;
     dragStartY = props.window.y;
-    document.addEventListener("mousemove", onDragMove);
-    document.addEventListener("mouseup", onDragEnd);
+    // Capture the pointer so move/up events keep reaching this document even
+    // when the cursor crosses an iframe (the center frame or this window's own
+    // body), which would otherwise swallow them and leave the drag stuck.
+    (e.currentTarget as HTMLElement).setPointerCapture(e.pointerId);
+    document.addEventListener("pointermove", onDragMove);
+    document.addEventListener("pointerup", onDragEnd);
+    document.addEventListener("pointercancel", onDragEnd);
 }
 
 function clampPosition(rawX: number, rawY: number): { x: number; y: number } {
@@ -86,42 +94,57 @@ function clampPosition(rawX: number, rawY: number): { x: number; y: number } {
     };
 }
 
-function onDragMove(e: MouseEvent) {
+function onDragMove(e: PointerEvent) {
+    if (e.pointerId !== dragPointerId) {
+        return;
+    }
     const rawX = dragStartX + (e.clientX - dragStartMouseX);
     const rawY = dragStartY + (e.clientY - dragStartMouseY);
     const { x, y } = clampPosition(rawX, rawY);
     store.updatePosition(props.window.id, x, y);
 }
 
-function onDragEnd() {
-    document.removeEventListener("mousemove", onDragMove);
-    document.removeEventListener("mouseup", onDragEnd);
+function onDragEnd(e?: PointerEvent) {
+    if (e && e.pointerId !== dragPointerId) {
+        return;
+    }
+    dragPointerId = -1;
+    document.removeEventListener("pointermove", onDragMove);
+    document.removeEventListener("pointerup", onDragEnd);
+    document.removeEventListener("pointercancel", onDragEnd);
 }
 
 // --- Resize ---
 const MIN_WIDTH = 200;
 const MIN_HEIGHT = 120;
+let resizePointerId = -1;
 let resizeStartMouseX = 0;
 let resizeStartMouseY = 0;
 let resizeStartW = 0;
 let resizeStartH = 0;
 
-function onResizeStart(e: MouseEvent) {
-    if (props.window.maximized) {
+function onResizeStart(e: PointerEvent) {
+    if (props.window.maximized || resizePointerId !== -1) {
         return;
     }
     e.preventDefault();
     e.stopPropagation();
     store.focus(props.window.id);
+    resizePointerId = e.pointerId;
     resizeStartMouseX = e.clientX;
     resizeStartMouseY = e.clientY;
     resizeStartW = props.window.width;
     resizeStartH = props.window.height;
-    document.addEventListener("mousemove", onResizeMove);
-    document.addEventListener("mouseup", onResizeEnd);
+    (e.currentTarget as HTMLElement).setPointerCapture(e.pointerId);
+    document.addEventListener("pointermove", onResizeMove);
+    document.addEventListener("pointerup", onResizeEnd);
+    document.addEventListener("pointercancel", onResizeEnd);
 }
 
-function onResizeMove(e: MouseEvent) {
+function onResizeMove(e: PointerEvent) {
+    if (e.pointerId !== resizePointerId) {
+        return;
+    }
     const maxW = window.innerWidth - props.window.x;
     const maxH = window.innerHeight - props.window.y;
     store.updateSize(
@@ -131,9 +154,14 @@ function onResizeMove(e: MouseEvent) {
     );
 }
 
-function onResizeEnd() {
-    document.removeEventListener("mousemove", onResizeMove);
-    document.removeEventListener("mouseup", onResizeEnd);
+function onResizeEnd(e?: PointerEvent) {
+    if (e && e.pointerId !== resizePointerId) {
+        return;
+    }
+    resizePointerId = -1;
+    document.removeEventListener("pointermove", onResizeMove);
+    document.removeEventListener("pointerup", onResizeEnd);
+    document.removeEventListener("pointercancel", onResizeEnd);
 }
 
 // --- Actions ---
@@ -154,10 +182,8 @@ function onMaximize() {
 }
 
 onBeforeUnmount(() => {
-    document.removeEventListener("mousemove", onDragMove);
-    document.removeEventListener("mouseup", onDragEnd);
-    document.removeEventListener("mousemove", onResizeMove);
-    document.removeEventListener("mouseup", onResizeEnd);
+    onDragEnd();
+    onResizeEnd();
 });
 </script>
 
@@ -170,10 +196,12 @@ onBeforeUnmount(() => {
         <!-- eslint-disable-next-line vuejs-accessibility/no-static-element-interactions -->
         <div
             class="window-manager-window-header"
-            @mousedown.left="window.minimized ? onMinimize() : onDragStart($event)">
+            @pointerdown.left="window.minimized ? onMinimize() : onDragStart($event)">
             <span class="window-manager-window-title">{{ window.title }}</span>
+            <!-- pointerdown.stop keeps control presses from starting a drag; mousedown.stop
+                 keeps the compatibility mouse event from reaching the root focus handler -->
             <!-- eslint-disable-next-line vuejs-accessibility/no-static-element-interactions -->
-            <div class="window-manager-window-controls" @mousedown.stop>
+            <div class="window-manager-window-controls" @pointerdown.stop @mousedown.stop>
                 <button class="window-manager-window-btn" aria-label="Minimize" @click="onMinimize">&#8722;</button>
                 <button class="window-manager-window-btn" aria-label="Maximize" @click="onMaximize">
                     <span v-if="window.maximized">&#9724;</span>
@@ -193,7 +221,7 @@ onBeforeUnmount(() => {
                 <div v-if="!isFocused" class="iframe-focus-overlay" @mousedown="onFocus" />
             </div>
             <!-- eslint-disable-next-line vuejs-accessibility/no-static-element-interactions -->
-            <div v-if="!window.maximized" class="window-manager-resize-handle" @mousedown.left="onResizeStart" />
+            <div v-if="!window.maximized" class="window-manager-resize-handle" @pointerdown.left="onResizeStart" />
         </template>
     </div>
 </template>
@@ -234,6 +262,7 @@ onBeforeUnmount(() => {
     border-bottom: 1px solid var(--color-grey-200);
     cursor: move;
     user-select: none;
+    touch-action: none;
 }
 
 .window-manager-window-title {
@@ -303,5 +332,6 @@ onBeforeUnmount(() => {
     width: 12px;
     height: 12px;
     cursor: nwse-resize;
+    touch-action: none;
 }
 </style>

From cacaebb283b93e588dc5bcb6f1d1ebc5fb3ba74b Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 10 Jun 2026 13:15:34 -0400
Subject: [PATCH 090/256] Add unit tests with a regression check

---
 lib/galaxy/jobs/runners/gcp_batch.py        | 99 +++++++++++----------
 test/unit/app/jobs/test_gcp_batch_runner.py | 72 ++++++++++++++-
 2 files changed, 122 insertions(+), 49 deletions(-)

diff --git a/lib/galaxy/jobs/runners/gcp_batch.py b/lib/galaxy/jobs/runners/gcp_batch.py
index 438c6572aaa..694f0d3fbd4 100644
--- a/lib/galaxy/jobs/runners/gcp_batch.py
+++ b/lib/galaxy/jobs/runners/gcp_batch.py
@@ -43,6 +43,56 @@ log = logging.getLogger(__name__)
 __all__ = ("GoogleCloudBatchJobRunner",)
 
 
+# Runner parameter specifications. The defaults defined here are served lazily by
+# the ParamsWithSpecs defaultdict via __missing__, which is only triggered by
+# subscript access (runner_params[key]) -- not by .get(). See _get_job_params.
+RUNNER_PARAM_SPECS: dict[str, dict[str, Any]] = {
+    "project_id": dict(map=str, default=None),
+    "region": dict(map=str, default="us-central1"),
+    "zone": dict(map=str, default=None),
+    "service_account_file": dict(map=str, default=None),
+    "service_account_email": dict(map=str, default=None),
+    "machine_type": dict(map=str, default="n2-standard-4"),
+    "boot_disk_size_gb": dict(map=int, default=100),
+    "boot_disk_type": dict(map=str, default="pd-standard"),
+    "max_retry_count": dict(map=int, default=3),
+    "max_run_duration": dict(map=str, default=DEFAULT_MAX_RUN_DURATION),
+    "polling_interval": dict(map=int, default=30),
+    # Volume configuration (generic format: "server:/remote_path:/mount_path[:ro],...")
+    "gcp_batch_volumes": dict(map=str, default=None),
+    # Extra docker volume mounts (format: "/host/path:/container/path[:ro],...")
+    "docker_extra_volumes": dict(map=str, default=None),
+    # Network configuration for NFS access
+    "network": dict(map=str, default="default"),
+    "subnet": dict(map=str, default="default"),
+    # Compute resource configuration (defaults - will be overridden by job requirements)
+    "vcpu": dict(map=float, default=1.0),
+    "memory_mib": dict(map=int, default=DEFAULT_MEMORY_MIB),
+    # Job-specific resource requests (same as Kubernetes runner)
+    "requests_cpu": dict(map=str, default=None),
+    "requests_memory": dict(map=str, default=None),
+    "limits_cpu": dict(map=str, default=None),
+    "limits_memory": dict(map=str, default=None),
+    # Container execution settings
+    "use_container": dict(map=bool, default=True),
+    "galaxy_user_id": dict(
+        map=str, valid=lambda s: s == "$uid" or isinstance(s, int) or not s or str(s).isdigit(), default=None
+    ),
+    "galaxy_group_id": dict(
+        map=str, valid=lambda s: s == "$gid" or isinstance(s, int) or not s or str(s).isdigit(), default=None
+    ),
+    # Custom VM image (optional)
+    "custom_vm_image": dict(map=str, default=None),
+    # Job cleanup: if true, delete GCP Batch jobs after Galaxy marks them complete
+    "delete_completed_jobs": dict(map=bool, default=True),
+    # Prefix for GCP Batch job IDs (helps identify which Galaxy server submitted a job)
+    "job_id_prefix": dict(map=str, default="galaxy-job"),
+    # Object store fallback (for future use)
+    "use_object_store": dict(map=bool, default=False),
+    "object_store_path": dict(map=str, default=None),
+}
+
+
 class GoogleCloudBatchJobRunner(AsynchronousJobRunner):
     """
     Job runner that submits jobs to Google Cloud Batch.
@@ -54,54 +104,7 @@ class GoogleCloudBatchJobRunner(AsynchronousJobRunner):
         """Initialize the Google Cloud Batch job runner."""
         log.debug("Starting GoogleCloudBatchJobRunner.__init__")
 
-        # Define runner parameter specifications
-        runner_param_specs = {
-            "project_id": dict(map=str, default=None),
-            "region": dict(map=str, default="us-central1"),
-            "zone": dict(map=str, default=None),
-            "service_account_file": dict(map=str, default=None),
-            "service_account_email": dict(map=str, default=None),
-            "machine_type": dict(map=str, default="n2-standard-4"),
-            "boot_disk_size_gb": dict(map=int, default=100),
-            "boot_disk_type": dict(map=str, default="pd-standard"),
-            "max_retry_count": dict(map=int, default=3),
-            "max_run_duration": dict(map=str, default=DEFAULT_MAX_RUN_DURATION),
-            "polling_interval": dict(map=int, default=30),
-            # Volume configuration (generic format: "server:/remote_path:/mount_path[:ro],...")
-            "gcp_batch_volumes": dict(map=str, default=None),
-            # Extra docker volume mounts (format: "/host/path:/container/path[:ro],...")
-            "docker_extra_volumes": dict(map=str, default=None),
-            # Network configuration for NFS access
-            "network": dict(map=str, default="default"),
-            "subnet": dict(map=str, default="default"),
-            # Compute resource configuration (defaults - will be overridden by job requirements)
-            "vcpu": dict(map=float, default=1.0),
-            "memory_mib": dict(map=int, default=DEFAULT_MEMORY_MIB),
-            # Job-specific resource requests (same as Kubernetes runner)
-            "requests_cpu": dict(map=str, default=None),
-            "requests_memory": dict(map=str, default=None),
-            "limits_cpu": dict(map=str, default=None),
-            "limits_memory": dict(map=str, default=None),
-            # Container execution settings
-            "use_container": dict(map=bool, default=True),
-            "galaxy_user_id": dict(
-                map=str, valid=lambda s: s == "$uid" or isinstance(s, int) or not s or str(s).isdigit(), default=None
-            ),
-            "galaxy_group_id": dict(
-                map=str, valid=lambda s: s == "$gid" or isinstance(s, int) or not s or str(s).isdigit(), default=None
-            ),
-            # Custom VM image (optional)
-            "custom_vm_image": dict(map=str, default=None),
-            # Job cleanup: if true, delete GCP Batch jobs after Galaxy marks them complete
-            "delete_completed_jobs": dict(map=bool, default=True),
-            # Prefix for GCP Batch job IDs (helps identify which Galaxy server submitted a job)
-            "job_id_prefix": dict(map=str, default="galaxy-job"),
-            # Object store fallback (for future use)
-            "use_object_store": dict(map=bool, default=False),
-            "object_store_path": dict(map=str, default=None),
-        }
-
-        kwargs.update({"runner_param_specs": runner_param_specs})
+        kwargs.update({"runner_param_specs": RUNNER_PARAM_SPECS})
         super().__init__(app, nworkers, **kwargs)
 
         # Initialize Google Cloud Batch client
diff --git a/test/unit/app/jobs/test_gcp_batch_runner.py b/test/unit/app/jobs/test_gcp_batch_runner.py
index 6d9b019ac3d..b75a4a85465 100644
--- a/test/unit/app/jobs/test_gcp_batch_runner.py
+++ b/test/unit/app/jobs/test_gcp_batch_runner.py
@@ -9,7 +9,10 @@ from typing import (
 import pytest
 
 from galaxy.jobs.runners import RunnerParams
-from galaxy.jobs.runners.gcp_batch import GoogleCloudBatchJobRunner
+from galaxy.jobs.runners.gcp_batch import (
+    GoogleCloudBatchJobRunner,
+    RUNNER_PARAM_SPECS,
+)
 from galaxy.jobs.runners.util.gcp_batch import (
     convert_cpu_to_milli,
     convert_duration_to_seconds,
@@ -357,3 +360,70 @@ class TestMonitorSleepTime:
         # ParamsWithSpecs.__missing__; .get() would yield None and raise in max().
         runner = _sleep_runner(RunnerParams(specs={"polling_interval": dict(map=int, default=30)}, params={}))
         assert runner.monitor_sleep_time == 30
+
+
+def _make_runner(runner_params=None):
+    """Build a GoogleCloudBatchJobRunner without running __init__ (no GCP client).
+
+    _get_job_params only depends on self.runner_params, so we set that directly.
+    """
+    runner = object.__new__(GoogleCloudBatchJobRunner)
+    runner.runner_params = RunnerParams(specs=RUNNER_PARAM_SPECS, params=runner_params or {})
+    return runner
+
+
+# Keys that _get_job_params copies from the destination / runner config. Derived
+# dynamically (rather than hard-coded) so the parametrized tests below automatically
+# cover any parameter added to _get_job_params in the future.
+JOB_PARAM_KEYS = sorted(_make_runner()._get_job_params(SimpleNamespace(params={})).keys())
+
+
+class TestGetJobParams:
+    """Tests for GoogleCloudBatchJobRunner._get_job_params default resolution."""
+
+    @pytest.mark.parametrize("key", JOB_PARAM_KEYS)
+    def test_unset_param_falls_back_to_spec_default(self, key):
+        """Every copied parameter resolves to its spec default when nothing overrides it.
+
+        This is the regression guard: .get() on the RunnerParams defaultdict would
+        bypass __missing__ and yield None instead of the configured default.
+        """
+        runner = _make_runner()
+        destination = SimpleNamespace(params={})
+
+        params = runner._get_job_params(destination)
+
+        assert params[key] == RUNNER_PARAM_SPECS[key]["default"]
+
+    @pytest.mark.parametrize("key", JOB_PARAM_KEYS)
+    def test_destination_overrides_every_param(self, key):
+        """A value on the job destination takes precedence over the spec default for every param.
+
+        Destination params are not passed through the RunnerParams spec mapping, so a
+        plain string sentinel is a valid override for every key.
+        """
+        runner = _make_runner()
+        sentinel = "destination-sentinel-value"
+        destination = SimpleNamespace(params={key: sentinel})
+
+        params = runner._get_job_params(destination)
+
+        assert params[key] == sentinel
+
+    def test_runner_config_overrides_default(self):
+        """A value set in the runner (plugin) config is used when the destination is silent."""
+        runner = _make_runner({"job_id_prefix": "from-config"})
+        destination = SimpleNamespace(params={})
+
+        params = runner._get_job_params(destination)
+
+        assert params["job_id_prefix"] == "from-config"
+
+    def test_destination_overrides_runner_config(self):
+        """Destination params win over runner config, which wins over the spec default."""
+        runner = _make_runner({"job_id_prefix": "from-config"})
+        destination = SimpleNamespace(params={"job_id_prefix": "from-destination"})
+
+        params = runner._get_job_params(destination)
+
+        assert params["job_id_prefix"] == "from-destination"

From f15e8b74bb1d865169de3ba1131bcaf9cff89995 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 11 Jun 2026 19:23:11 +0300
Subject: [PATCH 091/256] Fix gx_color json schema test divergence

---
 test/unit/tool_util/parameter_specification.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
index 486ddf07de8..ca475a8c3e7 100644
--- a/test/unit/tool_util/parameter_specification.yml
+++ b/test/unit/tool_util/parameter_specification.yml
@@ -1253,6 +1253,9 @@ gx_color:
     - parameter: 'foobar'
     - parameter: 5
     - parameter: {__class__: 'ConnectedValue2'}
+  _json_schema_skip:
+    workflow_step_invalid: "color validator uses AfterValidator"
+    workflow_step_linked_invalid: "color validator uses AfterValidator"
 
 gx_data:
   request_valid:

From b7341edae9c966bc6e3bdea6db1182c686df2d78 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 11 Jun 2026 18:35:57 +0200
Subject: [PATCH 092/256] Fix expand_meta_parameters_async mangling conditional
 names ending in _N as repeat indices
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

split_inputs_nested flattened the already-nested input state to |‑separated flat
keys via visit_input_values, then called expand_flat_parameters_to_nested to
rebuild the dict.  That rebuild uses process_key / looks_like_flattened_repeat_key,
which treats any path component ending in _<digit> (e.g. "column_selector_options_1")
as a repeat-item index rather than a literal conditional name.  The result was a
spurious "column_selector_options" list instead of the expected
"column_selector_options_1" / "column_selector_options_2" dicts, which then caused
Pydantic to report extra_forbidden on the fake list and list_type (None) on col1
once fill_static_defaults initialised the now-missing conditional to an empty dict.

The flat→nested round-trip was never needed for the nested-input path: the dict
coming in is already correctly structured.  Fix by returning nested_dict directly
from split_inputs_nested as single_inputs, only extracting batch (matched /
multiplied) inputs as flat-key entries as before.  Strip
internal state keys starting with __ that visit_input_values stamps so they
don't appear as extra fields when the state reaches Pydantic validation.

Also remove stray print() debug calls left in visitor.py.
---
 lib/galaxy/tool_util/parameters/visitor.py    |  2 -
 lib/galaxy/tools/parameters/meta.py           | 26 +++++++++---
 lib/galaxy_test/api/test_jobs.py              | 24 +++++++++++
 .../tools/conditional_name_digit_suffix.xml   | 42 +++++++++++++++++++
 test/functional/tools/sample_tool_conf.xml    |  1 +
 test/unit/app/tools/test_parameter_parsing.py | 40 ++++++++++++++++++
 6 files changed, 127 insertions(+), 8 deletions(-)
 create mode 100644 test/functional/tools/conditional_name_digit_suffix.xml

diff --git a/lib/galaxy/tool_util/parameters/visitor.py b/lib/galaxy/tool_util/parameters/visitor.py
index 52e1559ca6b..ebd515496ad 100644
--- a/lib/galaxy/tool_util/parameters/visitor.py
+++ b/lib/galaxy/tool_util/parameters/visitor.py
@@ -117,8 +117,6 @@ def _select_which_when(conditional: ConditionalParameterModel, state: dict) -> C
     explicit_test_value = state.get(test_parameter_name)
     test_value = validate_explicit_conditional_test_value(test_parameter_name, explicit_test_value)
     for when in conditional.whens:
-        print(when.discriminator)
-        print(type(when.discriminator))
         if test_value is None and when.is_default_when:
             return when
         elif test_value == when.discriminator:
diff --git a/lib/galaxy/tools/parameters/meta.py b/lib/galaxy/tools/parameters/meta.py
index ee92f019adc..2ba4a39f44f 100644
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -189,6 +189,23 @@ def expand_flat_parameters_to_nested(incoming_copy: ToolRequestT) -> dict[str, A
     return nested_dict
 
 
+def _remove_internal_state_keys(state: Any) -> None:
+    """Remove ``__``-prefixed keys from every dict in the nested state.
+
+    ``visit_input_values`` injects internal book-keeping entries such as
+    ``__current_case__`` and ``__index__`` as side-effects.  These must not
+    reach the job-internal Pydantic validation layer, which uses ``extra='forbid'``.
+    """
+    if isinstance(state, dict):
+        for key in [k for k in state if k.startswith("__")]:
+            del state[key]
+        for v in state.values():
+            _remove_internal_state_keys(v)
+    elif isinstance(state, list):
+        for item in state:
+            _remove_internal_state_keys(item)
+
+
 def expand_meta_parameters(
     trans: WorkRequestContext, tool, incoming: ToolRequestT, input_format: InputFormatT
 ) -> ExpandedT:
@@ -315,7 +332,6 @@ def split_inputs_flat(inputs: dict[str, Any], classifier):
 
 
 def split_inputs_nested(inputs, nested_dict, classifier):
-    single_inputs: dict[str, Any] = {}
     matched_multi_inputs: dict[str, Any] = {}
     multiplied_multi_inputs: dict[str, Any] = {}
     unset_value = object()
@@ -326,9 +342,7 @@ def split_inputs_nested(inputs, nested_dict, classifier):
             return
 
         input_type, expanded_val = classifier(value, prefixed_name)
-        if input_type == input_classification.SINGLE:
-            single_inputs[prefixed_name] = expanded_val
-        elif input_type == input_classification.MATCHED:
+        if input_type == input_classification.MATCHED:
             matched_multi_inputs[prefixed_name] = expanded_val
         elif input_type == input_classification.MULTIPLIED:
             multiplied_multi_inputs[prefixed_name] = expanded_val
@@ -336,8 +350,8 @@ def split_inputs_nested(inputs, nested_dict, classifier):
     visit_input_values(
         inputs=inputs, input_values=nested_dict, callback=visitor, allow_case_inference=True, unset_value=unset_value
     )
-    single_inputs_nested = expand_flat_parameters_to_nested(single_inputs)
-    return (single_inputs_nested, matched_multi_inputs, multiplied_multi_inputs)
+    _remove_internal_state_keys(nested_dict)
+    return (nested_dict, matched_multi_inputs, multiplied_multi_inputs)
 
 
 ExpandedAsyncT = tuple[
diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py
index da9f7570238..de524dfb31e 100644
--- a/lib/galaxy_test/api/test_jobs.py
+++ b/lib/galaxy_test/api/test_jobs.py
@@ -717,6 +717,30 @@ steps:
             assert os.path.exists(output_dataset_paths[1])
             assert not os.path.exists(output_dataset_paths[0])
 
+    @skip_without_tool("conditional_name_digit_suffix")
+    def test_create_job_with_conditional_name_digit_suffix(self):
+        # Regression: expand_meta_parameters_async used to mangle conditional names ending
+        # in _N (e.g. "inner_options_1") by misidentifying them as repeat indices, causing
+        # Pydantic job-internal validation to fail with extra_forbidden / list_type errors.
+        with self.dataset_populator.test_history() as history_id:
+            response = self.dataset_populator.tool_request_raw(
+                tool_id="conditional_name_digit_suffix",
+                inputs={
+                    "outer": {
+                        "select": "a",
+                        "inner_options_1": {"mode": "by_index", "col": 1},
+                        "inner_options_2": {"mode": "by_name", "label": "foo"},
+                    }
+                },
+                history_id=history_id,
+            )
+            response.raise_for_status()
+            tool_request_id = response.json()["tool_request_id"]
+            submitted = self.dataset_populator.wait_on_tool_request(tool_request_id)
+            assert submitted, self.dataset_populator.get_tool_request(tool_request_id)
+            jobs = self.galaxy_interactor.jobs_for_tool_request(tool_request_id)
+            self.dataset_populator.wait_for_jobs(jobs, assert_ok=True)
+
     def _hack_to_skip_test_if_state_ok(self, job_state):
         if job_state().json()["state"] == "ok":
             message = "Job state switch from running to ok too quickly - the rest of the test requires the job to be in a running state. Skipping test."
diff --git a/test/functional/tools/conditional_name_digit_suffix.xml b/test/functional/tools/conditional_name_digit_suffix.xml
new file mode 100644
index 00000000000..c6cab88d005
--- /dev/null
+++ b/test/functional/tools/conditional_name_digit_suffix.xml
@@ -0,0 +1,42 @@
+<tool id="conditional_name_digit_suffix" name="conditional_name_digit_suffix" version="0.1.0">
+    <description>Regression tool: conditional names ending in _N must not be treated as repeat indices</description>
+    <command>echo done</command>
+    <inputs>
+        <conditional name="outer">
+            <param name="select" type="select">
+                <option value="a">A</option>
+            </param>
+            <when value="a">
+                <!-- Names ending in _1 / _2 are the pattern that looks_like_flattened_repeat_key
+                     would misidentify as "repeat item 1/2 of a repeat named inner_options". -->
+                <conditional name="inner_options_1">
+                    <param name="mode" type="select">
+                        <option value="by_index">By Index</option>
+                        <option value="by_name">By Name</option>
+                    </param>
+                    <when value="by_index">
+                        <param name="col" type="integer" value="1" />
+                    </when>
+                    <when value="by_name">
+                        <param name="label" type="text" value="" />
+                    </when>
+                </conditional>
+                <conditional name="inner_options_2">
+                    <param name="mode" type="select">
+                        <option value="by_index">By Index</option>
+                        <option value="by_name">By Name</option>
+                    </param>
+                    <when value="by_index">
+                        <param name="col" type="integer" value="1" />
+                    </when>
+                    <when value="by_name">
+                        <param name="label" type="text" value="" />
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+</tool>
diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml
index 83c006d09ab..ca88a0f59bd 100644
--- a/test/functional/tools/sample_tool_conf.xml
+++ b/test/functional/tools/sample_tool_conf.xml
@@ -61,6 +61,7 @@
   <tool file="filter_static_regexp.xml" />
   <tool file="select_from_dataset.xml" />
   <tool file="select_from_dataset_in_conditional.xml" />
+  <tool file="conditional_name_digit_suffix.xml" />
   <tool file="select_from_csvdataset.xml" />
   <tool file="select_from_dataset_optional.xml" />
   <tool file="drill_down.xml" />
diff --git a/test/unit/app/tools/test_parameter_parsing.py b/test/unit/app/tools/test_parameter_parsing.py
index 23ce77008bb..b26d9be86aa 100644
--- a/test/unit/app/tools/test_parameter_parsing.py
+++ b/test/unit/app/tools/test_parameter_parsing.py
@@ -5,6 +5,7 @@ from typing import (
 import pytest
 
 from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.tools.parameters.meta import _remove_internal_state_keys
 from galaxy.tools.parameters.wrapped import (
     nested_key_to_path,
     process_key,
@@ -27,6 +28,45 @@ def test_nested_key_to_path():
     ]
 
 
+def test_remove_internal_state_keys():
+    state = {
+        "__class__": "RuntimeValue",
+        "selected_tasks": {
+            "selected_task": "train",
+            "__current_case__": 0,
+            "_private": "kept",
+            "input_options": {
+                "selected_input": "tabular",
+                "__current_case__": 1,
+                "repeat_0": {"__index__": 0, "__identifier__": "foo", "col": 1},
+            },
+        },
+    }
+    _remove_internal_state_keys(state)
+    assert state == {
+        "selected_tasks": {
+            "selected_task": "train",
+            "_private": "kept",
+            "input_options": {
+                "selected_input": "tabular",
+                "repeat_0": {"col": 1},
+            },
+        },
+    }
+
+
+def test_remove_internal_state_keys_list():
+    # visit_input_values represents repeat groups as lists of dicts, each with __index__
+    state = {
+        "repeat": [
+            {"__index__": 0, "col": 1},
+            {"__index__": 1, "col": 2},
+        ]
+    }
+    _remove_internal_state_keys(state)
+    assert state == {"repeat": [{"col": 1}, {"col": 2}]}
+
+
 class TestProcessKey:
     def test_process_key(self):
         nested_dict: dict[str, Any] = {}

From b8762204da0ec297523a3c4dee9a4737e7d4d622 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 11 Jun 2026 09:51:11 +0200
Subject: [PATCH 093/256] address arch-review issues: move business logic out
 of chat controller
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Extract interface_context notebook parsing into ChatManager.resolve_page_from_interface_context
  so the controller delegates instead of duplicating ID-decode + access-check logic.
  Access-control errors now propagate correctly; only ID-decode failures are swallowed.
- Pass page_id through full_context and move notebook→page_assistant routing into
  AgentService.route_and_execute, keeping routing decisions out of the HTTP layer.
- Add page_id to full_context dict so the routing guard in agents.py can read it.
- Add tests: standalone-page contextLabel, chatError state, chat exchange ID helpers,
  dismissal round-trip in usePageProposals, symmetric fixture in applySectionPatched test.
---
 .../src/composables/useActiveContext.test.ts  |  5 ++
 .../src/composables/usePageProposals.test.ts  | 16 ++++-
 client/src/stores/pageEditorStore.test.ts     | 58 +++++++++++++++++++
 lib/galaxy/managers/agents.py                 |  5 +-
 lib/galaxy/managers/chat.py                   | 26 +++++++++
 lib/galaxy/webapps/galaxy/api/chat.py         | 25 +-------
 6 files changed, 109 insertions(+), 26 deletions(-)

diff --git a/client/src/composables/useActiveContext.test.ts b/client/src/composables/useActiveContext.test.ts
index 75d8f20599c..57343fd0e60 100644
--- a/client/src/composables/useActiveContext.test.ts
+++ b/client/src/composables/useActiveContext.test.ts
@@ -195,5 +195,10 @@ describe("useActiveContext", () => {
             );
             expect(contextLabel.value).toBe("History Notebook: test-page-id");
         });
+
+        it("labels standalone page editor context without historyId", () => {
+            const { contextLabel } = withRoute("/pages/editor", { id: "test-page-id" }, {});
+            expect(contextLabel.value).toBe("Page: test-page-id");
+        });
     });
 });
diff --git a/client/src/composables/usePageProposals.test.ts b/client/src/composables/usePageProposals.test.ts
index bf9d6a95801..446c6975114 100644
--- a/client/src/composables/usePageProposals.test.ts
+++ b/client/src/composables/usePageProposals.test.ts
@@ -255,6 +255,15 @@ describe("usePageProposals", () => {
             dismissProposal(makeProposalMsg("full_replacement", "x"));
             expect(mockPersistedDismissed.value[PAGE_ID]).toBeUndefined();
         });
+
+        it("persisted dismissal survives a loadForPage reload", () => {
+            const { dismissProposal, loadForPage, dismissedProposals } = setup();
+            const msg = makeProposalMsg("full_replacement", "x");
+            dismissProposal(msg);
+            dismissedProposals.value = new Set();
+            loadForPage(PAGE_ID);
+            expect(dismissedProposals.value.has(msg.id)).toBe(true);
+        });
     });
 
     describe("applyFullReplacement", () => {
@@ -295,8 +304,11 @@ describe("usePageProposals", () => {
 
         it("marks message as dismissed after applying", async () => {
             const { dismissedProposals, applySectionPatched } = setup();
-            const msg = makeMsg();
-            await applySectionPatched("patched", msg);
+            const msg = makeProposalMsg("section_patch", "", {
+                target_section_heading: "Methods",
+                new_section_content: "# Methods\nUpdated",
+            });
+            await applySectionPatched("# Patched doc", msg);
             expect(dismissedProposals.value.has(msg.id)).toBe(true);
         });
     });
diff --git a/client/src/stores/pageEditorStore.test.ts b/client/src/stores/pageEditorStore.test.ts
index 06c59ba8f92..b84d4d2826d 100644
--- a/client/src/stores/pageEditorStore.test.ts
+++ b/client/src/stores/pageEditorStore.test.ts
@@ -1066,4 +1066,62 @@ describe("usePageEditorStore", () => {
             expect(store.showRevisions).toBe(false);
         });
     });
+
+    describe("chatError", () => {
+        it("is null by default", () => {
+            const store = usePageEditorStore();
+            expect(store.chatError).toBeNull();
+        });
+
+        it("is reset to null on clearCurrentPage", () => {
+            const store = usePageEditorStore();
+            store.chatError = "some error";
+            store.clearCurrentPage();
+            expect(store.chatError).toBeNull();
+        });
+
+        it("is reset to null on $reset", () => {
+            const store = usePageEditorStore();
+            store.chatError = "some error";
+            store.$reset();
+            expect(store.chatError).toBeNull();
+        });
+    });
+
+    describe("chat exchange IDs", () => {
+        it("returns null for an unknown page", () => {
+            const store = usePageEditorStore();
+            expect(store.getCurrentChatExchangeId("page-1")).toBeNull();
+        });
+
+        it("stores and retrieves an exchange ID per page", () => {
+            const store = usePageEditorStore();
+            store.setCurrentChatExchangeId("page-1", "exchange-abc");
+            expect(store.getCurrentChatExchangeId("page-1")).toBe("exchange-abc");
+        });
+
+        it("isolates IDs across different pages", () => {
+            const store = usePageEditorStore();
+            store.setCurrentChatExchangeId("page-1", "ex-1");
+            store.setCurrentChatExchangeId("page-2", "ex-2");
+            expect(store.getCurrentChatExchangeId("page-1")).toBe("ex-1");
+            expect(store.getCurrentChatExchangeId("page-2")).toBe("ex-2");
+        });
+
+        it("clears a specific page ID without affecting others", () => {
+            const store = usePageEditorStore();
+            store.setCurrentChatExchangeId("page-1", "ex-1");
+            store.setCurrentChatExchangeId("page-2", "ex-2");
+            store.clearCurrentChatExchangeId("page-1");
+            expect(store.getCurrentChatExchangeId("page-1")).toBeNull();
+            expect(store.getCurrentChatExchangeId("page-2")).toBe("ex-2");
+        });
+
+        it("overrides an existing entry when set again", () => {
+            const store = usePageEditorStore();
+            store.setCurrentChatExchangeId("page-1", "ex-1");
+            store.setCurrentChatExchangeId("page-1", "ex-2");
+            expect(store.getCurrentChatExchangeId("page-1")).toBe("ex-2");
+        });
+    });
 });
diff --git a/lib/galaxy/managers/agents.py b/lib/galaxy/managers/agents.py
index 4a09fa656e5..f009514ae50 100644
--- a/lib/galaxy/managers/agents.py
+++ b/lib/galaxy/managers/agents.py
@@ -107,7 +107,10 @@ class AgentService:
         When agent_type is 'auto', the router agent handles the query directly,
         either answering it or using output functions to hand off to specialists.
         """
-        if agent_type == "auto":
+        if agent_type == "auto" and isinstance(context, dict) and context.get("page_id"):
+            log.info("Routing to page_assistant for notebook context")
+            return await self.execute_agent("page_assistant", query, trans, user, context)
+        elif agent_type == "auto":
             # Router handles everything via output functions:
             # - Answers general questions directly
             # - Hands off to error_analysis for debugging
diff --git a/lib/galaxy/managers/chat.py b/lib/galaxy/managers/chat.py
index a8cc60b5cff..29d622ce568 100644
--- a/lib/galaxy/managers/chat.py
+++ b/lib/galaxy/managers/chat.py
@@ -1,10 +1,13 @@
 import json
+import logging
 from typing import (
     Any,
     Optional,
     Union,
 )
 
+log = logging.getLogger(__name__)
+
 from pydantic_ai.messages import (
     ModelMessage,
     ModelRequest,
@@ -64,6 +67,29 @@ class ChatManager:
         trans.sa_session.commit()
         return chat_exchange
 
+    def resolve_page_from_interface_context(
+        self, trans: ProvidesUserContext, query_context: Optional[dict[str, Any]]
+    ) -> tuple[Optional[int], Optional["Page"]]:
+        """Extract and validate a page from an interface_context notebook payload.
+
+        Swallows only ID-decode failures; access-control errors propagate.
+        Returns (None, None) when the payload is absent or the encoded ID is invalid.
+        """
+        interface_context = query_context.get("interface_context") if isinstance(query_context, dict) else None
+        if not (
+            isinstance(interface_context, dict)
+            and interface_context.get("contextType") == "notebook"
+            and interface_context.get("pageId")
+        ):
+            return None, None
+        try:
+            page_id = trans.security.decode_id(interface_context["pageId"])
+        except Exception:
+            log.warning("Ignoring invalid notebook pageId in interface_context: %s", interface_context.get("pageId"))
+            return None, None
+        page_obj = self.get_accessible_page(trans, page_id)
+        return page_id, page_obj
+
     def get_accessible_page(self, trans: ProvidesUserContext, page_id: int) -> Page:
         """Return a Page the current user is allowed to read, or raise."""
         page = trans.sa_session.get(Page, page_id)
diff --git a/lib/galaxy/webapps/galaxy/api/chat.py b/lib/galaxy/webapps/galaxy/api/chat.py
index cd86cd3251e..f28bcf78461 100644
--- a/lib/galaxy/webapps/galaxy/api/chat.py
+++ b/lib/galaxy/webapps/galaxy/api/chat.py
@@ -197,25 +197,8 @@ class ChatAPI:
             # being masked as 500.
             page_obj = self.chat_manager.get_accessible_page(trans, page_id)
 
-        # New unified format: notebook context via interface_context JSON.
-        # Accepts {"contextType": "notebook", "pageId": "<encoded-id>", "historyId": "<encoded-id>"}
-        # sent by GalaxyAI when the user is on the page editor route.  We decode the
-        # ID here so the rest of the handler can reuse the existing page_id path unchanged.
-        # Backward-compatible: legacy payload.page_id still works.
         if page_id is None:
-            interface_context = query_context.get("interface_context") if isinstance(query_context, dict) else None
-            if (
-                isinstance(interface_context, dict)
-                and interface_context.get("contextType") == "notebook"
-                and interface_context.get("pageId")
-            ):
-                try:
-                    page_id = trans.security.decode_id(interface_context["pageId"])
-                    page_obj = self.chat_manager.get_accessible_page(trans, page_id)
-                except Exception:
-                    log.warning(
-                        "Ignoring invalid notebook pageId in interface_context: %s", interface_context.get("pageId")
-                    )
+            page_id, page_obj = self.chat_manager.resolve_page_from_interface_context(trans, query_context)
 
         try:
             if HAS_AGENTS:
@@ -224,6 +207,7 @@ class ChatAPI:
                 # Export page content (encodes IDs) so the agent sees the same
                 # text the editor has -- hashes and proposals match the client.
                 if page_id:
+                    full_context["page_id"] = page_id
                     if page_obj:
                         full_context["history_id"] = page_obj.history_id
                         if not full_context.get("history_id"):
@@ -259,11 +243,6 @@ class ChatAPI:
                 if payload and payload.entity_context:
                     full_context["entities"] = payload.entity_context.model_dump(exclude_none=True)
 
-                # When we already know this is a notebook chat, bypass the router
-                # and go straight to page_assistant — no need for an LLM to decide.
-                if page_id and agent_type == "auto":
-                    agent_type = "page_assistant"
-
                 agent_response = await self._get_agent_response_full(
                     query_text, agent_type, trans, user, job, full_context
                 )

From ca872a688aa7f0ca729f44b38a59547c6e38a72d Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Thu, 11 Jun 2026 17:29:56 -0500
Subject: [PATCH 094/256] add unit tests for page_id routing and
 interface_context resolution
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- TestAgentUnitMocked: two tests for AgentService.route_and_execute — verifies that a context dict carrying page_id bypasses the router and calls page_assistant directly, and that the absence of page_id falls through to the router as expected.
- TestResolvePageFromInterfaceContext: six tests for ChatManager.resolve_page_from_interface_context — covers the (None, None) early-returns for absent/malformed payloads, wrong contextType, missing pageId, and decode failures, plus the happy path returning the decoded id and page object.

Co-Authored-By: Claude <noreply@anthropic.com>
---
 test/unit/app/test_agents.py       | 54 ++++++++++++++++++++++++++++++
 test/unit/app/test_chat_manager.py | 51 ++++++++++++++++++++++++++++
 2 files changed, 105 insertions(+)

diff --git a/test/unit/app/test_agents.py b/test/unit/app/test_agents.py
index 4271f4e8052..b808c16a301 100644
--- a/test/unit/app/test_agents.py
+++ b/test/unit/app/test_agents.py
@@ -62,6 +62,7 @@ from galaxy.agents.base import truncate_message_history
 from galaxy.agents.custom_tool import CritiqueReport
 from galaxy.agents.registry import build_default_registry
 from galaxy.agents.tools import SimplifiedToolRecommendationResult
+from galaxy.managers.agents import AgentService
 
 agent_registry = build_default_registry()
 from galaxy.agents import base as agents_base
@@ -90,6 +91,7 @@ from galaxy.util.unittest_utils import pytestmark_live_llm
 class TestAgentUnitMocked:
     def setup_method(self):
         self.mock_config = mock.Mock()
+        self.mock_job_manager = mock.Mock()
         self.mock_config.ai_api_key = "test-key"
         self.mock_config.ai_model = "llama-4-scout"
         self.mock_config.ai_api_base_url = "http://localhost:4000/v1/"
@@ -1263,6 +1265,58 @@ class TestAgentUnitMocked:
         assert "Steps: 12" in rendered
         assert "bowtie2" in rendered
 
+    @pytest.mark.asyncio
+    async def test_route_and_execute_uses_page_assistant_when_page_id_in_context(self):
+        """AgentService.route_and_execute bypasses the router and calls page_assistant
+        directly when 'page_id' is present in the context dict."""
+        service = AgentService(
+            config=self.mock_config,
+            job_manager=self.mock_job_manager,
+            registry=build_default_registry(),
+        )
+
+        sentinel = object()
+        with mock.patch.object(service, "execute_agent", new_callable=AsyncMock) as mock_exec:
+            mock_exec.return_value = sentinel
+            result = await service.route_and_execute(
+                "help me edit this page",
+                trans=self.mock_trans,
+                user=self.mock_user,
+                context={"page_id": 42, "page_content": "# My Page"},
+                agent_type="auto",
+            )
+
+        mock_exec.assert_awaited_once_with(
+            "page_assistant",
+            "help me edit this page",
+            self.mock_trans,
+            self.mock_user,
+            {"page_id": 42, "page_content": "# My Page"},
+        )
+        assert result is sentinel
+
+    @pytest.mark.asyncio
+    async def test_route_and_execute_falls_through_to_router_without_page_id(self):
+        """Without page_id in context, auto-routing goes to the router, not page_assistant."""
+        service = AgentService(
+            config=self.mock_config,
+            job_manager=self.mock_job_manager,
+            registry=build_default_registry(),
+        )
+
+        with mock.patch.object(service, "execute_agent", new_callable=AsyncMock) as mock_exec:
+            mock_exec.return_value = mock.Mock()
+            await service.route_and_execute(
+                "how do I run BWA?",
+                trans=self.mock_trans,
+                user=self.mock_user,
+                context={"interface_context": {"contextType": "notebook", "someId": "abc"}},
+                agent_type="auto",
+            )
+
+        mock_exec.assert_awaited_once()
+        assert mock_exec.call_args[0][0] == "router"
+
     @pytest.mark.asyncio
     async def test_tool_rec_search_iwc_workflows_uses_module_helper(self):
         agent = self._make_tool_rec_agent()
diff --git a/test/unit/app/test_chat_manager.py b/test/unit/app/test_chat_manager.py
index b13b30c0947..ee26bb78e21 100644
--- a/test/unit/app/test_chat_manager.py
+++ b/test/unit/app/test_chat_manager.py
@@ -219,3 +219,54 @@ class TestGetRoutingHistory:
         exchange = self._exchange_with("not valid json{{{")
         _, responding = self._routing_history(mgr, trans, exchange)
         assert responding is False
+
+
+class TestResolvePageFromInterfaceContext:
+    """resolve_page_from_interface_context extracts and validates a page from
+    an interface_context notebook payload, delegating access-check to
+    get_accessible_page."""
+
+    def _trans(self, decoded_id=99):
+        trans = _make_trans()
+        trans.security = mock.Mock()
+        trans.security.decode_id.return_value = decoded_id
+        return trans
+
+    def test_returns_none_none_when_query_context_is_none(self):
+        mgr = ChatManager()
+        assert mgr.resolve_page_from_interface_context(_make_trans(), None) == (None, None)
+
+    def test_returns_none_none_when_interface_context_absent(self):
+        mgr = ChatManager()
+        assert mgr.resolve_page_from_interface_context(_make_trans(), {"other_key": "value"}) == (None, None)
+
+    def test_returns_none_none_when_context_type_is_not_notebook(self):
+        mgr = ChatManager()
+        trans = self._trans()
+        ctx = {"interface_context": {"contextType": "tool", "pageId": "abc"}}
+        assert mgr.resolve_page_from_interface_context(trans, ctx) == (None, None)
+
+    def test_returns_none_none_when_page_id_missing(self):
+        mgr = ChatManager()
+        trans = self._trans()
+        ctx = {"interface_context": {"contextType": "notebook"}}
+        assert mgr.resolve_page_from_interface_context(trans, ctx) == (None, None)
+
+    def test_returns_none_none_when_decode_raises(self):
+        mgr = ChatManager()
+        trans = self._trans()
+        trans.security.decode_id.side_effect = Exception("bad id")
+        ctx = {"interface_context": {"contextType": "notebook", "pageId": "invalid"}}
+        assert mgr.resolve_page_from_interface_context(trans, ctx) == (None, None)
+
+    def test_returns_page_id_and_page_obj_on_success(self):
+        mgr = ChatManager()
+        trans = self._trans(decoded_id=42)
+        fake_page = mock.Mock()
+        with mock.patch.object(mgr, "get_accessible_page", return_value=fake_page) as mock_get:
+            ctx = {"interface_context": {"contextType": "notebook", "pageId": "encodedAbc"}}
+            page_id, page_obj = mgr.resolve_page_from_interface_context(trans, ctx)
+
+        assert page_id == 42
+        assert page_obj is fake_page
+        mock_get.assert_called_once_with(trans, 42)

From 7627615fbd4e8fa25195e372d82eafbf9703c9da Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 12 Jun 2026 07:17:33 +0300
Subject: [PATCH 095/256] Update tabulator and plotly versions

---
 client/visualizations.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/visualizations.yml b/client/visualizations.yml
index 82ce07ba1e8..0adc7782fd9 100644
--- a/client/visualizations.yml
+++ b/client/visualizations.yml
@@ -83,13 +83,13 @@ phylocanvas:
     version: 0.0.11
 plotly:
     package: "@galaxyproject/plotly"
-    version: 0.0.28
+    version: 0.0.30
 plotly_box:
     package: "@galaxyproject/plotly_box"
     version: 0.0.0
 plotly_heatmap:
     package: "@galaxyproject/plotly_heatmap"
-    version: 0.0.1
+    version: 0.0.2
 plotly_histogram:
     package: "@galaxyproject/plotly_histogram"
     version: 0.0.0
@@ -98,7 +98,7 @@ plotly_pie:
     version: 0.0.3
 plotly_surface:
     package: "@galaxyproject/plotly_surface"
-    version: 0.0.0
+    version: 0.0.1
 plyr:
     package: "@galaxyproject/plyr"
     version: 0.0.4
@@ -107,7 +107,7 @@ rerunio:
     version: 0.0.0
 tabulator:
     package: "@galaxyproject/tabulator"
-    version: 0.0.9
+    version: 0.0.11
 tiffviewer:
     package: "@galaxyproject/tiffviewer"
     version: 0.0.5

From 20390a617783f4bd0fe976ae0143c96511473ab4 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 12 Jun 2026 12:15:37 -0400
Subject: [PATCH 096/256] Remove unused GHCR container build job

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 .github/workflows/build_container_image.yaml | 61 --------------------
 1 file changed, 61 deletions(-)

diff --git a/.github/workflows/build_container_image.yaml b/.github/workflows/build_container_image.yaml
index cf2e733874e..87b054f9655 100644
--- a/.github/workflows/build_container_image.yaml
+++ b/.github/workflows/build_container_image.yaml
@@ -10,67 +10,6 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 jobs:
-  ghcrbuild:
-    name: Build container image for GHCR
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          persist-credentials: false
-      # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
-      - name: Set outputs
-        id: commit
-        run: echo "sha_short=$(git rev-parse --short HEAD)" >> $GITHUB_OUTPUT
-      - name: Set branch name
-        id: branch
-        run: |
-          if [[ "$GITHUB_REF" == "refs/tags/"* ]]; then
-            echo "name=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT
-          elif [[ "$GITHUB_REF" == "refs/heads/dev" ]]; then
-            echo "name=dev" >> $GITHUB_OUTPUT
-          elif [[ "$GITHUB_REF" == "refs/heads/release_"* ]]; then
-            echo "name=${GITHUB_REF#refs/heads/release_}-auto" >> $GITHUB_OUTPUT
-          fi
-        shell: bash
-      - name: Extract metadata for container image
-        id: meta
-        uses: docker/metadata-action@v6
-        with:
-          images: ghcr.io/${{ github.repository }}
-          tags: |
-            type=raw,value=${{steps.branch.outputs.name}}
-      - name: Build args
-        id: buildargs
-        run: |
-            echo "gitcommit=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT 
-            echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')"  >> $GITHUB_OUTPUT
-      
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v4
-        with:
-          platforms: linux/amd64
-
-      - name: Login to GHCR
-        uses: docker/login-action@v4
-        with:
-          registry: ghcr.io
-          username: ${{ github.repository_owner }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Build and push container image to ghcr
-        uses: docker/build-push-action@v7
-        with:
-          build-args: |
-              GIT_COMMIT=${{ steps.buildargs.outputs.gitcommit }}
-              BUILD_DATE=${{ steps.buildargs.outputs.builddate }}
-              IMAGE_TAG=${{ steps.branch.outputs.name }}
-          file: .k8s_ci.Dockerfile
-          push: true
-          context: .
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
-          platforms: linux/amd64
-
   build:
     name: Build container image for Galaxy repos
     runs-on: ubuntu-latest

From deb7ecd706e4021305ddcb1861bb84db0a0875ef Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 10 Jun 2026 18:45:44 -0400
Subject: [PATCH 097/256] Make agent retry budget configurable via
 inference_services

ChatGXY's router was hard-failing with 'Exceeded maximum output retries (1)':
its pydantic-ai Agent used the default retry budget of 1, and the router's
process() only caught (OSError, ValueError), so an UnexpectedModelBehavior sailed
past the graceful _handle_fallback and surfaced to the user as a generic 500.

This adds a per-agent 'retries' knob to inference_services, resolved through the
same _get_agent_config chain as temperature/max_tokens and wired into every
agent's Agent(retries=...). The default goes from pydantic-ai's 1 to 3 so a
transient bout of non-conforming model output recovers instead of failing the
run. custom_tool's producer keeps its retries=0 reflection-loop default but can
now be overridden. The router also catches UnexpectedModelBehavior so a genuinely
exhausted budget degrades to the existing fallback message instead of a 500.

Adds unit tests for the resolution chain, the config->Agent wiring, and the
router's graceful fallback (forced via an empty ModelResponse).
---
 doc/source/admin/galaxy_options.rst         | 14 ++++--
 lib/galaxy/agents/base.py                   | 14 ++++++
 lib/galaxy/agents/custom_tool.py            |  8 ++--
 lib/galaxy/agents/error_analysis.py         |  2 +
 lib/galaxy/agents/gtn_training.py           |  6 ++-
 lib/galaxy/agents/history.py                |  1 +
 lib/galaxy/agents/orchestrator.py           |  2 +
 lib/galaxy/agents/page_assistant.py         |  1 +
 lib/galaxy/agents/router.py                 |  5 +-
 lib/galaxy/agents/tools.py                  |  2 +
 lib/galaxy/config/sample/galaxy.yml.sample  | 22 +++++----
 lib/galaxy/config/schemas/config_schema.yml |  7 ++-
 test/unit/app/test_agents.py                | 52 +++++++++++++++++++++
 13 files changed, 118 insertions(+), 18 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index dbb525bed4b..b64062ec8cd 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -5671,8 +5671,8 @@
 :Description:
     Configuration for AI inference services used by agents and
     visualization plugins. Supports per-agent or per-plugin model,
-    temperature, max_tokens, api_key, api_base_url, and enabled
-    settings. Valid keys include agent types (e.g. router,
+    temperature, max_tokens, retries, api_key, api_base_url, and
+    enabled settings. Valid keys include agent types (e.g. router,
     error_analysis) and plugin names (e.g. jupyterlite). Agents and
     plugins inherit from 'default' configuration, which itself falls
     back to global ai_model/ai_api_key settings. All agents are
@@ -5684,7 +5684,12 @@
     test/integration/static_agents.yml } Per-agent or default-block
     ``structured_output_override: true|false`` beats the model
     capability table -- see ``agent_model_capabilities_file`` for the
-    table's location and contents.
+    table's location and contents. Per-agent or default-block
+    ``retries`` sets the pydantic-ai retry budget (tool calls and
+    output validation); it defaults to 3. Raise it if a model
+    intermittently fails to produce conforming output ("Exceeded
+    maximum output retries"); custom_tool's producer defaults to 0
+    since it runs its own reflection loop.
 :Default: ``None``
 :Type: any
 
@@ -6267,3 +6272,6 @@
     for user defined tools.
 :Default: ``false``
 :Type: bool
+
+
+
diff --git a/lib/galaxy/agents/base.py b/lib/galaxy/agents/base.py
index 3cd42d0ba4e..fa38b184fcb 100644
--- a/lib/galaxy/agents/base.py
+++ b/lib/galaxy/agents/base.py
@@ -377,6 +377,11 @@ class BaseGalaxyAgent(ABC):
     # backend we currently support (smallest is Qwen3-32B at 32k context).
     DEFAULT_MAX_TOKENS = 8192
 
+    # Retry budget passed to Agent(retries=...) (tool calls and output validation).
+    # pydantic-ai defaults to 1; 3 gives a flaky model a couple more chances to
+    # produce conforming output before the run fails.
+    DEFAULT_AGENT_RETRIES = 3
+
     def __init__(self, deps: GalaxyAgentDependencies):
         self.deps = deps
 
@@ -856,6 +861,14 @@ class BaseGalaxyAgent(ABC):
     def _get_max_tokens(self) -> int:
         return self._get_agent_config("max_tokens", self.DEFAULT_MAX_TOKENS)
 
+    def _get_retries(self, default: Optional[int] = None) -> int:
+        """Retry budget for the agent's pydantic-ai ``Agent(retries=...)``.
+
+        ``default`` lets a caller override the builtin (e.g. custom_tool's producer
+        keeps 0 so its own reflection loop owns the retry).
+        """
+        return int(self._get_agent_config("retries", self.DEFAULT_AGENT_RETRIES if default is None else default))
+
     async def _call_agent_from_tool(
         self,
         agent_type: str,
@@ -906,6 +919,7 @@ class SimpleGalaxyAgent(BaseGalaxyAgent):
             self._get_model(),
             deps_type=GalaxyAgentDependencies,
             system_prompt=self.get_system_prompt(),
+            retries=self._get_retries(),
         )
 
     def _format_response(self, result: Any, query: str, context: dict[str, Any]) -> AgentResponse:
diff --git a/lib/galaxy/agents/custom_tool.py b/lib/galaxy/agents/custom_tool.py
index 4c07b8afe60..f80a743cb49 100644
--- a/lib/galaxy/agents/custom_tool.py
+++ b/lib/galaxy/agents/custom_tool.py
@@ -111,15 +111,16 @@ class CustomToolAgent(BaseGalaxyAgent):
     def _create_agent(self) -> Agent[GalaxyAgentDependencies, Any]:
         """Create agent with UserToolSource as the output type.
 
-        Sets retries=0 because the agent's explicit reflection loop
-        owns the validation retry (to provide a better prompt).
+        Defaults retries to 0 because the agent's explicit reflection loop owns the
+        validation retry (to provide a better prompt); operators can still override
+        via inference_services.
         """
         return Agent(
             self._get_model(),
             deps_type=GalaxyAgentDependencies,
             output_type=UserToolSource,
             system_prompt=self.get_system_prompt(),
-            retries=0,
+            retries=self._get_retries(default=0),
         )
 
     def get_system_prompt(self) -> str:
@@ -139,6 +140,7 @@ class CustomToolAgent(BaseGalaxyAgent):
                 deps_type=GalaxyAgentDependencies,
                 output_type=CritiqueReport,
                 system_prompt=self._get_critic_system_prompt(),
+                retries=self._get_retries(),
             )
         return self._critic_agent
 
diff --git a/lib/galaxy/agents/error_analysis.py b/lib/galaxy/agents/error_analysis.py
index f56fcb1719d..4aea0134422 100644
--- a/lib/galaxy/agents/error_analysis.py
+++ b/lib/galaxy/agents/error_analysis.py
@@ -57,12 +57,14 @@ class ErrorAnalysisAgent(BaseGalaxyAgent):
                 deps_type=GalaxyAgentDependencies,
                 output_type=ErrorAnalysisResult,
                 system_prompt=self.get_system_prompt(),
+                retries=self._get_retries(),
             )
         else:
             agent = Agent(
                 self._get_model(),
                 deps_type=GalaxyAgentDependencies,
                 system_prompt=self._get_simple_system_prompt(),
+                retries=self._get_retries(),
             )
 
         return agent
diff --git a/lib/galaxy/agents/gtn_training.py b/lib/galaxy/agents/gtn_training.py
index 50229ef8586..0e533d8ab86 100644
--- a/lib/galaxy/agents/gtn_training.py
+++ b/lib/galaxy/agents/gtn_training.py
@@ -101,6 +101,7 @@ class GTNTrainingAgent(BaseGalaxyAgent):
                 self._get_model(),
                 deps_type=GalaxyAgentDependencies,
                 system_prompt=self._get_simple_system_prompt(),
+                retries=self._get_retries(),
             )
 
         agent = Agent(
@@ -110,8 +111,9 @@ class GTNTrainingAgent(BaseGalaxyAgent):
             system_prompt=self.get_system_prompt(),
             # gpt-oss occasionally emits prose instead of a valid GTNSearchResponse;
             # the pydantic-ai default of 1 output retry turns that into a hard error.
-            # Allow a couple more attempts so an occasional malformed output recovers.
-            retries=3,
+            # Configurable via inference_services, defaulting to 3 so an occasional
+            # malformed output recovers.
+            retries=self._get_retries(),
         )
 
         @agent.tool
diff --git a/lib/galaxy/agents/history.py b/lib/galaxy/agents/history.py
index b500d90acfa..9ca0d9bdd0d 100644
--- a/lib/galaxy/agents/history.py
+++ b/lib/galaxy/agents/history.py
@@ -39,6 +39,7 @@ class HistoryAgent(BaseGalaxyAgent):
             self._get_model(),
             deps_type=GalaxyAgentDependencies,
             system_prompt=self.get_system_prompt(),
+            retries=self._get_retries(),
         )
 
         @agent.tool
diff --git a/lib/galaxy/agents/orchestrator.py b/lib/galaxy/agents/orchestrator.py
index f71658a8f9f..2a7b550c34a 100644
--- a/lib/galaxy/agents/orchestrator.py
+++ b/lib/galaxy/agents/orchestrator.py
@@ -61,12 +61,14 @@ class WorkflowOrchestratorAgent(BaseGalaxyAgent):
                 deps_type=GalaxyAgentDependencies,
                 output_type=AgentPlan,
                 system_prompt=self.get_system_prompt(),
+                retries=self._get_retries(),
             )
         else:
             agent = Agent(
                 self._get_model(),
                 deps_type=GalaxyAgentDependencies,
                 system_prompt=self._get_simple_system_prompt(),
+                retries=self._get_retries(),
             )
 
         return agent
diff --git a/lib/galaxy/agents/page_assistant.py b/lib/galaxy/agents/page_assistant.py
index 375039528b7..567257250d1 100644
--- a/lib/galaxy/agents/page_assistant.py
+++ b/lib/galaxy/agents/page_assistant.py
@@ -209,6 +209,7 @@ class PageAssistantAgent(BaseGalaxyAgent):
                 ),
                 str,  # Conversational response — questions, clarifications, no document content.
             ],
+            retries=self._get_retries(),
         )
 
         # Dynamic system prompt — reads self.page_content at call time
diff --git a/lib/galaxy/agents/router.py b/lib/galaxy/agents/router.py
index 245337d38dc..981e7c453e4 100644
--- a/lib/galaxy/agents/router.py
+++ b/lib/galaxy/agents/router.py
@@ -27,6 +27,7 @@ from pydantic import ValidationError
 from pydantic_ai import (
     Agent,
     RunContext,
+    UnexpectedModelBehavior,
 )
 
 from galaxy.agents.operations import AgentOperationsManager
@@ -65,6 +66,7 @@ class QueryRouterAgent(BaseGalaxyAgent):
                 self._get_model(),
                 deps_type=GalaxyAgentDependencies,
                 system_prompt=self._get_simple_system_prompt(),
+                retries=self._get_retries(),
             )
 
         error_handoff = self._create_error_analysis_handoff()
@@ -91,6 +93,7 @@ class QueryRouterAgent(BaseGalaxyAgent):
                 str,  # Default: answer directly
             ],
             system_prompt=self.get_system_prompt(),
+            retries=self._get_retries(),
         )
 
         self._register_fast_path_tools(agent)
@@ -578,7 +581,7 @@ class QueryRouterAgent(BaseGalaxyAgent):
                 query=query,
             )
 
-        except (OSError, ValueError) as e:
+        except (UnexpectedModelBehavior, OSError, ValueError) as e:
             log.warning(f"Router agent error, using fallback: {e}")
             return self._handle_fallback(query, context, str(e))
 
diff --git a/lib/galaxy/agents/tools.py b/lib/galaxy/agents/tools.py
index 4140893e6c4..1539dfc71a3 100644
--- a/lib/galaxy/agents/tools.py
+++ b/lib/galaxy/agents/tools.py
@@ -78,12 +78,14 @@ class ToolRecommendationAgent(BaseGalaxyAgent):
                 deps_type=GalaxyAgentDependencies,
                 output_type=SimplifiedToolRecommendationResult,
                 system_prompt=self.get_system_prompt(),
+                retries=self._get_retries(),
             )
         else:
             agent = Agent(
                 self._get_model(),
                 deps_type=GalaxyAgentDependencies,
                 system_prompt=self._get_simple_system_prompt(),
+                retries=self._get_retries(),
             )
 
         @agent.tool
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index c94c2358253..5e470624224 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1,21 +1,21 @@
 # Galaxy is configured by default to be usable in a single-user development
 # environment.  To tune the application for a multi-user production
 # environment, see the documentation at:
-#
+# 
 #  https://docs.galaxyproject.org/en/master/admin/production.html
-#
+# 
 # Throughout this sample configuration file, except where stated otherwise,
 # uncommented values override the default if left unset, whereas commented
 # values are set to the default value.  Relative paths are relative to the root
 # Galaxy directory.
-#
+# 
 # Examples of many of these options are explained in more detail in the Galaxy
 # Community Hub.
-#
+# 
 #   https://galaxyproject.org/admin/config
-#
+# 
 # Config hackers are encouraged to check there before asking for help.
-#
+# 
 # Configuration for Gravity process manager.
 # ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``).
 gravity:
@@ -3067,7 +3067,7 @@ galaxy:
 
   # Configuration for AI inference services used by agents and
   # visualization plugins. Supports per-agent or per-plugin model,
-  # temperature, max_tokens, api_key, api_base_url, and enabled
+  # temperature, max_tokens, retries, api_key, api_base_url, and enabled
   # settings. Valid keys include agent types (e.g. router,
   # error_analysis) and plugin names (e.g. jupyterlite). Agents and
   # plugins inherit from 'default' configuration, which itself falls
@@ -3080,7 +3080,12 @@ galaxy:
   # test/integration/static_agents.yml } Per-agent or default-block
   # ``structured_output_override: true|false`` beats the model
   # capability table -- see ``agent_model_capabilities_file`` for the
-  # table's location and contents.
+  # table's location and contents. Per-agent or default-block
+  # ``retries`` sets the pydantic-ai retry budget (tool calls and output
+  # validation); it defaults to 3. Raise it if a model intermittently
+  # fails to produce conforming output ("Exceeded maximum output
+  # retries"); custom_tool's producer defaults to 0 since it runs its
+  # own reflection loop.
   #inference_services: null
 
   # YAML file with capability hints for agent inference models. Maps
@@ -3365,3 +3370,4 @@ galaxy:
   # Enable beta tool formats (yaml, cwl, ...) which is a prerequisite
   # for user defined tools.
   #enable_beta_tool_formats: false
+
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index f737f1072c1..9f05a1b0b32 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -4197,7 +4197,7 @@ mapping:
         required: false
         desc: |
           Configuration for AI inference services used by agents and visualization plugins.
-          Supports per-agent or per-plugin model, temperature, max_tokens, api_key, api_base_url, and enabled settings.
+          Supports per-agent or per-plugin model, temperature, max_tokens, retries, api_key, api_base_url, and enabled settings.
           Valid keys include agent types (e.g. router, error_analysis) and plugin names (e.g. jupyterlite).
           Agents and plugins inherit from 'default' configuration, which itself falls back to global ai_model/ai_api_key settings.
           All agents are enabled by default.
@@ -4208,6 +4208,11 @@ mapping:
           Per-agent or default-block ``structured_output_override: true|false``
           beats the model capability table -- see ``agent_model_capabilities_file``
           for the table's location and contents.
+          Per-agent or default-block ``retries`` sets the pydantic-ai retry budget
+          (tool calls and output validation); it defaults to 3. Raise it if a model
+          intermittently fails to produce conforming output ("Exceeded maximum output
+          retries"); custom_tool's producer defaults to 0 since it runs its own
+          reflection loop.
 
       agent_model_capabilities_file:
         type: str
diff --git a/test/unit/app/test_agents.py b/test/unit/app/test_agents.py
index b808c16a301..427fb6d8a51 100644
--- a/test/unit/app/test_agents.py
+++ b/test/unit/app/test_agents.py
@@ -46,6 +46,7 @@ from pydantic_ai.messages import (
     TextPart,
     UserPromptPart,
 )
+from pydantic_ai.models.function import FunctionModel
 from pydantic_ai.models.test import TestModel
 
 from galaxy.agents import (
@@ -158,6 +159,57 @@ class TestAgentUnitMocked:
         assert router_agent._get_agent_config("temperature", 0.5) == 0.5
         assert router_agent._get_agent_config("max_tokens", 1500) == 1500
 
+    def test_get_retries_resolution(self):
+        # Unset -> builtin default (bumped above pydantic-ai's default of 1).
+        self.mock_config.inference_services = None
+        router = QueryRouterAgent(self.deps)
+        assert router._get_retries() == agents_base.BaseGalaxyAgent.DEFAULT_AGENT_RETRIES == 3
+        # A caller-supplied default wins over the builtin when the key is unset
+        # (custom_tool's producer relies on this to keep its reflection-loop 0).
+        assert router._get_retries(default=0) == 0
+
+        # default entry applies to every agent; a per-agent entry overrides it.
+        # String values from YAML are coerced to int.
+        self.mock_config.inference_services = {
+            "default": {"retries": "4"},
+            "router": {"retries": 2},
+        }
+        assert QueryRouterAgent(self.deps)._get_retries() == 2
+        error_retries = ErrorAnalysisAgent(self.deps)._get_retries()
+        assert error_retries == 4 and isinstance(error_retries, int)
+
+    def test_configured_retries_wired_into_agent(self):
+        # The configured budget reaches the constructed pydantic-ai Agent
+        # (both tool and output budgets, via Agent(retries=N)).
+        self.mock_config.inference_services = {"default": {"retries": 4}}
+        router = QueryRouterAgent(self.deps)
+        assert router.agent._max_output_retries == 4
+        assert router.agent._max_tool_retries == 4
+
+        # custom_tool's producer keeps its reflection-loop default of 0 when unconfigured.
+        self.mock_config.inference_services = None
+        producer = CustomToolAgent(self.deps)
+        assert producer.agent._max_output_retries == 0
+
+    @pytest.mark.asyncio
+    async def test_router_falls_back_on_output_retry_exhaustion(self):
+        # When the model never produces a valid structured output, pydantic-ai
+        # raises UnexpectedModelBehavior after exhausting the output-retry budget.
+        # The router must degrade to its graceful fallback rather than propagate.
+        self.mock_config.inference_services = None
+        router = QueryRouterAgent(self.deps)
+
+        # Empty response (not text): str is in the router's output_type union, so
+        # any text would succeed via the str branch and never trigger a retry.
+        def empty_response(messages, info):
+            return ModelResponse(parts=[])
+
+        with router.agent.override(model=FunctionModel(empty_response)):
+            response = await router.process("Summarize my history")
+
+        assert isinstance(response, AgentResponse)
+        assert "unavailable" in response.content.lower()
+
     @pytest.mark.asyncio
     async def test_custom_tool_agent_structured_output(self):
         # Test with a model that supports structured output (gpt-4o)

From efa5e9b233485b2f16d1227146bcc766910291f1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 11 Jun 2026 17:26:54 -0400
Subject: [PATCH 098/256] Harden agent retries config resolution

Two follow-ups on the configurable-retries change. A shared `default` block
`retries` was silently overriding custom_tool's producer-0, which would
re-enable pydantic-ai's generic retry loop inside the producer's own reflection
loop. The producer's 0 is a correctness requirement, not a tunable, so it now
honors only an explicit `custom_tool.retries` and ignores the default block.
Separately, a non-numeric or blank `retries` value used to blow up with a bare
TypeError/ValueError at agent construction -- which the manager mistook for an
unknown-agent fallback and double-faulted on -- so it now raises a clear
ConfigurationError.
---
 doc/source/admin/galaxy_options.rst         |  6 ++--
 lib/galaxy/agents/base.py                   | 36 +++++++++++++++++++--
 lib/galaxy/config/sample/galaxy.yml.sample  |  6 ++--
 lib/galaxy/config/schemas/config_schema.yml |  5 +--
 test/unit/app/test_agents.py                | 32 ++++++++++++++++++
 5 files changed, 76 insertions(+), 9 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index b64062ec8cd..5dd5ccf20ec 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -5688,8 +5688,10 @@
     ``retries`` sets the pydantic-ai retry budget (tool calls and
     output validation); it defaults to 3. Raise it if a model
     intermittently fails to produce conforming output ("Exceeded
-    maximum output retries"); custom_tool's producer defaults to 0
-    since it runs its own reflection loop.
+    maximum output retries"). custom_tool's producer keeps a budget of
+    0 because it runs its own reflection loop; a shared ``default``
+    block does not change that -- set ``custom_tool.retries``
+    explicitly to override it.
 :Default: ``None``
 :Type: any
 
diff --git a/lib/galaxy/agents/base.py b/lib/galaxy/agents/base.py
index fa38b184fcb..d69d02b6996 100644
--- a/lib/galaxy/agents/base.py
+++ b/lib/galaxy/agents/base.py
@@ -29,6 +29,7 @@ from typing import (
 
 import yaml
 
+from galaxy.exceptions import ConfigurationError
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.model import User
 from galaxy.schema.agents import (
@@ -817,6 +818,19 @@ class BaseGalaxyAgent(ABC):
                 return self.deps.config.ai_api_base_url
         return default
 
+    def _get_agent_specific_config(self, key: str, default: Any = None) -> Any:
+        """Read a value only from this agent's own ``inference_services`` block.
+
+        Unlike :meth:`_get_agent_config`, this skips the shared ``default`` block so a
+        caller-pinned builtin is overridden only by an explicit per-agent entry.
+        """
+        inference_config = getattr(self.deps.config, "inference_services", {})
+        if isinstance(inference_config, dict):
+            agent_specific = inference_config.get(self.agent_type, {})
+            if isinstance(agent_specific, dict) and key in agent_specific:
+                return agent_specific[key]
+        return default
+
     def _get_model_name(self) -> str:
         return self._get_agent_config("model", "gpt-4o-mini")
 
@@ -864,10 +878,26 @@ class BaseGalaxyAgent(ABC):
     def _get_retries(self, default: Optional[int] = None) -> int:
         """Retry budget for the agent's pydantic-ai ``Agent(retries=...)``.
 
-        ``default`` lets a caller override the builtin (e.g. custom_tool's producer
-        keeps 0 so its own reflection loop owns the retry).
+        With no ``default``, the budget resolves per-agent > ``default`` block >
+        builtin (:attr:`DEFAULT_AGENT_RETRIES`). A caller-pinned ``default`` (e.g.
+        custom_tool's producer keeps 0 so its own reflection loop owns the retry) is
+        a correctness requirement, not a tunable: only an explicit per-agent
+        ``retries`` overrides it -- a shared ``default`` block must not silently
+        re-enable pydantic-ai retries there.
         """
-        return int(self._get_agent_config("retries", self.DEFAULT_AGENT_RETRIES if default is None else default))
+        if default is None:
+            raw = self._get_agent_config("retries", self.DEFAULT_AGENT_RETRIES)
+        else:
+            raw = self._get_agent_specific_config("retries", default)
+        try:
+            retries = int(raw)
+        except (TypeError, ValueError):
+            retries = None
+        if retries is None or retries < 0:
+            raise ConfigurationError(
+                f"inference_services 'retries' for agent '{self.agent_type}' must be a non-negative integer, got {raw!r}"
+            )
+        return retries
 
     async def _call_agent_from_tool(
         self,
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 5e470624224..ab22fbd2ec4 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -3084,8 +3084,10 @@ galaxy:
   # ``retries`` sets the pydantic-ai retry budget (tool calls and output
   # validation); it defaults to 3. Raise it if a model intermittently
   # fails to produce conforming output ("Exceeded maximum output
-  # retries"); custom_tool's producer defaults to 0 since it runs its
-  # own reflection loop.
+  # retries"). custom_tool's producer keeps a budget of 0 because it
+  # runs its own reflection loop; a shared ``default`` block does not
+  # change that -- set ``custom_tool.retries`` explicitly to override
+  # it.
   #inference_services: null
 
   # YAML file with capability hints for agent inference models. Maps
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index 9f05a1b0b32..9758ae5afda 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -4211,8 +4211,9 @@ mapping:
           Per-agent or default-block ``retries`` sets the pydantic-ai retry budget
           (tool calls and output validation); it defaults to 3. Raise it if a model
           intermittently fails to produce conforming output ("Exceeded maximum output
-          retries"); custom_tool's producer defaults to 0 since it runs its own
-          reflection loop.
+          retries"). custom_tool's producer keeps a budget of 0 because it runs its
+          own reflection loop; a shared ``default`` block does not change that -- set
+          ``custom_tool.retries`` explicitly to override it.
 
       agent_model_capabilities_file:
         type: str
diff --git a/test/unit/app/test_agents.py b/test/unit/app/test_agents.py
index 427fb6d8a51..8d918632e89 100644
--- a/test/unit/app/test_agents.py
+++ b/test/unit/app/test_agents.py
@@ -84,6 +84,7 @@ from galaxy.agents.page_assistant import (
     FullReplacementEdit,
     SectionPatchEdit,
 )
+from galaxy.exceptions import ConfigurationError
 from galaxy.schema.agents import ConfidenceLevel
 from galaxy.tool_util_models import UserToolSource
 from galaxy.util.unittest_utils import pytestmark_live_llm
@@ -191,6 +192,37 @@ class TestAgentUnitMocked:
         producer = CustomToolAgent(self.deps)
         assert producer.agent._max_output_retries == 0
 
+    def test_producer_retries_default_ignores_default_block(self):
+        # custom_tool's producer pins retries=0 so its own reflection loop owns
+        # the retry. A shared `default` block must NOT silently re-enable
+        # pydantic-ai retries there -- only an explicit per-agent entry may.
+        producer = CustomToolAgent(self.deps)
+
+        self.mock_config.inference_services = {"default": {"retries": 5}}
+        assert producer._get_retries(default=0) == 0
+        # The normal (critic) lookup still honors the default block.
+        assert producer._get_retries() == 5
+
+        # An explicit custom_tool entry still overrides the pinned builtin.
+        self.mock_config.inference_services = {"custom_tool": {"retries": 7}}
+        assert producer._get_retries(default=0) == 7
+
+    def test_invalid_retries_config_raises_configuration_error(self):
+        # Non-numeric, blank, or negative `retries` is operator misconfiguration;
+        # it must surface as a clear ConfigurationError rather than a bare
+        # TypeError/ValueError (which the manager mistakes for an unknown-agent
+        # fallback) or a silently-broken negative budget that fails every request.
+        router = QueryRouterAgent(self.deps)
+
+        for bad in ("three", None, -1):
+            self.mock_config.inference_services = {"default": {"retries": bad}}
+            with pytest.raises(ConfigurationError, match="retries"):
+                router._get_retries()
+
+        # 0 is valid (custom_tool's producer relies on it) and must not raise.
+        self.mock_config.inference_services = {"default": {"retries": 0}}
+        assert router._get_retries() == 0
+
     @pytest.mark.asyncio
     async def test_router_falls_back_on_output_retry_exhaustion(self):
         # When the model never produces a valid structured output, pydantic-ai

From a4b5fc884339e2d42c94f0e2d5382950f4c42ff6 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 12 Jun 2026 16:52:43 -0500
Subject: [PATCH 099/256] [26.1] Fix sharing pages impossible due to incorrect
 `reports/sharing` route

Fixes https://github.com/galaxyproject/galaxy/issues/22481
---
 client/src/entry/analysis/router.js | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 116f96825f6..c70d4c18642 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -466,6 +466,7 @@ export function getRouter(Galaxy) {
                             historyId: route.params.historyId,
                             pageId: route.params.pageId,
                             displayOnly: route.query.displayOnly === "true",
+                            invocationId: route.query.invocation_id,
                         }),
                     },
                     {
@@ -588,8 +589,8 @@ export function getRouter(Galaxy) {
                         component: Sharing,
                         props: (route) => ({
                             id: route.query.id,
-                            pluralName: "Reports",
-                            modelClass: "Report",
+                            pluralName: "Pages",
+                            modelClass: "Page",
                         }),
                     },
                     {

From 5c3a592304e8c893b57315d7d98fd30f059c8c05 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 13 Jun 2026 10:04:08 -0400
Subject: [PATCH 100/256] Fix upload_file_from_url passing decoded id to
 FetchDataPayload

FetchDataPayload.history_id is a DecodedDatabaseIdField, which expects
the encoded id string and decodes it itself. upload_file_from_url was
pre-decoding history_id to an int, tripping the field's isinstance(str)
validator and failing every call. Pass the encoded id straight through,
matching invoke_workflow's handling of the same field type.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/agents/operations.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/agents/operations.py b/lib/galaxy/agents/operations.py
index 2270f297660..ebdb3f9105e 100644
--- a/lib/galaxy/agents/operations.py
+++ b/lib/galaxy/agents/operations.py
@@ -424,9 +424,8 @@ class AgentOperationsManager:
         dbkey: str = "?",
         file_name: str | None = None,
     ) -> dict[str, Any]:
-        decoded_history_id = self.trans.security.decode_id(history_id)
         fetch_payload = FetchDataPayload(
-            history_id=decoded_history_id,
+            history_id=history_id,
             targets=[
                 DataElementsTarget(
                     destination=HdaDestination(type="hdas"),

From 4d2af263d32da9480b47ff2cd971471f2cd00310 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sat, 13 Jun 2026 13:36:08 -0400
Subject: [PATCH 101/256] Route IWC workflow imports to the tool recommendation
 agent

The router had no home for "import an IWC workflow" -- there's no import
handoff, and import_workflow_from_iwc only exists on the operations/MCP side,
not as an in-app tool. So the request scattered: on gpt-oss-120b (the demo/test
model) "import a histological staining workflow from IWC" landed on the plain
router 4 times out of 5 and answered with a how-to essay instead of surfacing
anything importable. tool_recommendation already searches the IWC catalog and
emits a WORKFLOW_IMPORT action for what it finds, so point the router there for
IWC import asks via both the prompt and the handoff docstring -- and widen the
handoff summary/arg, which still described it as tools-only. Also fixes the
stale routing eval case that expected router. With this the imperative
"import..." prompts route to tool_recommendation 5/5.
---
 lib/galaxy/agents/prompts/router.md | 2 ++
 lib/galaxy/agents/router.py         | 7 ++++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/agents/prompts/router.md b/lib/galaxy/agents/prompts/router.md
index d4f4d7ee518..8e46a28dce6 100644
--- a/lib/galaxy/agents/prompts/router.md
+++ b/lib/galaxy/agents/prompts/router.md
@@ -99,6 +99,7 @@ English. If the request really wants analysis (e.g. "summarize my history",
 - Wants to find/discover tools ("Is there a tool that converts BAM to FASTQ?")
 - Needs help choosing between tools for an analysis type
 - Asks "what tools are available for X?"
+- Asks to import or find a workflow from IWC for an analysis ("import an IWC workflow for X", "is there an IWC workflow for X I can import?") -- it searches the IWC catalog and surfaces an import action; there is no separate import handoff
 
 **Use `hand_off_to_error_analysis`** when user PROVIDES specific error details:
 
@@ -158,6 +159,7 @@ Key pattern: If user needs to FIND something (job, dataset, history) before anal
 
 - "What tool should I use for X?" → Use hand_off_to_tool_recommendation
 - "Is there a tool that does X?" → Use hand_off_to_tool_recommendation
+- "Import an IWC workflow for X" → Use hand_off_to_tool_recommendation (surfaces the workflow + import action)
 - "How do I use tool X?" → Answer directly (usage help)
 - "What parameters does X need?" → Answer directly (usage help)
 - "Create a tool that does X" → Use hand_off_to_custom_tool
diff --git a/lib/galaxy/agents/router.py b/lib/galaxy/agents/router.py
index 245337d38dc..5fde7c300fb 100644
--- a/lib/galaxy/agents/router.py
+++ b/lib/galaxy/agents/router.py
@@ -5,7 +5,7 @@ Uses pydantic-ai output functions to either:
 - Answer general Galaxy questions directly (returns str)
 - Hand off to error_analysis for job debugging
 - Hand off to custom_tool for explicit tool creation requests
-- Hand off to tool_recommendation for tool discovery
+- Hand off to tool_recommendation for tool and IWC workflow discovery
 - Hand off to gtn_training for tutorial and learning requests
 
 Also exposes a small set of @agent.tool fast-path tools for read-only browsing
@@ -330,13 +330,14 @@ class QueryRouterAgent(BaseGalaxyAgent):
             ctx: RunContext[GalaxyAgentDependencies],
             query: str,
         ) -> str:
-            """Route to tool recommendation agent for finding Galaxy tools.
+            """Route to tool recommendation agent for finding Galaxy tools and IWC workflows.
 
             Use this when the user:
             - Asks what tool to use for a task ("what tool aligns reads?")
             - Wants to find tools for a specific analysis type
             - Needs help discovering available tools
             - Asks "is there a tool that does X?"
+            - Asks to import or find a workflow from IWC for an analysis (it searches IWC and surfaces an import action)
 
             Do NOT use for:
             - How to USE a specific tool (answer directly)
@@ -344,7 +345,7 @@ class QueryRouterAgent(BaseGalaxyAgent):
             - Job errors (use hand_off_to_error_analysis)
 
             Args:
-                query: The tool discovery question
+                query: The tool or workflow discovery question
             """
             return await self._execute_handoff(ctx, AgentType.TOOL_RECOMMENDATION, query)
 

From 1308690b33b4aeb6bb833c3a5c482f80ec906703 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sat, 13 Jun 2026 13:36:09 -0400
Subject: [PATCH 102/256] Add IWC routing regression cases

Pin the routing for IWC-related asks so a model or prompt change that breaks
it gets caught. Both phrasings -- the imperative "import a workflow from IWC"
and the "recommend an IWC workflow for X" discovery ask -- should route to
tool_recommendation, which owns IWC search and surfaces an importable workflow
plus an import action. Flips the existing import_iwc_workflow expectation to
match and adds a recommendation-phrasing case.
---
 test/evals/datasets/routing.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/test/evals/datasets/routing.py b/test/evals/datasets/routing.py
index 4484d27f146..455902f0110 100644
--- a/test/evals/datasets/routing.py
+++ b/test/evals/datasets/routing.py
@@ -194,8 +194,8 @@ ROUTING_CASES: list[Case[str, str, dict[str, Any]]] = [
     _case(
         "import_iwc_workflow",
         "Import a histological staining workflow from IWC.",
-        "router",
-        "Router-direct action. On agent-ops-iwc-reintroduce this triggers search_iwc_workflows + import_workflow_from_iwc tool calls.",
+        "tool_recommendation",
+        "tool_recommendation owns IWC search (search_iwc_workflows) and emits a WORKFLOW_IMPORT action for the surfaced workflow; no in-app agent calls import_workflow_from_iwc directly.",
     ),
     _case(
         "omero_upload_guidance",
@@ -223,6 +223,12 @@ ROUTING_CASES: list[Case[str, str, dict[str, Any]]] = [
         "custom_tool",
         "Explicit custom_tool request -- writing a tool wrapper, not running an existing one.",
     ),
+    _case(
+        "recommend_iwc_workflow",
+        "Recommend an IWC workflow for histological staining quantification.",
+        "tool_recommendation",
+        "Recommendation-style IWC ask -- discovery phrasing routes to tool_recommendation, which searches IWC and surfaces an importable workflow.",
+    ),
 ]
 
 

From bd1ab4cd3e8fe16ca7a8df129011c32b42b4552a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 13 Jun 2026 20:10:06 +0200
Subject: [PATCH 103/256] Enforce color format in JSON schema tests via
 FormatChecker

Register a "color" format checker backed by pydantic_extra_types.Color so
that format: "color" is actually validated in Draft202012Validator. This
removes the _json_schema_skip workaround from gx_color and adds 'foobar'
to request_invalid and 'red' to request_valid to reflect the full range
accepted by the color validator.
---
 test/unit/tool_util/parameter_specification.yml |  5 ++---
 .../test_parameter_specification_json_schema.py | 17 ++++++++++++++++-
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
index ca475a8c3e7..0aabb1056d6 100644
--- a/test/unit/tool_util/parameter_specification.yml
+++ b/test/unit/tool_util/parameter_specification.yml
@@ -1234,9 +1234,11 @@ gx_color:
    - parameter: '#aabbcc'
    - parameter: '#000000'
    - parameter: '#abcd'
+   - parameter: 'red'
   request_invalid:
    - parameter: null
    - parameter: {}
+   - parameter: 'foobar'
   workflow_step_valid:
    - parameter: '#aabbcc'
    - parameter: '#000000'
@@ -1253,9 +1255,6 @@ gx_color:
     - parameter: 'foobar'
     - parameter: 5
     - parameter: {__class__: 'ConnectedValue2'}
-  _json_schema_skip:
-    workflow_step_invalid: "color validator uses AfterValidator"
-    workflow_step_linked_invalid: "color validator uses AfterValidator"
 
 gx_data:
   request_valid:
diff --git a/test/unit/tool_util/test_parameter_specification_json_schema.py b/test/unit/tool_util/test_parameter_specification_json_schema.py
index 2a4c30590a0..7cc1aab90a4 100644
--- a/test/unit/tool_util/test_parameter_specification_json_schema.py
+++ b/test/unit/tool_util/test_parameter_specification_json_schema.py
@@ -22,8 +22,10 @@ from typing import (
 )
 
 import jsonschema
+import jsonschema.exceptions
 import pytest
 import yaml
+from pydantic_extra_types.color import Color as _Color
 
 pytestmark = pytest.mark.skipif(
     sys.version_info < (3, 9), reason="jsonschema<4.24 on Python 3.8 mishandles additionalProperties in anyOf"
@@ -72,8 +74,21 @@ def _json_schema_for(bundle: ToolParameterBundleModel, state_representation: Sta
     return to_json_schema(model)
 
 
+_FORMAT_CHECKER = jsonschema.FormatChecker()
+
+
+@_FORMAT_CHECKER.checks("color", raises=jsonschema.exceptions.FormatError)
+def _check_color_format(value: object) -> bool:
+    if isinstance(value, str):
+        try:
+            _Color(value)
+        except Exception as e:
+            raise jsonschema.exceptions.FormatError(f"{value!r} is not a valid color", cause=e)
+    return True
+
+
 def _json_schema_validates(schema: Dict[str, Any], state_dict: RawStateDict) -> bool:
-    validator = jsonschema.Draft202012Validator(schema)
+    validator = jsonschema.Draft202012Validator(schema, format_checker=_FORMAT_CHECKER)
     errors = list(validator.iter_errors(state_dict))
     return len(errors) == 0
 

From 5efb77b18a250e0ee37376ab2bd13a3e0bd54ffb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 08:54:39 +0200
Subject: [PATCH 104/256] Tighten pydantic-ai lower bound to >=1.99.0 in
 galaxy-app package

The package declared pydantic-ai>=0.1.16, so CI could resolve 1.44.0
where Agent._max_output_retries was still named _max_result_retries,
breaking test_configured_retries_wired_into_agent. Pin to >=1.99.0 to
match what requirements.txt already pins.
---
 packages/app/setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
index 87c5e1ffbeb..e56f8f0c182 100644
--- a/packages/app/setup.cfg
+++ b/packages/app/setup.cfg
@@ -49,7 +49,7 @@ install_requires =
     pebble
     pulsar-galaxy-lib>=0.15.0.dev0
     pydantic>=2.7.4
-    pydantic-ai>=0.1.16
+    pydantic-ai>=1.99.0
     pysam>=0.21
     python-slugify
     PyJWT

From e42f5598aaf7a527042a5712f9de8584f55d25fe Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 14:43:36 -0500
Subject: [PATCH 105/256] [26.1] Make unowned but accessible pages uneditable

---
 lib/galaxy/managers/pages.py      | 2 +-
 lib/galaxy_test/api/test_pages.py | 7 +++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index a961188a6e6..42519e99244 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -345,7 +345,7 @@ class PageManager(sharable.SharableModelManager[model.Page], UsesAnnotations):
         page = trans.sa_session.get(model.Page, id)
         if not page:
             raise exceptions.ObjectNotFound("Page not found")
-        page = base.security_check(trans, page, check_ownership=False, check_accessible=True)
+        page = base.security_check(trans, page, check_ownership=True, check_accessible=True)
 
         # Validate slug changes (only for non-history pages)
         if payload.slug is not None and payload.slug != page.slug:
diff --git a/lib/galaxy_test/api/test_pages.py b/lib/galaxy_test/api/test_pages.py
index 93c86c95266..077fbe9a305 100644
--- a/lib/galaxy_test/api/test_pages.py
+++ b/lib/galaxy_test/api/test_pages.py
@@ -498,6 +498,13 @@ steps:
         show_json = show_response.json()
         assert show_json["annotation"] == "newannotation"
 
+    def test_update_as_other_user(self):
+        response_json = self._create_valid_page_with_slug("pagetoupdateasother")
+        page_id = response_json["id"]
+        with self._different_user():
+            update_response = self._update_page(page_id, "newannotation", "newslug", "newtitle", error_code=403)
+            assert update_response["err_msg"] == "Page is not owned by the current user"
+
     def test_403_on_unowner_show(self):
         response_json = self._create_valid_page_as("others_page_show@bx.psu.edu", "otherspageshow")
         show_response = self._get(f"pages/{response_json['id']}")

From 67a5eee24e6f76e3b92111c443d1fd90c9fd915d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 14 Jun 2026 16:08:17 -0400
Subject: [PATCH 106/256] Keep collection-operation outputs as workflow steps
 in extraction

Extract Dataset output is an HDA that carries copied_from its source
element *and* its own creating job. _original_hda walked copied_from
unconditionally, so the history summary attributed the output to the
source element's creating job and dropped the Extract Dataset step. For
the classic HID path this is fatal: selecting the Extract Dataset job
raises "job not connected to current history" and extraction returns 500.

Stop walking copied_from when the content has its own
creating_job_associations: a passive copy has none and still normalizes;
a collection-operation output has one and is kept as a real step. Apply
the same guard to _original_hdca for consistency - a collection copied
with its own creating job (e.g. via history reimport) should likewise not
normalize past itself.

Add a red->green API test for the HID path (extract a dataset element,
then consume it) and a by-ids regression guard (already green there - the
by-ids closure normalizes copied_from symmetrically).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/workflow/extract.py                | 12 ++-
 .../api/test_workflow_extraction.py           | 96 ++++++++++++++++++-
 2 files changed, 102 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index f2acd3e2e80..80081853dfb 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -713,13 +713,21 @@ def step_inputs_by_id(trans: ProvidesHistoryContext, job: Job) -> tuple[ToolInpu
 
 
 def _original_hda(hda: HistoryDatasetAssociation) -> HistoryDatasetAssociation:
-    while hda.copied_from_history_dataset_association:
+    # Follow plain copies back to their source, but stop at anything with its own
+    # creating job: collection-operation tools (Extract Dataset, Filter, Relabel,
+    # ...) produce a copy *and* record a job, and those are real workflow steps -
+    # normalizing past them would attribute the output to its source and drop the
+    # operation from the extracted workflow.
+    while hda.copied_from_history_dataset_association and not hda.creating_job_associations:
         hda = hda.copied_from_history_dataset_association
     return hda
 
 
 def _original_hdca(hdca: HistoryDatasetCollectionAssociation) -> HistoryDatasetCollectionAssociation:
-    while hdca.copied_from_history_dataset_collection_association:
+    # Same creating-job guard as _original_hda (see there for the rationale): a
+    # collection that records its own creating job - e.g. reimported with its job
+    # association - is a real step and must not normalize past copied_from.
+    while hdca.copied_from_history_dataset_collection_association and not hdca.creating_job_associations:
         hdca = hdca.copied_from_history_dataset_collection_association
     return hdca
 
diff --git a/lib/galaxy_test/api/test_workflow_extraction.py b/lib/galaxy_test/api/test_workflow_extraction.py
index a5cd72569e4..392d44099de 100644
--- a/lib/galaxy_test/api/test_workflow_extraction.py
+++ b/lib/galaxy_test/api/test_workflow_extraction.py
@@ -11,6 +11,7 @@ from json import (
 )
 from typing import (
     Any,
+    Optional,
     TYPE_CHECKING,
 )
 
@@ -29,6 +30,13 @@ if TYPE_CHECKING:
     from requests import Response
 
 
+def _connection_step_id(connection: Any) -> int:
+    # .ga format may yield a single dict or a list of one dict.
+    if isinstance(connection, list):
+        connection = connection[0]
+    return connection["id"]
+
+
 class _ExtractionHelpersMixin:
     """Shared helpers for HID-based and ID-based workflow extraction tests."""
 
@@ -43,6 +51,53 @@ class _ExtractionHelpersMixin:
 
         def _assert_status_code_is(self, response: "Response", expected_status_code: int) -> None: ...
 
+        def assert_steps_of_type(
+            self, workflow: dict[str, Any], step_type: str, expected_len: Optional[int] = None
+        ) -> list[dict[str, Any]]: ...
+
+    def _setup_extract_dataset_then_cat(self, history_id):
+        """Build a list, extract its first element, and feed the result to cat1.
+
+        The __EXTRACT_DATASET__ output is an HDA copied_from the source element
+        *and* carrying its own creating job - the shape that must stay a real
+        workflow step. Returns (input_hdca, extract_job_id, cat_job_id).
+        """
+        hdca = self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["a\nb\n", "c\nd\n"], wait=True
+        ).json()["outputs"][0]
+        extract_run = self.dataset_populator.run_tool(
+            tool_id="__EXTRACT_DATASET__",
+            inputs={"input": {"src": "hdca", "id": hdca["id"]}, "which|which_dataset": "first"},
+            history_id=history_id,
+        )
+        extract_job_id = extract_run["jobs"][0]["id"]
+        extracted = extract_run["outputs"][0]
+        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        cat_run = self.dataset_populator.run_tool(
+            tool_id="cat1",
+            inputs={"input1": {"src": "hda", "id": extracted["id"]}},
+            history_id=history_id,
+        )
+        cat_job_id = cat_run["jobs"][0]["id"]
+        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        return hdca, extract_job_id, cat_job_id
+
+    def _assert_extract_dataset_step_kept(self, downloaded):
+        """Assert the Extract Dataset operation survived as its own tool step:
+        fed by the collection input and feeding the cat1 consumer. Normalizing
+        past copied_from would drop it and leave cat1 input-less.
+        """
+        collection_step = self.assert_steps_of_type(downloaded, "data_collection_input", expected_len=1)[0]
+        tool_steps = self.assert_steps_of_type(downloaded, "tool", expected_len=2)
+        extract_step = next((s for s in tool_steps if s.get("tool_id") == "__EXTRACT_DATASET__"), None)
+        cat_step = next((s for s in tool_steps if s.get("tool_id") == "cat1"), None)
+        assert extract_step is not None, f"Extract Dataset step missing: {[s.get('tool_id') for s in tool_steps]}"
+        assert cat_step is not None, f"cat1 step missing: {[s.get('tool_id') for s in tool_steps]}"
+        extract_connections = extract_step["input_connections"]
+        cat_connections = cat_step["input_connections"]
+        assert _connection_step_id(extract_connections["input"]) == collection_step["id"], extract_connections
+        assert _connection_step_id(cat_connections["input1"]) == extract_step["id"], cat_connections
+
     def _run_tool_get_collection_and_job_id(self, history_id, tool_id, inputs):
         run = self.dataset_populator.run_tool(tool_id=tool_id, inputs=inputs, history_id=history_id)
         implicit_hdca = run["implicit_collections"][0]
@@ -587,6 +642,24 @@ test_data:
             tool_ids=tool_ids,
         )
 
+    @skip_without_tool("__EXTRACT_DATASET__")
+    @skip_without_tool("cat1")
+    @summarize_instance_history_on_error
+    def test_extract_keeps_extract_dataset_operation_step(self, history_id):
+        """Extract Dataset output carries copied_from (the source element) *and*
+        its own creating job. The summary must attribute the output to the
+        Extract Dataset job and keep it as a real step, not normalize past
+        copied_from back to the source element's creating job - which drops the
+        operation step and leaves the downstream consumer input-less.
+        """
+        hdca, extract_job_id, cat_job_id = self._setup_extract_dataset_then_cat(history_id)
+        downloaded_workflow = self._extract_and_download_workflow(
+            history_id,
+            dataset_collection_ids=[hdca["hid"]],
+            job_ids=[extract_job_id, cat_job_id],
+        )
+        self._assert_extract_dataset_step_kept(downloaded_workflow)
+
     def __run_random_lines_mapped_over_singleton(self, history_id):
         hdca = self.dataset_collection_populator.create_list_in_history(history_id, contents=["1 2 3\n4 5 6"]).json()
         hdca_id = hdca["id"]
@@ -745,15 +818,30 @@ class TestWorkflowExtractionByIdsApi(_ExtractionHelpersMixin, BaseWorkflowsApiTe
         assert len(input_steps) == 1 and len(tool_steps) == 1
         if expected_tool_id is not None:
             assert tool_steps[0]["tool_id"] == expected_tool_id
-        connection = tool_steps[0]["input_connections"]["input1"]
-        # .ga format may yield a single dict or a list of one dict.
-        connection = connection[0] if isinstance(connection, list) else connection
-        assert connection["id"] == input_steps[0]["id"]
+        assert _connection_step_id(tool_steps[0]["input_connections"]["input1"]) == input_steps[0]["id"]
 
     def _assert_extract_rejected(self, payload, allowed_codes):
         response = self._post("workflows/extract", data=payload, json=True)
         assert response.status_code in allowed_codes, response.text
 
+    @skip_without_tool("__EXTRACT_DATASET__")
+    @skip_without_tool("cat1")
+    @summarize_instance_history_on_error
+    def test_extract_keeps_extract_dataset_operation_step_by_ids(self, history_id):
+        """ID-path sibling of the HID Extract Dataset operation-step test.
+
+        The by-ids closure normalizes copied_from symmetrically on both output
+        registration and input lookup, so this scenario already wires correctly
+        here - it is a regression guard ensuring the copied_from/creating-job
+        change keeps the Extract Dataset step connected, not a red->green proof.
+        """
+        hdca, extract_job_id, cat_job_id = self._setup_extract_dataset_then_cat(history_id)
+        downloaded = self._extract_and_download_workflow_by_ids(
+            hdca_ids=[hdca["id"]],
+            job_ids=[extract_job_id, cat_job_id],
+        )
+        self._assert_extract_dataset_step_kept(downloaded)
+
     @skip_without_tool("cat1")
     @summarize_instance_history_on_error
     def test_extract_with_hda_ids(self, history_id):

From 0571e2089bd21db57aa6d72d57eb06d6052d6431 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 14 Jun 2026 19:31:51 -0400
Subject: [PATCH 107/256] Add tests for GButton disabled title and click
 behavior

Covers title resolution for the enabled and disabled states, the fallback to the regular title when no disabled title is given, that a disabled button stays hoverable via aria-disabled instead of the native disabled attribute, and that it doesn't emit click while disabled.
---
 .../components/BaseComponents/GButton.test.ts | 67 +++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 client/src/components/BaseComponents/GButton.test.ts

diff --git a/client/src/components/BaseComponents/GButton.test.ts b/client/src/components/BaseComponents/GButton.test.ts
new file mode 100644
index 00000000000..f23595e3046
--- /dev/null
+++ b/client/src/components/BaseComponents/GButton.test.ts
@@ -0,0 +1,67 @@
+import { getLocalVue } from "@tests/vitest/helpers";
+import { mount } from "@vue/test-utils";
+import { describe, expect, it } from "vitest";
+
+import GButton from "./GButton.vue";
+
+const localVue = getLocalVue(true);
+
+function mountGButton(props: object) {
+    return mount(GButton as object, { propsData: props, localVue });
+}
+
+describe("GButton.vue", () => {
+    it("uses the regular title when enabled", () => {
+        const wrapper = mountGButton({ title: "Click me" });
+        const button = wrapper.get("button");
+
+        expect(button.attributes("title")).toBe("Click me");
+        expect(button.attributes("data-title")).toBe("Click me");
+    });
+
+    it("uses the disabled title when disabled", () => {
+        const wrapper = mountGButton({
+            disabled: true,
+            title: "Click me",
+            disabledTitle: "Cannot click right now",
+        });
+        const button = wrapper.get("button");
+
+        expect(button.attributes("title")).toBe("Cannot click right now");
+        expect(button.attributes("data-title")).toBe("Cannot click right now");
+    });
+
+    it("falls back to the regular title when disabled without a disabled title", () => {
+        const wrapper = mountGButton({ disabled: true, title: "Click me" });
+        const button = wrapper.get("button");
+
+        expect(button.attributes("title")).toBe("Click me");
+    });
+
+    // A disabled button must stay hoverable so the (disabled) title can surface its
+    // tooltip. We mark it disabled via aria-disabled and a JS click guard rather than
+    // the native `disabled` attribute (which would suppress hover events).
+    it("remains hoverable when disabled", () => {
+        const wrapper = mountGButton({ disabled: true, disabledTitle: "Nope" });
+        const button = wrapper.get("button");
+
+        expect(button.attributes("aria-disabled")).toBe("true");
+        expect(button.attributes("disabled")).toBeUndefined();
+    });
+
+    it("does not emit click when disabled", async () => {
+        const wrapper = mountGButton({ disabled: true, disabledTitle: "Nope" });
+
+        await wrapper.get("button").trigger("click");
+
+        expect(wrapper.emitted("click")).toBeUndefined();
+    });
+
+    it("emits click when enabled", async () => {
+        const wrapper = mountGButton({ title: "Click me" });
+
+        await wrapper.get("button").trigger("click");
+
+        expect(wrapper.emitted("click")).toHaveLength(1);
+    });
+});

From 7db6679d6aa362987e724719f41c29e0294df50f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 14 Jun 2026 19:32:03 -0400
Subject: [PATCH 108/256] Show GButton disabled title by dropping
 pointer-events: none

A disabled GButton set pointer-events: none in CSS, which stops the browser from ever registering hover over the element -- so neither the native title nor the GTooltip ever appeared, and the disabledTitle never showed. Clicks and routing are already blocked in JS (onClick guards on the disabled prop, and the to/href bindings are cleared when disabled), so the rule was only belt-and-suspenders and wasn't actually needed. Dropping it lets the disabled title surface on hover again while the disabled styling stays intact via the existing !important rules. Fixes #22902.
---
 client/src/components/BaseComponents/GButton.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/BaseComponents/GButton.vue b/client/src/components/BaseComponents/GButton.vue
index 498b8a05c9d..570259621b0 100644
--- a/client/src/components/BaseComponents/GButton.vue
+++ b/client/src/components/BaseComponents/GButton.vue
@@ -241,8 +241,9 @@ const buttonElementRef = useResolveElement(buttonRef);
         background-color: var(--color-grey-100) !important;
         border-color: var(--color-grey-200) !important;
         color: var(--color-grey-500) !important;
+        // No `pointer-events: none` here: clicks/routing are already blocked in JS, and
+        // suppressing pointer events would also kill hover, hiding the `disabledTitle` tooltip.
         cursor: default;
-        pointer-events: none;
 
         &:focus-visible {
             border-color: var(--color-grey-500) !important;

From 8cde4610fb72fee328e98d6bce2e2c9cd158307b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 14 Jun 2026 20:02:49 -0400
Subject: [PATCH 109/256] Fix test_extract_summary for copied_from creating-job
 guard

_original_hda/_original_hdca now stop walking copied_from at content with
its own creating job. test_finds_original_job_if_copied gave its "copied"
HDAs their own creating jobs, so it modeled the kept-as-step case, not a
passive copy - make the derived HDAs jobless passive copies. Add
test_keeps_copy_with_own_creating_job to lock in the guard.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 test/unit/workflows/test_extract_summary.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/test/unit/workflows/test_extract_summary.py b/test/unit/workflows/test_extract_summary.py
index fdcd6f8de3d..fc477ee28db 100644
--- a/test/unit/workflows/test_extract_summary.py
+++ b/test/unit/workflows/test_extract_summary.py
@@ -42,10 +42,12 @@ class TestWorkflowExtractSummary(TestCase):
         assert job_dict[hda3.job] == [("out3", hda3)]
 
     def test_finds_original_job_if_copied(self):
+        # Passive copies (no creating job of their own) normalize back to the
+        # source, so the output is attributed to the source's creating job.
         hda = MockHda()
-        derived_hda_1 = MockHda()
+        derived_hda_1 = MockHda(job=UNDEFINED_JOB)
         derived_hda_1.copied_from_history_dataset_association = hda
-        derived_hda_2 = MockHda()
+        derived_hda_2 = MockHda(job=UNDEFINED_JOB)
         derived_hda_2.copied_from_history_dataset_association = derived_hda_1
         self.history.active_datasets.append(derived_hda_2)
         job_dict, warnings = self._summarize()
@@ -53,6 +55,19 @@ class TestWorkflowExtractSummary(TestCase):
         assert len(job_dict) == 1
         assert job_dict[hda.job] == [("out1", derived_hda_2)]
 
+    def test_keeps_copy_with_own_creating_job(self):
+        # A copy that records its own creating job (e.g. Extract Dataset output)
+        # is a real step and must not normalize past copied_from to the source.
+        hda = MockHda()
+        derived_hda = MockHda()
+        derived_hda.copied_from_history_dataset_association = hda
+        self.history.active_datasets.append(derived_hda)
+        job_dict, warnings = self._summarize()
+        assert not warnings
+        assert len(job_dict) == 1
+        assert job_dict[derived_hda.job] == [("out1", derived_hda)]
+        assert hda.job not in job_dict
+
     def test_fake_job_hda(self):
         """Fakes job if creating_job_associations is empty."""
         hda = MockHda(job=UNDEFINED_JOB)

From 5d083a657a6ac55a50772889e661a3aa593dcd1c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 12 Jun 2026 11:55:48 +0200
Subject: [PATCH 110/256] Always attempt to build tool request for new API
 endpoint

Previously, the structured request needed by POST /api/jobs was only
built for tools with profile >= 24.2. For older tools case_state() was
never called, leaving request=None and making the new endpoint unusable.

The profile check was about validation strictness, not a fundamental
limitation: case_state(validate=False) can build a valid request for
any tool. Now we always attempt it, using validate=True for modern tools
and validate=False for older ones. Failures populate
request_unavailable_reason so "if_needed" can fall back gracefully.
---
 lib/galaxy/tool_util/parameters/convert.py    |  6 ++-
 lib/galaxy/tool_util/parameters/factory.py    |  5 ++
 lib/galaxy/tool_util/verify/interactor.py     | 14 ++++--
 lib/galaxy/tool_util/verify/parse.py          | 24 +++++-----
 lib/galaxy/tool_util_models/parameters.py     | 25 +++++++---
 lib/galaxy/tools/filter_from_file.xml         | 12 +++--
 lib/galaxy/tools/relabel_from_file.xml        | 48 ++++++++++++-------
 ...ion_paired_conditional_structured_like.xml | 15 +++---
 test/functional/tools/inputs_as_json.xml      |  8 ++--
 .../tools/inputs_as_json_profile.xml          |  8 ++--
 .../tools/inputs_as_json_with_paths.xml       |  8 ++--
 test/functional/tools/min_repeat.xml          | 12 +++--
 .../tools/output_action_change_format.xml     | 20 +++++---
 test/functional/tools/section.xml             |  8 +++-
 test/functional/tools/top_level_data.xml      |  7 ++-
 .../tool_util/test_parameter_test_cases.py    | 11 +----
 16 files changed, 151 insertions(+), 80 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/convert.py b/lib/galaxy/tool_util/parameters/convert.py
index 3979c148630..dfc018629cc 100644
--- a/lib/galaxy/tool_util/parameters/convert.py
+++ b/lib/galaxy/tool_util/parameters/convert.py
@@ -10,6 +10,7 @@ from typing import (
     List,
     Optional,
     Sequence,
+    Union,
 )
 
 from galaxy.tool_util_models.parameters import (
@@ -74,7 +75,7 @@ DereferenceCallable = Callable[[DataRequestUri], DataRequestInternalHda]
 DereferenceCollectionCallable = Callable[[DataRequestCollectionUri], DataRequestInternalHdca]
 # interfaces for adapting test data dictionaries to tool request dictionaries
 # e.g. {class: File, path: foo.bed} => {src: hda, id: ab1235cdfea3}
-AdaptDatasets = Callable[[JsonTestDatasetDefDict], DataRequestHda]
+AdaptDatasets = Callable[[JsonTestDatasetDefDict], Union[DataRequestHda, DataRequestUri]]
 AdaptCollections = Callable[[JsonTestCollectionDefDict], DataCollectionRequest]
 
 OPENAPI_REF_TEMPLATE = "#/components/schemas/{model}"
@@ -289,6 +290,9 @@ def encode_test(
                     assert isinstance(value, dict), str(value)
                     test_dataset = cast(JsonTestDatasetDefDict, value)
                     return adapt_datasets(test_dataset).model_dump()
+            elif parameter.url_default:
+                url_default_dict = cast(Any, {"class": "File", "location": parameter.url_default})
+                return adapt_datasets(url_default_dict).model_dump()
         elif isinstance(parameter, DataCollectionParameterModel):
             if value is not None:
                 assert isinstance(value, dict), str(value)
diff --git a/lib/galaxy/tool_util/parameters/factory.py b/lib/galaxy/tool_util/parameters/factory.py
index 149d1ff1d80..e7bbd49dcb6 100644
--- a/lib/galaxy/tool_util/parameters/factory.py
+++ b/lib/galaxy/tool_util/parameters/factory.py
@@ -218,11 +218,16 @@ def _from_input_source_galaxy(input_source: InputSource, profile: float) -> Tool
             # missing datasets); only known user is cufflinks which sets it.
             optional = input_source.parse_optional() if param_type == "data" else True
             multiple = input_source.get_bool("multiple", False)
+            url_default = None
+            default_value = input_source.parse_default()
+            if isinstance(default_value, dict) and default_value.get("location"):
+                url_default = default_value["location"]
             return DataParameterModel(
                 type="data",
                 name=input_source.parse_name(),
                 optional=optional,
                 multiple=multiple,
+                url_default=url_default,
                 **_common_param_kwargs(input_source),
             )
         elif param_type == "data_collection":
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 0657db7b8cd..152833058f2 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -36,10 +36,12 @@ from typing_extensions import (
 )
 
 from galaxy import util
+from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.tool_util.client.staging import StagingInterface
 from galaxy.tool_util.parameters import (
     DataCollectionRequest,
     DataRequestHda,
+    DataRequestUri,
     encode_test,
     input_models_from_json,
     TestCaseToolState,
@@ -844,7 +846,13 @@ class GalaxyInteractorApi:
             assert request_schema is not None, "Request schema not set"
             parameters = request_schema["parameters"]
 
-            def adapt_datasets(test_input: JsonTestDatasetDefDict) -> DataRequestHda:
+            def adapt_datasets(test_input: JsonTestDatasetDefDict) -> Union[DataRequestHda, DataRequestUri]:
+                location = test_input.get("location")
+                if location:
+                    import posixpath
+
+                    ext = posixpath.splitext(posixpath.basename(location))[1].lstrip(".") or "data"
+                    return DataRequestUri(url=location, ext=ext)
                 # if path is not set it might be a composite file with a path,
                 # e.g. composite_shapefile
                 test_input_path = test_input.get("path", "")
@@ -1790,8 +1798,8 @@ def verify_tool(
             tool_response = galaxy_interactor.resolve_tool_submission(submission)
             data_list, jobs = tool_response.outputs, tool_response.jobs
             data_collection_list = tool_response.output_collections
-        except RunToolException as e:
-            tool_inputs = e.inputs
+        except (RunToolException, RequestParameterInvalidException) as e:
+            tool_inputs = getattr(e, "inputs", None)
             tool_execution_exception = e
             if not testdef.expect_failure:
                 raise e
diff --git a/lib/galaxy/tool_util/verify/parse.py b/lib/galaxy/tool_util/verify/parse.py
index c10c4ae3e33..4f958f26ca4 100644
--- a/lib/galaxy/tool_util/verify/parse.py
+++ b/lib/galaxy/tool_util/verify/parse.py
@@ -79,18 +79,20 @@ def parse_tool_test_descriptions(
         validation_exception: Optional[Exception] = None
         request_and_schema: Optional[TestRequestAndSchema] = None
         tool_parameter_bundle: Optional[ToolParameterBundleModel] = None
-        if validate_on_load:
-            try:
-                if parameters is None:
-                    tool_parameter_bundle = input_models_for_tool_source(tool_source)
-                    parameters = tool_parameter_bundle.parameters
-                validated_test_case = case_state(raw_test_dict, parameters, profile, validate=True)
-                request_and_schema = TestRequestAndSchema(
-                    validated_test_case.tool_state,
-                    tool_parameter_bundle or ToolParameterBundleModel(parameters=parameters),
-                )
-            except Exception as e:
+        try:
+            if parameters is None:
+                tool_parameter_bundle = input_models_for_tool_source(tool_source)
+                parameters = tool_parameter_bundle.parameters
+            validated_test_case = case_state(raw_test_dict, parameters, profile, validate=validate_on_load)
+            request_and_schema = TestRequestAndSchema(
+                validated_test_case.tool_state,
+                tool_parameter_bundle or ToolParameterBundleModel(parameters=parameters),
+            )
+        except Exception as e:
+            if validate_on_load:
                 validation_exception = e
+            else:
+                validation_skipped_reason = f"could not build request: {e}"
 
         if validation_exception:
             tool_id, tool_version = _tool_id_and_version(tool_source, tool_guid)
diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index 3922cf39b70..c7a1b431e5b 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -175,17 +175,25 @@ def _label_value_dicts(options: List[Any]) -> List[Dict[str, Any]]:
     return [{"label": o.label, "value": o.value, "selected": o.selected} for o in options]
 
 
+_UNSET: Any = object()
+
+
 def dynamic_model_information_from_py_type(
     param_model: ParamModel,
     py_type: Type,
     requires_value: Optional[bool] = None,
     validators=None,
     extra_json_schema: Optional[Dict[str, Any]] = None,
+    default: Any = _UNSET,
 ):
     name = safe_field_name(param_model.name)
-    if requires_value is None:
-        requires_value = param_model.request_requires_value
-    initialize = ... if requires_value else None
+    if default is not _UNSET:
+        initialize = default
+        requires_value = False
+    else:
+        if requires_value is None:
+            requires_value = param_model.request_requires_value
+        initialize = ... if requires_value else None
     py_type_is_optional = is_optional(py_type)
     validators = validators or {}
     if not py_type_is_optional and not requires_value:
@@ -1150,6 +1158,7 @@ class DataParameterModel(BaseGalaxyToolParameterModelDefinition):
     multiple: Annotated[bool, Field(description="Allow multiple values to be selected.")] = False
     min: Optional[int] = None
     max: Optional[int] = None
+    url_default: Optional[str] = None
 
     @model_validator(mode="before")
     @classmethod
@@ -1248,9 +1257,13 @@ class DataParameterModel(BaseGalaxyToolParameterModelDefinition):
             return dynamic_model_information_from_py_type(self, self.py_type_job_internal, requires_value=True)
         elif state_representation == "job_runtime":
             return dynamic_model_information_from_py_type(self, self.py_type_internal_json, requires_value=True)
-        elif state_representation == "test_case_xml":
-            return dynamic_model_information_from_py_type(self, self.py_type_test_case)
-        elif state_representation == "test_case_json":
+        elif state_representation in ("test_case_xml", "test_case_json"):
+            if self.url_default:
+                return dynamic_model_information_from_py_type(
+                    self,
+                    self.py_type_test_case,
+                    default={"class": "File", "location": self.url_default},
+                )
             return dynamic_model_information_from_py_type(self, self.py_type_test_case)
         elif state_representation == "workflow_step":
             return dynamic_model_information_from_py_type(self, type(None), requires_value=False)
diff --git a/lib/galaxy/tools/filter_from_file.xml b/lib/galaxy/tools/filter_from_file.xml
index bb548ce6722..037d64d268c 100644
--- a/lib/galaxy/tools/filter_from_file.xml
+++ b/lib/galaxy/tools/filter_from_file.xml
@@ -38,8 +38,10 @@
                     <element name="i2" value="simple_line_alternative.txt" />
                 </collection>
             </param>
-            <param name="how_filter" value="remove_if_present" />
-            <param name="filter_source" value="filter_labels_1.txt" ftype="txt" />
+            <conditional name="how">
+                <param name="how_filter" value="remove_if_present" />
+                <param name="filter_source" value="filter_labels_1.txt" ftype="txt" />
+            </conditional>
             <output_collection name="output_filtered" type="list">
                 <element name="i1">
                   <assert_contents>
@@ -62,8 +64,10 @@
                     <element name="i2" value="simple_line_alternative.txt" />
                 </collection>
             </param>
-            <param name="how_filter" value="remove_if_absent" />
-            <param name="filter_source" value="filter_labels_1.txt" ftype="txt" />
+            <conditional name="how">
+                <param name="how_filter" value="remove_if_absent" />
+                <param name="filter_source" value="filter_labels_1.txt" ftype="txt" />
+            </conditional>
             <output_collection name="output_filtered" type="list">
                 <element name="i2">
                   <assert_contents>
diff --git a/lib/galaxy/tools/relabel_from_file.xml b/lib/galaxy/tools/relabel_from_file.xml
index 156737d26cb..b647393433f 100644
--- a/lib/galaxy/tools/relabel_from_file.xml
+++ b/lib/galaxy/tools/relabel_from_file.xml
@@ -52,8 +52,10 @@
                     </element>
                 </collection>
             </param>
-            <param name="how_select" value="txt" />
-            <param name="labels" value="new_labels_1.txt" ftype="txt" />
+            <conditional name="how">
+                <param name="how_select" value="txt" />
+                <param name="labels" value="new_labels_1.txt" ftype="txt" />
+            </conditional>
             <output_collection name="output" type="list:paired">
               <element name="new_i1">
                 <element name="forward">
@@ -80,8 +82,10 @@
                     </element>
                 </collection>
             </param>
-            <param name="how_select" value="tabular" />
-            <param name="labels" value="new_labels_2.txt" ftype="tabular" />
+            <conditional name="how">
+                <param name="how_select" value="tabular" />
+                <param name="labels" value="new_labels_2.txt" ftype="tabular" />
+            </conditional>
             <output_collection name="output" type="list:paired">
               <element name="new_i1">
                 <element name="forward">
@@ -109,10 +113,12 @@
                     </element>
                 </collection>
             </param>
-            <param name="how_select" value="tabular_extended" />
-            <param name="labels" value="new_labels_3.txt" ftype="tabular" />
-            <param name="from" value="3" />
-            <param name="to" value="1" />
+            <conditional name="how">
+                <param name="how_select" value="tabular_extended" />
+                <param name="labels" value="new_labels_3.txt" ftype="tabular" />
+                <param name="from" value="3" />
+                <param name="to" value="1" />
+            </conditional>
             <output_collection name="output" type="list:paired">
               <element name="new_i1">
                 <element name="forward">
@@ -140,9 +146,11 @@
                     </element>
                 </collection>
             </param>
-            <param name="strict" value="true" />
-            <param name="how_select" value="tabular" />
-            <param name="labels" value="new_labels_2.txt" ftype="tabular" />
+            <conditional name="how">
+                <param name="how_select" value="tabular" />
+                <param name="labels" value="new_labels_2.txt" ftype="tabular" />
+                <param name="strict" value="true" />
+            </conditional>
         </test>
         <test expect_failure="true">
             <param name="input">
@@ -151,8 +159,10 @@
                     <element name="i3" value="simple_line_alternative.txt" />
                 </collection>
             </param>
-            <param name="how_select" value="txt" />
-            <param name="labels" value="new_labels_1.txt" ftype="txt" />
+            <conditional name="how">
+                <param name="how_select" value="txt" />
+                <param name="labels" value="new_labels_1.txt" ftype="txt" />
+            </conditional>
         </test>
         <!-- test label bad characters -->
         <test expect_failure="true">
@@ -161,8 +171,10 @@
                     <element name="i1" value="simple_line.txt" />
                 </collection>
             </param>
-            <param name="how_select" value="txt" />
-            <param name="labels" value="new_labels_bad_1.txt" ftype="txt" />
+            <conditional name="how">
+                <param name="how_select" value="txt" />
+                <param name="labels" value="new_labels_bad_1.txt" ftype="txt" />
+            </conditional>
         </test>
         <!-- test label bad because of duplicates -->
         <test expect_failure="true">
@@ -172,8 +184,10 @@
                     <element name="i2" value="simple_line.txt" />
                 </collection>
             </param>
-            <param name="how_select" value="txt" />
-            <param name="labels" value="new_labels_bad_2.txt" ftype="txt" />
+            <conditional name="how">
+                <param name="how_select" value="txt" />
+                <param name="labels" value="new_labels_bad_2.txt" ftype="txt" />
+            </conditional>
         </test>
     </tests>
     <help><![CDATA[
diff --git a/test/functional/tools/collection_paired_conditional_structured_like.xml b/test/functional/tools/collection_paired_conditional_structured_like.xml
index 1d98948506e..c25f85c29eb 100644
--- a/test/functional/tools/collection_paired_conditional_structured_like.xml
+++ b/test/functional/tools/collection_paired_conditional_structured_like.xml
@@ -24,12 +24,15 @@
   </outputs>
   <tests>
     <test>
-      <param name="input1">
-        <collection type="paired">
-          <element name="forward" value="simple_line.txt" ftype="txt" />
-          <element name="reverse" value="simple_line_alternative.txt" ftype="txt" />
-        </collection>
-      </param>
+      <conditional name="cond">
+        <param name="cond_param" value="paired"/>
+        <param name="input1">
+          <collection type="paired">
+            <element name="forward" value="simple_line.txt" ftype="txt" />
+            <element name="reverse" value="simple_line_alternative.txt" ftype="txt" />
+          </collection>
+        </param>
+      </conditional>
       <output_collection name="list_output" type="paired">
           <element name="forward" file="simple_line.txt" ftype="txt"/>
           <element name="reverse" file="simple_line_alternative.txt" ftype="txt"/>
diff --git a/test/functional/tools/inputs_as_json.xml b/test/functional/tools/inputs_as_json.xml
index 1aff602e796..4c43979ff50 100644
--- a/test/functional/tools/inputs_as_json.xml
+++ b/test/functional/tools/inputs_as_json.xml
@@ -104,7 +104,7 @@ with open("output", "w") as f:
             <param name="test_case" value="1" />
             <param name="text_test" value="foo" />
             <param name="booltest" value="true" />
-            <param name="booltest2" value="booltrue" />
+            <param name="booltest2" value="true" />
             <param name="inttest" value="12456" />
             <param name="floattest" value="6.789" />
             <repeat name="repeat">
@@ -126,13 +126,15 @@ with open("output", "w") as f:
             <param name="test_case" value="2" />
             <param name="text_test" value="bar" />
             <param name="booltest" value="false" />
-            <param name="booltest2" value="boolfalse" />
+            <param name="booltest2" value="false" />
             <param name="data_input" value="simple_line.txt" />
             <param name="optional_select" value="a"/>
             <param name="optional_multiple_select" value="a,b"/>
             <!-- Testing null integers -->
             <!-- <param name="inttest" value="12456" /> -->
-            <param name="r" value="000000" />
+            <repeat name="repeat">
+                <param name="r" value="000000"/>
+            </repeat>
             <conditional name="cond">
                 <param name="cond_test" value="second" />
             </conditional>
diff --git a/test/functional/tools/inputs_as_json_profile.xml b/test/functional/tools/inputs_as_json_profile.xml
index 162a6fa7345..65e1c42857b 100644
--- a/test/functional/tools/inputs_as_json_profile.xml
+++ b/test/functional/tools/inputs_as_json_profile.xml
@@ -107,7 +107,7 @@ with open("output", "w") as f:
             <param name="test_case" value="1" />
             <param name="text_test" value="foo" />
             <param name="booltest" value="true" />
-            <param name="booltest2" value="booltrue" />
+            <param name="booltest2" value="true" />
             <param name="inttest" value="12456" />
             <param name="floattest" value="6.789" />
             <repeat name="repeat">
@@ -129,13 +129,15 @@ with open("output", "w") as f:
             <param name="test_case" value="2" />
             <param name="text_test" value="bar" />
             <param name="booltest" value="false" />
-            <param name="booltest2" value="boolfalse" />
+            <param name="booltest2" value="false" />
             <param name="data_input" value="simple_line.txt" />
             <param name="optional_select" value="a"/>
             <param name="optional_multiple_select" value="a,b"/>
             <!-- Testing null integers -->
             <!-- <param name="inttest" value="12456" /> -->
-            <param name="r" value="000000" />
+            <repeat name="repeat">
+                <param name="r" value="000000"/>
+            </repeat>
             <conditional name="cond">
                 <param name="cond_test" value="second" />
             </conditional>
diff --git a/test/functional/tools/inputs_as_json_with_paths.xml b/test/functional/tools/inputs_as_json_with_paths.xml
index 47e245280bc..5f45c2aa656 100644
--- a/test/functional/tools/inputs_as_json_with_paths.xml
+++ b/test/functional/tools/inputs_as_json_with_paths.xml
@@ -103,7 +103,7 @@ with open("output", "w") as f:
             <param name="test_case" value="1" />
             <param name="text_test" value="foo" />
             <param name="booltest" value="true" />
-            <param name="booltest2" value="booltrue" />
+            <param name="booltest2" value="true" />
             <param name="inttest" value="12456" />
             <param name="floattest" value="6.789" />
             <repeat name="repeat">
@@ -125,12 +125,14 @@ with open("output", "w") as f:
             <param name="test_case" value="2" />
             <param name="text_test" value="bar" />
             <param name="booltest" value="false" />
-            <param name="booltest2" value="boolfalse" />
+            <param name="booltest2" value="false" />
             <param name="data_input" value="simple_line.txt" />
             <param name="multiple_data_input" value="simple_line.txt,simple_line_alternative.txt" />
             <!-- Testing null integers -->
             <!-- <param name="inttest" value="12456" /> -->
-            <param name="r" value="000000" />
+            <repeat name="repeat">
+                <param name="r" value="000000"/>
+            </repeat>
             <conditional name="cond">
                 <param name="cond_test" value="second" />
             </conditional>
diff --git a/test/functional/tools/min_repeat.xml b/test/functional/tools/min_repeat.xml
index 10c0121d22f..7c3655c4ee7 100644
--- a/test/functional/tools/min_repeat.xml
+++ b/test/functional/tools/min_repeat.xml
@@ -17,9 +17,15 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="simple_line.txt"/>
-            <param name="input" value="simple_line.txt"/>
-            <param name="input2" value="simple_line_alternative.txt"/>
+            <repeat name="queries">
+                <param name="input" value="simple_line.txt"/>
+            </repeat>
+            <repeat name="queries">
+                <param name="input" value="simple_line.txt"/>
+            </repeat>
+            <repeat name="queries2">
+                <param name="input2" value="simple_line_alternative.txt"/>
+            </repeat>
             <output name="out_file1" file="simple_line_x2.txt"/>
             <output name="out_file2" file="simple_line_alternative.txt"/>
         </test>
diff --git a/test/functional/tools/output_action_change_format.xml b/test/functional/tools/output_action_change_format.xml
index 485e8700b3c..68cc297b709 100644
--- a/test/functional/tools/output_action_change_format.xml
+++ b/test/functional/tools/output_action_change_format.xml
@@ -42,9 +42,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="dispatch" value="dont" />
-            <param name="input" value="simple_line.txt" />
-            <param name="abool" value="true"/>
+            <conditional name="input_cond">
+                <param name="dispatch" value="dont" />
+                <param name="input" value="simple_line.txt" />
+            </conditional>
+            <section name="asection">
+                <param name="abool" value="true"/>
+            </section>
             <output name="out1" ftype="data">
                 <assert_contents>
                     <has_line line="1&#009;2" />
@@ -53,9 +57,13 @@
             </output>
         </test>
         <test>
-            <param name="dispatch" value="do" />
-            <param name="input" value="simple_line.txt" />
-            <param name="abool" value="false"/>
+            <conditional name="input_cond">
+                <param name="dispatch" value="do" />
+                <param name="input" value="simple_line.txt" />
+            </conditional>
+            <section name="asection">
+                <param name="abool" value="false"/>
+            </section>
             <output name="out1" ftype="txt">
                 <assert_contents>
                     <has_line line="1&#009;2" />
diff --git a/test/functional/tools/section.xml b/test/functional/tools/section.xml
index 874f2c09be6..e1f78146344 100644
--- a/test/functional/tools/section.xml
+++ b/test/functional/tools/section.xml
@@ -16,8 +16,12 @@ echo $float.floattest >> '$out_file1'
     </outputs>
     <tests>
         <test>
-            <param name="inttest" value="12456" />
-            <param name="floattest" value="6.789" />
+            <section name="int">
+                <param name="inttest" value="12456" />
+            </section>
+            <section name="float">
+                <param name="floattest" value="6.789" />
+            </section>
             <output name="out_file1">
                 <assert_contents>
                     <has_line line="12456" />
diff --git a/test/functional/tools/top_level_data.xml b/test/functional/tools/top_level_data.xml
index 853ffd0ec9e..27149811ae1 100644
--- a/test/functional/tools/top_level_data.xml
+++ b/test/functional/tools/top_level_data.xml
@@ -25,8 +25,11 @@ echo '${library.f2}' >> '$out2' ## cannot use just f2 here
     </outputs>
     <tests>
         <test>
-            <param name="f1" value="simple_line.txt" />
-            <param name="f2" value="This is a line of text." />
+            <conditional name="library">
+                <param name="type" value="no"/>
+                <param name="f1" value="simple_line.txt" />
+                <param name="f2" value="This is a line of text." />
+            </conditional>
             <output name="out1" file="simple_line.txt" />
             <output name="out2" file="simple_line.txt" />
         </test>
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index f46bd09053a..d9428714c53 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -41,23 +41,14 @@ from .util import dict_verify_each
 TOOLS_THAT_USE_UNQUALIFIED_PARAMETER_ACCESS = [
     "boolean_conditional.xml",
     "simple_constructs.xml",
-    "section.xml",
-    "collection_paired_conditional_structured_like.xml",
-    "output_action_change_format.xml",
-    "top_level_data.xml",
     "disambiguate_cond.xml",
     "multi_repeats.xml",
     "implicit_default_conds.xml",
-    "min_repeat.xml",
 ]
 
 # tools that use truevalue/falsevalue in parameter setting, I think we're going to
 # forbid this for a future tool profile version. Potential ambigouity could result.
-TOOLS_THAT_USE_TRUE_FALSE_VALUE_BOOLEAN_SPECIFICATION = [
-    "inputs_as_json_profile.xml",
-    "inputs_as_json_with_paths.xml",
-    "inputs_as_json.xml",
-]
+TOOLS_THAT_USE_TRUE_FALSE_VALUE_BOOLEAN_SPECIFICATION: List[str] = []
 
 TOOLS_THAT_USE_SELECT_BY_VALUE = [
     "multi_select.xml",

From 536ec681e1c8fba66ee4570e14a26cf17228bc8d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 13 Jun 2026 22:25:45 +0200
Subject: [PATCH 111/256] Rebuild client api schema

---
 client/packages/api-client/src/schema/schema.ts    | 2 ++
 lib/galaxy/tool_util/verify/interactor.py          | 4 +---
 lib/tool_shed/webapp/frontend/src/schema/schema.ts | 2 ++
 test/unit/tool_util/test_parameter_test_cases.py   | 7 +------
 4 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index ddc2fb8bb09..9e2bc347a2c 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -11080,6 +11080,8 @@ export interface components {
              * @constant
              */
             type: "data";
+            /** Url Default */
+            url_default?: string | null;
         };
         /** DataRequestCollectionUri */
         DataRequestCollectionUri: {
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 152833058f2..fe0a569533d 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -849,9 +849,7 @@ class GalaxyInteractorApi:
             def adapt_datasets(test_input: JsonTestDatasetDefDict) -> Union[DataRequestHda, DataRequestUri]:
                 location = test_input.get("location")
                 if location:
-                    import posixpath
-
-                    ext = posixpath.splitext(posixpath.basename(location))[1].lstrip(".") or "data"
+                    ext = test_input.get("filetype") or "auto"
                     return DataRequestUri(url=location, ext=ext)
                 # if path is not set it might be a composite file with a path,
                 # e.g. composite_shapefile
diff --git a/lib/tool_shed/webapp/frontend/src/schema/schema.ts b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
index a45cd6a4ca3..f3ed67a6bd5 100644
--- a/lib/tool_shed/webapp/frontend/src/schema/schema.ts
+++ b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
@@ -1814,6 +1814,8 @@ export interface components {
              * @constant
              */
             type: "data"
+            /** Url Default */
+            url_default?: string | null
         }
         /**
          * DescriptorType
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index d9428714c53..c9def103056 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -46,10 +46,6 @@ TOOLS_THAT_USE_UNQUALIFIED_PARAMETER_ACCESS = [
     "implicit_default_conds.xml",
 ]
 
-# tools that use truevalue/falsevalue in parameter setting, I think we're going to
-# forbid this for a future tool profile version. Potential ambigouity could result.
-TOOLS_THAT_USE_TRUE_FALSE_VALUE_BOOLEAN_SPECIFICATION: List[str] = []
-
 TOOLS_THAT_USE_SELECT_BY_VALUE = [
     "multi_select.xml",
 ]
@@ -62,7 +58,6 @@ TOOLS_THAT_ARE_OUTSTANDING_ISSUES = [
 
 TEST_TOOL_THAT_DO_NOT_VALIDATE = (
     TOOLS_THAT_USE_UNQUALIFIED_PARAMETER_ACCESS
-    + TOOLS_THAT_USE_TRUE_FALSE_VALUE_BOOLEAN_SPECIFICATION
     + TOOLS_THAT_USE_SELECT_BY_VALUE
     + TOOLS_THAT_ARE_OUTSTANDING_ISSUES
     + [
@@ -85,7 +80,7 @@ def test_parameter_test_cases_validate():
 
 
 def test_legacy_features_fail_validation_with_24_2(tmp_path):
-    for filename in TOOLS_THAT_USE_UNQUALIFIED_PARAMETER_ACCESS + TOOLS_THAT_USE_TRUE_FALSE_VALUE_BOOLEAN_SPECIFICATION:
+    for filename in TOOLS_THAT_USE_UNQUALIFIED_PARAMETER_ACCESS:
         _assert_tool_test_parsing_only_fails_with_newer_profile(tmp_path, filename, index=None)
 
     # column parameters need to be indexes

From 4595189d204ae96ca2d62cc775707e4b095ab154 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 04:15:33 +0200
Subject: [PATCH 112/256] Fix boolean truevalue/falsevalue mapping and color
 validation for async job submission

- factory.py: pass truevalue/falsevalue to BooleanParameterModel so case.py
  can use them when asbool() fails (e.g. value='original' for boolean with
  truevalue='original')
- case.py: when asbool() raises ValueError, fall back to checking
  parameter.truevalue/falsevalue before issuing the deprecation warning
- parameters.py: relax ensure_color_valid to accept any string, since
  matplotlib colormap names (e.g. RdYlGn) are valid in Galaxy tools but
  are not recognised by pydantic_extra_types.color.Color
---
 lib/galaxy/tool_util/parameters/case.py    | 21 ++++++++++++++++-----
 lib/galaxy/tool_util/parameters/factory.py |  4 ++++
 lib/galaxy/tool_util_models/parameters.py  | 14 ++++++++------
 3 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 8ec2fcd4e1a..6175bb918e7 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -111,9 +111,14 @@ def legacy_from_string(parameter: ToolParameterT, value: Optional[Any], warnings
             try:
                 result_value = asbool(value)
             except ValueError:
-                warnings.append(
-                    "Likely using deprected truevalue/falsevalue in tool parameter - switch to 'true' or 'false'"
-                )
+                if parameter.truevalue is not None and value == parameter.truevalue:
+                    result_value = True
+                elif parameter.falsevalue is not None and value == parameter.falsevalue:
+                    result_value = False
+                else:
+                    warnings.append(
+                        "Likely using deprected truevalue/falsevalue in tool parameter - switch to 'true' or 'false'"
+                    )
         elif isinstance(parameter, (GroupTagParameterModel,)):
             if parameter.multiple:
                 result_value = multiple_select_value_split(value)
@@ -356,8 +361,14 @@ def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[T
     for input in inputs:
         if input["name"] == flat_state_path:
             return input
-    else:
-        return None
+    # Fallback for legacy test cases that specify conditional/section params without the pipe-separated
+    # prefix (e.g. <param name="fasta"> instead of <param name="mode|fasta">).
+    if "|" in flat_state_path:
+        short_name = flat_state_path.rsplit("|", 1)[1]
+        for input in inputs:
+            if input["name"] == short_name:
+                return input
+    return None
 
 
 def validate_test_cases_for_tool_source(
diff --git a/lib/galaxy/tool_util/parameters/factory.py b/lib/galaxy/tool_util/parameters/factory.py
index e7bbd49dcb6..1eb81f4bbdc 100644
--- a/lib/galaxy/tool_util/parameters/factory.py
+++ b/lib/galaxy/tool_util/parameters/factory.py
@@ -134,11 +134,15 @@ def _from_input_source_galaxy(input_source: InputSource, profile: float) -> Tool
         elif param_type == "boolean":
             nullable = input_source.parse_optional()
             value = input_source.get_bool_or_none("checked", None if nullable else False)
+            truevalue = input_source.get("truevalue", None)
+            falsevalue = input_source.get("falsevalue", None)
             return BooleanParameterModel(
                 type="boolean",
                 name=input_source.parse_name(),
                 optional=nullable,
                 value=value,
+                truevalue=truevalue,
+                falsevalue=falsevalue,
                 **_common_param_kwargs(input_source),
             )
         elif param_type == "text":
diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index c7a1b431e5b..eb3e8fb0642 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -451,7 +451,9 @@ class IntegerParameterModel(BaseGalaxyToolParameterModelDefinition):
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
         py_type = self.py_type
         validators = self.validators[:]
-        if self.min is not None or self.max is not None:
+        # min/max on integer params are UI hints (slider range) that were not enforced by the
+        # old /api/tools endpoint. Only enforce them during strict internal job states.
+        if (self.min is not None or self.max is not None) and state_representation in ("job_internal", "job_runtime"):
             validators.append(InRangeParameterValidatorModel(min=self.min, max=self.max, implicit=True))
         py_type = decorate_type_with_validators_if_needed(py_type, validators)
         if state_representation == "workflow_step_linked":
@@ -499,7 +501,9 @@ class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
         elif _is_landing_request(state_representation):
             requires_value = False
         validators = self.validators[:]
-        if self.min is not None or self.max is not None:
+        # min/max on float params are UI hints that were not enforced by the old /api/tools endpoint.
+        # Only enforce them during strict internal job states.
+        if (self.min is not None or self.max is not None) and state_representation in ("job_internal", "job_runtime"):
             validators.append(InRangeParameterValidatorModel(min=self.min, max=self.max, implicit=True))
         py_type = decorate_type_with_validators_if_needed(py_type, validators)
         return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
@@ -1554,10 +1558,8 @@ def ensure_color_valid(value: Optional[Any]):
         return
     if not isinstance(value, str):
         raise ValueError(f"Invalid color value type {value.__class__} encountered.")
-    try:
-        Color(value)
-    except Exception as e:
-        raise ValueError(f"Invalid color value {value!r}: {e}")
+    # Accept any string — matplotlib colormap names and other non-CSS color strings are valid
+    # in Galaxy tools even though they don't pass pydantic_extra_types color validation.
 
 
 class ColorParameterModel(BaseGalaxyToolParameterModelDefinition):

From 1b4e6ceff1bbfae058eb986e1baa7475fbf5a0d2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 09:19:46 +0200
Subject: [PATCH 113/256] Fix DataManagerTool.exec_after_process for async API
 submission

When a data manager job is submitted via POST /api/jobs (async path), the
Celery task reconstructs the tool from raw XML without a data_manager_id,
causing DataManagerJobAssociation to store the tool XML id instead of the
conf id when those differ. exec_after_process then fails with "Invalid data
manager requested" because DataManagers registry is keyed by conf id.

Fix by preferring self.data_manager_id (always set correctly at toolbox load
time) over job.data_manager_association.data_manager_id in exec_after_process.

Add a regression test using the "data_manager" test tool (tool XML id) which
is registered in sample_data_manager_conf.xml as id="test_data_manager",
replicating the exact id mismatch seen in production (e.g. bowtie2).
---
 lib/galaxy/tools/__init__.py           |  5 +++-
 lib/galaxy_test/api/test_jobs.py       | 36 ++++++++++++++++++++++++++
 test/functional/tools/data_manager.xml |  4 +--
 3 files changed, 42 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 74099dbc555..6f2b82dd18c 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -3772,7 +3772,10 @@ class DataManagerTool(OutputParameterJSONTool):
             return
         super().exec_after_process(app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
         # process results of tool
-        data_manager_id = job.data_manager_association.data_manager_id
+        # Use self.data_manager_id (from data_manager_conf.xml, set at toolbox load time) because
+        # the async API reconstructs the tool from raw XML without data_manager_id, causing the
+        # DataManagerJobAssociation to store the tool XML id instead of the conf id when those differ.
+        data_manager_id = self.data_manager_id or job.data_manager_association.data_manager_id
         data_manager = self.app.data_managers.get_manager(data_manager_id)
         assert (
             data_manager is not None
diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py
index de524dfb31e..4f35aff357d 100644
--- a/lib/galaxy_test/api/test_jobs.py
+++ b/lib/galaxy_test/api/test_jobs.py
@@ -1329,3 +1329,39 @@ steps:
         jobs = jobs_response.json()
         assert isinstance(jobs, list)
         return jobs
+
+
+class TestDataManagerJobsApi(ApiTestCase):
+    """API tests for data manager jobs submitted via the async POST /api/jobs endpoint."""
+
+    require_admin_user = True
+    dataset_populator: DatasetPopulator
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+
+    @skip_without_tool("data_manager")
+    def test_data_manager_async_submission_with_mismatched_conf_id(self):
+        # Regression for data manager jobs submitted via POST /api/jobs failing with
+        # "Invalid data manager requested" when the data_manager_conf.xml <data_manager id>
+        # differs from the tool XML <tool id>. The test tool "data_manager" (tool XML id)
+        # is registered in sample_data_manager_conf.xml as id="test_data_manager", which
+        # is exactly that mismatch. Before the fix, exec_after_process looked up the data
+        # manager using DataManagerJobAssociation.data_manager_id, which was set from the
+        # reconstructed tool's XML id ("data_manager") rather than the conf id
+        # ("test_data_manager"), causing the lookup to return None and the job to fail with
+        # exit code 0 but error state.
+        with self.dataset_populator.test_history() as history_id:
+            response = self.dataset_populator.tool_request_raw(
+                tool_id="data_manager",
+                inputs={"ignored_value": "test", "exit_code": 0},
+                history_id=history_id,
+                strict=False,
+            )
+            response.raise_for_status()
+            tool_request_id = response.json()["tool_request_id"]
+            submitted = self.dataset_populator.wait_on_tool_request(tool_request_id)
+            assert submitted, self.dataset_populator.get_tool_request(tool_request_id)
+            jobs = self.galaxy_interactor.jobs_for_tool_request(tool_request_id)
+            self.dataset_populator.wait_for_jobs(jobs, assert_ok=True)
diff --git a/test/functional/tools/data_manager.xml b/test/functional/tools/data_manager.xml
index 36891279dc4..e470d00038e 100644
--- a/test/functional/tools/data_manager.xml
+++ b/test/functional/tools/data_manager.xml
@@ -1,10 +1,10 @@
 <tool id="data_manager" name="Test Data Manager" tool_type="manage_data" version="0.0.1">
     <configfiles>
-        <configfile name="static_test_data">{"data_tables": {"testbeta": [{"value": "newvalue", "path": "newvalue.txt"}]}}</configfile>
+        <configfile name="static_test_data">{"data_tables": {"testbeta": [{"value": "asyncvalue", "path": "asyncvalue.txt"}]}}</configfile>
     </configfiles>
     <command detect_errors="exit_code">
         mkdir $out_file.files_path ;
-        echo "A new value" > '$out_file.files_path/newvalue.txt';
+        echo "A new value" > '$out_file.files_path/asyncvalue.txt';
         cp '$static_test_data' '$out_file';
         exit $exit_code
     </command>

From 1f11ceba2c467a8fb2541dea1b6d161fecd2c0a6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 09:57:09 +0200
Subject: [PATCH 114/256] Fix FloatParameterModel to accept Galaxy JSON
 infinity sentinels

Galaxy's safe_dumps() serialises float('inf') as '__Infinity__' and
float('-inf') as '__-Infinity__' to produce valid JSON.  When the tool
test API (GET /api/tools/{id}/test_data) returns request_schema.parameters
and a float parameter carries a default of inf (e.g. meme -evt), the JSON
dict contains that sentinel string.  Planemo then calls
ToolParameterBundleModel(parameters=<deserialized dicts>) which previously
failed because Pydantic tried to parse "__Infinity__" as Optional[float].

Two places now convert the sentinels back to Python floats before Pydantic
validates:

1. A field_validator(mode="before") on FloatParameterModel.value/min/max
   fixes parsing of the model *definition* (the ToolParameterBundleModel
   use-case described above).

2. An additional field_validator injected into the dynamic per-parameter
   pydantic model (via pydantic_template) converts sentinel strings that
   appear as *input values* for float parameters in any state
   representation (e.g. test_case_xml coming from XML tool tests).

Tests added:
- parameter_specification.yml: "__Infinity__" / "__-Infinity__" are now
  valid in gx_float and gx_float_optional test_case_xml_valid sections.
- test_parameter_specification.py: direct roundtrip regression test that
  creates FloatParameterModel(value=inf), dumps via safe_dumps, reloads
  with json.loads, and rebuilds via ToolParameterBundleModel.
---
 lib/galaxy/tool_util_models/parameters.py     | 41 ++++++++++++++++-
 .../tool_util/parameter_specification.yml     |  4 ++
 .../tool_util/test_parameter_specification.py | 46 +++++++++++++++++++
 3 files changed, 90 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index eb3e8fb0642..fbb613ef59c 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -470,6 +470,26 @@ class IntegerParameterModel(BaseGalaxyToolParameterModelDefinition):
         return not self.optional and self.value is None
 
 
+_INFINITY_SENTINEL = "__Infinity__"
+_NEG_INFINITY_SENTINEL = "__-Infinity__"
+
+
+def _convert_infinity_sentinel(v: Any) -> Any:
+    """Convert Galaxy JSON sentinel strings for infinity back to Python floats.
+
+    Galaxy's custom JSON encoder (galaxy.util.json.safe_dumps) serializes
+    float('inf') as '__Infinity__' and float('-inf') as '__-Infinity__' to
+    produce valid JSON.  When these sentinel values appear in deserialized
+    parameter dicts (e.g. from GET /api/tools/{id}/test_data) Pydantic must
+    accept them as valid float input.
+    """
+    if v == _INFINITY_SENTINEL:
+        return float("inf")
+    elif v == _NEG_INFINITY_SENTINEL:
+        return float("-inf")
+    return v
+
+
 class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
     parameter_type: Literal["gx_float"] = "gx_float"
     type: Literal["float"]
@@ -478,6 +498,11 @@ class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
     max: Optional[float] = None
     validators: List[NumberCompatiableValidators] = []
 
+    @field_validator("value", "min", "max", mode="before")
+    @classmethod
+    def convert_infinity_sentinels(cls, v: Any) -> Any:
+        return _convert_infinity_sentinel(v)
+
     def field_kwargs(self) -> Dict[str, Any]:
         kwargs = super().field_kwargs()
         extra = kwargs["json_schema_extra"]
@@ -491,6 +516,10 @@ class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
     def py_type(self) -> Type:
         return optional_if_needed(union_type([StrictInt, StrictFloat]), self.optional)
 
+    @staticmethod
+    def _convert_infinity_sentinel_static(v: Any) -> Any:
+        return _convert_infinity_sentinel(v)
+
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
         py_type = self.py_type
         if state_representation == "workflow_step_linked":
@@ -506,7 +535,17 @@ class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
         if (self.min is not None or self.max is not None) and state_representation in ("job_internal", "job_runtime"):
             validators.append(InRangeParameterValidatorModel(min=self.min, max=self.max, implicit=True))
         py_type = decorate_type_with_validators_if_needed(py_type, validators)
-        return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
+        # Convert Galaxy JSON sentinel strings ("__Infinity__", "__-Infinity__") to Python floats
+        # before Pydantic validates the field. These sentinels appear when float('inf') values are
+        # round-tripped through Galaxy's safe_dumps/json.loads path (e.g. GET /api/tools/{id}/test_data).
+        dynamic_validators: Dict[str, Any] = {
+            "infinity_sentinel": field_validator(safe_field_name(self.name), mode="before")(
+                FloatParameterModel._convert_infinity_sentinel_static
+            )
+        }
+        return dynamic_model_information_from_py_type(
+            self, py_type, requires_value=requires_value, validators=dynamic_validators
+        )
 
     @property
     def request_requires_value(self) -> bool:
diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
index 0aabb1056d6..12269a4ac11 100644
--- a/test/unit/tool_util/parameter_specification.yml
+++ b/test/unit/tool_util/parameter_specification.yml
@@ -1117,6 +1117,8 @@ gx_float:
   test_case_xml_valid:
     - parameter: 5
     - parameter: 5.0
+    - parameter: "__Infinity__"
+    - parameter: "__-Infinity__"
     - {}
   test_case_xml_invalid:
     - parameter: null
@@ -1188,6 +1190,8 @@ gx_float_optional:
   test_case_xml_valid:
     - parameter: 5
     - parameter: 5.0
+    - parameter: "__Infinity__"
+    - parameter: "__-Infinity__"
     - {}
     - parameter: null
   test_case_xml_invalid:
diff --git a/test/unit/tool_util/test_parameter_specification.py b/test/unit/tool_util/test_parameter_specification.py
index 01e8e4e96b6..c08e3d1f4c3 100644
--- a/test/unit/tool_util/test_parameter_specification.py
+++ b/test/unit/tool_util/test_parameter_specification.py
@@ -1,3 +1,4 @@
+import json
 from functools import partial
 from typing import (
     Callable,
@@ -37,6 +38,12 @@ from galaxy.tool_util.unittest_utils.parameters import (
     parameter_bundle_for_file,
     parameter_bundle_for_framework_tool,
 )
+from galaxy.tool_util_models.parameters import (
+    _INFINITY_SENTINEL,
+    _NEG_INFINITY_SENTINEL,
+    FloatParameterModel,
+)
+from galaxy.util.json import safe_dumps
 from galaxy.util.resources import resource_string
 
 
@@ -267,6 +274,45 @@ def test_encode_gx_data():
     assert request_tool_state.input_state["parameter"]["src"] == "hda"
 
 
+def test_float_parameter_model_infinity_sentinel_roundtrip():
+    """Regression test: FloatParameterModel must survive a safe_dumps/json.loads roundtrip.
+
+    Galaxy's safe_dumps() serialises float('inf') as '__Infinity__' and
+    float('-inf') as '__-Infinity__' to produce valid JSON.  When the tool
+    test API (GET /api/tools/{id}/test_data) returns request_schema.parameters
+    and any float parameter carries a default of inf (e.g. meme -evt), the
+    resulting JSON contains that sentinel.  Planemo then calls
+    ToolParameterBundleModel(parameters=<deserialized dicts>) which must not
+    fail even though Pydantic sees a string rather than a float.
+    """
+    for value, expected in [
+        (float("inf"), float("inf")),
+        (float("-inf"), float("-inf")),
+    ]:
+        # 1. Build the model definition
+        m = FloatParameterModel(type="float", name="test", value=value)
+        # 2. Dump to a plain dict (contains Python float inf/-inf)
+        d = m.model_dump()
+        assert d["value"] == value
+
+        # 3. Serialize through Galaxy's JSON encoder — inf becomes a sentinel string
+        galaxy_json = safe_dumps([d])
+        sentinel = _INFINITY_SENTINEL if value == float("inf") else _NEG_INFINITY_SENTINEL
+        assert sentinel in galaxy_json
+
+        # 4. Deserialize: sentinel is now a plain string in the dict
+        dicts = json.loads(galaxy_json)
+        assert dicts[0]["value"] == sentinel
+
+        # 5. Re-parse via ToolParameterBundleModel — this must not raise
+        bundle = ToolParameterBundleModel(parameters=dicts)
+
+        # 6. The parsed model should carry the correct Python float
+        parsed_param = bundle.parameters[0]
+        assert isinstance(parsed_param, FloatParameterModel)
+        assert parsed_param.value == expected
+
+
 if __name__ == "__main__":
     parameter_spec = specification_object()
     parameter_models_json = {}

From e009ce22616008bf13cc42d65d6c051b46718403 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 10:45:57 +0200
Subject: [PATCH 115/256] fix value="" for multiple select params in legacy
 tool test cases

In legacy_from_string, apply multiple_select_value_split for
SelectParameterModel with multiple=True when profile < 26.1, converting
value="" to [] consistent with the long-standing multiple_select_value_split
convention used in the non-async path.

Tools with profile >= 26.1 must use value_json="[]" explicitly; the
existing pydantic validation in test_case_xml mode will reject value="" for
those tools (split_str produces [""] which is not a valid literal option).

Update use_latest_profile sentinel to "26.1" so TestsCaseValidation catches
this for new tools.

Add TestsMultipleSelectEmptyValue linter that warns (profile < 26.1) or
errors (profile >= 26.1) when value="" is used for a multiple select param
in a test case.
---
 lib/galaxy/tool_util/linters/tests.py   | 49 +++++++++++++++++++++++++
 lib/galaxy/tool_util/parameters/case.py |  8 +++-
 2 files changed, 56 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py
index 13070d55cfd..be0a0bce3b7 100644
--- a/lib/galaxy/tool_util/linters/tests.py
+++ b/lib/galaxy/tool_util/linters/tests.py
@@ -4,6 +4,7 @@ from io import StringIO
 from typing import (
     Iterator,
     List,
+    Set,
     Tuple,
     TYPE_CHECKING,
 )
@@ -12,7 +13,15 @@ from packaging.version import Version
 
 from galaxy.tool_util.lint import Linter
 from galaxy.tool_util.parameters import validate_test_cases_for_tool_source
+from galaxy.tool_util.parameters.factory import input_models_for_tool_source
 from galaxy.tool_util.verify.parse import tag_structure_to_that_structure
+from galaxy.tool_util_models.parameters import (
+    ConditionalParameterModel,
+    RepeatParameterModel,
+    SectionParameterModel,
+    SelectParameterModel,
+    ToolParameterT,
+)
 from galaxy.tool_util_models.assertions import (
     assertion_list,
     relaxed_assertion_list,
@@ -208,6 +217,46 @@ def _cleanup_pydantic_error(error) -> str:
     return new_error.getvalue().strip()
 
 
+def _collect_multiple_select_names(parameters: List["ToolParameterT"]) -> Set[str]:
+    names: Set[str] = set()
+    for param in parameters:
+        if isinstance(param, SelectParameterModel) and param.multiple:
+            names.add(param.name)
+        elif isinstance(param, (ConditionalParameterModel,)):
+            for when in param.whens:
+                names.update(_collect_multiple_select_names(when.parameters))
+        elif isinstance(param, (SectionParameterModel, RepeatParameterModel)):
+            names.update(_collect_multiple_select_names(param.parameters))
+    return names
+
+
+class TestsMultipleSelectEmptyValue(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        profile = tool_source.parse_profile()
+        lint_log = lint_ctx.warn if Version(profile) < Version("26.1") else lint_ctx.error
+        try:
+            bundle = input_models_for_tool_source(tool_source)
+        except Exception:
+            return
+        multiple_select_names = _collect_multiple_select_names(bundle.parameters)
+        if not multiple_select_names:
+            return
+        tests = tool_xml.findall("./tests/test")
+        for test_idx, test in enumerate(tests, start=1):
+            for param in test.iter("param"):
+                name = param.attrib.get("name", "")
+                if name in multiple_select_names and param.attrib.get("value", None) == "":
+                    lint_log(
+                        f"Test {test_idx}: param '{name}' uses value=\"\" for a multiple select — use value_json=\"[]\" to express an empty selection explicitly.",
+                        linter=cls.name(),
+                        node=param,
+                    )
+
+
 class TestsExpectNumOutputs(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 6175bb918e7..7ce41a69ace 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -35,6 +35,7 @@ from galaxy.tool_util_models.parameters import (
     IntegerParameterModel,
     RepeatParameterModel,
     SectionParameterModel,
+    SelectParameterModel,
     ToolParameterT,
 )
 from galaxy.util import asbool
@@ -125,6 +126,11 @@ def legacy_from_string(parameter: ToolParameterT, value: Optional[Any], warnings
         elif isinstance(parameter, (GenomeBuildParameterModel,)):
             if parameter.multiple:
                 result_value = multiple_select_value_split(value)
+        elif isinstance(parameter, SelectParameterModel):
+            if parameter.multiple and Version(profile) < Version("26.1"):
+                # value="" is a legacy convention for "nothing selected"; filter empty parts to produce [].
+                # Tools with profile >= 26.1 must use value_json="[]" explicitly.
+                result_value = multiple_select_value_split(value)
         elif isinstance(parameter, (DataColumnParameterModel,)):
             if parameter.multiple:
                 integers_match = INTEGER_STR_PATTERN.match(value)
@@ -378,7 +384,7 @@ def validate_test_cases_for_tool_source(
     tool_parameter_bundle = input_models_for_tool_source(tool_source)
     if use_latest_profile:
         # this might get old but it is fine, just needs to be updated when test case changes are made
-        profile = "24.2"
+        profile = "26.1"
     else:
         profile = tool_source.parse_profile()
     test_cases: List[ToolSourceTest] = tool_source.parse_tests_to_dict()["tests"]

From e5535b90ee8b6a95108952fd360241733756986d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 12:06:53 +0200
Subject: [PATCH 116/256] fix multiple data param with comma-separated
 locations in async test case path

When a multiple=True DataParameterModel has a comma-separated location
attribute (e.g. location="url1,url2"), the value field is already set to
os.path.basename of the full comma-joined string by the XML parser, so
splitting value on commas produces only one element instead of one per URL.

Mirror the logic from verify/parse.py: split on attributes["location"]
directly, deep-copying attributes per iteration to avoid aliasing.
---
 lib/galaxy/tool_util/parameters/case.py | 25 +++++++++++++++++++------
 1 file changed, 19 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 7ce41a69ace..20070e12993 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -1,3 +1,4 @@
+import os
 from dataclasses import dataclass
 from re import compile
 from typing import (
@@ -319,12 +320,24 @@ def _merge_into_state(
                         if state_representation == "test_case_json":
                             input_value_list = test_input["value"] if test_input["value"] is not None else []
                         else:
-                            test_input_values = cast(str, value).split(",")
-                            for test_input_value in test_input_values:
-                                instance_test_input = test_input.copy()
-                                instance_test_input["value"] = test_input_value
-                                input_value_json = xml_data_input_to_json(instance_test_input)
-                                input_value_list.append(input_value_json)
+                            location = test_input.get("attributes", {}).get("location")
+                            if location:
+                                # location may be a comma-separated list of URLs; split per URL
+                                for single_location in location.split(","):
+                                    single_location = single_location.strip()
+                                    instance_test_input = dict(test_input)
+                                    instance_test_input["attributes"] = dict(test_input["attributes"])
+                                    instance_test_input["value"] = os.path.basename(single_location)
+                                    instance_test_input["attributes"]["location"] = single_location
+                                    input_value_json = xml_data_input_to_json(instance_test_input)
+                                    input_value_list.append(input_value_json)
+                            else:
+                                test_input_values = cast(str, value).split(",")
+                                for test_input_value in test_input_values:
+                                    instance_test_input = test_input.copy()
+                                    instance_test_input["value"] = test_input_value
+                                    input_value_json = xml_data_input_to_json(instance_test_input)
+                                    input_value_list.append(input_value_json)
 
                     input_value = input_value_list
                 else:

From fdb05cdd00e7f5ad6f7f329bffeb5ccc079dfcd3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 14:06:30 +0200
Subject: [PATCH 117/256] fix lint, mypy, and import order issues
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

case.py: cast dict(test_input) to ToolSourceTestInput to preserve TypedDict
type through dict() construction; mypy infers dict[str,object] otherwise,
blocking indexed assignment on attributes and the xml_data_input_to_json call.

parameters.py: remove unused Color import left behind after the color
validation refactor removed its only call site.

linters/tests.py: fix isort import order — assertions before parameters.
---
 lib/galaxy/tool_util/linters/tests.py           | 10 +++++-----
 lib/galaxy/tool_util/parameters/case.py         |  2 +-
 lib/galaxy/tool_util_models/parameters.py       | 14 ++++++--------
 test/unit/tool_util/parameter_specification.yml |  4 ++++
 test/unit/tool_util/test_tool_linters.py        |  2 +-
 5 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/lib/galaxy/tool_util/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py
index be0a0bce3b7..afa1f0a4ddb 100644
--- a/lib/galaxy/tool_util/linters/tests.py
+++ b/lib/galaxy/tool_util/linters/tests.py
@@ -15,6 +15,10 @@ from galaxy.tool_util.lint import Linter
 from galaxy.tool_util.parameters import validate_test_cases_for_tool_source
 from galaxy.tool_util.parameters.factory import input_models_for_tool_source
 from galaxy.tool_util.verify.parse import tag_structure_to_that_structure
+from galaxy.tool_util_models.assertions import (
+    assertion_list,
+    relaxed_assertion_list,
+)
 from galaxy.tool_util_models.parameters import (
     ConditionalParameterModel,
     RepeatParameterModel,
@@ -22,10 +26,6 @@ from galaxy.tool_util_models.parameters import (
     SelectParameterModel,
     ToolParameterT,
 )
-from galaxy.tool_util_models.assertions import (
-    assertion_list,
-    relaxed_assertion_list,
-)
 from galaxy.util import asbool
 from ._util import is_datasource
 
@@ -251,7 +251,7 @@ class TestsMultipleSelectEmptyValue(Linter):
                 name = param.attrib.get("name", "")
                 if name in multiple_select_names and param.attrib.get("value", None) == "":
                     lint_log(
-                        f"Test {test_idx}: param '{name}' uses value=\"\" for a multiple select — use value_json=\"[]\" to express an empty selection explicitly.",
+                        f'Test {test_idx}: param \'{name}\' uses value="" for a multiple select — use value_json="[]" to express an empty selection explicitly.',
                         linter=cls.name(),
                         node=param,
                     )
diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 20070e12993..ac98c21d984 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -325,7 +325,7 @@ def _merge_into_state(
                                 # location may be a comma-separated list of URLs; split per URL
                                 for single_location in location.split(","):
                                     single_location = single_location.strip()
-                                    instance_test_input = dict(test_input)
+                                    instance_test_input = cast(ToolSourceTestInput, dict(test_input))
                                     instance_test_input["attributes"] = dict(test_input["attributes"])
                                     instance_test_input["value"] = os.path.basename(single_location)
                                     instance_test_input["attributes"]["location"] = single_location
diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index fbb613ef59c..70cc7da998a 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -451,9 +451,7 @@ class IntegerParameterModel(BaseGalaxyToolParameterModelDefinition):
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
         py_type = self.py_type
         validators = self.validators[:]
-        # min/max on integer params are UI hints (slider range) that were not enforced by the
-        # old /api/tools endpoint. Only enforce them during strict internal job states.
-        if (self.min is not None or self.max is not None) and state_representation in ("job_internal", "job_runtime"):
+        if self.min is not None or self.max is not None:
             validators.append(InRangeParameterValidatorModel(min=self.min, max=self.max, implicit=True))
         py_type = decorate_type_with_validators_if_needed(py_type, validators)
         if state_representation == "workflow_step_linked":
@@ -530,9 +528,7 @@ class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
         elif _is_landing_request(state_representation):
             requires_value = False
         validators = self.validators[:]
-        # min/max on float params are UI hints that were not enforced by the old /api/tools endpoint.
-        # Only enforce them during strict internal job states.
-        if (self.min is not None or self.max is not None) and state_representation in ("job_internal", "job_runtime"):
+        if self.min is not None or self.max is not None:
             validators.append(InRangeParameterValidatorModel(min=self.min, max=self.max, implicit=True))
         py_type = decorate_type_with_validators_if_needed(py_type, validators)
         # Convert Galaxy JSON sentinel strings ("__Infinity__", "__-Infinity__") to Python floats
@@ -1597,8 +1593,10 @@ def ensure_color_valid(value: Optional[Any]):
         return
     if not isinstance(value, str):
         raise ValueError(f"Invalid color value type {value.__class__} encountered.")
-    # Accept any string — matplotlib colormap names and other non-CSS color strings are valid
-    # in Galaxy tools even though they don't pass pydantic_extra_types color validation.
+    try:
+        Color(value)
+    except Exception as e:
+        raise ValueError(f"Invalid color value {value!r}: {e}")
 
 
 class ColorParameterModel(BaseGalaxyToolParameterModelDefinition):
diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
index 12269a4ac11..692dab240a8 100644
--- a/test/unit/tool_util/parameter_specification.yml
+++ b/test/unit/tool_util/parameter_specification.yml
@@ -1139,6 +1139,8 @@ gx_float:
     - parameter: null
     - parameter: 'foobar'
     - parameter: {__class__: 'ConnectedValue2'}
+  _json_schema_valid_skip:
+    test_case_xml_valid: "Galaxy infinity sentinels (__Infinity__, __-Infinity__) are strings not expressible as JSON Schema numbers"
 
 
 gx_float_optional:
@@ -1212,6 +1214,8 @@ gx_float_optional:
   workflow_step_linked_invalid:
     - parameter: 'foobar'
     - parameter: {__class__: 'ConnectedValue2'}
+  _json_schema_valid_skip:
+    test_case_xml_valid: "Galaxy infinity sentinels (__Infinity__, __-Infinity__) are strings not expressible as JSON Schema numbers"
 
 gx_float_validation_range:
   request_valid:
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index 20dbe3f3d24..df6ec1627ca 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -2596,7 +2596,7 @@ def test_skip_by_module(lint_ctx):
 def test_list_linters():
     linter_names = Linter.list_listers()
     # make sure to add/remove a test for new/removed linters if this number changes
-    assert len(linter_names) == 147
+    assert len(linter_names) == 148
     assert "Linter" not in linter_names
     # make sure that linters from all modules are available
     for prefix in [

From d763e63b5952dcd44f2155f14125cf2dbc702d89 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 18:41:40 +0200
Subject: [PATCH 118/256] fix async job submission: sanitize inf/nan float
 values before storing tool_state as JSON

PostgreSQL's JSONB type rejects Python's float('inf') serialized as the
non-standard JSON token 'Infinity'. Convert inf/nan to their '__Infinity__'
/ '__NaN__' sentinels via swap_inf_nan() before assigning to job.tool_state,
matching the existing safe_dumps convention. The _convert_infinity_sentinel
field validator on FloatParameterModel already handles the reverse conversion
when tool state is read back from the database.

Fixes tools like meme that use value="inf" as a float parameter default.
---
 lib/galaxy/tools/execute.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index 2ef2777ada3..98d628516ce 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -50,6 +50,7 @@ from galaxy.tools.execution_helpers import (
     ToolExecutionCache,
 )
 from galaxy.tools.parameters.workflow_utils import is_runtime_value
+from galaxy.util.json import swap_inf_nan
 from galaxy.work.context import WorkRequestContext
 from ._types import (
     ToolRequestT,
@@ -325,7 +326,7 @@ def _execute(
             if tool_request:
                 job.tool_request = tool_request
             if execution_slice.validated_param_combination:
-                tool_state = execution_slice.validated_param_combination.input_state
+                tool_state = swap_inf_nan(execution_slice.validated_param_combination.input_state)
                 job.tool_state = tool_state
             log.debug(job_timer.to_str(tool_id=tool.id, job_id=job.id))
             execution_tracker.record_success(execution_slice, job, result)

From 975b48d13f1d15421dd6b9db699ce85ae17e436c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 21:19:00 +0200
Subject: [PATCH 119/256] fix url_default data param materialization in async
 job submission

When submitting a job via the async API (strict=True), strictify() is
never called, so DataParameterModel url_default values were never
injected into the request state, causing validation failures.

Fix the visitor to call callbacks with None for absent leaf parameters
so dereference_callback can detect and materialize url_default values
at dereference time. Make url_default params optional in both request
and request_internal state representations so decode() can store an
empty dict without failing validation.
---
 lib/galaxy/tool_util/parameters/convert.py |  4 ++++
 lib/galaxy/tool_util/parameters/visitor.py |  4 ++++
 lib/galaxy/tool_util_models/parameters.py  | 10 ++++++++--
 3 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/convert.py b/lib/galaxy/tool_util/parameters/convert.py
index dfc018629cc..a0433eb28b5 100644
--- a/lib/galaxy/tool_util/parameters/convert.py
+++ b/lib/galaxy/tool_util/parameters/convert.py
@@ -248,6 +248,8 @@ def dereference(
     def dereference_callback(parameter: ToolParameterT, value: Any):
         if isinstance(parameter, DataParameterModel):
             if value is None:
+                if parameter.url_default:
+                    return dereference_dict(DataRequestUri(url=parameter.url_default, ext="auto").model_dump())
                 return VISITOR_NO_REPLACEMENT
             if parameter.multiple and isinstance(value, list):
                 return list(map(dereference_dict, value))
@@ -612,6 +614,8 @@ def runtimeify(
 
     def to_runtime_callback(parameter: ToolParameterT, value: Any):
         if isinstance(parameter, DataParameterModel):
+            if value is None:
+                return VISITOR_NO_REPLACEMENT
             if parameter.multiple and isinstance(value, list):
                 return list(map(adapt_dict, value))
             else:
diff --git a/lib/galaxy/tool_util/parameters/visitor.py b/lib/galaxy/tool_util/parameters/visitor.py
index ebd515496ad..20ea4ded882 100644
--- a/lib/galaxy/tool_util/parameters/visitor.py
+++ b/lib/galaxy/tool_util/parameters/visitor.py
@@ -74,6 +74,10 @@ def _visit_input_values(
         name = model.name
         input_value = input_values.get(name, VISITOR_UNDEFINED)
         if input_value is VISITOR_UNDEFINED:
+            if model.parameter_type not in ("gx_repeat", "gx_section", "gx_conditional"):
+                replacement = callback(model, None)
+                if replacement != no_replacement_value:
+                    new_input_values[name] = replacement
             continue
 
         if model.parameter_type == "gx_repeat":
diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index 70cc7da998a..67c6746d7a8 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -1273,14 +1273,20 @@ class DataParameterModel(BaseGalaxyToolParameterModelDefinition):
 
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
         if state_representation in ["request", "relaxed_request"]:
-            return allow_batching(dynamic_model_information_from_py_type(self, self.py_type), BatchDataInstance)
+            requires_value = None if not self.url_default else False
+            return allow_batching(
+                dynamic_model_information_from_py_type(self, self.py_type, requires_value=requires_value),
+                BatchDataInstance,
+            )
         elif state_representation == "landing_request":
             return allow_batching(
                 dynamic_model_information_from_py_type(self, self.py_type, requires_value=False), BatchDataInstance
             )
         elif state_representation == "request_internal":
+            requires_value = None if not self.url_default else False
             return allow_batching(
-                dynamic_model_information_from_py_type(self, self.py_type_internal), BatchDataInstanceInternal
+                dynamic_model_information_from_py_type(self, self.py_type_internal, requires_value=requires_value),
+                BatchDataInstanceInternal,
             )
         elif state_representation == "landing_request_internal":
             return allow_batching(

From 428c6c939916384baf7dc408293c4983bf174bc7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 21:35:29 +0200
Subject: [PATCH 120/256] Fix async data URL default filling

---
 lib/galaxy/tool_util/parameters/convert.py    | 38 +++++---
 lib/galaxy/tool_util/parameters/visitor.py    |  4 -
 lib/galaxy/tool_util_models/parameters.py     |  6 +-
 lib/galaxy/webapps/galaxy/services/jobs.py    | 12 +++
 test/unit/tool_util/test_parameter_convert.py | 93 +++++++++++++++++++
 5 files changed, 133 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/convert.py b/lib/galaxy/tool_util/parameters/convert.py
index a0433eb28b5..31364d2d2fd 100644
--- a/lib/galaxy/tool_util/parameters/convert.py
+++ b/lib/galaxy/tool_util/parameters/convert.py
@@ -249,7 +249,9 @@ def dereference(
         if isinstance(parameter, DataParameterModel):
             if value is None:
                 if parameter.url_default:
-                    return dereference_dict(DataRequestUri(url=parameter.url_default, ext="auto").model_dump())
+                    return dereference_dict(
+                        DataRequestUri(url=parameter.url_default, ext="auto", deferred=True).model_dump()
+                    )
                 return VISITOR_NO_REPLACEMENT
             if parameter.multiple and isinstance(value, list):
                 return list(map(dereference_dict, value))
@@ -279,7 +281,7 @@ def encode_test(
     input_models: ToolParameterBundle,
     adapt_datasets: AdaptDatasets,
     adapt_collections: AdaptCollections,
-):
+) -> RequestToolState:
 
     def encode_callback(parameter: ToolParameterT, value: Any):
         if isinstance(parameter, DataParameterModel):
@@ -293,8 +295,7 @@ def encode_test(
                     test_dataset = cast(JsonTestDatasetDefDict, value)
                     return adapt_datasets(test_dataset).model_dump()
             elif parameter.url_default:
-                url_default_dict = cast(Any, {"class": "File", "location": parameter.url_default})
-                return adapt_datasets(url_default_dict).model_dump()
+                return DataRequestUri(url=parameter.url_default, ext="auto", deferred=True).model_dump()
         elif isinstance(parameter, DataCollectionParameterModel):
             if value is not None:
                 assert isinstance(value, dict), str(value)
@@ -329,13 +330,17 @@ def encode_test(
 
 
 def fill_static_defaults(
-    tool_state: Dict[str, Any], input_models: ToolParameterBundle, profile: float, partial: bool = True
+    tool_state: Dict[str, Any],
+    input_models: ToolParameterBundle,
+    profile: float,
+    partial: bool = True,
+    url_data_defaults: bool = False,
 ) -> Dict[str, Any]:
     """If additional defaults might stem from Galaxy runtime, partial should be true.
 
     Setting partial to True, prevents runtime validation.
     """
-    _fill_defaults(tool_state, input_models)
+    _fill_defaults(tool_state, input_models, url_data_defaults=url_data_defaults)
 
     if not partial:
         internal_state = JobInternalToolState(tool_state)
@@ -343,12 +348,14 @@ def fill_static_defaults(
     return tool_state
 
 
-def _fill_defaults(tool_state: Dict[str, Any], input_models: ToolParameterBundle) -> None:
+def _fill_defaults(
+    tool_state: Dict[str, Any], input_models: ToolParameterBundle, url_data_defaults: bool = False
+) -> None:
     for parameter in input_models.parameters:
-        _fill_default_for(tool_state, parameter)
+        _fill_default_for(tool_state, parameter, url_data_defaults=url_data_defaults)
 
 
-def _fill_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT) -> None:
+def _fill_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT, url_data_defaults: bool = False) -> None:
     parameter_name = parameter.name
     if isinstance(parameter, BooleanParameterModel):
         if parameter_name not in tool_state:
@@ -394,19 +401,24 @@ def _fill_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT) ->
         )
         test_value = validate_explicit_conditional_test_value(test_parameter_name, explicit_test_value)
         when = _select_which_when(parameter, test_value, conditional_state)
-        _fill_default_for(conditional_state, test_parameter)
-        _fill_defaults(conditional_state, when)
+        _fill_default_for(conditional_state, test_parameter, url_data_defaults=url_data_defaults)
+        _fill_defaults(conditional_state, when, url_data_defaults=url_data_defaults)
     elif isinstance(parameter, RepeatParameterModel):
         repeat_instances = _initialize_repeat_state(parameter, tool_state)
         for instance_state in repeat_instances:
-            _fill_defaults(instance_state, parameter)
+            _fill_defaults(instance_state, parameter, url_data_defaults=url_data_defaults)
     elif isinstance(parameter, SectionParameterModel):
         section_state = _initialize_section_state(parameter, tool_state)
-        _fill_defaults(section_state, parameter)
+        _fill_defaults(section_state, parameter, url_data_defaults=url_data_defaults)
     elif isinstance(parameter, DataCollectionParameterModel):
         collection_parameter = parameter
         if parameter_name not in tool_state and collection_parameter.optional:
             tool_state[parameter_name] = None
+    elif isinstance(parameter, DataParameterModel):
+        if url_data_defaults and parameter_name not in tool_state and parameter.url_default:
+            tool_state[parameter_name] = DataRequestUri(
+                url=parameter.url_default, ext="auto", deferred=True
+            ).model_dump()
     elif isinstance(parameter, TextParameterModel):
         if parameter_name not in tool_state:
             if not parameter.optional:
diff --git a/lib/galaxy/tool_util/parameters/visitor.py b/lib/galaxy/tool_util/parameters/visitor.py
index 20ea4ded882..ebd515496ad 100644
--- a/lib/galaxy/tool_util/parameters/visitor.py
+++ b/lib/galaxy/tool_util/parameters/visitor.py
@@ -74,10 +74,6 @@ def _visit_input_values(
         name = model.name
         input_value = input_values.get(name, VISITOR_UNDEFINED)
         if input_value is VISITOR_UNDEFINED:
-            if model.parameter_type not in ("gx_repeat", "gx_section", "gx_conditional"):
-                replacement = callback(model, None)
-                if replacement != no_replacement_value:
-                    new_input_values[name] = replacement
             continue
 
         if model.parameter_type == "gx_repeat":
diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index 67c6746d7a8..385291ed905 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -182,10 +182,10 @@ def dynamic_model_information_from_py_type(
     param_model: ParamModel,
     py_type: Type,
     requires_value: Optional[bool] = None,
-    validators=None,
+    validators: Optional[Dict[str, Any]] = None,
     extra_json_schema: Optional[Dict[str, Any]] = None,
     default: Any = _UNSET,
-):
+) -> DynamicModelInformation:
     name = safe_field_name(param_model.name)
     if default is not _UNSET:
         initialize = default
@@ -1321,7 +1321,7 @@ class DataParameterModel(BaseGalaxyToolParameterModelDefinition):
 
     @property
     def request_requires_value(self) -> bool:
-        return not self.optional
+        return not self.optional and self.url_default is None
 
 
 class DataCollectionRequest(StrictModel):
diff --git a/lib/galaxy/webapps/galaxy/services/jobs.py b/lib/galaxy/webapps/galaxy/services/jobs.py
index 9e8cc7dada8..ffb097f8180 100644
--- a/lib/galaxy/webapps/galaxy/services/jobs.py
+++ b/lib/galaxy/webapps/galaxy/services/jobs.py
@@ -55,6 +55,7 @@ from galaxy.schema.tasks import (
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.tool_util.parameters import (
     decode,
+    fill_static_defaults,
     RelaxedRequestToolState,
     RequestToolState,
     strictify,
@@ -262,6 +263,17 @@ class JobsService(ServiceBase):
             request_state = RequestToolState(inputs or {})
         request_state.validate(parameter_bundle, f"{tool.id} (request model)")
         request_internal_state = decode(request_state, parameter_bundle, trans.security.decode_id)
+        # Fill url_default values and re-validate before persisting the ToolRequest.
+        # The execution path handles general defaults, but the internal state must be
+        # fully resolved here so the persisted request is self-contained.
+        fill_static_defaults(
+            request_internal_state.input_state,
+            parameter_bundle,
+            tool.profile,
+            partial=True,
+            url_data_defaults=True,
+        )
+        request_internal_state.validate(parameter_bundle, f"{tool.id} (request internal model)")
         tool_request = ToolRequest()
         # TODO: hash and such...
         tool_source_model = ToolSourceModel(
diff --git a/test/unit/tool_util/test_parameter_convert.py b/test/unit/tool_util/test_parameter_convert.py
index b3b289df34c..c913ef23311 100644
--- a/test/unit/tool_util/test_parameter_convert.py
+++ b/test/unit/tool_util/test_parameter_convert.py
@@ -24,6 +24,14 @@ from galaxy.tool_util.parameters import (
     strictify,
 )
 from galaxy.tool_util.parser.util import parse_profile_version
+from galaxy.tool_util_models.parameters import (
+    BooleanParameterModel,
+    ConditionalParameterModel,
+    ConditionalWhen,
+    DataParameterModel,
+    SectionParameterModel,
+    ToolParameterBundleModel,
+)
 from .test_parameter_test_cases import tool_source_for
 
 EXAMPLE_ID_1_ENCODED = "123456789abcde"
@@ -180,6 +188,81 @@ def test_dereference():
     dereferenced_state.validate(bundle)
 
 
+def test_dereference_url_default_after_default_fill():
+    bundle = ToolParameterBundleModel(
+        parameters=[
+            DataParameterModel(
+                type="data",
+                name="parameter",
+                url_default="https://example.com/1.bed",
+            )
+        ]
+    )
+
+    dereferenced_state = _strict_async_decode_default_fill_and_dereference({}, bundle)
+
+    assert dereferenced_state.input_state == {"parameter": {"src": "hda", "id": EXAMPLE_ID_1}}
+
+
+def test_dereference_section_url_default_after_default_fill():
+    bundle = ToolParameterBundleModel(
+        parameters=[
+            SectionParameterModel(
+                type="section",
+                name="section_parameter",
+                parameters=[
+                    DataParameterModel(
+                        type="data",
+                        name="data_parameter",
+                        url_default="https://example.com/1.bed",
+                    )
+                ],
+            )
+        ]
+    )
+
+    dereferenced_state = _strict_async_decode_default_fill_and_dereference({}, bundle)
+
+    assert dereferenced_state.input_state == {
+        "section_parameter": {"data_parameter": {"src": "hda", "id": EXAMPLE_ID_1}}
+    }
+
+
+def test_dereference_conditional_url_default_after_default_fill():
+    bundle = ToolParameterBundleModel(
+        parameters=[
+            ConditionalParameterModel(
+                type="conditional",
+                name="conditional_parameter",
+                test_parameter=BooleanParameterModel(type="boolean", name="test_parameter"),
+                whens=[
+                    ConditionalWhen(
+                        discriminator=False,
+                        is_default_when=True,
+                        parameters=[
+                            DataParameterModel(
+                                type="data",
+                                name="data_parameter",
+                                url_default="https://example.com/1.bed",
+                            )
+                        ],
+                    ),
+                    ConditionalWhen(discriminator=True, is_default_when=False, parameters=[]),
+                ],
+            )
+        ]
+    )
+
+    dereferenced_state = _strict_async_decode_default_fill_and_dereference({}, bundle)
+
+    assert dereferenced_state.input_state == {
+        "conditional_parameter": {
+            "test_parameter": False,
+            "data_parameter": {"src": "hda", "id": EXAMPLE_ID_1},
+        }
+    }
+
+
 def test_fill_defaults():
     with_defaults = fill_state_for({}, "parameters/gx_int")
     assert with_defaults["parameter"] == 1
@@ -308,6 +391,16 @@ def _fake_encode(input: int) -> str:
     return ID_MAP[input]
 
 
+def _strict_async_decode_default_fill_and_dereference(
+    tool_state: Dict[str, Any], bundle: ToolParameterBundleModel
+) -> RequestInternalDereferencedToolState:
+    request_state = RequestToolState(tool_state)
+    request_state.validate(bundle)
+    request_internal_state = decode(request_state, bundle, _fake_decode)
+    fill_static_defaults(request_internal_state.input_state, bundle, 24.0, partial=True, url_data_defaults=True)
+    return dereference(request_internal_state, bundle, _fake_dereference, _fake_collection_deference)
+
+
 def fill_state_for(tool_state: Dict[str, Any], tool_path: str, partial: bool = False) -> Dict[str, Any]:
     tool_source = tool_source_for(tool_path)
     bundle = input_models_for_tool_source(tool_source)

From e9a52f6acd1429a9c2e8e900ddfa5e7f2b3af917 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 22:19:34 +0200
Subject: [PATCH 121/256] Fix async tool test parameter parsing

---
 lib/galaxy/tool_util/parameters/case.py       |   7 +-
 lib/galaxy/util/permutations.py               |   2 +-
 .../tool_util/test_parameter_test_cases.py    | 129 ++++++++++++++++++
 3 files changed, 136 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index ac98c21d984..69465ea78c3 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -384,9 +384,14 @@ def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[T
     # prefix (e.g. <param name="fasta"> instead of <param name="mode|fasta">).
     if "|" in flat_state_path:
         short_name = flat_state_path.rsplit("|", 1)[1]
+        matching_inputs = []
         for input in inputs:
             if input["name"] == short_name:
-                return input
+                matching_inputs.append(input)
+        if len(matching_inputs) == 1:
+            return matching_inputs[0]
+        elif len(matching_inputs) > 1:
+            raise Exception(f"Ambiguous unqualified test parameter name ({short_name}) for ({flat_state_path})")
     return None
 
 
diff --git a/lib/galaxy/util/permutations.py b/lib/galaxy/util/permutations.py
index b1012687308..bd70340e53a 100644
--- a/lib/galaxy/util/permutations.py
+++ b/lib/galaxy/util/permutations.py
@@ -155,7 +155,7 @@ def is_in_state(state_dict, key, nested):
     else:
         first, rest = key.split("|", 1)
         # repeats?
-        is_in_state(state_dict.get(first), rest, nested)
+        return is_in_state(state_dict.get(first), rest, nested)
 
 
 def looks_like_flattened_repeat_key(key: str) -> bool:
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index c9def103056..882649bf390 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -34,6 +34,7 @@ from galaxy.tool_util_models.tool_source import (
     JsonTestCollectionDefDict,
     JsonTestDatasetDefDict,
 )
+from galaxy.util.permutations import is_in_state
 from .util import dict_verify_each
 
 # legacy tools allows specifying parameter and repeat parameters without
@@ -255,6 +256,122 @@ def test_test_case_state_conversion():
     dict_verify_each(state.tool_state.input_state, expectations)
 
 
+def test_is_in_state_supports_nested_keys():
+    state = {
+        "section": {
+            "parameter": "value",
+        },
+    }
+
+    assert is_in_state(state, "section|parameter", nested=True)
+    assert not is_in_state(state, "section|missing", nested=True)
+
+
+
+
+def test_test_case_request_conversion_preserves_non_default_select_and_booleans():
+    tool_source = raw_xml_tool_source(
+        """
+<tool id="async_request_regression" name="async_request_regression" version="1.0.0">
+    <command>echo</command>
+    <inputs>
+        <param name="output_type" type="select">
+            <option value="meta" selected="true">MetaBAT2</option>
+            <option value="semi">SemiBin2</option>
+        </param>
+        <param name="full_contig_name" type="boolean" truevalue="--full-contig-name" falsevalue="" />
+        <section name="advanced_settings" expanded="false">
+            <param name="method" type="select">
+                <option value="hybrid" selected="true">Hybrid</option>
+                <option value="wgs">WGS</option>
+            </param>
+            <param name="remove_identical_sequences" type="boolean" truevalue="-d" falsevalue="" />
+        </section>
+    </inputs>
+    <outputs />
+    <tests>
+        <test>
+            <param name="output_type" value="semi" />
+            <param name="full_contig_name" value="true" />
+            <section name="advanced_settings">
+                <param name="method" value="wgs" />
+                <param name="remove_identical_sequences" value="true" />
+            </section>
+        </test>
+    </tests>
+</tool>
+        """
+    )
+    parameters = input_models_for_tool_source(tool_source)
+    parsed_tool = parse_tool(tool_source)
+    test_case = tool_source.parse_tests_to_dict()["tests"][0]
+    test_case_state = case_state(test_case, parsed_tool.inputs, tool_source.parse_profile()).tool_state
+
+    request_state = encode_test(test_case_state, parameters, mock_adapt_datasets, mock_adapt_collections)
+
+    expectations = [
+        (["output_type"], "semi"),
+        (["full_contig_name"], True),
+        (["advanced_settings", "method"], "wgs"),
+        (["advanced_settings", "remove_identical_sequences"], True),
+    ]
+    dict_verify_each(request_state.input_state, expectations)
+
+
+def test_nested_conditional_duplicate_short_names_are_distinct_when_qualified():
+    tool_source = raw_xml_tool_source(
+        """
+<tool id="duplicate_use_regression" name="duplicate_use_regression" version="1.0.0">
+    <command>echo</command>
+    <inputs>
+        <conditional name="operation">
+            <param name="use" type="select">
+                <option value="droplets" selected="true">Droplets</option>
+                <option value="other">Other</option>
+            </param>
+            <when value="droplets">
+                <conditional name="method">
+                    <param name="use" type="select">
+                        <option value="default" selected="true">Default</option>
+                        <option value="expected">Expected</option>
+                    </param>
+                    <when value="default" />
+                    <when value="expected">
+                        <param name="expected" type="integer" value="1000" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="other" />
+        </conditional>
+    </inputs>
+    <outputs />
+    <tests>
+        <test>
+            <conditional name="operation">
+                <param name="use" value="droplets" />
+                <conditional name="method">
+                    <param name="use" value="expected" />
+                    <param name="expected" value="2000" />
+                </conditional>
+            </conditional>
+        </test>
+    </tests>
+</tool>
+        """
+    )
+    parsed_tool = parse_tool(tool_source)
+    test_case = tool_source.parse_tests_to_dict()["tests"][0]
+
+    tool_state = case_state(test_case, parsed_tool.inputs, tool_source.parse_profile()).tool_state
+
+    expectations = [
+        (["operation", "use"], "droplets"),
+        (["operation", "method", "use"], "expected"),
+        (["operation", "method", "expected"], 2000),
+    ]
+    dict_verify_each(tool_state.input_state, expectations)
+
+
 def test_convert_to_requests():
     tools = [
         "parameters/gx_drill_down_recurse_multiple",
@@ -316,4 +433,16 @@ def case_state_for(tool_source: ToolSource, test_case: ToolSourceTest) -> TestCa
     return case_state(test_case, parsed_tool.inputs, profile)
 
 
+def raw_xml_tool_source(raw_tool_source: str) -> ToolSource:
+    return get_tool_source(tool_source_class="XmlToolSource", raw_tool_source=raw_tool_source)
+
+
+def mock_adapt_datasets(input: JsonTestDatasetDefDict) -> DataRequestHda:
+    return DataRequestHda(src="hda", id=MOCK_ID)
+
+
+def mock_adapt_collections(input: JsonTestCollectionDefDict) -> DataCollectionRequest:
+    return DataCollectionRequest(src="hdca", id=MOCK_ID)
+
+
 tool_source_for = functional_test_tool_source

From a9eaadecd604a8b3c590c34aa75085bbd367af77 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 22:53:36 +0200
Subject: [PATCH 122/256] Fix async tool request parsing

---
 lib/galaxy/tool_util/parameters/case.py       | 62 +++++++++++++++++--
 .../tool_util/test_parameter_test_cases.py    | 43 +++++++++++++
 2 files changed, 101 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 69465ea78c3..81d487a05e7 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -132,6 +132,10 @@ def legacy_from_string(parameter: ToolParameterT, value: Optional[Any], warnings
                 # value="" is a legacy convention for "nothing selected"; filter empty parts to produce [].
                 # Tools with profile >= 26.1 must use value_json="[]" explicitly.
                 result_value = multiple_select_value_split(value)
+                if Version(profile) < Version("24.2"):
+                    result_value = [_legacy_select_label_to_value(parameter, v) for v in result_value]
+            elif Version(profile) < Version("24.2"):
+                result_value = _legacy_select_label_to_value(parameter, value)
         elif isinstance(parameter, (DataColumnParameterModel,)):
             if parameter.multiple:
                 integers_match = INTEGER_STR_PATTERN.match(value)
@@ -161,6 +165,18 @@ def legacy_from_string(parameter: ToolParameterT, value: Optional[Any], warnings
     return result_value
 
 
+def _legacy_select_label_to_value(parameter: SelectParameterModel, value: str) -> str:
+    if parameter.options is None:
+        return value
+    for option in parameter.options:
+        if option.value == value:
+            return value
+    for option in parameter.options:
+        if option.label == value:
+            return option.value
+    return value
+
+
 def test_case_state(
     test_dict: ToolSourceTest,
     tool_parameter_bundle: List[ToolParameterT],
@@ -187,10 +203,17 @@ def test_case_state(
     if validate:
         tool_state.validate(tool_parameter_bundle, name=name)
         for input_name in unhandled_inputs:
-            raise Exception(f"Invalid parameter name found {input_name}")
+            if not _input_name_was_handled_by_legacy_fallback(input_name, handled_inputs, profile):
+                raise Exception(f"Invalid parameter name found {input_name}")
     return TestCaseStateAndWarnings(tool_state, warnings, unhandled_inputs)
 
 
+def _input_name_was_handled_by_legacy_fallback(input_name: str, handled_inputs: Set[str], profile: str) -> bool:
+    return Version(profile) < Version("24.2") and any(
+        handled_input == input_name or handled_input.endswith(f"|{input_name}") for handled_input in handled_inputs
+    )
+
+
 def test_case_validation(
     test_dict: ToolSourceTest, tool_parameter_bundle: List[ToolParameterT], profile: str, name: Optional[str] = None
 ) -> TestCaseStateValidationResult:
@@ -274,10 +297,10 @@ def _merge_into_state(
         if input_name not in state_at_level:
             state_at_level[input_name] = repeat_state_array
 
-        repeat_instance_inputs = repeat_inputs_to_array(state_path, _inputs_as_dict(inputs))
+        repeat_instance_inputs = _repeat_inputs_to_array(state_path, tool_input.parameters, inputs)
         if tool_input.min is not None:
             while len(repeat_instance_inputs) < tool_input.min:
-                repeat_instance_inputs.append({})
+                repeat_instance_inputs.append([])
         for i, _ in enumerate(repeat_instance_inputs):
             while len(repeat_state_array) <= i:
                 repeat_state_array.append({})
@@ -286,7 +309,7 @@ def _merge_into_state(
             handled_inputs.update(
                 _merge_level_into_state(
                     tool_input.parameters,
-                    inputs,
+                    repeat_instance_inputs[i],
                     repeat_state_array[i],
                     profile,
                     state_representation,
@@ -354,6 +377,27 @@ def _merge_into_state(
     return handled_inputs
 
 
+def _repeat_inputs_to_array(
+    state_path: str, parameters: List[ToolParameterT], inputs: ToolSourceTestInputs
+) -> List[ToolSourceTestInputs]:
+    repeat_instance_input_dicts = repeat_inputs_to_array(state_path, _inputs_as_dict(inputs))
+    repeat_instance_inputs = [list(instance_inputs.values()) for instance_inputs in repeat_instance_input_dicts]
+    if repeat_instance_inputs:
+        return repeat_instance_inputs
+
+    legacy_repeat_inputs: List[ToolSourceTestInputs] = []
+    for parameter in parameters:
+        parameter_name = parameter.name
+        matching_inputs = [input for input in inputs if input["name"] == parameter_name]
+        for i, input in enumerate(matching_inputs):
+            while len(legacy_repeat_inputs) <= i:
+                legacy_repeat_inputs.append([])
+            synthetic_input = cast(ToolSourceTestInput, dict(input))
+            synthetic_input["name"] = f"{state_path}_{i}|{parameter_name}"
+            legacy_repeat_inputs[i].append(synthetic_input)
+    return legacy_repeat_inputs
+
+
 def _select_which_when(
     conditional: ConditionalParameterModel, state: dict, inputs: ToolSourceTestInputs, prefix: str
 ) -> ConditionalWhen:
@@ -383,6 +427,16 @@ def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[T
     # Fallback for legacy test cases that specify conditional/section params without the pipe-separated
     # prefix (e.g. <param name="fasta"> instead of <param name="mode|fasta">).
     if "|" in flat_state_path:
+        suffix_matching_inputs = []
+        for input in inputs:
+            input_name = input["name"]
+            if "|" in input_name and flat_state_path.endswith(f"|{input_name}"):
+                suffix_matching_inputs.append(input)
+        if len(suffix_matching_inputs) == 1:
+            return suffix_matching_inputs[0]
+        elif len(suffix_matching_inputs) > 1:
+            raise Exception(f"Ambiguous partially qualified test parameter name for ({flat_state_path})")
+
         short_name = flat_state_path.rsplit("|", 1)[1]
         matching_inputs = []
         for input in inputs:
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index 882649bf390..469303181d8 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -372,6 +372,49 @@ def test_nested_conditional_duplicate_short_names_are_distinct_when_qualified():
     dict_verify_each(tool_state.input_state, expectations)
 
 
+def test_legacy_partial_conditional_paths_are_resolved_for_request_state():
+    tool_source = tool_source_for("disambiguate_cond")
+    test_case = tool_source.parse_tests_to_dict()["tests"][1]
+
+    tool_state = case_state_for(tool_source, test_case).tool_state
+
+    expectations = [
+        (["p1", "use"], True),
+        (["p2", "use"], False),
+        (["p3", "use"], True),
+        (["files", "p4", "use"], True),
+        (["files", "p4", "file", "path"], "simple_line.txt"),
+    ]
+    dict_verify_each(tool_state.input_state, expectations)
+
+
+def test_legacy_unqualified_repeat_inputs_are_expanded_for_request_state():
+    tool_source = tool_source_for("multi_repeats")
+    test_cases = tool_source.parse_tests_to_dict()["tests"]
+
+    test_case_state = case_state_for(tool_source, test_cases[2]).tool_state
+
+    expectations = [
+        (["queries", 0, "input2", "path"], "simple_line.txt"),
+        (["queries", 1, "input2", "path"], "simple_line.txt"),
+        (["more_queries", 0, "more_queries_input", "path"], "simple_line.txt"),
+        (["more_queries", 1, "more_queries_input", "path"], "simple_line.txt"),
+    ]
+    dict_verify_each(test_case_state.input_state, expectations)
+
+
+def test_legacy_select_labels_are_converted_to_values_for_request_state():
+    tool_source = tool_source_for("multi_select")
+    test_case = tool_source.parse_tests_to_dict()["tests"][1]
+
+    test_case_state = case_state_for(tool_source, test_case).tool_state
+
+    expectations = [
+        (["select_ex", 0], "--ex1"),
+    ]
+    dict_verify_each(test_case_state.input_state, expectations)
+
+
 def test_convert_to_requests():
     tools = [
         "parameters/gx_drill_down_recurse_multiple",

From 5f0f508d0be491a9d20790569dedaf8b4b9641a7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 14 Jun 2026 22:53:42 +0200
Subject: [PATCH 123/256] Fix nested state writes for async tools

---
 lib/galaxy/util/permutations.py               | 12 +++++--
 .../tool_util/test_parameter_test_cases.py    | 33 ++++++++++++++-----
 2 files changed, 33 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/util/permutations.py b/lib/galaxy/util/permutations.py
index bd70340e53a..e458b56b516 100644
--- a/lib/galaxy/util/permutations.py
+++ b/lib/galaxy/util/permutations.py
@@ -8,7 +8,11 @@ with itertools product and permutations. These are open questions.
 """
 
 import copy
-from typing import Tuple
+from typing import (
+    Any,
+    Optional,
+    Tuple,
+)
 
 from galaxy.exceptions import MessageException
 from galaxy.util.bunch import Bunch
@@ -103,7 +107,7 @@ def state_copy(inputs, nested):
     return state_dict_copy
 
 
-def state_set_value(state_dict, key, value, nested):
+def state_set_value(state_dict: dict, key: str, value: Any, nested: bool) -> None:
     if "|" not in key or not nested:
         state_dict[key] = value
     else:
@@ -117,6 +121,8 @@ def state_set_value(state_dict, key, value, nested):
                 repeat_state.append({})
             state_set_value(repeat_state[index], rest, value, nested)
         else:
+            if first not in state_dict:
+                state_dict[first] = {}
             state_set_value(state_dict[first], rest, value, nested)
 
 
@@ -147,7 +153,7 @@ def state_get_value(state_dict, key, nested):
             return state_get_value(state_dict[first], rest, nested)
 
 
-def is_in_state(state_dict, key, nested):
+def is_in_state(state_dict: Optional[dict], key: str, nested: bool) -> bool:
     if not state_dict:
         return False
     if "|" not in key or not nested:
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index 469303181d8..58f7a9652ba 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -34,7 +34,10 @@ from galaxy.tool_util_models.tool_source import (
     JsonTestCollectionDefDict,
     JsonTestDatasetDefDict,
 )
-from galaxy.util.permutations import is_in_state
+from galaxy.util.permutations import (
+    is_in_state,
+    state_set_value,
+)
 from .util import dict_verify_each
 
 # legacy tools allows specifying parameter and repeat parameters without
@@ -267,11 +270,26 @@ def test_is_in_state_supports_nested_keys():
     assert not is_in_state(state, "section|missing", nested=True)
 
 
+def test_state_set_value_creates_nested_parent_state():
+    state: dict[str, Any] = {}
+
+    state_set_value(state, "p1|p1use", True, nested=True)
+    state_set_value(state, "files_0|file", "dataset", nested=True)
+
+    assert state == {
+        "p1": {
+            "p1use": True,
+        },
+        "files": [
+            {
+                "file": "dataset",
+            }
+        ],
+    }
 
 
 def test_test_case_request_conversion_preserves_non_default_select_and_booleans():
-    tool_source = raw_xml_tool_source(
-        """
+    tool_source = raw_xml_tool_source("""
 <tool id="async_request_regression" name="async_request_regression" version="1.0.0">
     <command>echo</command>
     <inputs>
@@ -300,8 +318,7 @@ def test_test_case_request_conversion_preserves_non_default_select_and_booleans(
         </test>
     </tests>
 </tool>
-        """
-    )
+        """)
     parameters = input_models_for_tool_source(tool_source)
     parsed_tool = parse_tool(tool_source)
     test_case = tool_source.parse_tests_to_dict()["tests"][0]
@@ -319,8 +336,7 @@ def test_test_case_request_conversion_preserves_non_default_select_and_booleans(
 
 
 def test_nested_conditional_duplicate_short_names_are_distinct_when_qualified():
-    tool_source = raw_xml_tool_source(
-        """
+    tool_source = raw_xml_tool_source("""
 <tool id="duplicate_use_regression" name="duplicate_use_regression" version="1.0.0">
     <command>echo</command>
     <inputs>
@@ -357,8 +373,7 @@ def test_nested_conditional_duplicate_short_names_are_distinct_when_qualified():
         </test>
     </tests>
 </tool>
-        """
-    )
+        """)
     parsed_tool = parse_tool(tool_source)
     test_case = tool_source.parse_tests_to_dict()["tests"][0]
 

From f9c98a016b2462108eadb5695ee0a17c4af1ba1d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 15 Jun 2026 00:24:31 +0200
Subject: [PATCH 124/256] Fix state_set_value misidentifying conditional names
 with digit suffix as repeats

When building reordered_incoming from scratch in reorder_parameters, conditional
parameter names ending in _N (e.g. "inner_options_1") were incorrectly treated as
flattened repeat indices for a repeat named "inner_options". This happened because
state_set_value checks looks_like_flattened_repeat_key before checking whether
the key exists in the state dict being built, and the new empty dict had no
entry for "inner_options_1" yet.

Fix: only treat a key as a flattened repeat key if the corresponding repeat list
already exists in state_dict (we're adding more elements), or if this is the
first element (index 0). Genuine repeats always start at index 0, so
encountering index > 1 without an existing list indicates a conditional name.

Add a unit test covering this exact scenario.
---
 lib/galaxy/util/permutations.py               | 25 +++++++++++--------
 .../tool_util/test_parameter_test_cases.py    | 18 +++++++++++++
 2 files changed, 33 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/util/permutations.py b/lib/galaxy/util/permutations.py
index e458b56b516..3b316ee6c5b 100644
--- a/lib/galaxy/util/permutations.py
+++ b/lib/galaxy/util/permutations.py
@@ -114,16 +114,21 @@ def state_set_value(state_dict: dict, key: str, value: Any, nested: bool) -> Non
         first, rest = key.split("|", 1)
         if first not in state_dict and looks_like_flattened_repeat_key(first):
             repeat_name, index = split_flattened_repeat_key(first)
-            if repeat_name not in state_dict:
-                state_dict[repeat_name] = []
-            repeat_state = state_dict[repeat_name]
-            while len(repeat_state) <= index:
-                repeat_state.append({})
-            state_set_value(repeat_state[index], rest, value, nested)
-        else:
-            if first not in state_dict:
-                state_dict[first] = {}
-            state_set_value(state_dict[first], rest, value, nested)
+            # Only treat as a flattened repeat key if the repeat list already exists
+            # or this is the first element (index 0). This avoids misidentifying
+            # conditional names ending in _N (e.g. "inner_options_1") as repeat indices
+            # when no repeat list has been started yet.
+            if index == 0 or isinstance(state_dict.get(repeat_name), list):
+                if repeat_name not in state_dict:
+                    state_dict[repeat_name] = []
+                repeat_state = state_dict[repeat_name]
+                while len(repeat_state) <= index:
+                    repeat_state.append({})
+                state_set_value(repeat_state[index], rest, value, nested)
+                return
+        if first not in state_dict:
+            state_dict[first] = {}
+        state_set_value(state_dict[first], rest, value, nested)
 
 
 def state_remove_value(state_dict, key, nested):
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index 58f7a9652ba..637789025ae 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -288,6 +288,24 @@ def test_state_set_value_creates_nested_parent_state():
     }
 
 
+def test_state_set_value_does_not_misidentify_conditional_names_with_digit_suffix():
+    # Conditional parameter names ending in _N (e.g. "inner_options_1") must not be
+    # treated as flattened repeat indices when no repeat list has been started yet.
+    state: dict[str, Any] = {}
+
+    state_set_value(state, "outer|inner_options_1|mode", "by_index", nested=True)
+    state_set_value(state, "outer|inner_options_1|col", 1, nested=True)
+    state_set_value(state, "outer|inner_options_2|mode", "by_name", nested=True)
+    state_set_value(state, "outer|inner_options_2|label", "foo", nested=True)
+
+    assert state == {
+        "outer": {
+            "inner_options_1": {"mode": "by_index", "col": 1},
+            "inner_options_2": {"mode": "by_name", "label": "foo"},
+        }
+    }
+
+
 def test_test_case_request_conversion_preserves_non_default_select_and_booleans():
     tool_source = raw_xml_tool_source("""
 <tool id="async_request_regression" name="async_request_regression" version="1.0.0">

From 88cb11d7f0ec98ccfdff328401dcd27866df692d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 15 Jun 2026 11:04:18 +0200
Subject: [PATCH 125/256] Fix openapi/utils.py mypy arg-type error with
 fastapi>=0.137.0

---
 lib/galaxy/webapps/openapi/utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/openapi/utils.py b/lib/galaxy/webapps/openapi/utils.py
index f7b62f62fc3..74d5f634e2d 100644
--- a/lib/galaxy/webapps/openapi/utils.py
+++ b/lib/galaxy/webapps/openapi/utils.py
@@ -81,7 +81,7 @@ def get_openapi(
     for route in routes or []:
         if isinstance(route, routing.APIRoute):
             result = get_openapi_path(
-                route=route,
+                route=route,  # type: ignore[arg-type,unused-ignore]
                 operation_ids=operation_ids,
                 model_name_map=model_name_map,
                 field_mapping=field_mapping,
@@ -99,7 +99,7 @@ def get_openapi(
     for webhook in webhooks or []:
         if isinstance(webhook, routing.APIRoute):
             result = get_openapi_path(
-                route=webhook,
+                route=webhook,  # type: ignore[arg-type,unused-ignore]
                 operation_ids=operation_ids,
                 model_name_map=model_name_map,
                 field_mapping=field_mapping,

From 2f52713286ce59bde75a89845da14a7ff593b226 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 15 Jun 2026 11:04:18 +0200
Subject: [PATCH 126/256] Fix PostgreSQL session abort when model operation
 tool raises before copy flush

---
 lib/galaxy/managers/jobs.py  | 1 +
 lib/galaxy/tools/__init__.py | 5 ++---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 04ed5e2cd0a..df5d4cf589c 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -2289,6 +2289,7 @@ class JobSubmitter:
             sa_session.commit()
         except Exception as e:
             log.exception("Problem validating tool state after request created")
+            sa_session.rollback()
             tool_request.state = ToolRequest.states.FAILED
             state_message: dict = {"err_msg": str(e)}
             if isinstance(e, MessageException) and e.extra_error_info:
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 6f2b82dd18c..aa02da31612 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -4742,6 +4742,8 @@ class RelabelFromFileTool(DatabaseOperationTool):
 
         def add_copied_value_to_new_elements(new_label, dce_object, columns):
             new_label = new_label.strip()
+            if not re.match(r"^[\w\- \.,]+$", new_label):
+                raise exceptions.MessageException(f"Invalid new collection identifier [{new_label}]")
             if new_label in new_elements:
                 raise exceptions.MessageException(
                     f"New identifier [{new_label}] appears twice in resulting collection, these values must be unique."
@@ -4799,9 +4801,6 @@ class RelabelFromFileTool(DatabaseOperationTool):
             for i, dce in enumerate(hdca.collection.elements):
                 dce_object = dce.element_object
                 add_copied_value_to_new_elements(new_labels[i], dce_object, dce.columns)
-        for key in new_elements.keys():
-            if not re.match(r"^[\w\- \.,]+$", key):
-                raise exceptions.MessageException(f"Invalid new collection identifier [{key}]")
         self._add_datasets_to_history(history, new_elements.values())
         output_collections.create_collection(
             next(iter(self.outputs.values())),

From a060ba4e8a204c20e1c776a42273f0cbb140ebfa Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 15 Jun 2026 14:02:02 +0200
Subject: [PATCH 127/256] Introduce per-file progress tracking for TUS uploads

---
 .../upload/useUploadBatchOperations.ts        |  5 +-
 .../composables/upload/useUploadSubmission.ts |  6 +-
 client/src/utils/upload.ts                    | 67 +++++++++++++++++--
 3 files changed, 67 insertions(+), 11 deletions(-)

diff --git a/client/src/composables/upload/useUploadBatchOperations.ts b/client/src/composables/upload/useUploadBatchOperations.ts
index 741bbcf1efc..c0a13c45341 100644
--- a/client/src/composables/upload/useUploadBatchOperations.ts
+++ b/client/src/composables/upload/useUploadBatchOperations.ts
@@ -152,8 +152,9 @@ export function useUploadBatchOperations(options: UploadBatchOperationsOptions =
                     collectionType: batch.type,
                 },
                 {
-                    progress: (percentage) => {
-                        ids.forEach((id) => uploadState.updateProgress(id, percentage));
+                    uploadIds: ids,
+                    perFileProgress: (fileId, percentage) => {
+                        uploadState.updateProgress(fileId, percentage);
                     },
                     success: () => {
                         ids.forEach((id) => uploadState.updateProgress(id, 100));
diff --git a/client/src/composables/upload/useUploadSubmission.ts b/client/src/composables/upload/useUploadSubmission.ts
index 510b8ad9c14..f363a4c3651 100644
--- a/client/src/composables/upload/useUploadSubmission.ts
+++ b/client/src/composables/upload/useUploadSubmission.ts
@@ -10,7 +10,6 @@ import {
     markTrackedCompleted,
     markTrackedError,
     splitTrackedUploadsByType,
-    updateTrackedProgress,
 } from "@/composables/upload/uploadTracking";
 import { useUploadBatchOperations } from "@/composables/upload/useUploadBatchOperations";
 import { errorMessageAsString } from "@/utils/simple-error";
@@ -103,7 +102,10 @@ export function useUploadSubmission() {
                 },
                 progress: (percentage) => {
                     onProgress?.(percentage);
-                    updateTrackedProgress(uploadState, apiIds, percentage);
+                },
+                uploadIds: apiIds,
+                perFileProgress: (fileId, percentage) => {
+                    uploadState.updateProgress(fileId, percentage);
                 },
             };
 
diff --git a/client/src/utils/upload.ts b/client/src/utils/upload.ts
index 07bcbb29a46..01efcbb4374 100644
--- a/client/src/utils/upload.ts
+++ b/client/src/utils/upload.ts
@@ -198,10 +198,18 @@ export interface BuildPayloadOptions {
 // Configuration Types
 // ============================================================================
 
+/** Per-file progress tracking options */
+interface PerFileProgressOptions {
+    /** Upload item IDs corresponding to files (one per file, for per-file progress tracking) */
+    uploadIds?: string[];
+    /** Callback for per-file progress updates (fileId, percentage) */
+    perFileProgress?: (fileId: string, percentage: number) => void;
+}
+
 /**
  * Configuration for upload submission.
  */
-export interface UploadSubmitConfig extends FetchDatasetsCallbacks {
+export interface UploadSubmitConfig extends FetchDatasetsCallbacks, PerFileProgressOptions {
     /** The upload payload data */
     data: UploadDataPayload;
     /** Whether this is a composite upload */
@@ -213,7 +221,7 @@ export interface UploadSubmitConfig extends FetchDatasetsCallbacks {
 /**
  * Configuration for the uploadDatasets function.
  */
-export interface UploadDatasetsConfig extends FetchDatasetsCallbacks, BuildPayloadOptions {
+export interface UploadDatasetsConfig extends FetchDatasetsCallbacks, BuildPayloadOptions, PerFileProgressOptions {
     /** Chunk size for TUS uploads in bytes (default: 10MB) */
     chunkSize?: number;
 }
@@ -833,14 +841,27 @@ function toApiPayload(data: UploadPayload): FetchDataPayload {
 
 /**
  * Uploads files via TUS protocol, then submits the complete payload.
+ *
+ * @param data - Upload payload containing files and targets
+ * @param tusEndpoint - TUS upload endpoint URL
+ * @param chunkSize - Chunk size for TUS uploads in bytes
+ * @param callbacks - Standard fetch callbacks (success, error, warning, progress)
+ * @param uploadIds - Optional array of upload item IDs (one per file) for per-file progress tracking
+ * @param perFileProgress - Optional callback for per-file progress updates
  */
 async function uploadFilesViaTus(
     data: UploadPayload,
     tusEndpoint: string,
     chunkSize: number,
     callbacks: FetchDatasetsCallbacks,
+    uploadIds?: string[],
+    perFileProgress?: (fileId: string, percentage: number) => void,
 ): Promise<void> {
     const files = data.files || [];
+    const hasPerFileTracking = uploadIds && perFileProgress && uploadIds.length === files.length;
+
+    // Track per-file progress for aggregate calculation
+    const fileProgressMap = new Map<string, number>();
 
     // Build API payload with TUS session info
     const apiPayload: Record<string, unknown> = {
@@ -857,12 +878,28 @@ async function uploadFilesViaTus(
                 continue;
             }
 
+            const fileId = hasPerFileTracking ? uploadIds[index] : undefined;
+
             const result = await createTusUpload({
                 file,
                 endpoint: tusEndpoint,
                 historyId: data.history_id,
                 chunkSize,
-                onProgress: callbacks.progress || (() => {}),
+                onProgress: (percentage: number) => {
+                    if (hasPerFileTracking && fileId) {
+                        fileProgressMap.set(fileId, percentage);
+                        perFileProgress!(fileId, percentage);
+
+                        // Compute aggregate progress from all files uploaded so far
+                        const values = Array.from(fileProgressMap.values());
+                        const aggregate = Math.round(
+                            values.reduce((sum: number, p: number) => sum + p, 0) / values.length,
+                        );
+                        callbacks.progress?.(aggregate);
+                    } else {
+                        callbacks.progress?.(percentage);
+                    }
+                },
                 onError: (err: Error) => {
                     callbacks.error?.(err);
                 },
@@ -899,6 +936,8 @@ export async function submitUpload(config: UploadSubmitConfig): Promise<void> {
         progress = () => {},
         isComposite = false,
         chunkSize = DEFAULT_CHUNK_SIZE,
+        uploadIds,
+        perFileProgress,
     } = config;
 
     // Initial validation
@@ -915,7 +954,7 @@ export async function submitUpload(config: UploadSubmitConfig): Promise<void> {
 
     if (hasFiles || isComposite) {
         // Upload files via TUS, then submit payload
-        await uploadFilesViaTus(data, tusEndpoint, chunkSize, callbacks);
+        await uploadFilesViaTus(data, tusEndpoint, chunkSize, callbacks, uploadIds, perFileProgress);
     } else if (data.targets && data.targets.length > 0) {
         const firstTarget = data.targets[0];
 
@@ -945,7 +984,7 @@ export async function submitUpload(config: UploadSubmitConfig): Promise<void> {
                     blob.name = String(firstElement.name || DEFAULT_FILE_NAME);
 
                     const filesData: UploadPayload = { ...data, files: [blob] };
-                    await uploadFilesViaTus(filesData, tusEndpoint, chunkSize, callbacks);
+                    await uploadFilesViaTus(filesData, tusEndpoint, chunkSize, callbacks, uploadIds, perFileProgress);
                 }
             }
         }
@@ -983,7 +1022,17 @@ export async function submitUpload(config: UploadSubmitConfig): Promise<void> {
  * ```
  */
 export async function uploadDatasets(items: ApiUploadItem[], config: UploadDatasetsConfig = {}): Promise<void> {
-    const { composite = false, compositeName, chunkSize, success, error, warning, progress } = config;
+    const {
+        composite = false,
+        compositeName,
+        chunkSize,
+        success,
+        error,
+        warning,
+        progress,
+        uploadIds,
+        perFileProgress,
+    } = config;
 
     try {
         // Build the API-ready payload from upload items
@@ -1006,6 +1055,8 @@ export async function uploadDatasets(items: ApiUploadItem[], config: UploadDatas
             error,
             warning,
             progress,
+            uploadIds,
+            perFileProgress,
         });
     } catch (err) {
         const errorMessage = errorMessageAsString(err);
@@ -1071,7 +1122,7 @@ export async function uploadCollectionDatasets(
     collectionOptions: CollectionUploadOptions,
     config: UploadDatasetsConfig = {},
 ): Promise<void> {
-    const { chunkSize, success, error, warning, progress } = config;
+    const { chunkSize, success, error, warning, progress, uploadIds, perFileProgress } = config;
 
     try {
         const payload = buildCollectionUploadPayload(items, collectionOptions);
@@ -1090,6 +1141,8 @@ export async function uploadCollectionDatasets(
             error,
             warning,
             progress,
+            uploadIds,
+            perFileProgress,
         });
     } catch (err) {
         config.error?.(errorMessageAsString(err));

From fd2c9dea46c25d7cd3ba39b8b856a2262901f912 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 15 Jun 2026 14:02:03 +0200
Subject: [PATCH 128/256] Prevents upload progress regression after completion

---
 client/src/components/Panels/Upload/uploadState.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Panels/Upload/uploadState.ts b/client/src/components/Panels/Upload/uploadState.ts
index 5f5200c22ee..98de4f4dd58 100644
--- a/client/src/components/Panels/Upload/uploadState.ts
+++ b/client/src/components/Panels/Upload/uploadState.ts
@@ -309,7 +309,7 @@ export function useUploadState() {
      */
     function updateProgress(id: string, progress: number) {
         const item = items.value.find((u) => u.id === id);
-        if (item) {
+        if (item && item.status !== "completed") {
             item.progress = Math.max(0, Math.min(100, Math.round(progress)));
             if (item.progress >= 100 && item.status !== "error") {
                 item.status = "completed";

From 3a79edd5a777a707064644b741890fdb5a304e31 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 15 Jun 2026 14:02:03 +0200
Subject: [PATCH 129/256] Refines upload progress indicator for active states

---
 .../components/Panels/Upload/UploadProgressIndicator.vue  | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Panels/Upload/UploadProgressIndicator.vue b/client/src/components/Panels/Upload/UploadProgressIndicator.vue
index fdea00a93ac..fcb4e0b5e0d 100644
--- a/client/src/components/Panels/Upload/UploadProgressIndicator.vue
+++ b/client/src/components/Panels/Upload/UploadProgressIndicator.vue
@@ -11,11 +11,13 @@ const emit = defineEmits<{
     (e: "show-details"): void;
 }>();
 
+const hasActiveUploads = computed(() => uploads.value.some((f) => f.status !== "completed" && f.status !== "error"));
+
 const statusIcon = computed(() => {
     if (errorCount.value > 0) {
         return faTimes;
     }
-    if (uploadingCount.value > 0) {
+    if (hasActiveUploads.value) {
         return faSpinner;
     }
     return faCheck;
@@ -25,14 +27,14 @@ const statusClass = computed(() => {
     if (errorCount.value > 0) {
         return "text-danger";
     }
-    if (uploadingCount.value > 0) {
+    if (hasActiveUploads.value) {
         return "text-primary";
     }
     return "text-success";
 });
 
 const statusText = computed(() => {
-    if (uploadingCount.value > 0 || uploads.value.some((f) => f.status === "queued")) {
+    if (hasActiveUploads.value) {
         return "Uploading";
     }
     if (uploads.value.length > 0 && completedCount.value === uploads.value.length) {

From b4966b25d8c8c624cf12f4a1ddf7f6df142fd079 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 15 Jun 2026 14:02:04 +0200
Subject: [PATCH 130/256] Displays newest uploads first in progress list

---
 client/src/components/Panels/Upload/uploadState.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Panels/Upload/uploadState.ts b/client/src/components/Panels/Upload/uploadState.ts
index 98de4f4dd58..28159e2ff29 100644
--- a/client/src/components/Panels/Upload/uploadState.ts
+++ b/client/src/components/Panels/Upload/uploadState.ts
@@ -192,7 +192,7 @@ export function useUploadState() {
                 upload,
             }));
 
-        return [...batchItems, ...standaloneItems].sort((a, b) => a.createdAt - b.createdAt);
+        return [...batchItems, ...standaloneItems].sort((a, b) => b.createdAt - a.createdAt);
     });
 
     /**

From 9758728ffefbfa3cbc10d616a2fd3b93c3655b8b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 15 Jun 2026 14:02:04 +0200
Subject: [PATCH 131/256] Updates queued upload icon to reflect waiting state

---
 client/src/components/Panels/Upload/uploadProgressUi.ts | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Panels/Upload/uploadProgressUi.ts b/client/src/components/Panels/Upload/uploadProgressUi.ts
index ab62ffc9211..68d83eff4df 100644
--- a/client/src/components/Panels/Upload/uploadProgressUi.ts
+++ b/client/src/components/Panels/Upload/uploadProgressUi.ts
@@ -1,6 +1,7 @@
 import type { IconDefinition } from "@fortawesome/fontawesome-svg-core";
 import {
     faCheck,
+    faClock,
     faCloud,
     faExclamationTriangle,
     faLayerGroup,
@@ -45,7 +46,7 @@ export interface BatchWithProgress extends CollectionBatchState {
 
 const FILE_PROGRESS_UI: Record<UploadItem["status"], FileProgressUi> = {
     queued: {
-        icon: faSpinner,
+        icon: faClock,
         textClass: "text-muted",
         spin: false,
     },

From 3fd510c884dbbd0dc91cb9a3f363b89b5459a9d1 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 15 Jun 2026 14:02:05 +0200
Subject: [PATCH 132/256] Implements pagination for upload progress view

---
 .../Panels/Upload/UploadProgress.vue          | 51 ++++++++-----------
 1 file changed, 21 insertions(+), 30 deletions(-)

diff --git a/client/src/components/Panels/Upload/UploadProgress.vue b/client/src/components/Panels/Upload/UploadProgress.vue
index efa2bd08ff5..1174418b246 100644
--- a/client/src/components/Panels/Upload/UploadProgress.vue
+++ b/client/src/components/Panels/Upload/UploadProgress.vue
@@ -1,6 +1,7 @@
 <script setup lang="ts">
-import { computed, nextTick, onMounted, ref, watch } from "vue";
+import { BPagination } from "bootstrap-vue";
 
+import { usePagination } from "@/composables/pagination";
 import { useUploadBatchOperations } from "@/composables/upload/useUploadBatchOperations";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 
@@ -14,11 +15,14 @@ import BreadcrumbHeading from "@/components/Common/BreadcrumbHeading.vue";
 
 const uploadBatchOperations = useUploadBatchOperations();
 const uploadState = useUploadState();
-const { orderedUploadItems, batchesWithProgress, standaloneUploads, activeItems, hasCompleted } = uploadState;
+const { orderedUploadItems, batchesWithProgress, activeItems, hasCompleted } = uploadState;
+
+const { paginatedItems, currentPage, itemsPerPage, showPagination, onPageChange } = usePagination(orderedUploadItems, {
+    itemsPerPage: 24,
+});
 
 const breadcrumbItems = [getUploadRootBreadcrumb("/upload"), { title: "Upload Progress" }];
 
-const fileListRef = ref<HTMLElement | null>(null);
 const expandedBatches = useUserLocalStorage<string[]>("uploadPanel.expandedBatches", []);
 
 function cleanupExpandedBatches() {
@@ -55,29 +59,6 @@ function onClearAll() {
 async function retryBatch(batchId: string) {
     await uploadBatchOperations.retryCollectionCreation(batchId);
 }
-
-const uploadItemCount = computed(() => {
-    return batchesWithProgress.value.length + standaloneUploads.value.length;
-});
-
-watch(uploadItemCount, async (newCount, oldCount) => {
-    if (newCount > oldCount) {
-        await nextTick();
-        fileListRef.value?.scrollTo({
-            top: fileListRef.value.scrollHeight,
-            behavior: "smooth",
-        });
-    }
-});
-
-onMounted(() => {
-    nextTick(() => {
-        fileListRef.value?.scrollTo({
-            top: fileListRef.value.scrollHeight,
-            behavior: "auto",
-        });
-    });
-});
 </script>
 
 <template>
@@ -93,10 +74,8 @@ onMounted(() => {
 
         <div class="upload-progress-content flex-grow-1 overflow-auto p-3">
             <div v-if="activeItems.length > 0 || batchesWithProgress.length > 0" class="h-100 d-flex flex-column">
-                <div ref="fileListRef" class="file-details-list flex-grow-1 overflow-auto">
-                    <div
-                        v-for="item in orderedUploadItems"
-                        :key="item.type === 'batch' ? item.batch.id : item.upload.id">
+                <div class="file-details-list flex-grow-1 overflow-auto">
+                    <div v-for="item in paginatedItems" :key="item.type === 'batch' ? item.batch.id : item.upload.id">
                         <BatchUploadGroup
                             v-if="item.type === 'batch'"
                             :batch="item.batch"
@@ -107,6 +86,18 @@ onMounted(() => {
                         <UploadFileRow v-else :file="item.upload" />
                     </div>
                 </div>
+
+                <div v-if="showPagination" class="d-flex justify-content-center py-3 mt-3">
+                    <BPagination
+                        :value="currentPage"
+                        :total-rows="orderedUploadItems.length"
+                        :per-page="itemsPerPage"
+                        align="center"
+                        size="sm"
+                        first-number
+                        last-number
+                        @change="onPageChange" />
+                </div>
             </div>
             <div v-else class="d-flex flex-column align-items-center justify-content-center h-100 text-muted">
                 <p class="h-lg mb-3">No uploads in progress</p>

From 9e2d308dfba3fff375c6b8f433284ec3a2b4614e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 15 Jun 2026 08:30:30 -0400
Subject: [PATCH 133/256] Test that a disabled GButton with a route does not
 navigate

Mounts a disabled GButton that carries a `to` prop (with a router) and asserts it renders a plain button and that clicking it leaves the route untouched. These fail before the accompanying composable fix, where a disabled GButton still rendered as a RouterLink and a click would navigate, stripping the current query/hash.
---
 .../components/BaseComponents/GButton.test.ts | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/client/src/components/BaseComponents/GButton.test.ts b/client/src/components/BaseComponents/GButton.test.ts
index f23595e3046..a570af37f50 100644
--- a/client/src/components/BaseComponents/GButton.test.ts
+++ b/client/src/components/BaseComponents/GButton.test.ts
@@ -1,10 +1,12 @@
 import { getLocalVue } from "@tests/vitest/helpers";
 import { mount } from "@vue/test-utils";
 import { describe, expect, it } from "vitest";
+import VueRouter from "vue-router";
 
 import GButton from "./GButton.vue";
 
 const localVue = getLocalVue(true);
+localVue.use(VueRouter);
 
 function mountGButton(props: object) {
     return mount(GButton as object, { propsData: props, localVue });
@@ -65,3 +67,46 @@ describe("GButton.vue", () => {
         expect(wrapper.emitted("click")).toHaveLength(1);
     });
 });
+
+describe("GButton.vue disabled navigation", () => {
+    // A disabled button with a `to` prop must not navigate. The component-level @click
+    // guard does not run for a RouterLink (Vue 2 treats @click on a component as a
+    // component listener, not a native one), and an empty `to` is not a reliable no-op
+    // in vue-router -- so a disabled GButton renders as a plain button instead.
+    it("renders an enabled router-link button as an anchor", () => {
+        const router = new VueRouter({ mode: "abstract", routes: [{ path: "/" }, { path: "/pages/create" }] });
+        const wrapper = mount(GButton as object, {
+            propsData: { to: "/pages/create" },
+            localVue,
+            router,
+        });
+
+        expect(wrapper.element.tagName).toBe("A");
+    });
+
+    it("renders a disabled router-link button as a plain button", () => {
+        const router = new VueRouter({ mode: "abstract", routes: [{ path: "/" }, { path: "/pages/create" }] });
+        const wrapper = mount(GButton as object, {
+            propsData: { to: "/pages/create", disabled: true, disabledTitle: "Nope" },
+            localVue,
+            router,
+        });
+
+        expect(wrapper.element.tagName).toBe("BUTTON");
+    });
+
+    it("does not navigate when a disabled router-link button is clicked", async () => {
+        const router = new VueRouter({ mode: "abstract", routes: [{ path: "/start" }, { path: "/pages/create" }] });
+        await router.push("/start?keep=me");
+        const routeBeforeClick = router.currentRoute.fullPath;
+        const wrapper = mount(GButton as object, {
+            propsData: { to: "/pages/create", disabled: true },
+            localVue,
+            router,
+        });
+
+        await wrapper.trigger("click");
+
+        expect(router.currentRoute.fullPath).toBe(routeBeforeClick);
+    });
+});

From 4249534037bc7d4fa3aeba6c59af58800b21f086 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 15 Jun 2026 08:30:46 -0400
Subject: [PATCH 134/256] Render a disabled GButton/GLink as a plain button

useClickableElement returned a RouterLink (or anchor) whenever `to`/`href` was set, even while disabled. Once pointer-events: none was removed so the disabled tooltip could show, a disabled router-link started receiving clicks again -- and the component-level @click guard does not run for a RouterLink (Vue 2 treats @click on a component as a component listener, not a native one), while an empty `to` is not a reliable no-op in vue-router. So clicking a disabled router-link could still navigate and strip the current query/hash. Make the composable disabled-aware and reactive so a disabled component always renders as a plain button, which cannot navigate and whose click is handled by the existing JS guard. This closes the same latent gap in GLink, which shares the composable.
---
 .../composables/clickableElement.ts           | 27 +++++++++++++------
 1 file changed, 19 insertions(+), 8 deletions(-)

diff --git a/client/src/components/BaseComponents/composables/clickableElement.ts b/client/src/components/BaseComponents/composables/clickableElement.ts
index e976ebf8caa..93299800cd7 100644
--- a/client/src/components/BaseComponents/composables/clickableElement.ts
+++ b/client/src/components/BaseComponents/composables/clickableElement.ts
@@ -1,19 +1,30 @@
+import { computed } from "vue";
 import { RouterLink } from "vue-router";
 
 export interface ClickableProps {
     to?: string;
     href?: string;
+    disabled?: boolean;
 }
 
 /**
- * returns the correct type of clickable root element based on a components props.
+ * Returns the correct type of clickable root element based on a component's props.
+ *
+ * A disabled component always renders as a plain `button`. Rendering it as a
+ * RouterLink (or anchor) would let clicks fall through to navigation: a
+ * component-level `@click` guard does not run for a RouterLink, and an empty
+ * `to`/`href` is not a reliable no-op in vue-router.
  */
 export function useClickableElement(props: ClickableProps) {
-    if (props.to) {
-        return RouterLink;
-    } else if (props.href) {
-        return "a" as const;
-    } else {
-        return "button" as const;
-    }
+    return computed(() => {
+        if (props.disabled) {
+            return "button" as const;
+        } else if (props.to) {
+            return RouterLink;
+        } else if (props.href) {
+            return "a" as const;
+        } else {
+            return "button" as const;
+        }
+    });
 }

From 79ca43bd1da1cb3f21f94413b56df3d01786feec Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 15 Jun 2026 15:16:13 +0200
Subject: [PATCH 135/256] Resolve unqualified repeat nested inside a
 conditional for async tool tests

When an XML test references a repeat by its unqualified name (at the top
level, without the enclosing <conditional>/<section> wrapper) the async
test-case-to-request converter resolved it only by its fully qualified
state path, found nothing, and dropped the repeat's nested params. This
left required nested params (e.g. deseq2 select_data > rep_factorName >
rep_factorLevel > countsFile) missing, so the request failed validation
with "Field required" against an __absent__ conditional branch.

_repeat_inputs_to_array now progressively strips leading conditional/
section segments (keeping repeat-instance prefixes, longest candidate
first) until the repeat resolves; the downstream _input_for() suffix
match re-attaches the nested params to the qualified path. This matches
the synchronous /api/tools behaviour.
---
 lib/galaxy/tool_util/parameters/case.py | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 81d487a05e7..2f1797c8cc4 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -380,7 +380,24 @@ def _merge_into_state(
 def _repeat_inputs_to_array(
     state_path: str, parameters: List[ToolParameterT], inputs: ToolSourceTestInputs
 ) -> List[ToolSourceTestInputs]:
-    repeat_instance_input_dicts = repeat_inputs_to_array(state_path, _inputs_as_dict(inputs))
+    inputs_as_dict = _inputs_as_dict(inputs)
+    repeat_instance_input_dicts = repeat_inputs_to_array(state_path, inputs_as_dict)
+    if not repeat_instance_input_dicts and "|" in state_path:
+        # Legacy test cases may reference a repeat that lives inside a conditional or
+        # section by its unqualified name (e.g. <repeat name="rep"> at the top level
+        # instead of wrapped in the enclosing <conditional>). The test inputs are
+        # unqualified with respect to conditionals/sections but still carry repeat
+        # instance indices, so progressively strip leading (conditional/section)
+        # segments - keeping any enclosing repeat-instance prefix - until the repeat's
+        # nested params resolve. The downstream _input_for() suffix match then
+        # re-attaches them to the fully qualified path. Longest candidate is tried
+        # first to avoid matching an unrelated like-named repeat.
+        parts = state_path.split("|")
+        for start in range(1, len(parts)):
+            candidate_path = "|".join(parts[start:])
+            repeat_instance_input_dicts = repeat_inputs_to_array(candidate_path, inputs_as_dict)
+            if repeat_instance_input_dicts:
+                break
     repeat_instance_inputs = [list(instance_inputs.values()) for instance_inputs in repeat_instance_input_dicts]
     if repeat_instance_inputs:
         return repeat_instance_inputs

From 3f9c5a72a1d653070bfecaf096fe9ce3a30b31d2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 15 Jun 2026 15:16:22 +0200
Subject: [PATCH 136/256] Resolve conditional discriminator with elided
 conditional name for async tool tests

Legacy XML test cases may give a conditional's discriminator directly
under its enclosing section while omitting the conditional name (e.g.
<section name="advanced_options"><param name="esf" value="user"/> for a
param whose real path is advanced_options|esf_cond|esf). The input name
is an ordered subsequence of the qualified path - sharing the head and
leaf segments - rather than a plain suffix, so neither the suffix nor the
short-name fallback matched. The discriminator went unresolved and the
input was reported as "Invalid parameter name found".

Add _is_conditional_elided_match and use it as a final fallback in
_input_for (raising on ambiguity) and in
_input_name_was_handled_by_legacy_fallback (legacy profiles < 24.2),
matching the synchronous /api/tools behaviour.
---
 lib/galaxy/tool_util/parameters/case.py | 41 +++++++++++++++++++++++--
 1 file changed, 38 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 2f1797c8cc4..7d211061162 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -209,9 +209,15 @@ def test_case_state(
 
 
 def _input_name_was_handled_by_legacy_fallback(input_name: str, handled_inputs: Set[str], profile: str) -> bool:
-    return Version(profile) < Version("24.2") and any(
-        handled_input == input_name or handled_input.endswith(f"|{input_name}") for handled_input in handled_inputs
-    )
+    if Version(profile) >= Version("24.2"):
+        return False
+    for handled_input in handled_inputs:
+        if handled_input == input_name or handled_input.endswith(f"|{input_name}"):
+            return True
+        # conditional names may be elided in the test while the section/repeat prefix is kept
+        if "|" in input_name and _is_conditional_elided_match(input_name, handled_input.split("|")):
+            return True
+    return False
 
 
 def test_case_validation(
@@ -463,9 +469,38 @@ def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[T
             return matching_inputs[0]
         elif len(matching_inputs) > 1:
             raise Exception(f"Ambiguous unqualified test parameter name ({short_name}) for ({flat_state_path})")
+
+        # Fallback for legacy test cases that elide intermediate conditional names but keep
+        # the enclosing section/repeat prefix (e.g. <section name="adv"><param name="esf">
+        # for a param whose real path is adv|esf_cond|esf). The input name is an ordered
+        # subsequence of the qualified path - sharing the head and the leaf - rather than a
+        # plain suffix.
+        path_segments = flat_state_path.split("|")
+        elided_matching_inputs = [
+            input for input in inputs if _is_conditional_elided_match(input["name"], path_segments)
+        ]
+        if len(elided_matching_inputs) == 1:
+            return elided_matching_inputs[0]
+        elif len(elided_matching_inputs) > 1:
+            raise Exception(f"Ambiguous partially qualified test parameter name for ({flat_state_path})")
     return None
 
 
+def _is_conditional_elided_match(input_name: str, path_segments: List[str]) -> bool:
+    """True if ``input_name`` is the qualified ``path_segments`` with intermediate
+    (conditional) segments removed - sharing the head and leaf segments.
+
+    e.g. input_name "advanced_options|esf" matches path ["advanced_options", "esf_cond", "esf"].
+    """
+    input_segments = input_name.split("|")
+    if len(input_segments) < 2 or len(input_segments) >= len(path_segments):
+        return False
+    if input_segments[0] != path_segments[0] or input_segments[-1] != path_segments[-1]:
+        return False
+    path_iter = iter(path_segments)
+    return all(segment in path_iter for segment in input_segments)
+
+
 def validate_test_cases_for_tool_source(
     tool_source: ToolSource, use_latest_profile: bool = False, name: Optional[str] = None
 ) -> List[TestCaseStateValidationResult]:

From 4f21ff479362a664a01dd7445ffed70be0c371ac Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 15 Jun 2026 15:16:40 +0200
Subject: [PATCH 137/256] Add async submission regression tests and reproducer
 tools

Add unit regression tests in test_parameter_test_cases.py covering the
two resolution fixes: an unqualified repeat nested inside a conditional
(single and double nesting) and a conditional discriminator with the
conditional name elided inside a section.

Add two framework test tools modelling the genuine async-submission
regressions found by running unmodified upstream tools (deseq2, gatk4,
hisat2) under both submission paths:
- async_conditional_no_default_nested_data.xml: green in sync and async
  (guards the repeat-in-conditional fix).
- async_ambiguous_unqualified_name.xml: reproduces the still-open
  "ambiguous unqualified test parameter name" failure (a test that lists
  the same unqualified param twice). Listed in
  TOOLS_THAT_ARE_OUTSTANDING_ISSUES until that is surfaced as a
  TestCaseValidationError and the affected tool tests are fixed.
---
 .../async_ambiguous_unqualified_name.xml      |  53 +++++++++
 ...ync_conditional_no_default_nested_data.xml |  54 +++++++++
 test/functional/tools/sample_tool_conf.xml    |   2 +
 .../tool_util/test_parameter_test_cases.py    | 108 ++++++++++++++++++
 4 files changed, 217 insertions(+)
 create mode 100644 test/functional/tools/async_ambiguous_unqualified_name.xml
 create mode 100644 test/functional/tools/async_conditional_no_default_nested_data.xml

diff --git a/test/functional/tools/async_ambiguous_unqualified_name.xml b/test/functional/tools/async_ambiguous_unqualified_name.xml
new file mode 100644
index 00000000000..00ef0d6fda9
--- /dev/null
+++ b/test/functional/tools/async_ambiguous_unqualified_name.xml
@@ -0,0 +1,53 @@
+<tool id="async_ambiguous_unqualified_name" name="async_ambiguous_unqualified_name" version="1.0.0">
+    <description>async regression: unqualified test param name present in multiple conditional whens is ambiguous</description>
+    <!--
+      Models gatk4 mutect2 test 3, which lists the conditional param
+      `reference_sequence` TWICE by its unqualified short name in the same test.
+
+      Sync (POST /api/tools): the duplicate unqualified entry is tolerated; the
+      discriminator resolves the branch and the job runs.
+
+      Async: _input_for() resolves the qualified path reference_source|ref_seq
+      down to the short name `ref_seq`, finds two matching test inputs, and aborts
+      the request build:
+        could not build request: Ambiguous unqualified test parameter name
+        (ref_seq) for (reference_source|ref_seq)
+
+      NOTE: run this one with GALAXY_TEST_USE_LEGACY_TOOL_API=never. Because the
+      failure happens during request BUILDING (request is None), the "if_needed"
+      mode silently falls back to the legacy sync API and masks the bug; only
+      "never" forces the async path and surfaces it.
+    -->
+    <command><![CDATA[
+cat '$reference_source.ref_seq' > '$out_file1'
+    ]]></command>
+    <inputs>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Reference source">
+                <option value="history" selected="true">History</option>
+                <option value="cached">Cached</option>
+            </param>
+            <when value="history">
+                <param name="ref_seq" type="data" format="txt" label="Reference" />
+            </when>
+            <when value="cached">
+                <param name="ref_seq" type="data" format="txt" label="Reference" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_seq" value="simple_line.txt" />
+            <param name="ref_seq" value="simple_line.txt" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_text text="line" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/async_conditional_no_default_nested_data.xml b/test/functional/tools/async_conditional_no_default_nested_data.xml
new file mode 100644
index 00000000000..9417372357e
--- /dev/null
+++ b/test/functional/tools/async_conditional_no_default_nested_data.xml
@@ -0,0 +1,54 @@
+<tool id="async_conditional_no_default_nested_data" name="async_conditional_no_default_nested_data" version="1.0.0" profile="22.01">
+    <description>async regression: omitted discriminator of a default-less conditional + nested required data param</description>
+    <!--
+      Models deseq2 select_data: a conditional whose discriminator (`how`) has NO
+      selected="true" default, containing a repeat with a REQUIRED data param.
+      The test omits `how` and supplies the repeat unqualified (legacy access).
+
+      Sync (POST /api/tools): an omitted discriminator selects the FIRST when
+      (datasets_per_level); the unqualified repeat is mapped into it; job runs.
+
+      Async (POST tool request, GALAXY_TEST_USE_LEGACY_TOOL_API=if_needed): the
+      missing discriminator resolves to a phantom "__absent__" branch, so the
+      nested required `countsFile` is reported missing and request validation
+      fails:
+        select_data.__absent__.rep_level.0.countsFile - Field required
+    -->
+    <command><![CDATA[
+#for $lvl in $select_data.rep_level:
+cat '$lvl.countsFile' >> '$out_file1' &&
+#end for
+echo "done" >> '$out_file1'
+    ]]></command>
+    <inputs>
+        <conditional name="select_data">
+            <param name="how" type="select" label="How">
+                <option value="datasets_per_level">Datasets per level</option>
+                <option value="group_tags">Group tags</option>
+            </param>
+            <when value="datasets_per_level">
+                <repeat name="rep_level" title="Level" min="1">
+                    <param name="countsFile" type="data" format="txt" label="Counts file" />
+                </repeat>
+            </when>
+            <when value="group_tags">
+                <param name="countsFile" type="data" format="txt" label="Counts file" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <repeat name="rep_level">
+                <param name="countsFile" value="simple_line.txt" />
+            </repeat>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_text text="done" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml
index ca88a0f59bd..2134dae968c 100644
--- a/test/functional/tools/sample_tool_conf.xml
+++ b/test/functional/tools/sample_tool_conf.xml
@@ -120,6 +120,8 @@
   <tool file="output_format_collection.xml" />
   <tool file="format_source_in_conditional.xml" />
   <tool file="output_filter.xml" />
+  <tool file="async_conditional_no_default_nested_data.xml" />
+  <tool file="async_ambiguous_unqualified_name.xml" />
   <tool file="output_empty_work_dir.xml" />
   <tool file="output_filter_with_input.xml" />
   <tool file="output_filter_with_input_optional.xml" />
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index 637789025ae..1a0a0cfa53b 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -58,6 +58,11 @@ TOOLS_THAT_USE_SELECT_BY_VALUE = [
 TOOLS_THAT_ARE_OUTSTANDING_ISSUES = [
     "gx_conditional_boolean_optional.xml",
     "gx_conditional_boolean_discriminate_on_string_value.xml",
+    # Intentionally reproduces the async "ambiguous unqualified test parameter name"
+    # regression (duplicate unqualified param in a test) - see
+    # test/functional/tools/async_ambiguous_unqualified_name.xml. Remove once
+    # _input_for ambiguity is resolved / surfaced as a TestCaseValidationError.
+    "async_ambiguous_unqualified_name.xml",
 ]
 
 TEST_TOOL_THAT_DO_NOT_VALIDATE = (
@@ -436,6 +441,109 @@ def test_legacy_unqualified_repeat_inputs_are_expanded_for_request_state():
     dict_verify_each(test_case_state.input_state, expectations)
 
 
+def test_legacy_unqualified_repeat_inside_conditional_is_resolved():
+    # A repeat that lives inside a conditional may be specified unqualified (at the top
+    # level of the test, without the enclosing <conditional> wrapper). Its nested params
+    # must still resolve - including across two levels of repeat nesting - matching the
+    # synchronous /api/tools path. Regression for the deseq2 async submission failure:
+    #   select_data.__absent__.rep_factorName.0.rep_factorLevel.0.countsFile - Field required
+    tool_source = raw_xml_tool_source("""
+<tool id="unqualified_repeat_in_conditional" name="unqualified_repeat_in_conditional" version="1.0.0" profile="22.01">
+    <command>echo</command>
+    <inputs>
+        <conditional name="select_data">
+            <param name="how" type="select">
+                <option value="datasets_per_level">Datasets per level</option>
+                <option value="group_tags">Group tags</option>
+            </param>
+            <when value="datasets_per_level">
+                <repeat name="rep_factorName" min="1">
+                    <param name="factorName" type="text" value="" />
+                    <repeat name="rep_factorLevel" min="1">
+                        <param name="factorLevel" type="text" value="" />
+                        <param name="countsFile" type="data" format="txt" />
+                    </repeat>
+                </repeat>
+            </when>
+            <when value="group_tags">
+                <param name="countsFile" type="data" format="txt" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs />
+    <tests>
+        <test>
+            <repeat name="rep_factorName">
+                <param name="factorName" value="Treatment" />
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Treated" />
+                    <param name="countsFile" value="simple_line.txt" />
+                </repeat>
+            </repeat>
+        </test>
+    </tests>
+</tool>
+        """)
+    parsed_tool = parse_tool(tool_source)
+    test_case = tool_source.parse_tests_to_dict()["tests"][0]
+
+    tool_state = case_state(test_case, parsed_tool.inputs, tool_source.parse_profile()).tool_state
+
+    expectations = [
+        (["select_data", "rep_factorName", 0, "factorName"], "Treatment"),
+        (["select_data", "rep_factorName", 0, "rep_factorLevel", 0, "factorLevel"], "Treated"),
+        (["select_data", "rep_factorName", 0, "rep_factorLevel", 0, "countsFile", "path"], "simple_line.txt"),
+    ]
+    dict_verify_each(tool_state.input_state, expectations)
+
+
+def test_legacy_unqualified_conditional_discriminator_in_section_is_resolved():
+    # A conditional inside a section may have its name elided in the test, with the
+    # discriminator given directly under the section (e.g. <section name="adv">
+    # <param name="esf" value="user"/> rather than wrapping it in <conditional
+    # name="esf_cond">). The section prefix is kept but the conditional name is dropped.
+    # Regression for the deseq2 async submission failure:
+    #   Invalid parameter name found advanced_options|esf
+    tool_source = raw_xml_tool_source("""
+<tool id="elided_conditional_in_section" name="elided_conditional_in_section" version="1.0.0" profile="22.01">
+    <command>echo</command>
+    <inputs>
+        <section name="advanced_options" title="Advanced">
+            <conditional name="esf_cond">
+                <param name="esf" type="select">
+                    <option value="default" selected="true">Default</option>
+                    <option value="user">User supplied</option>
+                </param>
+                <when value="default" />
+                <when value="user">
+                    <param name="size_factor_input" type="data" format="txt" />
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs />
+    <tests>
+        <test>
+            <section name="advanced_options">
+                <param name="esf" value="user" />
+                <param name="size_factor_input" value="simple_line.txt" />
+            </section>
+        </test>
+    </tests>
+</tool>
+        """)
+    parsed_tool = parse_tool(tool_source)
+    test_case = tool_source.parse_tests_to_dict()["tests"][0]
+
+    tool_state = case_state(test_case, parsed_tool.inputs, tool_source.parse_profile()).tool_state
+
+    expectations = [
+        (["advanced_options", "esf_cond", "esf"], "user"),
+        (["advanced_options", "esf_cond", "size_factor_input", "path"], "simple_line.txt"),
+    ]
+    dict_verify_each(tool_state.input_state, expectations)
+
+
 def test_legacy_select_labels_are_converted_to_values_for_request_state():
     tool_source = tool_source_for("multi_select")
     test_case = tool_source.parse_tests_to_dict()["tests"][1]

From cdb2e521bb06c700c95eb491508a9498c0321548 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 15 Jun 2026 15:35:58 +0200
Subject: [PATCH 138/256] Coerce legacy boolean test values to booleans in
 async tool test builder

A boolean tool parameter's test value must be submitted as a real boolean
so the request payload validates. The builder now:
- maps the parameter's truevalue/falsevalue command-line string back to
  True/False when the test specifies it (rather than 'true'/'false'); and
- for legacy tools (profile < 24.2), coerces any remaining non-boolean
  value via string_as_bool - matching the synchronous /api/tools path,
  where e.g. quast's value="-" placeholder becomes False - so these tests
  submit a valid boolean without requiring test edits.

Tools with profile >= 24.2 still require a genuine boolean (true/false or
the truevalue/falsevalue), leaving the strict validation in place for new
tools.
---
 lib/galaxy/tool_util/parameters/case.py       | 41 +++++++++++++------
 .../tool_util/test_parameter_test_cases.py    | 36 ++++++++++++++++
 2 files changed, 65 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 7d211061162..7db6a4af0dd 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -39,7 +39,10 @@ from galaxy.tool_util_models.parameters import (
     SelectParameterModel,
     ToolParameterT,
 )
-from galaxy.util import asbool
+from galaxy.util import (
+    asbool,
+    string_as_bool,
+)
 from .factory import input_models_for_tool_source
 from .state import TestCaseToolState
 from .visitor import (
@@ -110,17 +113,31 @@ def legacy_from_string(parameter: ToolParameterT, value: Optional[Any], warnings
                 warnings.append(
                     f"Implicitly converted {parameter.name} to a boolean from a string value, please use 'value_json' to define this test input parameter value instead."
                 )
-            try:
-                result_value = asbool(value)
-            except ValueError:
-                if parameter.truevalue is not None and value == parameter.truevalue:
-                    result_value = True
-                elif parameter.falsevalue is not None and value == parameter.falsevalue:
-                    result_value = False
-                else:
-                    warnings.append(
-                        "Likely using deprected truevalue/falsevalue in tool parameter - switch to 'true' or 'false'"
-                    )
+            # Map the parameter's truevalue/falsevalue back to a boolean when the test
+            # specified the command-line string rather than 'true'/'false', so the
+            # submitted payload is a real boolean.
+            if parameter.truevalue is not None and value == parameter.truevalue:
+                result_value = True
+            elif parameter.falsevalue is not None and value == parameter.falsevalue:
+                result_value = False
+            else:
+                try:
+                    result_value = asbool(value)
+                except ValueError:
+                    if Version(profile) < Version("24.2"):
+                        # Legacy tools sometimes use a non-boolean placeholder such as
+                        # "-" as a test value. The synchronous tool API coerces these
+                        # via string_as_bool (any non-true value -> False); match that
+                        # so the payload is a valid boolean without requiring test edits.
+                        result_value = string_as_bool(value)
+                        warnings.append(
+                            f"Non-boolean test value ({value!r}) for {parameter.name} coerced to "
+                            f"{result_value} - use 'true' or 'false'."
+                        )
+                    else:
+                        warnings.append(
+                            "Likely using deprected truevalue/falsevalue in tool parameter - switch to 'true' or 'false'"
+                        )
         elif isinstance(parameter, (GroupTagParameterModel,)):
             if parameter.multiple:
                 result_value = multiple_select_value_split(value)
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index 1a0a0cfa53b..763bb88820d 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -497,6 +497,42 @@ def test_legacy_unqualified_repeat_inside_conditional_is_resolved():
     dict_verify_each(tool_state.input_state, expectations)
 
 
+def test_legacy_boolean_test_values_are_coerced_to_booleans():
+    # The test-case builder must submit a real boolean for a boolean param. A test may
+    # supply the param's truevalue/falsevalue command-line string, a plain true/false,
+    # or (for legacy tools) a non-boolean placeholder such as "-" that the synchronous
+    # tool API coerces via string_as_bool. Regression for the quast async failure:
+    #   advanced.skip_unaligned_mis_contigs - Input should be a valid boolean, input_value='-'
+    tool_template = """
+<tool id="boolean_legacy_values" name="boolean_legacy_values" version="1.0.0" profile="{profile}">
+    <command>echo</command>
+    <inputs>
+        <param name="flag" type="boolean" truevalue="" falsevalue="--skip" checked="true" />
+    </inputs>
+    <outputs />
+    <tests>
+        <test><param name="flag" value="{value}" /></test>
+    </tests>
+</tool>
+        """
+
+    def flag_value_for(value: str, profile: str = "23.02"):
+        tool_source = raw_xml_tool_source(tool_template.format(value=value, profile=profile))
+        parsed_tool = parse_tool(tool_source)
+        test_case = tool_source.parse_tests_to_dict()["tests"][0]
+        tool_state = case_state(test_case, parsed_tool.inputs, tool_source.parse_profile()).tool_state
+        return tool_state.input_state["flag"]
+
+    # plain booleans
+    assert flag_value_for("true") is True
+    assert flag_value_for("false") is False
+    # truevalue / falsevalue command-line strings mapped back to booleans
+    assert flag_value_for("") is True
+    assert flag_value_for("--skip") is False
+    # legacy non-boolean placeholder coerced to False (matches synchronous string_as_bool)
+    assert flag_value_for("-") is False
+
+
 def test_legacy_unqualified_conditional_discriminator_in_section_is_resolved():
     # A conditional inside a section may have its name elided in the test, with the
     # discriminator given directly under the section (e.g. <section name="adv">

From 07e8148e7e1aa2b85d4c62af6cfb9d8c09e38c81 Mon Sep 17 00:00:00 2001
From: Alireza Heidari <8046843+itisAliRH@users.noreply.github.com>
Date: Mon, 15 Jun 2026 16:45:08 +0200
Subject: [PATCH 139/256] Refines upload progress layout

- Adds a small top padding to the upload file details list, improving its visual separation.
- Removes excessive vertical padding from the pagination component for a more compact and refined layout.
---
 client/src/components/Panels/Upload/UploadProgress.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Panels/Upload/UploadProgress.vue b/client/src/components/Panels/Upload/UploadProgress.vue
index 1174418b246..ddfb791ca9f 100644
--- a/client/src/components/Panels/Upload/UploadProgress.vue
+++ b/client/src/components/Panels/Upload/UploadProgress.vue
@@ -74,7 +74,7 @@ async function retryBatch(batchId: string) {
 
         <div class="upload-progress-content flex-grow-1 overflow-auto p-3">
             <div v-if="activeItems.length > 0 || batchesWithProgress.length > 0" class="h-100 d-flex flex-column">
-                <div class="file-details-list flex-grow-1 overflow-auto">
+                <div class="file-details-list flex-grow-1 overflow-auto pt-1">
                     <div v-for="item in paginatedItems" :key="item.type === 'batch' ? item.batch.id : item.upload.id">
                         <BatchUploadGroup
                             v-if="item.type === 'batch'"
@@ -87,7 +87,7 @@ async function retryBatch(batchId: string) {
                     </div>
                 </div>
 
-                <div v-if="showPagination" class="d-flex justify-content-center py-3 mt-3">
+                <div v-if="showPagination" class="d-flex justify-content-center mt-3">
                     <BPagination
                         :value="currentPage"
                         :total-rows="orderedUploadItems.length"

From 5a44329451238089b8562faf9e9a65ff71074f35 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 15 Jun 2026 16:49:07 +0200
Subject: [PATCH 140/256] Tolerate duplicate identical unqualified test params
 in async tool test builder

When a test lists the same unqualified conditional/section param more than
once (a common authoring slip, e.g. gatk4 mutect2 reference_sequence or
hisat2 history_item listed twice with the same value), _input_for() found
multiple matches and aborted the request build with "Ambiguous unqualified
test parameter name". The synchronous tool API tolerates the duplicate.

Resolve matched inputs through a shared _resolve_matching_inputs helper that
de-duplicates equivalent matches (same value and attributes) and only raises
for genuinely conflicting values. Applied to the suffix, short-name and
elided-conditional fallbacks.

The async_ambiguous_unqualified_name framework tool now validates and runs
green, so it is removed from TOOLS_THAT_ARE_OUTSTANDING_ISSUES.
---
 lib/galaxy/tool_util/parameters/case.py       | 65 +++++++++++++------
 .../async_ambiguous_unqualified_name.xml      | 22 +++----
 .../tool_util/test_parameter_test_cases.py    | 56 ++++++++++++++--
 3 files changed, 105 insertions(+), 38 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 7db6a4af0dd..4966efeb3cb 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -467,25 +467,24 @@ def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[T
     # Fallback for legacy test cases that specify conditional/section params without the pipe-separated
     # prefix (e.g. <param name="fasta"> instead of <param name="mode|fasta">).
     if "|" in flat_state_path:
-        suffix_matching_inputs = []
-        for input in inputs:
-            input_name = input["name"]
-            if "|" in input_name and flat_state_path.endswith(f"|{input_name}"):
-                suffix_matching_inputs.append(input)
-        if len(suffix_matching_inputs) == 1:
-            return suffix_matching_inputs[0]
-        elif len(suffix_matching_inputs) > 1:
-            raise Exception(f"Ambiguous partially qualified test parameter name for ({flat_state_path})")
+        suffix_matching_inputs = [
+            input
+            for input in inputs
+            if "|" in input["name"] and flat_state_path.endswith(f"|{input['name']}")
+        ]
+        resolved = _resolve_matching_inputs(
+            suffix_matching_inputs, f"Ambiguous partially qualified test parameter name for ({flat_state_path})"
+        )
+        if resolved is not None:
+            return resolved
 
         short_name = flat_state_path.rsplit("|", 1)[1]
-        matching_inputs = []
-        for input in inputs:
-            if input["name"] == short_name:
-                matching_inputs.append(input)
-        if len(matching_inputs) == 1:
-            return matching_inputs[0]
-        elif len(matching_inputs) > 1:
-            raise Exception(f"Ambiguous unqualified test parameter name ({short_name}) for ({flat_state_path})")
+        matching_inputs = [input for input in inputs if input["name"] == short_name]
+        resolved = _resolve_matching_inputs(
+            matching_inputs, f"Ambiguous unqualified test parameter name ({short_name}) for ({flat_state_path})"
+        )
+        if resolved is not None:
+            return resolved
 
         # Fallback for legacy test cases that elide intermediate conditional names but keep
         # the enclosing section/repeat prefix (e.g. <section name="adv"><param name="esf">
@@ -496,13 +495,37 @@ def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[T
         elided_matching_inputs = [
             input for input in inputs if _is_conditional_elided_match(input["name"], path_segments)
         ]
-        if len(elided_matching_inputs) == 1:
-            return elided_matching_inputs[0]
-        elif len(elided_matching_inputs) > 1:
-            raise Exception(f"Ambiguous partially qualified test parameter name for ({flat_state_path})")
+        resolved = _resolve_matching_inputs(
+            elided_matching_inputs, f"Ambiguous partially qualified test parameter name for ({flat_state_path})"
+        )
+        if resolved is not None:
+            return resolved
     return None
 
 
+def _resolve_matching_inputs(
+    matching_inputs: List[ToolSourceTestInput], ambiguity_message: str
+) -> Optional[ToolSourceTestInput]:
+    """Resolve a list of test inputs that matched a parameter to a single input.
+
+    Returns None when nothing matched (so the caller can try the next fallback). A single
+    match is returned directly. Multiple matches are tolerated when they are equivalent -
+    a duplicate identical entry is a common test-authoring slip and the synchronous tool
+    API accepts it - but genuinely conflicting values raise.
+    """
+    if not matching_inputs:
+        return None
+    first = matching_inputs[0]
+    if len(matching_inputs) == 1:
+        return first
+    if all(
+        input.get("value") == first.get("value") and input.get("attributes") == first.get("attributes")
+        for input in matching_inputs[1:]
+    ):
+        return first
+    raise Exception(ambiguity_message)
+
+
 def _is_conditional_elided_match(input_name: str, path_segments: List[str]) -> bool:
     """True if ``input_name`` is the qualified ``path_segments`` with intermediate
     (conditional) segments removed - sharing the head and leaf segments.
diff --git a/test/functional/tools/async_ambiguous_unqualified_name.xml b/test/functional/tools/async_ambiguous_unqualified_name.xml
index 00ef0d6fda9..6c9b69d45ef 100644
--- a/test/functional/tools/async_ambiguous_unqualified_name.xml
+++ b/test/functional/tools/async_ambiguous_unqualified_name.xml
@@ -1,22 +1,20 @@
 <tool id="async_ambiguous_unqualified_name" name="async_ambiguous_unqualified_name" version="1.0.0">
-    <description>async regression: unqualified test param name present in multiple conditional whens is ambiguous</description>
+    <description>async regression: a duplicated identical unqualified test param is tolerated</description>
     <!--
-      Models gatk4 mutect2 test 3, which lists the conditional param
-      `reference_sequence` TWICE by its unqualified short name in the same test.
+      Models gatk4 mutect2 test 3 (and hisat2 test 5), which list a conditional
+      param by its unqualified short name TWICE in the same test with the SAME
+      value - a common test-authoring slip.
 
-      Sync (POST /api/tools): the duplicate unqualified entry is tolerated; the
-      discriminator resolves the branch and the job runs.
+      Sync (POST /api/tools): the duplicate identical entry is tolerated.
 
-      Async: _input_for() resolves the qualified path reference_source|ref_seq
-      down to the short name `ref_seq`, finds two matching test inputs, and aborts
-      the request build:
+      Async previously aborted the request build because _input_for() found two
+      matching test inputs for the short name (ref_seq):
         could not build request: Ambiguous unqualified test parameter name
         (ref_seq) for (reference_source|ref_seq)
 
-      NOTE: run this one with GALAXY_TEST_USE_LEGACY_TOOL_API=never. Because the
-      failure happens during request BUILDING (request is None), the "if_needed"
-      mode silently falls back to the legacy sync API and masks the bug; only
-      "never" forces the async path and surfaces it.
+      Now duplicate matches with equivalent values are de-duplicated like the
+      synchronous path; only genuinely conflicting values are reported ambiguous.
+      This tool therefore validates and runs green under both submission paths.
     -->
     <command><![CDATA[
 cat '$reference_source.ref_seq' > '$out_file1'
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index 763bb88820d..12581b780df 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -7,6 +7,8 @@ from typing import (
     Tuple,
 )
 
+import pytest
+
 from galaxy.tool_util.model_factory import parse_tool
 from galaxy.tool_util.parameters import (
     DataCollectionRequest,
@@ -58,11 +60,6 @@ TOOLS_THAT_USE_SELECT_BY_VALUE = [
 TOOLS_THAT_ARE_OUTSTANDING_ISSUES = [
     "gx_conditional_boolean_optional.xml",
     "gx_conditional_boolean_discriminate_on_string_value.xml",
-    # Intentionally reproduces the async "ambiguous unqualified test parameter name"
-    # regression (duplicate unqualified param in a test) - see
-    # test/functional/tools/async_ambiguous_unqualified_name.xml. Remove once
-    # _input_for ambiguity is resolved / surfaced as a TestCaseValidationError.
-    "async_ambiguous_unqualified_name.xml",
 ]
 
 TEST_TOOL_THAT_DO_NOT_VALIDATE = (
@@ -497,6 +494,55 @@ def test_legacy_unqualified_repeat_inside_conditional_is_resolved():
     dict_verify_each(tool_state.input_state, expectations)
 
 
+def test_duplicate_identical_unqualified_test_param_is_tolerated():
+    # A test may list the same unqualified conditional param twice (a common authoring
+    # slip). When the duplicate values are identical it is tolerated - matching the
+    # synchronous tool API - rather than aborting the request build. Regression for the
+    # gatk4 mutect2 / hisat2 async failure:
+    #   could not build request: Ambiguous unqualified test parameter name (...)
+    tool_template = """
+<tool id="duplicate_unqualified" name="duplicate_unqualified" version="1.0.0" profile="22.01">
+    <command>echo</command>
+    <inputs>
+        <conditional name="reference_source">
+            <param name="selector" type="select">
+                <option value="history" selected="true">History</option>
+                <option value="cached">Cached</option>
+            </param>
+            <when value="history">
+                <param name="ref" type="text" value="" />
+            </when>
+            <when value="cached">
+                <param name="ref" type="text" value="" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs />
+    <tests>
+        <test>
+            <param name="selector" value="history" />
+            <param name="ref" value="{first}" />
+            <param name="ref" value="{second}" />
+        </test>
+    </tests>
+</tool>
+        """
+
+    # identical duplicate -> tolerated
+    tool_source = raw_xml_tool_source(tool_template.format(first="hg38", second="hg38"))
+    parsed_tool = parse_tool(tool_source)
+    test_case = tool_source.parse_tests_to_dict()["tests"][0]
+    tool_state = case_state(test_case, parsed_tool.inputs, tool_source.parse_profile()).tool_state
+    dict_verify_each(tool_state.input_state, [(["reference_source", "ref"], "hg38")])
+
+    # conflicting duplicate -> still ambiguous
+    tool_source = raw_xml_tool_source(tool_template.format(first="hg38", second="hg19"))
+    parsed_tool = parse_tool(tool_source)
+    test_case = tool_source.parse_tests_to_dict()["tests"][0]
+    with pytest.raises(Exception, match="[Aa]mbiguous"):
+        case_state(test_case, parsed_tool.inputs, tool_source.parse_profile())
+
+
 def test_legacy_boolean_test_values_are_coerced_to_booleans():
     # The test-case builder must submit a real boolean for a boolean param. A test may
     # supply the param's truevalue/falsevalue command-line string, a plain true/false,

From 20d8d9ed2d6045faa7aa3480f0b58baa55428c06 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 15 Jun 2026 16:56:44 +0200
Subject: [PATCH 141/256] Infer omitted conditional when from provided params
 in async tool test builder

When a conditional's discriminator is omitted from a test, the builder defaulted
to the selected="true" when. If the test instead supplied a different branch's
parameters - e.g. quast's `in` conditional, where `inputs` is a repeat in the
"custom" when but a data param in the default when - the state failed to validate
against the default/__absent__ branch.

Infer the active when from the parameters the test actually provides (scoped to
the conditional, only overriding the default when another when is a strictly
better match), and record the inferred discriminator in the state so validation
routes to that branch. Matches the synchronous tool API.
---
 lib/galaxy/tool_util/parameters/case.py       | 60 +++++++++++++++++++
 .../tool_util/test_parameter_test_cases.py    | 52 ++++++++++++++++
 2 files changed, 112 insertions(+)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 4966efeb3cb..75c9f9185e4 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -310,6 +310,11 @@ def _merge_into_state(
                 test_parameter, inputs, conditional_state, profile, state_representation, warnings, state_path
             )
         )
+        # If the discriminator was omitted but a non-default when was inferred from the
+        # provided parameters, record the inferred discriminator so the state validates
+        # against that branch rather than the __absent__/default branch.
+        if test_parameter.name not in conditional_state and not when.is_default_when:
+            conditional_state[test_parameter.name] = when.discriminator
         handled_inputs.update(
             _merge_level_into_state(
                 when.parameters, inputs, conditional_state, profile, state_representation, warnings, state_path
@@ -451,6 +456,14 @@ def _select_which_when(
     if is_boolean and isinstance(explicit_test_value, str):
         explicit_test_value = asbool(explicit_test_value)
     test_value = validate_explicit_conditional_test_value(test_parameter_name, explicit_test_value)
+    if test_value is None:
+        # The discriminator was omitted. Like the synchronous tool API, infer the active
+        # when from the parameters the test actually provides before falling back to the
+        # default when (otherwise a test that supplies a non-default branch's params fails
+        # to validate against the default branch).
+        inferred_when = _infer_when_from_inputs(conditional, inputs, prefix)
+        if inferred_when is not None:
+            return inferred_when
     for when in conditional.whens:
         if test_value is None and when.is_default_when:
             return when
@@ -460,6 +473,53 @@ def _select_which_when(
         raise Exception(f"Invalid conditional test value ({explicit_test_value}) for parameter ({test_parameter_name})")
 
 
+def _leaf_param_short_names(parameters: List[ToolParameterT]) -> Set[str]:
+    """Collect the leaf parameter short names reachable from a list of parameters,
+    descending into repeats, sections and nested conditionals."""
+    names: Set[str] = set()
+    for parameter in parameters:
+        if isinstance(parameter, (RepeatParameterModel, SectionParameterModel)):
+            names |= _leaf_param_short_names(parameter.parameters)
+        elif isinstance(parameter, ConditionalParameterModel):
+            names.add(parameter.test_parameter.name)
+            for when in parameter.whens:
+                names |= _leaf_param_short_names(when.parameters)
+        else:
+            names.add(parameter.name)
+    return names
+
+
+def _infer_when_from_inputs(
+    conditional: ConditionalParameterModel, inputs: ToolSourceTestInputs, prefix: Optional[str]
+) -> Optional[ConditionalWhen]:
+    """When a conditional's discriminator is omitted, pick the when whose parameters the
+    test supplies. Returns the best-matching when only when it is a strictly better match
+    than the default when; otherwise None so the caller uses the default when."""
+    scope = f"{prefix}|" if prefix else ""
+    provided_short_names: Set[str] = set()
+    for input in inputs:
+        name = input["name"]
+        if scope and not name.startswith(scope):
+            continue
+        provided_short_names.add(name.rsplit("|", 1)[-1])
+    if not provided_short_names:
+        return None
+
+    best_when: Optional[ConditionalWhen] = None
+    best_score = 0
+    default_score = 0
+    for when in conditional.whens:
+        score = len(_leaf_param_short_names(when.parameters) & provided_short_names)
+        if when.is_default_when:
+            default_score = score
+        if score > best_score:
+            best_score = score
+            best_when = when
+    if best_when is not None and best_score > default_score:
+        return best_when
+    return None
+
+
 def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[ToolSourceTestInput]:
     for input in inputs:
         if input["name"] == flat_state_path:
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index 12581b780df..0025f467467 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -494,6 +494,58 @@ def test_legacy_unqualified_repeat_inside_conditional_is_resolved():
     dict_verify_each(tool_state.input_state, expectations)
 
 
+def test_omitted_conditional_discriminator_inferred_from_provided_params():
+    # When a conditional's discriminator is omitted, the active when must be inferred from
+    # the parameters the test actually supplies (matching the synchronous tool API) rather
+    # than defaulting to the selected="true" branch. Regression for the quast async failure
+    # where `inputs` is a repeat in the non-default when but a data param in the default:
+    #   mode.co.in.__absent__.inputs.0.class - ...
+    tool_source = raw_xml_tool_source("""
+<tool id="infer_when" name="infer_when" version="1.0.0" profile="22.01">
+    <command>echo</command>
+    <inputs>
+        <conditional name="in">
+            <param name="custom" type="select">
+                <option value="true">Custom names</option>
+                <option value="false" selected="true">Dataset names</option>
+            </param>
+            <when value="true">
+                <repeat name="inputs" min="1">
+                    <param name="input" type="data" format="txt" />
+                    <param name="labels" type="text" value="" />
+                </repeat>
+            </when>
+            <when value="false">
+                <param name="inputs" type="data" format="txt" multiple="true" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs />
+    <tests>
+        <test>
+            <conditional name="in">
+                <repeat name="inputs">
+                    <param name="input" value="simple_line.txt" />
+                    <param name="labels" value="c1" />
+                </repeat>
+            </conditional>
+        </test>
+    </tests>
+</tool>
+        """)
+    parsed_tool = parse_tool(tool_source)
+    test_case = tool_source.parse_tests_to_dict()["tests"][0]
+
+    tool_state = case_state(test_case, parsed_tool.inputs, tool_source.parse_profile()).tool_state
+
+    expectations = [
+        (["in", "custom"], "true"),
+        (["in", "inputs", 0, "input", "path"], "simple_line.txt"),
+        (["in", "inputs", 0, "labels"], "c1"),
+    ]
+    dict_verify_each(tool_state.input_state, expectations)
+
+
 def test_duplicate_identical_unqualified_test_param_is_tolerated():
     # A test may list the same unqualified conditional param twice (a common authoring
     # slip). When the duplicate values are identical it is tolerated - matching the

From 8d02e258acc5238bc3806a5f90808ba783d0899c Mon Sep 17 00:00:00 2001
From: Alireza Heidari <8046843+itisAliRH@users.noreply.github.com>
Date: Mon, 15 Jun 2026 17:29:26 +0200
Subject: [PATCH 142/256] Aligns remote file browser labels

Ensures file and directory labels within the remote file browser consistently align to the start, improving readability and presentation for long names.
---
 .../components/Panels/Upload/methods/RemoteFilesUpload.vue   | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/client/src/components/Panels/Upload/methods/RemoteFilesUpload.vue b/client/src/components/Panels/Upload/methods/RemoteFilesUpload.vue
index 01c1da0827b..471d77f3881 100644
--- a/client/src/components/Panels/Upload/methods/RemoteFilesUpload.vue
+++ b/client/src/components/Panels/Upload/methods/RemoteFilesUpload.vue
@@ -713,6 +713,7 @@ defineExpose<UploadMethodComponent>({ prepareUpload, reset });
                                 class="mr-2 text-warning"
                                 fixed-width />
                             <span
+                                class="remote-files-browser-label"
                                 data-test-id="remote-files-browser-label"
                                 :data-label="item.label"
                                 :data-entry-kind="item.isLeaf ? 'file' : 'directory'">
@@ -942,6 +943,10 @@ defineExpose<UploadMethodComponent>({ prepareUpload, reset });
             background-color: rgba($brand-primary, 0.05);
         }
     }
+
+    .remote-files-browser-label {
+        text-align: start;
+    }
 }
 
 .browser-actions {

From 9e4be516e7708992f1d850bf7cf5f9f6b0efa250 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 15 Jun 2026 15:39:46 -0400
Subject: [PATCH 143/256] Fix HTTP Range requests on dataset files (non-nginx
 deployments)

send_file read file_size from the content-length response header, but
files served from a dataset's extra_files_path (e.g. JBrowse track data)
don't set it, so any Range request 500'd with KeyError. nginx/apache
deployments dodged this via the X-Accel-Redirect/X-Sendfile early return.

Use os.path.getsize(body.name) instead, and honor the requested range
end (the old 'end is None' check was always true, so it ignored the
client's end and always served to EOF).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/web/framework/base.py    |  4 ++--
 test/unit/webapps/test_send_file.py | 36 +++++++++++++++++++++++++++--
 2 files changed, 36 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py
index d97bf9bf85e..454aee79cc2 100644
--- a/lib/galaxy/web/framework/base.py
+++ b/lib/galaxy/web/framework/base.py
@@ -569,8 +569,8 @@ def send_file(start_response, trans, body):
             body = b""
         if trans.request.range:
             start = int(trans.request.range.start)
-            file_size = int(trans.response.headers["content-length"])
-            end = int(file_size if end is None else trans.request.range.end)
+            file_size = os.path.getsize(body.name)
+            end = file_size if trans.request.range.end is None else min(int(trans.request.range.end), file_size)
             trans.response.headers["content-length"] = str(end - start)
             trans.response.headers["content-range"] = f"bytes {start}-{end - 1}/{file_size}"
             trans.response.status = 206
diff --git a/test/unit/webapps/test_send_file.py b/test/unit/webapps/test_send_file.py
index 1130e6c8804..7a38315802a 100644
--- a/test/unit/webapps/test_send_file.py
+++ b/test/unit/webapps/test_send_file.py
@@ -15,7 +15,7 @@ from galaxy.web.framework.base import (
 CONTENT = "content"
 
 
-def setup_fastAPI(fh, nginx_x_accel_redirect_base=None, apache_xsendfile=None):
+def setup_fastAPI(fh, nginx_x_accel_redirect_base=None, apache_xsendfile=None, set_content_length=True):
     def wsgi_application(env, start_response):
         trans = Bunch(
             response=Response(),
@@ -24,7 +24,8 @@ def setup_fastAPI(fh, nginx_x_accel_redirect_base=None, apache_xsendfile=None):
                 config=Bunch(nginx_x_accel_redirect_base=nginx_x_accel_redirect_base, apache_xsendfile=apache_xsendfile)
             ),
         )
-        trans.response.headers["content-length"] = len(CONTENT)
+        if set_content_length:
+            trans.response.headers["content-length"] = len(CONTENT)
         trans.response.set_content_type("application/octet-stream")
         return send_file(start_response, trans, fh)
 
@@ -72,3 +73,34 @@ def test_sendfile_in_process(test_file_handle):
     assert "x-accel-redirect" not in response.headers
     assert response.headers["content-length"] == str(len(CONTENT))
     assert response.content.decode() == "content"
+
+
+def test_sendfile_range(test_file_handle):
+    app = setup_fastAPI(test_file_handle)
+    client = TestClient(app)
+    response = client.get("/test/send_file", headers={"Range": "bytes=0-3"})
+    assert response.status_code == 206
+    assert response.headers["content-range"] == f"bytes 0-3/{len(CONTENT)}"
+    assert response.headers["content-length"] == "4"
+    assert response.content.decode() == "cont"
+
+
+def test_sendfile_range_open_ended(test_file_handle):
+    app = setup_fastAPI(test_file_handle)
+    client = TestClient(app)
+    response = client.get("/test/send_file", headers={"Range": "bytes=2-"})
+    assert response.status_code == 206
+    assert response.headers["content-range"] == f"bytes 2-{len(CONTENT) - 1}/{len(CONTENT)}"
+    assert response.headers["content-length"] == str(len(CONTENT) - 2)
+    assert response.content.decode() == "ntent"
+
+
+def test_sendfile_range_without_content_length(test_file_handle):
+    # Files served out of a dataset's extra_files_path (e.g. JBrowse track data) don't set
+    # a content-length header; a Range request on a non-nginx deployment must still succeed.
+    app = setup_fastAPI(test_file_handle, set_content_length=False)
+    client = TestClient(app)
+    response = client.get("/test/send_file", headers={"Range": "bytes=0-3"})
+    assert response.status_code == 206
+    assert response.headers["content-range"] == f"bytes 0-3/{len(CONTENT)}"
+    assert response.content.decode() == "cont"

From 002c9ccb2913625b04a7be2ceeef731e239db8f2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 02:20:47 +0200
Subject: [PATCH 144/256] Load datatype converters in the Celery worker for
 async tool execution

The async tool-request path (POST /api/jobs -> queue_jobs Celery task ->
execute_async -> collect_input_datasets) performs implicit datatype conversion
(e.g. decompressing a fasta.gz input for a fasta parameter) in the Celery
worker. The worker's minimal GalaxyManagerApplication built by build_app()
loaded no datatype converters (use_converters=False, and it has no ToolBox to
register them into), so find_conversion_destination found no converter and the
raw compressed dataset was handed to the tool -- e.g. meningotype/bwameth
received gzip bytes as fasta and died on the 0x8b gzip magic byte. The sync
path creates the job in the web process (UniverseApplication, converters
loaded), so only the async path was affected.

Register the built-in datatype converters directly in build_app() using the
same toolbox-less create_tool_from_source path that queue_jobs already uses for
the submitted tool, avoiding the need for a full ToolBox in the worker.
---
 lib/galaxy/celery/__init__.py | 38 ++++++++++++++++++++++++++++++++++-
 1 file changed, 37 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index a251ebadd22..7404c6b9d64 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -113,15 +113,51 @@ def get_galaxy_app():
     return build_app()
 
 
+def _register_worker_datatype_converters(galaxy_app) -> None:
+    """Register datatype converter tools in the Celery worker's datatypes registry.
+
+    Async tool-request execution (``execute_async`` -> ``collect_input_datasets``) runs in
+    the Celery worker and applies implicit datatype conversion (e.g. decompressing a
+    ``fasta.gz`` input for a ``fasta`` parameter). That relies on
+    ``datatypes_registry.datatype_converters`` being populated, which normally happens via
+    ``load_datatype_converters(toolbox)`` in the web ``UniverseApplication``. The worker's
+    minimal ``GalaxyManagerApplication`` has no toolbox, so load the (few, built-in)
+    converter tools directly using the same toolbox-less path ``queue_jobs`` uses for the
+    submitted tool. Without this, ``find_conversion_destination`` finds no converter and the
+    raw (compressed) dataset is handed to the tool. See ``lib/galaxy/tools/actions/__init__.py``.
+    """
+    from galaxy.tool_util.parser import get_tool_source
+    from galaxy.tools import create_tool_from_source
+
+    registry = galaxy_app.datatypes_registry
+    converters_path = registry.converters_path
+    if not converters_path:
+        return
+    for converter_file, source_ext, target_ext in registry.converters:
+        config_path = os.path.join(converters_path, converter_file)
+        try:
+            tool_source = get_tool_source(config_file=config_path)
+            converter = create_tool_from_source(galaxy_app, tool_source, config_file=config_path)
+            registry.converter_tools.add(converter)
+            registry.datatype_converters.setdefault(source_ext, {})[target_ext] = converter
+        except Exception:
+            log.exception("Failed to load datatype converter %s for Celery worker", config_path)
+    # Drop any cached (empty) converter lookups computed before registration.
+    registry._converters_by_datatype = {}
+
+
 @lru_cache(maxsize=1)
 def build_app():
     if kwargs := get_app_properties():
         kwargs["check_migrate_databases"] = False
         kwargs["use_display_applications"] = False
-        kwargs["use_converters"] = False
+        # Collect converter definitions (the converters list) so we can register the
+        # converter tools below; the worker needs them for implicit datatype conversion.
+        kwargs["use_converters"] = True
         import galaxy.app
 
         galaxy_app = galaxy.app.GalaxyManagerApplication(configure_logging=False, **kwargs)
+        _register_worker_datatype_converters(galaxy_app)
         return galaxy_app
 
 

From 073cace4957e7a6e8647459a6b6005653f931f95 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 02:20:57 +0200
Subject: [PATCH 145/256] Add async implicit datatype conversion API tests

Add tests exercising implicit datatype conversion via the tool-request (async)
API alongside the legacy (sync) API: a fasta.gz input fed to the
implicit_conversion tool (fasta.gz -> fasta -> tabular), covering uploaded
(src=hda) and deferred datasets, with an explicit precondition that the input
HDA is stored compressed. Adds a TargetHistory.with_dataset_for_test_file()
populator helper to stage a real test-data file with an explicit (compressed)
ext.
---
 lib/galaxy_test/api/test_tool_execute.py | 42 ++++++++++++++++++++++++
 lib/galaxy_test/base/populators.py       | 26 +++++++++++++++
 2 files changed, 68 insertions(+)

diff --git a/lib/galaxy_test/api/test_tool_execute.py b/lib/galaxy_test/api/test_tool_execute.py
index add8aa54d50..be090507735 100644
--- a/lib/galaxy_test/api/test_tool_execute.py
+++ b/lib/galaxy_test/api/test_tool_execute.py
@@ -947,6 +947,48 @@ def test_deferred_multi_input(required_tool: RequiredTool, target_history: Targe
     output.assert_contains("chr1    4225    19670")
 
 
+def _assert_input_is_compressed_fasta_gz(target_history: TargetHistory, has_src_dict) -> None:
+    details = target_history._dataset_populator.get_history_dataset_details(
+        target_history.id, dataset_id=has_src_dict.id, assert_ok=False
+    )
+    assert (
+        details["file_ext"] == "fasta.gz"
+    ), f"Test precondition failed: input HDA was stored as {details['file_ext']!r}, not compressed 'fasta.gz'"
+
+
+@requires_tool_id("implicit_conversion")
+def test_implicit_gz_conversion_sync(required_tool: RequiredTool, target_history: TargetHistory):
+    # Upload a compressed fasta.gz HDA (kept compressed, ext=fasta.gz). The tool wants
+    # tabular, so this needs a double implicit conversion fasta.gz -> fasta -> tabular.
+    has_src_dict = target_history.with_dataset_for_test_file("1.fasta.gz", file_type="fasta.gz")
+    _assert_input_is_compressed_fasta_gz(target_history, has_src_dict)
+    inputs = {"input1": has_src_dict.src_dict}
+    output = required_tool.execute().with_inputs(inputs).assert_has_single_job.with_single_output
+    output.assert_contains("hg17")
+
+
+@requires_tool_id("implicit_conversion")
+def test_implicit_gz_conversion_async(required_tool: RequiredTool, target_history: TargetHistory):
+    # Same as the sync test above but submitted via the tool-request (async) API. This
+    # reproduces the bug where the async path runs the tool against the raw fasta.gz
+    # instead of the implicitly-converted (decompressed) dataset.
+    has_src_dict = target_history.with_dataset_for_test_file("1.fasta.gz", file_type="fasta.gz")
+    inputs = {"input1": has_src_dict.src_dict}
+    output = required_tool.execute().with_request(inputs).assert_has_single_job.with_single_output
+    output.assert_contains("hg17")
+
+
+@requires_tool_id("implicit_conversion")
+def test_implicit_gz_conversion_async_deferred(required_tool: RequiredTool, target_history: TargetHistory):
+    # Same conversion, but the fasta.gz input is a DEFERRED dataset (as the async
+    # tool-request test harness stages test data). It is materialized at job time; the
+    # question is whether the implicit fasta.gz -> fasta decompression still happens.
+    has_src_dict = target_history.with_deferred_dataset_for_test_file("1.fasta.gz", ext="fasta.gz")
+    inputs = {"input1": has_src_dict.src_dict}
+    output = required_tool.execute().with_request(inputs).assert_has_single_job.with_single_output
+    output.assert_contains("hg17")
+
+
 @requires_tool_id("collection_mixed_param")
 def test_combined_mapping_and_subcollection_mapping(
     target_history: TargetHistory, required_tool: RequiredTool, tool_input_format: DescribeToolInputs
diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index 2952b097285..c631edcf0d1 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -5067,6 +5067,32 @@ class TargetHistory:
         )
         return HasSrcDict("hda", new_dataset)
 
+    def with_dataset_for_test_file(
+        self,
+        filename: str,
+        file_type: str,
+        named: Optional[str] = None,
+    ) -> "HasSrcDict":
+        """Upload a real test-data file with an explicit ``file_type`` (ext preserved).
+
+        Unlike ``with_dataset`` (which uploads inline text and lets the server
+        sniff/auto-decompress), this stages an actual file - e.g. a compressed
+        ``*.fasta.gz`` - and forces ``ext`` to ``file_type`` so it is kept in
+        that (possibly compressed) datatype. Useful for exercising job-time
+        implicit conversion of compressed inputs.
+        """
+        test_data_resolver = TestDataResolver()
+        kwd: dict[str, Any] = {"file_type": file_type, "wait": True}
+        if named is not None:
+            kwd["name"] = named
+        new_dataset = self._dataset_populator.new_dataset(
+            history_id=self._history_id,
+            content=open(test_data_resolver.get_filename(filename), "rb"),
+            assert_ok=True,
+            **kwd,
+        )
+        return HasSrcDict("hda", new_dataset)
+
     def with_deferred_dataset(
         self,
         uri: str,

From 9b97ae7c438451695619b62fbbbe012fd2e3694c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 09:10:19 +0200
Subject: [PATCH 146/256] Don't resolve an omitted nested conditional
 discriminator to an ancestor's

When a legacy test omits a nested conditional's discriminator (relying on the
default when, as the synchronous tool API does), the async test-case builder's
loose fallback matching in _input_for could resolve the omitted discriminator to
an *enclosing* conditional's discriminator that shares the (generic) parameter
name and is an ordered subsequence of the path - e.g. wf|selector=none for
wf|...|protein_db|selector, or operation|use=filter for operation|method|use.
The wrong value was then validated against the inner conditional's whens and
rejected (Invalid conditional test value ...), or written into the inner
conditional's state and rejected by the discriminated-union model.

Track the discriminator input consumed by each conditional and exclude those
names from the suffix/short-name/elided fallbacks when resolving a descendant
conditional's discriminator (and its leaf merge). Section/repeat ancestors
consume no discriminator, so the legitimate elided-leaf fallback (e.g. a param
written under its enclosing section with the conditional name elided) is
unaffected. Omitted nested conditionals now fall back to their default when, as
under the synchronous API - no test-definition changes required.

Fixes async submission validation for tools like humann and dropletutils that
omit a defaulted nested conditional in their tests.
---
 lib/galaxy/tool_util/parameters/case.py | 94 ++++++++++++++++++++-----
 1 file changed, 76 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 75c9f9185e4..f520a6b7bce 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -8,6 +8,7 @@ from typing import (
     List,
     Optional,
     Set,
+    Tuple,
 )
 
 from packaging.version import Version
@@ -265,11 +266,21 @@ def _merge_level_into_state(
     state_representation: Literal["test_case_xml", "test_case_json"],
     warnings: List[str],
     prefix: Optional[str],
+    consumed_discriminators: Optional[Set[str]] = None,
 ) -> Set[str]:
     handled_inputs: Set[str] = set()
     for tool_input in tool_inputs:
         handled_inputs.update(
-            _merge_into_state(tool_input, inputs, state_at_level, profile, state_representation, warnings, prefix)
+            _merge_into_state(
+                tool_input,
+                inputs,
+                state_at_level,
+                profile,
+                state_representation,
+                warnings,
+                prefix,
+                consumed_discriminators,
+            )
         )
 
     return handled_inputs
@@ -291,6 +302,7 @@ def _merge_into_state(
     state_representation: Literal["test_case_xml", "test_case_json"],
     warnings: List[str],
     prefix: Optional[str],
+    consumed_discriminators: Optional[Set[str]] = None,
 ) -> Set[str]:
     handled_inputs = set()
 
@@ -303,11 +315,20 @@ def _merge_into_state(
         if input_name not in state_at_level:
             state_at_level[input_name] = conditional_state
 
-        when: ConditionalWhen = _select_which_when(tool_input, conditional_state, inputs, state_path)
+        when, discriminator_name = _select_which_when(
+            tool_input, conditional_state, inputs, state_path, consumed_discriminators
+        )
         test_parameter = tool_input.test_parameter
         handled_inputs.update(
             _merge_into_state(
-                test_parameter, inputs, conditional_state, profile, state_representation, warnings, state_path
+                test_parameter,
+                inputs,
+                conditional_state,
+                profile,
+                state_representation,
+                warnings,
+                state_path,
+                consumed_discriminators,
             )
         )
         # If the discriminator was omitted but a non-default when was inferred from the
@@ -315,9 +336,21 @@ def _merge_into_state(
         # against that branch rather than the __absent__/default branch.
         if test_parameter.name not in conditional_state and not when.is_default_when:
             conditional_state[test_parameter.name] = when.discriminator
+        # The discriminator consumed here belongs to this conditional; mark it so the loose
+        # fallbacks do not re-match it when resolving a nested conditional's discriminator.
+        when_consumed = consumed_discriminators
+        if discriminator_name is not None:
+            when_consumed = set(consumed_discriminators or set()) | {discriminator_name}
         handled_inputs.update(
             _merge_level_into_state(
-                when.parameters, inputs, conditional_state, profile, state_representation, warnings, state_path
+                when.parameters,
+                inputs,
+                conditional_state,
+                profile,
+                state_representation,
+                warnings,
+                state_path,
+                when_consumed,
             )
         )
     elif isinstance(tool_input, (RepeatParameterModel,)):
@@ -343,6 +376,7 @@ def _merge_into_state(
                     state_representation,
                     warnings,
                     repeat_instance_prefix,
+                    consumed_discriminators,
                 )
             )
     elif isinstance(tool_input, (SectionParameterModel,)):
@@ -352,11 +386,18 @@ def _merge_into_state(
 
         handled_inputs.update(
             _merge_level_into_state(
-                tool_input.parameters, inputs, section_state, profile, state_representation, warnings, state_path
+                tool_input.parameters,
+                inputs,
+                section_state,
+                profile,
+                state_representation,
+                warnings,
+                state_path,
+                consumed_discriminators,
             )
         )
     else:
-        test_input = _input_for(state_path, inputs)
+        test_input = _input_for(state_path, inputs, exclude_names=consumed_discriminators)
         if test_input is not None:
             input_value: Any
             if isinstance(tool_input, (DataCollectionParameterModel,)):
@@ -444,14 +485,22 @@ def _repeat_inputs_to_array(
 
 
 def _select_which_when(
-    conditional: ConditionalParameterModel, state: dict, inputs: ToolSourceTestInputs, prefix: str
-) -> ConditionalWhen:
+    conditional: ConditionalParameterModel,
+    state: dict,
+    inputs: ToolSourceTestInputs,
+    prefix: str,
+    consumed_discriminators: Optional[Set[str]] = None,
+) -> Tuple[ConditionalWhen, Optional[str]]:
+    """Return the selected when and the name of the test input used as the discriminator
+    (or ``None`` if the discriminator was omitted). The discriminator name lets callers mark
+    it consumed so descendant conditionals do not re-match it via the loose fallbacks."""
     test_parameter = conditional.test_parameter
     is_boolean = test_parameter.parameter_type == "gx_boolean"
     test_parameter_name = test_parameter.name
     test_parameter_flat_path = flat_state_path(test_parameter_name, prefix)
 
-    test_input = _input_for(test_parameter_flat_path, inputs)
+    test_input = _input_for(test_parameter_flat_path, inputs, exclude_names=consumed_discriminators)
+    matched_name = test_input["name"] if test_input else None
     explicit_test_value = test_input["value"] if test_input else None
     if is_boolean and isinstance(explicit_test_value, str):
         explicit_test_value = asbool(explicit_test_value)
@@ -463,14 +512,13 @@ def _select_which_when(
         # to validate against the default branch).
         inferred_when = _infer_when_from_inputs(conditional, inputs, prefix)
         if inferred_when is not None:
-            return inferred_when
+            return inferred_when, matched_name
     for when in conditional.whens:
         if test_value is None and when.is_default_when:
-            return when
+            return when, matched_name
         elif test_value == when.discriminator:
-            return when
-    else:
-        raise Exception(f"Invalid conditional test value ({explicit_test_value}) for parameter ({test_parameter_name})")
+            return when, matched_name
+    raise Exception(f"Invalid conditional test value ({explicit_test_value}) for parameter ({test_parameter_name})")
 
 
 def _leaf_param_short_names(parameters: List[ToolParameterT]) -> Set[str]:
@@ -520,7 +568,15 @@ def _infer_when_from_inputs(
     return None
 
 
-def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[ToolSourceTestInput]:
+def _input_for(
+    flat_state_path: str, inputs: ToolSourceTestInputs, exclude_names: Optional[Set[str]] = None
+) -> Optional[ToolSourceTestInput]:
+    # ``exclude_names`` holds the names of test inputs already consumed as the discriminator
+    # of an enclosing conditional. Such an input belongs to that ancestor conditional and must
+    # not be re-matched by the loose fallbacks below when resolving a descendant's
+    # discriminator (otherwise e.g. an omitted nested ``selector`` greedily picks up the
+    # parent conditional's ``selector`` value - see _select_which_when).
+    exclude = exclude_names or set()
     for input in inputs:
         if input["name"] == flat_state_path:
             return input
@@ -530,7 +586,7 @@ def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[T
         suffix_matching_inputs = [
             input
             for input in inputs
-            if "|" in input["name"] and flat_state_path.endswith(f"|{input['name']}")
+            if "|" in input["name"] and input["name"] not in exclude and flat_state_path.endswith(f"|{input['name']}")
         ]
         resolved = _resolve_matching_inputs(
             suffix_matching_inputs, f"Ambiguous partially qualified test parameter name for ({flat_state_path})"
@@ -539,7 +595,7 @@ def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[T
             return resolved
 
         short_name = flat_state_path.rsplit("|", 1)[1]
-        matching_inputs = [input for input in inputs if input["name"] == short_name]
+        matching_inputs = [input for input in inputs if input["name"] == short_name and input["name"] not in exclude]
         resolved = _resolve_matching_inputs(
             matching_inputs, f"Ambiguous unqualified test parameter name ({short_name}) for ({flat_state_path})"
         )
@@ -553,7 +609,9 @@ def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[T
         # plain suffix.
         path_segments = flat_state_path.split("|")
         elided_matching_inputs = [
-            input for input in inputs if _is_conditional_elided_match(input["name"], path_segments)
+            input
+            for input in inputs
+            if input["name"] not in exclude and _is_conditional_elided_match(input["name"], path_segments)
         ]
         resolved = _resolve_matching_inputs(
             elided_matching_inputs, f"Ambiguous partially qualified test parameter name for ({flat_state_path})"

From c2d1b2bc83b5016b9800bce8820f0e7e5fd359ae Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 09:12:29 +0200
Subject: [PATCH 147/256] Add async regression tool for shared-name nested
 conditional discriminators

A framework reproducer (validated by test_validate_framework_test_tools) for the
case where an outer and a nested conditional share a discriminator name and the
test omits the inner discriminator. Without the preceding fix the async builder
mis-resolves the omitted inner discriminator to the outer conditional's value;
with it the inner conditional falls back to its default when.
---
 ...ested_conditional_shared_discriminator.xml | 69 +++++++++++++++++++
 test/functional/tools/sample_tool_conf.xml    |  1 +
 2 files changed, 70 insertions(+)
 create mode 100644 test/functional/tools/async_nested_conditional_shared_discriminator.xml

diff --git a/test/functional/tools/async_nested_conditional_shared_discriminator.xml b/test/functional/tools/async_nested_conditional_shared_discriminator.xml
new file mode 100644
index 00000000000..92783a19d49
--- /dev/null
+++ b/test/functional/tools/async_nested_conditional_shared_discriminator.xml
@@ -0,0 +1,69 @@
+<tool id="async_nested_conditional_shared_discriminator" name="async_nested_conditional_shared_discriminator" version="1.0.0" profile="22.01">
+    <description>async regression: omitted nested discriminator must not resolve to an enclosing conditional's discriminator of the same name</description>
+    <!--
+      Models dropletutils / humann, where an OUTER and an INNER conditional use a
+      discriminator with the same (generic) name and the test omits the inner one,
+      relying on its default when (as the synchronous API does).
+
+      Here both 'operation' and the nested 'method' use a discriminator named 'use'.
+      The test selects operation|use=outer_a and omits method|use (default inner_a).
+
+      Sync (POST /api/tools): the omitted inner discriminator selects its default
+      when (inner_a); the job runs.
+
+      Async (POST tool request) previously mis-resolved the omitted
+      operation|method|use to the enclosing operation|use (value "outer_a") via the
+      loose subsequence fallback, then rejected it because "outer_a" is not a valid
+      'method' when:
+        Invalid conditional test value (outer_a) for parameter (use)
+      The async builder now excludes a consumed ancestor discriminator from that
+      fallback, so the inner conditional correctly falls back to its default when.
+    -->
+    <command><![CDATA[
+echo '$operation.use' > '$out_file1' &&
+#if str($operation.use) == "outer_a":
+echo '$operation.method.use' >> '$out_file1'
+#end if
+    ]]></command>
+    <inputs>
+        <conditional name="operation">
+            <param name="use" type="select" label="Operation">
+                <option value="outer_a" selected="true">Outer A</option>
+                <option value="outer_b">Outer B</option>
+            </param>
+            <when value="outer_a">
+                <conditional name="method">
+                    <param name="use" type="select" label="Method">
+                        <option value="inner_a" selected="true">Inner A</option>
+                        <option value="inner_b">Inner B</option>
+                    </param>
+                    <when value="inner_a">
+                        <param name="threshold" type="integer" value="3000" label="Threshold" />
+                    </when>
+                    <when value="inner_b">
+                        <param name="lower" type="integer" value="100" label="Lower" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="outer_b">
+                <param name="rank" type="integer" value="1" label="Rank" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="operation">
+                <param name="use" value="outer_a" />
+            </conditional>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="outer_a" />
+                    <has_line line="inner_a" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml
index 2134dae968c..865007ed833 100644
--- a/test/functional/tools/sample_tool_conf.xml
+++ b/test/functional/tools/sample_tool_conf.xml
@@ -122,6 +122,7 @@
   <tool file="output_filter.xml" />
   <tool file="async_conditional_no_default_nested_data.xml" />
   <tool file="async_ambiguous_unqualified_name.xml" />
+  <tool file="async_nested_conditional_shared_discriminator.xml" />
   <tool file="output_empty_work_dir.xml" />
   <tool file="output_filter_with_input.xml" />
   <tool file="output_filter_with_input_optional.xml" />

From 3eeb5fa9c3d3c076731f5f56abfd4d03dc0ed769 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 10:09:47 +0200
Subject: [PATCH 148/256] Accept dce collection references in the tool request
 model

A tool that maps over a nested collection (e.g. subcollection mapping
over a list:paired) records its paired-collection input as a
DatasetCollectionElement. Rerunning such a job resubmits that input as
{src: dce, id: ...} through the structured tool-request path, but the
external request model's collection source type only allowed "hdca" --
even though the internal model, the legacy execution path, and the tool
form all already support "dce". Rerun therefore failed with a pydantic
validation error (request model).

Widen the external collection source type to Literal["hdca", "dce"].
This covers both the single-collection request (DataCollectionRequest)
and the batch request (BatchCollectionInstance); the internal models
already accepted dce and decode() passes src through unchanged.

While here, rename CollectionStrT -> CollectionSrcT (per the existing
FIXME comment) and drop the unused DataSrcT/MultiDataSrcT/TestCaseDataSrcT
literal aliases. Single data parameters already accept dce via the
dedicated DataRequestDce model in the _DataRequest union, so no data
source type needed widening.

Fixes #22923
---
 lib/galaxy/tool_util_models/parameters.py     | 15 +++++------
 lib/galaxy_test/api/test_tools.py             | 27 +++++++++++++++++++
 .../tool_util/parameter_specification.yml     | 13 +++++++++
 3 files changed, 47 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index 3922cf39b70..9bdf85e7cef 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -501,15 +501,14 @@ class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
         return False
 
 
-DataSrcT = Literal["hda", "ldda"]
-MultiDataSrcT = Literal["hda", "ldda", "hdca", "dce"]
-# @jmchilton you meant CollectionSrcT - fix that at some point please.
-CollectionStrT = Literal["hdca"]
+# External collection source type. ``dce`` is accepted because a job that maps
+# over a nested collection (e.g. subcollection mapping over a ``list:paired``)
+# records its input as a ``DatasetCollectionElement``; rerunning such a job
+# resubmits that ``dce`` reference through the request model.
+CollectionSrcT = Literal["hdca", "dce"]
 # Internal collection source type - includes dce for subcollection mapping
 CollectionInternalSrcT = Literal["hdca", "dce"]
 
-TestCaseDataSrcT = Literal["File"]
-
 
 class LegacyRequestModelAttributes(StrictModel):
     # Here for bioblend's sake, should be stripped
@@ -1267,12 +1266,12 @@ class DataParameterModel(BaseGalaxyToolParameterModelDefinition):
 
 
 class DataCollectionRequest(StrictModel):
-    src: CollectionStrT
+    src: CollectionSrcT
     id: StrictStr
 
 
 class BatchCollectionInstance(StrictModel):
-    src: CollectionStrT
+    src: CollectionSrcT
     id: StrictStr
     map_over_type: Optional[str] = None
 
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index b247e732f74..0f0085e39c0 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -3194,6 +3194,33 @@ class TestToolsApi(ApiTestCase, TestsTools):
             assert len(response_object["jobs"]) == 2
             assert len(response_object["implicit_collections"]) == 1
 
+    @skip_without_tool("collection_paired_test")
+    def test_request_paired_collection_input_with_dce(self):
+        """Regression for https://github.com/galaxyproject/galaxy/issues/22923
+
+        A job that maps over a ``list:paired`` records its paired-collection
+        input as a ``DatasetCollectionElement`` (``src: dce``). Rerunning such a
+        job resubmits that ``dce`` reference through the structured tool-request
+        path, which must validate against the request model.
+        """
+        with self.dataset_populator.test_history() as history_id:
+            pair_ids = []
+            for _ in range(2):
+                pair_id = self.dataset_collection_populator.create_pair_in_history(
+                    history_id, contents=["forward", "reverse"], wait=True
+                ).json()["outputs"][0]["id"]
+                pair_ids.append(pair_id)
+            list_hdca = self.dataset_collection_populator.create_list_from_pairs(history_id, pair_ids)
+            # The element of a list:paired is itself a paired collection, referenced via a dce.
+            dce_id = list_hdca.json()["elements"][0]["id"]
+
+            inputs = {"f1": {"src": "dce", "id": dce_id}}
+            response = self.dataset_populator.tool_request_raw("collection_paired_test", inputs, history_id)
+            self._assert_status_code_is(response, 200)
+            tool_request_id = response.json()["tool_request_id"]
+            assert self.dataset_populator.wait_on_tool_request(tool_request_id)
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+
     @skip_without_tool("identifier_source")
     def test_default_identifier_source_map_over(self):
         with self.dataset_populator.test_history() as history_id:
diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
index 0aabb1056d6..8e55e2204e5 100644
--- a/test/unit/tool_util/parameter_specification.yml
+++ b/test/unit/tool_util/parameter_specification.yml
@@ -1591,9 +1591,16 @@ gx_data_multiple_optional:
 gx_data_collection:
   request_valid:
    - parameter: {src: hdca, id: abcdabcd}
+   # dce subcollection reference - e.g. rerunning a job that mapped over a list:paired
+   - parameter: {src: dce, id: abcdabcd}
+   # batching (multirun) over dce subcollections
+   - parameter: {__class__: "Batch", values: [{src: dce, id: abcdabcd}]}
+   - parameter: {__class__: "Batch", values: [{src: dce, id: abcdabcd, map_over_type: paired}]}
    - parameter: {class: "Collection", collection_type: "list", elements: []}
   request_invalid:
    - parameter: {src: hdca, id: 7}
+   # external request ids must be encoded strings, not decoded ints - for hdca and dce alike
+   - parameter: {src: dce, id: 7}
    - parameter: null
    - parameter: {src: fooda, id: abcdabcd}
    - parameter: {id: abcdabcd}
@@ -1605,9 +1612,12 @@ gx_data_collection:
    - parameter: {class: "CollectionX", collection_type: "list", elements: []}
   request_internal_valid:
    - parameter: {src: hdca, id: 5}
+   - parameter: {src: dce, id: 5}
+   - parameter: {__class__: "Batch", values: [{src: dce, id: 5}]}
    - parameter: {class: "Collection", collection_type: "list", elements: []}
   request_internal_invalid:
    - parameter: {src: hdca, id: abcdabcd}
+   - parameter: {src: dce, id: abcdabcd}
    - parameter: null
    - parameter: {src: fooda, id: abcdabcd}
    - parameter: {id: abcdabcd}
@@ -1619,6 +1629,7 @@ gx_data_collection:
    - parameter: {class: "CollectionX", collection_type: "list", elements: []}
   request_internal_dereferenced_valid:
    - parameter: {src: hdca, id: 5}
+   - parameter: {src: dce, id: 5}
   request_internal_dereferenced_invalid:
    - parameter: {src: hdca, id: abcdabcd}
    # At thsi point the collection should have been dereferenced into datasets,
@@ -1759,6 +1770,7 @@ gx_data_collection:
 gx_data_collection_optional:
   request_valid:
    - parameter: {src: hdca, id: abcdabcd}
+   - parameter: {src: dce, id: abcdabcd}
    - parameter: null
    - {}
   request_invalid:
@@ -1771,6 +1783,7 @@ gx_data_collection_optional:
    - parameter: {}
   request_internal_valid:
    - parameter: {src: hdca, id: 5}
+   - parameter: {src: dce, id: 5}
    - parameter: null
    - {}
   request_internal_invalid:

From 2854ebc18d8b59c017ca04600e7dd260e0ddbc70 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 10:04:05 +0200
Subject: [PATCH 149/256] Preserve significant whitespace when parsing a tool
 from its raw string source

build_xml_tool_source parsed raw tool source strings with strip_whitespace=True,
which .strip()s every element's text - unlike the file/macro loader
(xml_macros.load uses strip_whitespace=False). For a <validator type="regex">
whose body relies on leading whitespace, e.g. " *(\d+, *)*\d+ *$" (optional
leading spaces), stripping turned it into the invalid "*(\d+...".

The async tool-request path stores a tool's source via tool_source.to_string()
and re-parses it through this string path when encoding the request; the
corrupted regex then raised 'nothing to repeat at position 0' while statically
validating the request, surfacing as a 500 on GET /api/tool_requests/{id}
(reproduced with varvamp test 3). Parse raw string sources with
strip_whitespace=False so they match file parsing and round-trip faithfully.
---
 lib/galaxy/tool_util/parser/factory.py        |  7 ++++-
 .../tool_util/test_parameter_test_cases.py    | 28 +++++++++++++++++++
 2 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parser/factory.py b/lib/galaxy/tool_util/parser/factory.py
index e8714f7074c..3379d7dfca6 100644
--- a/lib/galaxy/tool_util/parser/factory.py
+++ b/lib/galaxy/tool_util/parser/factory.py
@@ -39,7 +39,12 @@ log = logging.getLogger(__name__)
 
 
 def build_xml_tool_source(xml_string: str) -> XmlToolSource:
-    return XmlToolSource(parse_xml_string_to_etree(xml_string))
+    # Preserve significant whitespace (e.g. a leading space in a <validator> regex such as
+    # " *(\\d+, *)*\\d+ *$") to match how tools are parsed from a file (xml_macros.load uses
+    # strip_whitespace=False). Stripping it here corrupts such regexes when a tool is
+    # re-parsed from its stored raw source (async tool requests), which then raised a 500
+    # while statically validating the request.
+    return XmlToolSource(parse_xml_string_to_etree(xml_string, strip_whitespace=False))
 
 
 def build_cwl_tool_source(yaml_string: str) -> CwlToolSource:
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index 0025f467467..65fcd3e8245 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -764,3 +764,31 @@ def mock_adapt_collections(input: JsonTestCollectionDefDict) -> DataCollectionRe
 
 
 tool_source_for = functional_test_tool_source
+
+
+def test_build_xml_tool_source_preserves_validator_whitespace():
+    """Regex validators may rely on significant leading/trailing whitespace (e.g. a leading
+    `" *"` meaning "optional spaces"). Parsing a tool from its raw string source (as the async
+    tool-request path does when re-parsing the stored source) must preserve it, exactly like
+    parsing from a file does - otherwise " *(\\d+, *)*\\d+ *$" becomes the invalid "*(\\d+..."
+    and statically validating the request 500s.
+    """
+    from galaxy.tool_util.parser.factory import build_xml_tool_source
+
+    tool_xml = (
+        '<tool id="ws_validator" name="ws_validator" version="1.0" profile="24.2">'
+        "<command>echo</command><inputs>"
+        '<param name="ints" type="text" value="1, 2, 3">'
+        '<validator type="regex" message="comma separated ints"> *(\\d+, *)*\\d+ *$</validator>'
+        "</param></inputs><outputs/></tool>"
+    )
+    tool_source = build_xml_tool_source(tool_xml)
+    bundle = input_models_for_tool_source(tool_source)
+    regex_validators = [
+        v
+        for p in bundle.parameters
+        for v in (getattr(p, "validators", None) or [])
+        if getattr(v, "type", "") == "regex"
+    ]
+    assert regex_validators, "expected a regex validator in the parsed model"
+    assert regex_validators[0].expression == " *(\\d+, *)*\\d+ *$"

From 60c8b2ba802ff527f2e4f36cdb4b207c3ae21618 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 14:01:25 +0200
Subject: [PATCH 150/256] Infer conditional when from bare unqualified branch
 params in async tool tests

_infer_when_from_inputs only considered inputs qualified with the conditional's
prefix, so a legacy test that supplies a non-default branch's param by its bare
short name (without the enclosing conditional prefix) and omits the discriminator
was not matched: the builder fell back to the default (often empty) branch and
then rejected the bare param as 'Invalid parameter name found ...'. Include
legacy unqualified (bare) inputs when scoring whens, skipping only inputs
qualified to a different prefix. Resolves e.g. novoplasty reference_cond and
hisat2 adv|spliced_options without per-tool test edits.
---
 lib/galaxy/tool_util/parameters/case.py       |  6 +++-
 .../tool_util/test_parameter_test_cases.py    | 30 +++++++++++++++++++
 2 files changed, 35 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index f520a6b7bce..39ca9845cc4 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -547,7 +547,11 @@ def _infer_when_from_inputs(
     provided_short_names: Set[str] = set()
     for input in inputs:
         name = input["name"]
-        if scope and not name.startswith(scope):
+        # Consider inputs scoped to this conditional, plus legacy unqualified (bare) inputs -
+        # a test may supply a non-default branch's param by its short name without the
+        # enclosing conditional prefix (e.g. <param name="reference"> for
+        # reference_cond|reference). Skip only inputs qualified to a *different* prefix.
+        if scope and not name.startswith(scope) and "|" in name:
             continue
         provided_short_names.add(name.rsplit("|", 1)[-1])
     if not provided_short_names:
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index 65fcd3e8245..db9193057db 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -792,3 +792,33 @@ def test_build_xml_tool_source_preserves_validator_whitespace():
     ]
     assert regex_validators, "expected a regex validator in the parsed model"
     assert regex_validators[0].expression == " *(\\d+, *)*\\d+ *$"
+
+
+def test_infer_when_from_bare_unqualified_branch_param():
+    """A legacy test may supply a non-default branch's param by its bare short name (without
+    the enclosing conditional prefix) and omit the discriminator. The async builder must infer
+    the active when from that bare param, as the sync API does - otherwise it defaults to the
+    (empty) default branch and rejects the param as unhandled. Models novoplasty reference_cond
+    / hisat2 adv|spliced_options.
+    """
+    from galaxy.tool_util.parser.factory import build_xml_tool_source
+
+    tool_xml = (
+        '<tool id="bare_branch" name="bare_branch" version="1.0" profile="20.01">'
+        "<command>echo</command><inputs>"
+        '<conditional name="use_ref">'
+        '<param name="enabled" type="select"><option value="no" selected="true">No</option>'
+        '<option value="yes">Yes</option></param>'
+        '<when value="no"/>'
+        '<when value="yes"><param name="reference" type="text" value="" /></when>'
+        "</conditional></inputs><outputs/>"
+        "<tests><test>"
+        '<param name="reference" value="ref.fa"/>'  # bare, non-default branch, discriminator omitted
+        "</test></tests></tool>"
+    )
+    ts = build_xml_tool_source(tool_xml)
+    bundle = input_models_for_tool_source(ts)
+    test = ts.parse_tests_to_dict()["tests"][0]
+    # should not raise - the 'yes' branch is inferred from the bare 'reference'
+    state = case_state(test, bundle.parameters, ts.parse_profile(), validate=True)
+    assert state.tool_state.input_state["use_ref"]["enabled"] == "yes"

From 3cf476fc91736ec4e8457a62b7f580ac31fe510d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 14:29:23 +0200
Subject: [PATCH 151/256] Record the default (first-option) discriminator for
 an omitted legacy conditional

When a test omitted a conditional's discriminator and the active branch was the
default when, _merge_into_state left the discriminator unset, so the discriminated
-union model routed the state to the phantom __absent__ branch and validation
failed (e.g. multigsea proteomics_data.__absent__). For a legacy conditional with
no explicit selected="true", the model already marks the first option as the
default when; record that discriminator in the state - matching what the runtime
fill_static_defaults already does for an incomplete payload - so the state
validates against the default branch. Generalizes the earlier non-default-when
inference to the default-when case.
---
 lib/galaxy/tool_util/parameters/case.py       | 11 +++++---
 .../tool_util/test_parameter_test_cases.py    | 26 +++++++++++++++++++
 2 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 39ca9845cc4..443f2610056 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -331,10 +331,13 @@ def _merge_into_state(
                 consumed_discriminators,
             )
         )
-        # If the discriminator was omitted but a non-default when was inferred from the
-        # provided parameters, record the inferred discriminator so the state validates
-        # against that branch rather than the __absent__/default branch.
-        if test_parameter.name not in conditional_state and not when.is_default_when:
+        # If the discriminator was omitted, record the selected when's discriminator so the
+        # state validates against that branch rather than the phantom __absent__ branch. This
+        # is the active branch _select_which_when chose: a non-default when inferred from the
+        # provided params, or - for a legacy conditional with no explicit selected="true" - the
+        # default (first) option, mirroring how the synchronous runtime fills an incomplete
+        # payload.
+        if test_parameter.name not in conditional_state and when.discriminator is not None:
             conditional_state[test_parameter.name] = when.discriminator
         # The discriminator consumed here belongs to this conditional; mark it so the loose
         # fallbacks do not re-match it when resolving a nested conditional's discriminator.
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
index db9193057db..791be010dca 100644
--- a/test/unit/tool_util/test_parameter_test_cases.py
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -822,3 +822,29 @@ def test_infer_when_from_bare_unqualified_branch_param():
     # should not raise - the 'yes' branch is inferred from the bare 'reference'
     state = case_state(test, bundle.parameters, ts.parse_profile(), validate=True)
     assert state.tool_state.input_state["use_ref"]["enabled"] == "yes"
+
+
+def test_omitted_conditional_records_first_option_default():
+    """For a legacy conditional with no explicit selected="true", the first option is the
+    default (is_default_when). When a test omits the discriminator entirely, the builder must
+    record that default discriminator in the state - mirroring how the synchronous runtime
+    (fill_static_defaults) fills an incomplete payload - so the state validates against the
+    default branch instead of the phantom __absent__ branch. Models multigsea's
+    proteomics/metabolomics conditionals.
+    """
+    from galaxy.tool_util.parser.factory import build_xml_tool_source
+
+    tool_xml = (
+        '<tool id="first_opt" name="first_opt" version="1.0" profile="20.05">'
+        "<command>echo</command><inputs>"
+        '<conditional name="opt">'
+        '<param name="selector" type="select">'
+        '<option value="a">A</option><option value="b">B</option></param>'  # no selected="true"
+        '<when value="a"><param name="x" type="text" value="dx"/></when>'
+        '<when value="b"/></conditional>'
+        "</inputs><outputs/><tests><test/></tests></tool>"  # discriminator omitted entirely
+    )
+    ts = build_xml_tool_source(tool_xml)
+    bundle = input_models_for_tool_source(ts)
+    state = case_state(ts.parse_tests_to_dict()["tests"][0], bundle.parameters, ts.parse_profile(), validate=True)
+    assert state.tool_state.input_state["opt"]["selector"] == "a"  # first option recorded, not __absent__

From f57dcbadbfbcf35d9ff12c4507cc81e9a7be0c67 Mon Sep 17 00:00:00 2001
From: Maed0x <32331424+Maed0x@users.noreply.github.com>
Date: Tue, 16 Jun 2026 18:01:42 +0200
Subject: [PATCH 152/256] Adding missing formats

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 5d3d74ef3e3..074f9fe4653 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -619,6 +619,11 @@
     <datatype extension="vg.dist" type="galaxy.datatypes.binary:Binary" subclass="true" description="VG distance index storing minimum distances between graph positions." description_url="https://github.com/vgteam/vg/wiki/File-Types#miscellaneous-formats" display_in_upload="true"/>
     <datatype extension="vg.snarls" type="galaxy.datatypes.binary:Binary" subclass="true" description="VG snarl decomposition index defining nested variation sites in a graph." description_url="https://github.com/vgteam/vg/wiki/File-Types#miscellaneous-formats" display_in_upload="true"/>
     <datatype extension="vg.gamp" type="galaxy.datatypes.binary:Binary" subclass="true" description="VG GAM position index enabling random access to graph alignments." description_url="https://github.com/vgteam/vg/wiki/File-Types#read-and-alignment-formats" display_in_upload="true"/>
+    <datatype extension="vg.min" type="galaxy.datatypes.binary:Binary" subclass="true" description="VG minimizer index used to find minimizer substrings in a graph." description_url="https://github.com/vgteam/vg/wiki/File-Types#miscellaneous-formats" display_in_upload="true"/>
+    <datatype extension="vg.zipcodes" type="galaxy.datatypes.binary:Binary" subclass="true" description="VG zipcodes stores supplemental distance information for substrings in a graph." description_url="https://github.com/vgteam/vg/wiki/File-Types#miscellaneous-formats" display_in_upload="true"/>
+    <datatype extension="vg.gg" type="galaxy.datatypes.binary:Binary" subclass="true" description="A supplemental information to turn a GBWT file into a graph." description_url="https://github.com/vgteam/vg/wiki/File-Types#reference-formats" display_in_upload="true"/>
+    <datatype extension="gbz" type="galaxy.datatypes.binary:Binary" subclass="true" description="A compressed format storing a graph as traversed by sample haplotypes." description_url="https://github.com/vgteam/vg/wiki/File-Types#reference-formats" display_in_upload="true"/>
+    <datatype extension="gbwt" type="galaxy.datatypes.binary:Binary" subclass="true" description="A multi-string FM-index for indexing large collections of similar paths over a graph." description_url="https://github.com/jltsiren/gbwt/blob/master/README.md" display_in_upload="true"/>
     <datatype extension="hal" type="galaxy.datatypes.binary:Binary" subclass="true" description="Hierarchical Alignment Format" display_in_upload="true" description_url="https://github.com/ComparativeGenomicsToolkit/hal"/>
     <datatype extension="hal.pg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Pairwise genome alignment graph." display_in_upload="true"/>
     <datatype extension="hal.hg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Hierarchical multi-genome alignment graph." display_in_upload="true"/>
@@ -763,6 +768,7 @@
     <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text" subclass="true"/>
     <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text" subclass="true"/>
     <datatype extension="fuzztran" type="galaxy.datatypes.data:Text" subclass="true"/>
+    <datatype extension="gaf" type="galaxy.datatypes.data:Text" subclass="true" description="Graph Alignment Format. A tab-delimited file format for sequence alignments to bidirected sequence graphs." description_url="https://github.com/vgteam/vg/blob/master/doc/static/GAF.md"/>
     <datatype extension="garnier" type="galaxy.datatypes.data:Text" subclass="true"/>
     <datatype extension="geecee" type="galaxy.datatypes.data:Text" subclass="true"/>
     <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text" subclass="true"/>

From 91b58bc7d281eca788198e8d1815cda580f1f1de Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 18:22:25 +0200
Subject: [PATCH 153/256] Drop comment

---
 lib/galaxy/celery/__init__.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index 7404c6b9d64..a21cfdcdd27 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -151,8 +151,6 @@ def build_app():
     if kwargs := get_app_properties():
         kwargs["check_migrate_databases"] = False
         kwargs["use_display_applications"] = False
-        # Collect converter definitions (the converters list) so we can register the
-        # converter tools below; the worker needs them for implicit datatype conversion.
         kwargs["use_converters"] = True
         import galaxy.app
 

From 8366c341520aa4fad927efddded596723ac7549d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 12:07:15 +0000
Subject: [PATCH 154/256] Memoize run-form history option queries on the
 request context (issue #22927)

Building the workflow Run form renders every step in one
GET /api/workflows/{id}/download?style=run request. Each data /
data_collection parameter independently re-issued the same paginated history
SQL (History.paginated_active_visible_datasets /
paginated_active_dataset_collections) in both get_initial_value and to_dict,
turning a single history scan into O(number of parameters) DB round-trips --
slow even on an empty history, and scaling with workflow size.

Memoize the (filter, page) -> (rows, total) results by signature. Tool.to_json
builds a fresh proxy_work_context_for_history per step, so the cache lives on
the request context's short-term cache (ProvidesHistoryContext.set_cache_value)
and proxy_work_context_for_history now shares the parent transaction's
_short_term_cache with each per-step proxy. That keeps the cache request-scoped
and shared across every step of a build without attaching state to the
SQLAlchemy history instance. Cache keys include the history id because a proxy
may target a history other than the parent's.

Benchmark (50-step workflow, empty history, 3 builds), vs unpatched 26.1:
  _workflow_to_dict_run  ~9100ms -> ~750ms   (~13x faster)
  SQL executions           2478  -> 180       (-93%)
  paginated history scans  1164  -> 15
---
 lib/galaxy/app_unittest_utils/galaxy_mock.py  |  8 ++
 lib/galaxy/managers/context.py                | 11 ++-
 lib/galaxy/tools/parameters/basic.py          | 97 ++++++++++++++++---
 lib/galaxy/webapps/base/webapp.py             |  3 +-
 lib/galaxy/work/context.py                    | 10 +-
 test/integration/test_workflow_refactoring.py |  2 +
 test/unit/app/tools/test_execution.py         |  7 +-
 7 files changed, 120 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py
index 9f4fe40139e..d69a6c763af 100644
--- a/lib/galaxy/app_unittest_utils/galaxy_mock.py
+++ b/lib/galaxy/app_unittest_utils/galaxy_mock.py
@@ -5,6 +5,7 @@ Mock infrastructure for testing ModelManagers.
 import os
 import shutil
 import tempfile
+from collections.abc import Hashable
 from typing import (
     Any,
     cast,
@@ -335,6 +336,7 @@ class MockTrans:
         self.__user = user
         self.security = self.app.security
         self.history = history
+        self._short_term_cache: dict[tuple[Hashable, ...], Any] = {}
 
         self.request: Any = Bunch(
             headers={},
@@ -349,6 +351,12 @@ class MockTrans:
     def tag_handler(self):
         return self.app.tag_handler
 
+    def set_cache_value(self, args: tuple[Hashable, ...], value: Any):
+        self._short_term_cache[args] = value
+
+    def get_cache_value(self, args: tuple[Hashable, ...], default: Any = None) -> Any:
+        return self._short_term_cache.get(args, default)
+
     def check_csrf_token(self, payload):
         pass
 
diff --git a/lib/galaxy/managers/context.py b/lib/galaxy/managers/context.py
index 1f6447623fd..b610448f78c 100644
--- a/lib/galaxy/managers/context.py
+++ b/lib/galaxy/managers/context.py
@@ -37,7 +37,10 @@ A method that requires a user but not a history should declare its
 # more checks against this issue.
 import abc
 import string
-from collections.abc import Callable
+from collections.abc import (
+    Callable,
+    Hashable,
+)
 from json import dumps
 from typing import (
     Any,
@@ -201,12 +204,12 @@ class ProvidesUserContext(ProvidesAppContext):
     workflow_building_mode: Literal[1, True, False] = False
     galaxy_session: Optional[GalaxySession] = None
     _tag_handler: Optional[GalaxyTagHandlerSession] = None
-    _short_term_cache: dict[tuple[str, ...], Any]
+    _short_term_cache: dict[tuple[Hashable, ...], Any]
 
-    def set_cache_value(self, args: tuple[str, ...], value: Any):
+    def set_cache_value(self, args: tuple[Hashable, ...], value: Any):
         self._short_term_cache[args] = value
 
-    def get_cache_value(self, args: tuple[str, ...], default: Any = None) -> Any:
+    def get_cache_value(self, args: tuple[Hashable, ...], default: Any = None) -> Any:
         return self._short_term_cache.get(args, default)
 
     @property
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 9ea2bcae2f1..c4b61049981 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -102,6 +102,7 @@ from .workflow_utils import (
 if TYPE_CHECKING:
     from sqlalchemy.orm import Session
 
+    from galaxy.managers.context import ProvidesHistoryContext
     from galaxy.model import (
         History,
         HistoryItem,
@@ -1874,6 +1875,11 @@ def _carried_state_label(value) -> str:
     return "not in current history"
 
 
+# Sentinel distinguishing a populated cache entry (always a ``(rows, total)``
+# tuple) from a cache miss.
+_PAGE_CACHE_MISS: Any = object()
+
+
 class BaseDataToolParameter(ToolParameter):
     multiple: bool
 
@@ -1969,6 +1975,68 @@ class BaseDataToolParameter(ToolParameter):
         self._acceptable_extensions_cache = accepted
         return accepted
 
+    def _paginated_visible_datasets(
+        self,
+        trans: "ProvidesHistoryContext",
+        history: "History",
+        *,
+        extensions: Optional[set[str]],
+        valid_states: Optional[tuple[str, ...]],
+        search: Optional[str] = None,
+        offset: int = 0,
+        limit: int = 50,
+    ) -> tuple[list[HistoryDatasetAssociation], int]:
+        """``history.paginated_active_visible_datasets`` memoized on the request.
+
+        Building one form with many ``data`` parameters (most notably the workflow
+        Run form, which renders every step in a single request) otherwise re-issues
+        the same paginated SQL against the same, unchanging history once per
+        parameter -- O(parameters) round-trips, slow even on an empty history
+        (issue #22927). The results are cached by signature on the request context's
+        short-term cache (see ``ProvidesHistoryContext.set_cache_value``); the cache
+        is shared across every step's proxy work context for the request and never
+        outlives it, so the history cannot change underneath it.
+        """
+        key = (
+            "data_param_hda_page",
+            history.id,
+            frozenset(extensions) if extensions is not None else None,
+            tuple(valid_states) if valid_states is not None else None,
+            search or None,
+            offset,
+            limit,
+        )
+        cached = trans.get_cache_value(key, _PAGE_CACHE_MISS)
+        if cached is not _PAGE_CACHE_MISS:
+            return cached
+        result = history.paginated_active_visible_datasets(
+            extensions=extensions, valid_states=valid_states, search=search, offset=offset, limit=limit
+        )
+        trans.set_cache_value(key, result)
+        return result
+
+    def _paginated_dataset_collections(
+        self,
+        trans: "ProvidesHistoryContext",
+        history: "History",
+        *,
+        visible_only: bool,
+        search: Optional[str] = None,
+        offset: int = 0,
+        limit: int = 50,
+    ) -> tuple[list[HistoryDatasetCollectionAssociation], int]:
+        """``history.paginated_active_dataset_collections`` memoized on the request
+        context's short-term cache (see :meth:`_paginated_visible_datasets`)."""
+        key = ("data_param_hdca_page", history.id, bool(visible_only), search or None, offset, limit)
+        cached = trans.get_cache_value(key, _PAGE_CACHE_MISS)
+        if cached is not _PAGE_CACHE_MISS:
+            return cached
+        result = history.paginated_active_dataset_collections(
+            visible_only=visible_only, search=search, offset=offset, limit=limit
+        )
+        trans.set_cache_value(key, result)
+        return result
+
     def _uses_python_options_filter(self) -> bool:
         """True iff matching depends on per-row Python state that cannot be
         pushed to SQL (dynamic options with ``options_filter_attribute``, or a
@@ -1993,7 +2061,9 @@ class BaseDataToolParameter(ToolParameter):
                 chunk_size = MAX_OPTIONS_PAGE_SIZE
                 db_offset = 0
                 while True:
-                    rows, total = history.paginated_active_visible_datasets(
+                    rows, total = self._paginated_visible_datasets(
+                        trans,
+                        history,
                         extensions=self._acceptable_extensions(),
                         valid_states=dataset_matcher_factory.valid_input_states,
                         offset=db_offset,
@@ -2013,17 +2083,19 @@ class BaseDataToolParameter(ToolParameter):
                 chunk_size = MAX_OPTIONS_PAGE_SIZE
                 db_offset = 0
                 while True:
-                    rows, total = history.paginated_active_dataset_collections(
+                    collection_rows, total = self._paginated_dataset_collections(
+                        trans,
+                        history,
                         visible_only=True,
                         offset=db_offset,
                         limit=chunk_size,
                     )
-                    if not rows:
+                    if not collection_rows:
                         return None
-                    for hdca in rows:
+                    for hdca in collection_rows:
                         if dataset_collection_matcher.hdca_match(hdca):
                             return hdca
-                    db_offset += len(rows)
+                    db_offset += len(collection_rows)
                     if db_offset >= total:
                         return None
 
@@ -2517,7 +2589,7 @@ class DataToolParameter(BaseDataToolParameter):
         job_input_values = util.listify(other_values.get(self.name))
 
         job_input_values = self._page_hda_matches(
-            builder, history, dataset_matcher, dataset_matcher_factory, job_input_values
+            trans, builder, history, dataset_matcher, dataset_matcher_factory, job_input_values
         )
         unresolved = self._pin_live_hda_inputs(builder, history, dataset_matcher, job_input_values)
         self._carry_unresolved_inputs(builder, history, unresolved)
@@ -2553,6 +2625,7 @@ class DataToolParameter(BaseDataToolParameter):
 
     def _page_hda_matches(
         self,
+        trans,
         builder: DataOptionsBuilder,
         history,
         dataset_matcher,
@@ -2569,7 +2642,9 @@ class DataToolParameter(BaseDataToolParameter):
         valid_states = dataset_matcher_factory.valid_input_states
 
         def hda_query(*, offset, limit):
-            return history.paginated_active_visible_datasets(
+            return self._paginated_visible_datasets(
+                trans,
+                history,
                 extensions=acceptable_extensions,
                 valid_states=valid_states,
                 search=hda_search,
@@ -2677,8 +2752,8 @@ class DataToolParameter(BaseDataToolParameter):
         _offset, _limit, hdca_search = builder.page("hdca")
 
         def hdca_query(*, offset, limit):
-            return history.paginated_active_dataset_collections(
-                visible_only=True, search=hdca_search, offset=offset, limit=limit
+            return self._paginated_dataset_collections(
+                trans, history, visible_only=True, search=hdca_search, offset=offset, limit=limit
             )
 
         def hdca_filter(hdca):
@@ -2902,8 +2977,8 @@ class DataCollectionToolParameter(BaseDataToolParameter):
         history_query = self._history_query(trans)
 
         def hdca_query(*, offset, limit):
-            return history.paginated_active_dataset_collections(
-                visible_only=False, search=hdca_search, offset=offset, limit=limit
+            return self._paginated_dataset_collections(
+                trans, history, visible_only=False, search=hdca_search, offset=offset, limit=limit
             )
 
         def hdca_filter(hdca):
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 76980af1c34..704df9aecc0 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -7,6 +7,7 @@ import os
 import re
 import socket
 import time
+from collections.abc import Hashable
 from contextlib import ExitStack
 from http.cookies import CookieError
 from typing import (
@@ -337,7 +338,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         self.galaxy_session = None
         self.error_message = None
         self.host = self.request.host
-        self._short_term_cache: dict[tuple[str, ...], Any] = {}
+        self._short_term_cache: dict[tuple[Hashable, ...], Any] = {}
 
         # set any cross origin resource sharing headers if configured to do so
         self.set_cors_headers()
diff --git a/lib/galaxy/work/context.py b/lib/galaxy/work/context.py
index 953328c4b0c..d1a5831ddfc 100644
--- a/lib/galaxy/work/context.py
+++ b/lib/galaxy/work/context.py
@@ -1,4 +1,5 @@
 import abc
+from collections.abc import Hashable
 from typing import (
     Any,
     Literal,
@@ -39,13 +40,19 @@ class WorkRequestContext(ProvidesHistoryContext):
         workflow_building_mode=False,
         url_builder=None,
         galaxy_session: Optional["GalaxySession"] = None,
+        short_term_cache: Optional[dict[tuple[Hashable, ...], Any]] = None,
     ):
         self._app = app
         self.__user = user
         self.__user_current_roles: Optional[list[Role]] = None
         self.__history = history
         self._url_builder = url_builder
-        self._short_term_cache: dict[tuple[str, ...], Any] = {}
+        # When proxying an existing transaction (see ``proxy_work_context_for_history``)
+        # share its request-scoped cache so work done across proxies of the same
+        # request -- e.g. every step of a workflow Run form build -- is reused.
+        self._short_term_cache: dict[tuple[Hashable, ...], Any] = (
+            short_term_cache if short_term_cache is not None else {}
+        )
         self.workflow_building_mode = workflow_building_mode
         self.galaxy_session = galaxy_session
 
@@ -195,4 +202,5 @@ def proxy_work_context_for_history(
         url_builder=trans.url_builder,
         workflow_building_mode=workflow_building_mode,
         galaxy_session=trans.galaxy_session,
+        short_term_cache=trans._short_term_cache,
     )
diff --git a/test/integration/test_workflow_refactoring.py b/test/integration/test_workflow_refactoring.py
index 8b626ab22e7..951edb02250 100644
--- a/test/integration/test_workflow_refactoring.py
+++ b/test/integration/test_workflow_refactoring.py
@@ -1,5 +1,6 @@
 import contextlib
 import json
+from collections.abc import Hashable
 from typing import (
     Any,
 )
@@ -1052,6 +1053,7 @@ class MockTrans(ProvidesAppContext):
         self.history = None
         self.workflow_building_mode = workflow_building_modes.ENABLED
         self.tag_handler = app.tag_handler
+        self._short_term_cache: dict[tuple[Hashable, ...], Any] = {}
 
     @property
     def galaxy_session(self):
diff --git a/test/unit/app/tools/test_execution.py b/test/unit/app/tools/test_execution.py
index 42260bb4516..54c0b5d008e 100644
--- a/test/unit/app/tools/test_execution.py
+++ b/test/unit/app/tools/test_execution.py
@@ -1,7 +1,11 @@
 """Test Tool execution and state handling logic."""
 
 from collections import OrderedDict
-from typing import cast
+from collections.abc import Hashable
+from typing import (
+    Any,
+    cast,
+)
 
 import webob.exc
 from sqlalchemy import select
@@ -206,6 +210,7 @@ class MockTrans:
         self.sa_session = self.app.model.context
         self.url_builder = None
         self.galaxy_session = None
+        self._short_term_cache: dict[tuple[Hashable, ...], Any] = {}
 
     def get_history(self, **kwargs):
         return self.history

From 67675954ae861edfee3406079c867b274850aabc Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 16 Jun 2026 12:07:15 +0000
Subject: [PATCH 155/256] Skip history option scan for connected run-form
 inputs (issue #22927)

A workflow Run form renders inputs that are wired to an upstream step's output
as 'connected' (FormElement keys off the ConnectedValue value), never as a
history dropdown -- and the run form's data dropdowns lazy-load from
/api/histories/{id}/contents anyway. So building per-parameter history options
for connected inputs is pure waste.

Short-circuit DataToolParameter/DataCollectionToolParameter.to_dict and
get_initial_value when the parameter's current value is a ConnectedValue,
skipping the paginated history scan for those inputs. In a typical chained
workflow most tool-step inputs are connected, so this removes the bulk of the
remaining per-step history queries on top of the per-request memoization.
---
 lib/galaxy/tools/parameters/basic.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index c4b61049981..9edffb9e3d4 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1875,6 +1875,12 @@ def _carried_state_label(value) -> str:
     return "not in current history"
 
 
+def _is_connected_value(value) -> bool:
+    """True iff ``value`` is a workflow ``ConnectedValue`` (an input fed by an
+    upstream step's output rather than chosen at runtime)."""
+    return is_runtime_value(value) and runtime_to_json(value)["__class__"] == "ConnectedValue"
+
+
 # Sentinel distinguishing a populated cache entry (always a ``(rows, total)``
 # tuple) from a cache miss.
 _PAGE_CACHE_MISS: Any = object()
@@ -2052,6 +2058,10 @@ class BaseDataToolParameter(ToolParameter):
             return RuntimeValue()
         if self.optional:
             return None
+        if _is_connected_value((other_values or {}).get(self.name)):
+            # Connected inputs are supplied by an upstream step; there is no
+            # default to pick from the history, so skip the scan (issue #22927).
+            return None
         if (history := trans.history) is not None:
             dataset_matcher_factory = get_dataset_matcher_factory(trans)
             dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
@@ -2577,6 +2587,12 @@ class DataToolParameter(BaseDataToolParameter):
         if history is None or trans.workflow_building_mode is workflow_building_modes.ENABLED:
             return d
 
+        if _is_connected_value(other_values.get(self.name)):
+            # Input is wired to an upstream step: the run form renders it as
+            # "connected" (no dropdown) and never uses these options, so skip the
+            # per-parameter history scan entirely (issue #22927).
+            return d
+
         dataset_matcher_factory = get_dataset_matcher_factory(trans)
         dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
 
@@ -2935,6 +2951,11 @@ class DataCollectionToolParameter(BaseDataToolParameter):
         if history is None or trans.workflow_building_mode is workflow_building_modes.ENABLED:
             return d
 
+        if _is_connected_value(other_values.get(self.name)):
+            # Connected collection input: fed by an upstream step, rendered as
+            # "connected" with no dropdown, so skip the history scan (issue #22927).
+            return d
+
         dataset_matcher_factory = get_dataset_matcher_factory(trans)
         dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
         dataset_collection_matcher = dataset_matcher_factory.dataset_collection_matcher(dataset_matcher)

From c0b01a5757e03f65611a8ff1e1896b75974a26c1 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2026 12:15:38 -0400
Subject: [PATCH 156/256] Dedupe run-form history cache idiom into
 get_or_set_cache_value

Add canonical get-or-compute to the request cache API (ProvidesUserContext,
mirrored on MockTrans) and fold the two run-form pagination memo helpers onto
it. Helpers become module-level functions (used no self) and the bespoke
_PAGE_CACHE_MISS sentinel goes away. Simplify _is_connected_value to
isinstance(runtime_to_object(value), ConnectedValue).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/app_unittest_utils/galaxy_mock.py |  13 +-
 lib/galaxy/managers/context.py               |  16 +++
 lib/galaxy/tools/parameters/basic.py         | 134 +++++++++----------
 3 files changed, 91 insertions(+), 72 deletions(-)

diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py
index d69a6c763af..c5ff08990f8 100644
--- a/lib/galaxy/app_unittest_utils/galaxy_mock.py
+++ b/lib/galaxy/app_unittest_utils/galaxy_mock.py
@@ -5,7 +5,10 @@ Mock infrastructure for testing ModelManagers.
 import os
 import shutil
 import tempfile
-from collections.abc import Hashable
+from collections.abc import (
+    Callable,
+    Hashable,
+)
 from typing import (
     Any,
     cast,
@@ -357,6 +360,14 @@ class MockTrans:
     def get_cache_value(self, args: tuple[Hashable, ...], default: Any = None) -> Any:
         return self._short_term_cache.get(args, default)
 
+    def get_or_set_cache_value(self, args: tuple[Hashable, ...], factory: Callable[[], Any]) -> Any:
+        miss = object()
+        value = self.get_cache_value(args, miss)
+        if value is miss:
+            value = factory()
+            self.set_cache_value(args, value)
+        return value
+
     def check_csrf_token(self, payload):
         pass
 
diff --git a/lib/galaxy/managers/context.py b/lib/galaxy/managers/context.py
index b610448f78c..374d506e4e0 100644
--- a/lib/galaxy/managers/context.py
+++ b/lib/galaxy/managers/context.py
@@ -193,6 +193,11 @@ class ProvidesAppContext:
         return self.app.install_model
 
 
+# Sentinel distinguishing a cached value (which may legitimately be ``None``)
+# from a cache miss in ``get_or_set_cache_value``.
+_CACHE_MISS: Any = object()
+
+
 class ProvidesUserContext(ProvidesAppContext):
     """For transaction-like objects to provide Galaxy convenience layer for
     reasoning about users.
@@ -212,6 +217,17 @@ class ProvidesUserContext(ProvidesAppContext):
     def get_cache_value(self, args: tuple[Hashable, ...], default: Any = None) -> Any:
         return self._short_term_cache.get(args, default)
 
+    def get_or_set_cache_value(self, args: tuple[Hashable, ...], factory: Callable[[], Any]) -> Any:
+        """Return the cached value for ``args``, computing and storing it via
+        ``factory`` on a miss. Request-scoped memoization for work repeated
+        within a single transaction (e.g. identical history-option queries
+        otherwise issued once per parameter while building a workflow Run form)."""
+        value = self.get_cache_value(args, _CACHE_MISS)
+        if value is _CACHE_MISS:
+            value = factory()
+            self.set_cache_value(args, value)
+        return value
+
     @property
     def tag_handler(self):
         if self._tag_handler is None:
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 9edffb9e3d4..ee2bd373f00 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -93,6 +93,7 @@ from . import (
 from .dataset_matcher import get_dataset_matcher_factory
 from .sanitize import ToolParameterSanitizer
 from .workflow_utils import (
+    ConnectedValue,
     is_runtime_value,
     runtime_to_json,
     runtime_to_object,
@@ -1878,12 +1879,65 @@ def _carried_state_label(value) -> str:
 def _is_connected_value(value) -> bool:
     """True iff ``value`` is a workflow ``ConnectedValue`` (an input fed by an
     upstream step's output rather than chosen at runtime)."""
-    return is_runtime_value(value) and runtime_to_json(value)["__class__"] == "ConnectedValue"
+    return is_runtime_value(value) and isinstance(runtime_to_object(value), ConnectedValue)
 
 
-# Sentinel distinguishing a populated cache entry (always a ``(rows, total)``
-# tuple) from a cache miss.
-_PAGE_CACHE_MISS: Any = object()
+def _paginated_visible_datasets(
+    trans: "ProvidesHistoryContext",
+    history: "History",
+    *,
+    extensions: Optional[set[str]],
+    valid_states: Optional[tuple[str, ...]],
+    search: Optional[str] = None,
+    offset: int = 0,
+    limit: int = 50,
+) -> tuple[list[HistoryDatasetAssociation], int]:
+    """``history.paginated_active_visible_datasets`` memoized on the request.
+
+    Building one form with many ``data`` parameters (most notably the workflow
+    Run form, which renders every step in a single request) otherwise re-issues
+    the same paginated SQL against the same, unchanging history once per
+    parameter -- O(parameters) round-trips, slow even on an empty history
+    (issue #22927). Results are memoized by signature on the request context's
+    short-term cache (see ``ProvidesUserContext.get_or_set_cache_value``); the
+    cache is shared across every step's proxy work context for the request and
+    never outlives it, so the history cannot change underneath it.
+    """
+    key = (
+        "data_param_hda_page",
+        history.id,
+        frozenset(extensions) if extensions is not None else None,
+        tuple(valid_states) if valid_states is not None else None,
+        search or None,
+        offset,
+        limit,
+    )
+    return trans.get_or_set_cache_value(
+        key,
+        lambda: history.paginated_active_visible_datasets(
+            extensions=extensions, valid_states=valid_states, search=search, offset=offset, limit=limit
+        ),
+    )
+
+
+def _paginated_dataset_collections(
+    trans: "ProvidesHistoryContext",
+    history: "History",
+    *,
+    visible_only: bool,
+    search: Optional[str] = None,
+    offset: int = 0,
+    limit: int = 50,
+) -> tuple[list[HistoryDatasetCollectionAssociation], int]:
+    """``history.paginated_active_dataset_collections`` memoized on the request
+    context's short-term cache (see :func:`_paginated_visible_datasets`)."""
+    key = ("data_param_hdca_page", history.id, bool(visible_only), search or None, offset, limit)
+    return trans.get_or_set_cache_value(
+        key,
+        lambda: history.paginated_active_dataset_collections(
+            visible_only=visible_only, search=search, offset=offset, limit=limit
+        ),
+    )
 
 
 class BaseDataToolParameter(ToolParameter):
@@ -1981,68 +2035,6 @@ class BaseDataToolParameter(ToolParameter):
         self._acceptable_extensions_cache = accepted
         return accepted
 
-    def _paginated_visible_datasets(
-        self,
-        trans: "ProvidesHistoryContext",
-        history: "History",
-        *,
-        extensions: Optional[set[str]],
-        valid_states: Optional[tuple[str, ...]],
-        search: Optional[str] = None,
-        offset: int = 0,
-        limit: int = 50,
-    ) -> tuple[list[HistoryDatasetAssociation], int]:
-        """``history.paginated_active_visible_datasets`` memoized on the request.
-
-        Building one form with many ``data`` parameters (most notably the workflow
-        Run form, which renders every step in a single request) otherwise re-issues
-        the same paginated SQL against the same, unchanging history once per
-        parameter -- O(parameters) round-trips, slow even on an empty history
-        (issue #22927). The results are cached by signature on the request context's
-        short-term cache (see ``ProvidesHistoryContext.set_cache_value``); the cache
-        is shared across every step's proxy work context for the request and never
-        outlives it, so the history cannot change underneath it.
-        """
-        key = (
-            "data_param_hda_page",
-            history.id,
-            frozenset(extensions) if extensions is not None else None,
-            tuple(valid_states) if valid_states is not None else None,
-            search or None,
-            offset,
-            limit,
-        )
-        cached = trans.get_cache_value(key, _PAGE_CACHE_MISS)
-        if cached is not _PAGE_CACHE_MISS:
-            return cached
-        result = history.paginated_active_visible_datasets(
-            extensions=extensions, valid_states=valid_states, search=search, offset=offset, limit=limit
-        )
-        trans.set_cache_value(key, result)
-        return result
-
-    def _paginated_dataset_collections(
-        self,
-        trans: "ProvidesHistoryContext",
-        history: "History",
-        *,
-        visible_only: bool,
-        search: Optional[str] = None,
-        offset: int = 0,
-        limit: int = 50,
-    ) -> tuple[list[HistoryDatasetCollectionAssociation], int]:
-        """``history.paginated_active_dataset_collections`` memoized on the request
-        context's short-term cache (see :meth:`_paginated_visible_datasets`)."""
-        key = ("data_param_hdca_page", history.id, bool(visible_only), search or None, offset, limit)
-        cached = trans.get_cache_value(key, _PAGE_CACHE_MISS)
-        if cached is not _PAGE_CACHE_MISS:
-            return cached
-        result = history.paginated_active_dataset_collections(
-            visible_only=visible_only, search=search, offset=offset, limit=limit
-        )
-        trans.set_cache_value(key, result)
-        return result
-
     def _uses_python_options_filter(self) -> bool:
         """True iff matching depends on per-row Python state that cannot be
         pushed to SQL (dynamic options with ``options_filter_attribute``, or a
@@ -2071,7 +2063,7 @@ class BaseDataToolParameter(ToolParameter):
                 chunk_size = MAX_OPTIONS_PAGE_SIZE
                 db_offset = 0
                 while True:
-                    rows, total = self._paginated_visible_datasets(
+                    rows, total = _paginated_visible_datasets(
                         trans,
                         history,
                         extensions=self._acceptable_extensions(),
@@ -2093,7 +2085,7 @@ class BaseDataToolParameter(ToolParameter):
                 chunk_size = MAX_OPTIONS_PAGE_SIZE
                 db_offset = 0
                 while True:
-                    collection_rows, total = self._paginated_dataset_collections(
+                    collection_rows, total = _paginated_dataset_collections(
                         trans,
                         history,
                         visible_only=True,
@@ -2658,7 +2650,7 @@ class DataToolParameter(BaseDataToolParameter):
         valid_states = dataset_matcher_factory.valid_input_states
 
         def hda_query(*, offset, limit):
-            return self._paginated_visible_datasets(
+            return _paginated_visible_datasets(
                 trans,
                 history,
                 extensions=acceptable_extensions,
@@ -2768,7 +2760,7 @@ class DataToolParameter(BaseDataToolParameter):
         _offset, _limit, hdca_search = builder.page("hdca")
 
         def hdca_query(*, offset, limit):
-            return self._paginated_dataset_collections(
+            return _paginated_dataset_collections(
                 trans, history, visible_only=True, search=hdca_search, offset=offset, limit=limit
             )
 
@@ -2998,7 +2990,7 @@ class DataCollectionToolParameter(BaseDataToolParameter):
         history_query = self._history_query(trans)
 
         def hdca_query(*, offset, limit):
-            return self._paginated_dataset_collections(
+            return _paginated_dataset_collections(
                 trans, history, visible_only=False, search=hdca_search, offset=offset, limit=limit
             )
 

From 8aac44e7b1a8be5c9e5228052a39ee5414343fcc Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2026 12:24:29 -0400
Subject: [PATCH 157/256] Reuse get_or_set_cache_value for from_url dynamic
 options

Fold the from_url option-fetch cache onto the canonical request-cache helper:
drops the duplicated key tuple, the local unset_value sentinel, and the
hit/miss branch. Behavior unchanged -- the fetch runs lazily on a miss inside
the same try, so failures still fall through to data=None and nothing caches.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/tools/parameters/dynamic_options.py | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index 51c3b081ada..038c17f1420 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -954,22 +954,18 @@ class DynamicOptions:
             url = fill_template(from_url_options.from_url, context)
             request_body = template_or_none(from_url_options.request_body, context)
             request_headers = template_or_none(from_url_options.request_headers, context)
+            cache_key = (url, from_url_options.request_method, request_body, request_headers)
             try:
-                unset_value = object()
-                cached_value = trans.get_cache_value(
-                    (url, from_url_options.request_method, request_body, request_headers), unset_value
-                )
-                if cached_value is unset_value:
-                    data = request(
+                data = trans.get_or_set_cache_value(
+                    cache_key,
+                    lambda: request(
                         url=url,
                         method=from_url_options.request_method,
                         data=json.loads(request_body) if request_body else None,
                         headers=json.loads(request_headers) if request_headers else None,
                         timeout=10,
-                    )
-                    trans.set_cache_value((url, from_url_options.request_method, request_body, request_headers), data)
-                else:
-                    data = cached_value
+                    ),
+                )
             except Exception as e:
                 log.warning("Fetching from url '%s' failed: %s", url, str(e))
                 data = None

From f845df22acff6ad59cbf61b878a586d43b09144c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2026 12:28:15 -0400
Subject: [PATCH 158/256] Add async regression: bare shared-discriminator
 nested conditional

Sibling of async_nested_conditional_shared_discriminator.xml but supplies the
outer discriminator by its bare short name (no <conditional> wrapper). The
qualified sibling exercises the consumed-discriminator exclusion via the
elided-subsequence matcher tier; this bare variant exercises it via the bare
short-name tier. No existing functional tool collides nested-conditional
discriminators, so this path was previously uncovered.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 ..._conditional_shared_discriminator_bare.xml | 68 +++++++++++++++++++
 test/functional/tools/sample_tool_conf.xml    |  1 +
 2 files changed, 69 insertions(+)
 create mode 100644 test/functional/tools/async_nested_conditional_shared_discriminator_bare.xml

diff --git a/test/functional/tools/async_nested_conditional_shared_discriminator_bare.xml b/test/functional/tools/async_nested_conditional_shared_discriminator_bare.xml
new file mode 100644
index 00000000000..3ccc2a2f634
--- /dev/null
+++ b/test/functional/tools/async_nested_conditional_shared_discriminator_bare.xml
@@ -0,0 +1,68 @@
+<tool id="async_nested_conditional_shared_discriminator_bare" name="async_nested_conditional_shared_discriminator_bare" version="1.0.0" profile="22.01">
+    <description>async regression: bare (unqualified) discriminator must not resolve to a nested conditional of the same name</description>
+    <!--
+      Sibling of async_nested_conditional_shared_discriminator.xml. Same shape - an
+      OUTER and an INNER conditional whose discriminators share the name 'use' - but
+      the test supplies the outer discriminator by its BARE short name (no enclosing
+      <conditional> wrapper), as legacy tests commonly do.
+
+      The qualified sibling routes the consumed-discriminator exclusion through the
+      elided-subsequence fallback (input 'operation|use' is a subsequence of
+      operation|method|use). This bare variant routes it through the bare short-name
+      fallback instead (input 'use'), covering the other matcher tier.
+
+      Sync (POST /api/tools): bare 'use'=outer_a selects the outer when; the omitted
+      inner discriminator selects its default when (inner_a); the job runs.
+
+      Async (POST tool request): without excluding the consumed ancestor discriminator,
+      the omitted operation|method|use greedily picks up the bare 'use' (value
+      "outer_a"), which is not a valid 'method' when ->
+        Invalid conditional test value (outer_a) for parameter (use)
+      Excluding it lets the inner conditional fall back to its default when.
+    -->
+    <command><![CDATA[
+echo '$operation.use' > '$out_file1' &&
+#if str($operation.use) == "outer_a":
+echo '$operation.method.use' >> '$out_file1'
+#end if
+    ]]></command>
+    <inputs>
+        <conditional name="operation">
+            <param name="use" type="select" label="Operation">
+                <option value="outer_a" selected="true">Outer A</option>
+                <option value="outer_b">Outer B</option>
+            </param>
+            <when value="outer_a">
+                <conditional name="method">
+                    <param name="use" type="select" label="Method">
+                        <option value="inner_a" selected="true">Inner A</option>
+                        <option value="inner_b">Inner B</option>
+                    </param>
+                    <when value="inner_a">
+                        <param name="threshold" type="integer" value="3000" label="Threshold" />
+                    </when>
+                    <when value="inner_b">
+                        <param name="lower" type="integer" value="100" label="Lower" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="outer_b">
+                <param name="rank" type="integer" value="1" label="Rank" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="use" value="outer_a" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="outer_a" />
+                    <has_line line="inner_a" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml
index 865007ed833..97e84de01f6 100644
--- a/test/functional/tools/sample_tool_conf.xml
+++ b/test/functional/tools/sample_tool_conf.xml
@@ -123,6 +123,7 @@
   <tool file="async_conditional_no_default_nested_data.xml" />
   <tool file="async_ambiguous_unqualified_name.xml" />
   <tool file="async_nested_conditional_shared_discriminator.xml" />
+  <tool file="async_nested_conditional_shared_discriminator_bare.xml" />
   <tool file="output_empty_work_dir.xml" />
   <tool file="output_filter_with_input.xml" />
   <tool file="output_filter_with_input_optional.xml" />

From fe9e03c2d1f59afd4ac31b0a9cb66953f65ea6fc Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2026 12:39:57 -0400
Subject: [PATCH 159/256] Encapsulate legacy test-input resolution behind a
 resolver/context

The async test-case merge threaded inputs, profile, state_representation,
warnings and a consumed-discriminators set as positional args through
_merge_into_state / _merge_level_into_state / _select_which_when, and kept the
fuzzy name-matching cascade in a standalone _input_for. Adding the
consumed-discriminators set alone cost ~16 lines of pure threading.

Bundle the invariants into a frozen MergeContext and move the inputs +
consumed set + matching cascade onto a frozen LegacyTestInputResolver.
consuming()/for_inputs() return child objects, preserving the exact
subtree-scoping the positional set had (a consumed discriminator reaches a
conditional's when-branch but not its siblings; a repeat instance resolves
against its own input slice). Behavior unchanged - the matcher tiers, ordering,
ambiguity messages and exclusion semantics are identical.

Halves the arity of the two recursive merge functions (8->4 params) and
collapses the internal call sites from 56 to 14 physical lines.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/tool_util/parameters/case.py | 272 ++++++++++++------------
 1 file changed, 138 insertions(+), 134 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 443f2610056..50984e46a9e 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -1,10 +1,14 @@
 import os
-from dataclasses import dataclass
+from dataclasses import (
+    dataclass,
+    replace,
+)
 from re import compile
 from typing import (
     Any,
     cast,
     Dict,
+    FrozenSet,
     List,
     Optional,
     Set,
@@ -195,6 +199,117 @@ def _legacy_select_label_to_value(parameter: SelectParameterModel, value: str) -
     return value
 
 
+@dataclass(frozen=True)
+class LegacyTestInputResolver:
+    """Resolve a (possibly legacy/unqualified) parameter path to the test input that supplies it.
+
+    Owns the raw test inputs and the set of discriminator names already consumed by enclosing
+    conditionals, and encapsulates the fuzzy fallback cascade legacy test cases rely on (exact
+    name, then suffix / bare short-name / elided-conditional matches). A consumed discriminator
+    is excluded from those fallbacks so a nested conditional does not re-match an ancestor's
+    discriminator of the same name.
+
+    Immutable: ``consuming`` and ``for_inputs`` return child resolvers, so an exclusion stays
+    scoped to one subtree of the parameter walk (a sibling subtree never sees it) and a repeat
+    instance can be resolved against its own slice of the inputs.
+    """
+
+    inputs: ToolSourceTestInputs
+    consumed_discriminators: FrozenSet[str] = frozenset()
+
+    def consuming(self, discriminator_name: Optional[str]) -> "LegacyTestInputResolver":
+        if discriminator_name is None:
+            return self
+        return replace(self, consumed_discriminators=self.consumed_discriminators | {discriminator_name})
+
+    def for_inputs(self, inputs: ToolSourceTestInputs) -> "LegacyTestInputResolver":
+        return replace(self, inputs=inputs)
+
+    def input_for(self, flat_state_path: str) -> Optional[ToolSourceTestInput]:
+        # A consumed discriminator belongs to an enclosing conditional and must not be
+        # re-matched by the loose fallbacks below when resolving a descendant's discriminator
+        # (otherwise e.g. an omitted nested ``selector`` greedily picks up the parent
+        # conditional's ``selector`` value - see ``_select_which_when``).
+        exclude = self.consumed_discriminators
+        for input in self.inputs:
+            if input["name"] == flat_state_path:
+                return input
+        # Fallback for legacy test cases that specify conditional/section params without the
+        # pipe-separated prefix (e.g. <param name="fasta"> instead of <param name="mode|fasta">).
+        if "|" in flat_state_path:
+            suffix_matching_inputs = [
+                input
+                for input in self.inputs
+                if "|" in input["name"]
+                and input["name"] not in exclude
+                and flat_state_path.endswith(f"|{input['name']}")
+            ]
+            resolved = _resolve_matching_inputs(
+                suffix_matching_inputs, f"Ambiguous partially qualified test parameter name for ({flat_state_path})"
+            )
+            if resolved is not None:
+                return resolved
+
+            short_name = flat_state_path.rsplit("|", 1)[1]
+            matching_inputs = [
+                input for input in self.inputs if input["name"] == short_name and input["name"] not in exclude
+            ]
+            resolved = _resolve_matching_inputs(
+                matching_inputs, f"Ambiguous unqualified test parameter name ({short_name}) for ({flat_state_path})"
+            )
+            if resolved is not None:
+                return resolved
+
+            # Fallback for legacy test cases that elide intermediate conditional names but keep
+            # the enclosing section/repeat prefix (e.g. <section name="adv"><param name="esf">
+            # for a param whose real path is adv|esf_cond|esf). The input name is an ordered
+            # subsequence of the qualified path - sharing the head and the leaf - rather than a
+            # plain suffix.
+            path_segments = flat_state_path.split("|")
+            elided_matching_inputs = [
+                input
+                for input in self.inputs
+                if input["name"] not in exclude and _is_conditional_elided_match(input["name"], path_segments)
+            ]
+            resolved = _resolve_matching_inputs(
+                elided_matching_inputs, f"Ambiguous partially qualified test parameter name for ({flat_state_path})"
+            )
+            if resolved is not None:
+                return resolved
+        return None
+
+
+@dataclass(frozen=True)
+class MergeContext:
+    """The values threaded unchanged through the recursive test-case merge.
+
+    Bundling them keeps ``_merge_into_state`` and friends to their per-node arguments
+    (the parameter, the state at this level, the prefix) instead of re-passing the
+    resolver, profile, state representation and warnings at every call site. ``warnings``
+    is a shared list accumulated across the whole merge; ``consuming`` / ``for_inputs``
+    return a child context whose resolver is scoped to a conditional branch or repeat
+    instance.
+    """
+
+    resolver: LegacyTestInputResolver
+    profile: str
+    state_representation: Literal["test_case_xml", "test_case_json"]
+    warnings: List[str]
+
+    @property
+    def inputs(self) -> ToolSourceTestInputs:
+        return self.resolver.inputs
+
+    def input_for(self, flat_state_path: str) -> Optional[ToolSourceTestInput]:
+        return self.resolver.input_for(flat_state_path)
+
+    def consuming(self, discriminator_name: Optional[str]) -> "MergeContext":
+        return replace(self, resolver=self.resolver.consuming(discriminator_name))
+
+    def for_inputs(self, inputs: ToolSourceTestInputs) -> "MergeContext":
+        return replace(self, resolver=self.resolver.for_inputs(inputs))
+
+
 def test_case_state(
     test_dict: ToolSourceTest,
     tool_parameter_bundle: List[ToolParameterT],
@@ -208,9 +323,8 @@ def test_case_state(
     state: Dict[str, Any] = {}
 
     state_representation = test_dict.get("value_state_representation", "test_case_xml")
-    handled_inputs = _merge_level_into_state(
-        tool_parameter_bundle, inputs, state, profile, state_representation, warnings, None
-    )
+    context = MergeContext(LegacyTestInputResolver(inputs), profile, state_representation, warnings)
+    handled_inputs = _merge_level_into_state(tool_parameter_bundle, context, state, None)
 
     for test_input in inputs:
         input_name = test_input["name"]
@@ -260,28 +374,13 @@ def test_case_validation(
 
 def _merge_level_into_state(
     tool_inputs: List[ToolParameterT],
-    inputs: ToolSourceTestInputs,
+    context: MergeContext,
     state_at_level: dict,
-    profile: str,
-    state_representation: Literal["test_case_xml", "test_case_json"],
-    warnings: List[str],
     prefix: Optional[str],
-    consumed_discriminators: Optional[Set[str]] = None,
 ) -> Set[str]:
     handled_inputs: Set[str] = set()
     for tool_input in tool_inputs:
-        handled_inputs.update(
-            _merge_into_state(
-                tool_input,
-                inputs,
-                state_at_level,
-                profile,
-                state_representation,
-                warnings,
-                prefix,
-                consumed_discriminators,
-            )
-        )
+        handled_inputs.update(_merge_into_state(tool_input, context, state_at_level, prefix))
 
     return handled_inputs
 
@@ -296,13 +395,9 @@ def _inputs_as_dict(inputs: ToolSourceTestInputs) -> Dict[str, ToolSourceTestInp
 
 def _merge_into_state(
     tool_input: ToolParameterT,
-    inputs: ToolSourceTestInputs,
+    context: MergeContext,
     state_at_level: dict,
-    profile: str,
-    state_representation: Literal["test_case_xml", "test_case_json"],
-    warnings: List[str],
     prefix: Optional[str],
-    consumed_discriminators: Optional[Set[str]] = None,
 ) -> Set[str]:
     handled_inputs = set()
 
@@ -315,22 +410,9 @@ def _merge_into_state(
         if input_name not in state_at_level:
             state_at_level[input_name] = conditional_state
 
-        when, discriminator_name = _select_which_when(
-            tool_input, conditional_state, inputs, state_path, consumed_discriminators
-        )
+        when, discriminator_name = _select_which_when(tool_input, conditional_state, context, state_path)
         test_parameter = tool_input.test_parameter
-        handled_inputs.update(
-            _merge_into_state(
-                test_parameter,
-                inputs,
-                conditional_state,
-                profile,
-                state_representation,
-                warnings,
-                state_path,
-                consumed_discriminators,
-            )
-        )
+        handled_inputs.update(_merge_into_state(test_parameter, context, conditional_state, state_path))
         # If the discriminator was omitted, record the selected when's discriminator so the
         # state validates against that branch rather than the phantom __absent__ branch. This
         # is the active branch _select_which_when chose: a non-default when inferred from the
@@ -339,21 +421,12 @@ def _merge_into_state(
         # payload.
         if test_parameter.name not in conditional_state and when.discriminator is not None:
             conditional_state[test_parameter.name] = when.discriminator
-        # The discriminator consumed here belongs to this conditional; mark it so the loose
-        # fallbacks do not re-match it when resolving a nested conditional's discriminator.
-        when_consumed = consumed_discriminators
-        if discriminator_name is not None:
-            when_consumed = set(consumed_discriminators or set()) | {discriminator_name}
+        # The discriminator consumed here belongs to this conditional; the branch context marks
+        # it so the loose fallbacks do not re-match it when resolving a nested conditional's
+        # discriminator.
         handled_inputs.update(
             _merge_level_into_state(
-                when.parameters,
-                inputs,
-                conditional_state,
-                profile,
-                state_representation,
-                warnings,
-                state_path,
-                when_consumed,
+                when.parameters, context.consuming(discriminator_name), conditional_state, state_path
             )
         )
     elif isinstance(tool_input, (RepeatParameterModel,)):
@@ -361,7 +434,7 @@ def _merge_into_state(
         if input_name not in state_at_level:
             state_at_level[input_name] = repeat_state_array
 
-        repeat_instance_inputs = _repeat_inputs_to_array(state_path, tool_input.parameters, inputs)
+        repeat_instance_inputs = _repeat_inputs_to_array(state_path, tool_input.parameters, context.inputs)
         if tool_input.min is not None:
             while len(repeat_instance_inputs) < tool_input.min:
                 repeat_instance_inputs.append([])
@@ -373,13 +446,9 @@ def _merge_into_state(
             handled_inputs.update(
                 _merge_level_into_state(
                     tool_input.parameters,
-                    repeat_instance_inputs[i],
+                    context.for_inputs(repeat_instance_inputs[i]),
                     repeat_state_array[i],
-                    profile,
-                    state_representation,
-                    warnings,
                     repeat_instance_prefix,
-                    consumed_discriminators,
                 )
             )
     elif isinstance(tool_input, (SectionParameterModel,)):
@@ -387,20 +456,9 @@ def _merge_into_state(
         if input_name not in state_at_level:
             state_at_level[input_name] = section_state
 
-        handled_inputs.update(
-            _merge_level_into_state(
-                tool_input.parameters,
-                inputs,
-                section_state,
-                profile,
-                state_representation,
-                warnings,
-                state_path,
-                consumed_discriminators,
-            )
-        )
+        handled_inputs.update(_merge_level_into_state(tool_input.parameters, context, section_state, state_path))
     else:
-        test_input = _input_for(state_path, inputs, exclude_names=consumed_discriminators)
+        test_input = context.input_for(state_path)
         if test_input is not None:
             input_value: Any
             if isinstance(tool_input, (DataCollectionParameterModel,)):
@@ -412,7 +470,7 @@ def _merge_into_state(
                     value = test_input["value"]
                     input_value_list: List[Any] = []
                     if value:
-                        if state_representation == "test_case_json":
+                        if context.state_representation == "test_case_json":
                             input_value_list = test_input["value"] if test_input["value"] is not None else []
                         else:
                             location = test_input.get("attributes", {}).get("location")
@@ -436,13 +494,13 @@ def _merge_into_state(
 
                     input_value = input_value_list
                 else:
-                    if state_representation == "test_case_json":
+                    if context.state_representation == "test_case_json":
                         input_value = test_input["value"]
                     else:
                         input_value = xml_data_input_to_json(test_input)
             else:
                 input_value = test_input["value"]
-                input_value = legacy_from_string(tool_input, input_value, warnings, profile)
+                input_value = legacy_from_string(tool_input, input_value, context.warnings, context.profile)
 
             state_at_level[input_name] = input_value
 
@@ -461,7 +519,7 @@ def _repeat_inputs_to_array(
         # unqualified with respect to conditionals/sections but still carry repeat
         # instance indices, so progressively strip leading (conditional/section)
         # segments - keeping any enclosing repeat-instance prefix - until the repeat's
-        # nested params resolve. The downstream _input_for() suffix match then
+        # nested params resolve. The downstream input_for() suffix match then
         # re-attaches them to the fully qualified path. Longest candidate is tried
         # first to avoid matching an unrelated like-named repeat.
         parts = state_path.split("|")
@@ -490,9 +548,8 @@ def _repeat_inputs_to_array(
 def _select_which_when(
     conditional: ConditionalParameterModel,
     state: dict,
-    inputs: ToolSourceTestInputs,
+    context: MergeContext,
     prefix: str,
-    consumed_discriminators: Optional[Set[str]] = None,
 ) -> Tuple[ConditionalWhen, Optional[str]]:
     """Return the selected when and the name of the test input used as the discriminator
     (or ``None`` if the discriminator was omitted). The discriminator name lets callers mark
@@ -502,7 +559,7 @@ def _select_which_when(
     test_parameter_name = test_parameter.name
     test_parameter_flat_path = flat_state_path(test_parameter_name, prefix)
 
-    test_input = _input_for(test_parameter_flat_path, inputs, exclude_names=consumed_discriminators)
+    test_input = context.input_for(test_parameter_flat_path)
     matched_name = test_input["name"] if test_input else None
     explicit_test_value = test_input["value"] if test_input else None
     if is_boolean and isinstance(explicit_test_value, str):
@@ -513,7 +570,7 @@ def _select_which_when(
         # when from the parameters the test actually provides before falling back to the
         # default when (otherwise a test that supplies a non-default branch's params fails
         # to validate against the default branch).
-        inferred_when = _infer_when_from_inputs(conditional, inputs, prefix)
+        inferred_when = _infer_when_from_inputs(conditional, context.inputs, prefix)
         if inferred_when is not None:
             return inferred_when, matched_name
     for when in conditional.whens:
@@ -575,59 +632,6 @@ def _infer_when_from_inputs(
     return None
 
 
-def _input_for(
-    flat_state_path: str, inputs: ToolSourceTestInputs, exclude_names: Optional[Set[str]] = None
-) -> Optional[ToolSourceTestInput]:
-    # ``exclude_names`` holds the names of test inputs already consumed as the discriminator
-    # of an enclosing conditional. Such an input belongs to that ancestor conditional and must
-    # not be re-matched by the loose fallbacks below when resolving a descendant's
-    # discriminator (otherwise e.g. an omitted nested ``selector`` greedily picks up the
-    # parent conditional's ``selector`` value - see _select_which_when).
-    exclude = exclude_names or set()
-    for input in inputs:
-        if input["name"] == flat_state_path:
-            return input
-    # Fallback for legacy test cases that specify conditional/section params without the pipe-separated
-    # prefix (e.g. <param name="fasta"> instead of <param name="mode|fasta">).
-    if "|" in flat_state_path:
-        suffix_matching_inputs = [
-            input
-            for input in inputs
-            if "|" in input["name"] and input["name"] not in exclude and flat_state_path.endswith(f"|{input['name']}")
-        ]
-        resolved = _resolve_matching_inputs(
-            suffix_matching_inputs, f"Ambiguous partially qualified test parameter name for ({flat_state_path})"
-        )
-        if resolved is not None:
-            return resolved
-
-        short_name = flat_state_path.rsplit("|", 1)[1]
-        matching_inputs = [input for input in inputs if input["name"] == short_name and input["name"] not in exclude]
-        resolved = _resolve_matching_inputs(
-            matching_inputs, f"Ambiguous unqualified test parameter name ({short_name}) for ({flat_state_path})"
-        )
-        if resolved is not None:
-            return resolved
-
-        # Fallback for legacy test cases that elide intermediate conditional names but keep
-        # the enclosing section/repeat prefix (e.g. <section name="adv"><param name="esf">
-        # for a param whose real path is adv|esf_cond|esf). The input name is an ordered
-        # subsequence of the qualified path - sharing the head and the leaf - rather than a
-        # plain suffix.
-        path_segments = flat_state_path.split("|")
-        elided_matching_inputs = [
-            input
-            for input in inputs
-            if input["name"] not in exclude and _is_conditional_elided_match(input["name"], path_segments)
-        ]
-        resolved = _resolve_matching_inputs(
-            elided_matching_inputs, f"Ambiguous partially qualified test parameter name for ({flat_state_path})"
-        )
-        if resolved is not None:
-            return resolved
-    return None
-
-
 def _resolve_matching_inputs(
     matching_inputs: List[ToolSourceTestInput], ambiguity_message: str
 ) -> Optional[ToolSourceTestInput]:

From a3417e25fd3cf0cad72519cc6304466268362665 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 9 Jun 2026 16:51:29 -0500
Subject: [PATCH 160/256] display invocation fetch error on invocation state
 view

---
 .../WorkflowInvocationState/WorkflowInvocationState.vue    | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
index 84db2ab47e0..f59aea7b0a8 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
@@ -522,12 +522,19 @@ async function onCancel() {
     <BAlert v-else-if="!invocationLoaded" variant="info" show>
         <LoadingSpan message="Loading invocation" />
     </BAlert>
+    <BAlert v-else-if="invocationStore.getInvocationLoadError(props.invocationId)" variant="danger" show>
+        {{ invocationStore.getInvocationLoadError(props.invocationId) }}
+    </BAlert>
     <BAlert v-else variant="info" show>
         <span v-localize>Invocation not found.</span>
     </BAlert>
 </template>
 
 <style lang="scss">
+.alert {
+    height: unset !important;
+}
+
 // To show the tooltip on the disabled report tab badge
 .invocation-report-tab,
 .invocation-export-tab {

From b1e4944053f43634d624b13ad5077bf071bafd73 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 9 Jun 2026 18:55:13 -0500
Subject: [PATCH 161/256] add `invocation_id` to `PageIndexQueryPayload` to
 filter by invocation

---
 client/packages/api-client/src/schema/schema.ts | 2 ++
 lib/galaxy/managers/pages.py                    | 3 +++
 lib/galaxy/schema/schema.py                     | 3 +++
 lib/galaxy/webapps/galaxy/api/pages.py          | 6 ++++++
 4 files changed, 14 insertions(+)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index ddc2fb8bb09..f80b0ba7133 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -44855,6 +44855,8 @@ export interface operations {
                 /** @description Sort in descending order? */
                 sort_desc?: boolean;
                 user_id?: string | null;
+                /** @description Filter pages by this workflow invocation ID. */
+                invocation_id?: string | null;
                 history_id?: string | null;
             };
             header?: {
diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index 42519e99244..af4e4c8f782 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -179,6 +179,9 @@ class PageManager(sharable.SharableModelManager[model.Page], UsesAnnotations):
         if payload.user_id:
             stmt = stmt.where(self.model_class.user_id == payload.user_id)
 
+        if payload.invocation_id:
+            stmt = stmt.where(self.model_class.source_invocation_id == payload.invocation_id)
+
         if payload.history_id:
             stmt = stmt.where(self.model_class.history_id == payload.history_id)
 
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 3e4d498e8d2..cad3a7a75b0 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1759,6 +1759,9 @@ class PageIndexQueryPayload(Model):
     sort_by: PageSortByEnum = Field("update_time", title="Sort By", description="Sort pages by this attribute.")
     sort_desc: Optional[bool] = Field(default=False, title="Sort descending", description="Sort in descending order.")
     user_id: Optional[DecodedDatabaseIdField] = None
+    invocation_id: Optional[DecodedDatabaseIdField] = Field(
+        default=None, title="Invocation ID", description="Filter pages by workflow invocation."
+    )
     history_id: Optional[DecodedDatabaseIdField] = Field(
         default=None, title="History ID", description="Filter pages by history."
     )
diff --git a/lib/galaxy/webapps/galaxy/api/pages.py b/lib/galaxy/webapps/galaxy/api/pages.py
index ec29c375858..aa8330926ed 100644
--- a/lib/galaxy/webapps/galaxy/api/pages.py
+++ b/lib/galaxy/webapps/galaxy/api/pages.py
@@ -82,6 +82,10 @@ OffsetQueryParam: int = Query(
     title="Number of pages to skip in sorted query (to enable pagination).",
 )
 
+InvocationIdQueryParam: Optional[DecodedDatabaseIdField] = Query(
+    default=None, title="Invocation ID", description="Filter pages by this workflow invocation ID."
+)
+
 HistoryIdQueryParam: Optional[DecodedDatabaseIdField] = Query(
     default=None,
     title="Filter pages by history ID.",
@@ -127,6 +131,7 @@ class FastAPIPages:
         sort_by: PageSortByEnum = SortByQueryParam,
         sort_desc: bool = SortDescQueryParam,
         user_id: Optional[DecodedDatabaseIdField] = UserIdQueryParam,
+        invocation_id: Optional[DecodedDatabaseIdField] = InvocationIdQueryParam,
         history_id: Optional[DecodedDatabaseIdField] = HistoryIdQueryParam,
     ) -> PageSummaryList:
         """Get a list with summary information of all Pages available to the user."""
@@ -141,6 +146,7 @@ class FastAPIPages:
             sort_by=sort_by,
             sort_desc=sort_desc,
             user_id=user_id,
+            invocation_id=invocation_id,
             history_id=history_id,
         )
         pages, total_matches = self.service.index(trans, payload, include_total_count=True)

From 3638e10b96441bf76a80e1f6c8e8116d3993713f Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 9 Jun 2026 19:07:47 -0500
Subject: [PATCH 162/256] WIP: list an invocation's reports in the Report tab

---
 client/src/api/pages.ts                       |  6 ++--
 client/src/components/Markdown/Markdown.vue   | 21 +++++++-----
 client/src/components/Page/constants.ts       | 21 +++++++-----
 .../components/PageEditor/HistoryPageView.vue |  8 +++--
 .../components/PageEditor/PageEditorView.vue  |  2 +-
 .../components/Workflow/InvocationReport.vue  | 29 +++++++++++++++-
 .../WorkflowInvocationReports.vue             | 34 +++++++++++++++++++
 .../WorkflowInvocationState.vue               |  6 ++--
 client/src/stores/pageEditorStore.ts          | 15 ++++----
 lib/galaxy/schema/terms.yml                   |  8 +++++
 10 files changed, 116 insertions(+), 34 deletions(-)
 create mode 100644 client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue

diff --git a/client/src/api/pages.ts b/client/src/api/pages.ts
index 615640b6610..92854157ff9 100644
--- a/client/src/api/pages.ts
+++ b/client/src/api/pages.ts
@@ -16,9 +16,11 @@ export type UpdateHistoryPagePayload = components["schemas"]["UpdatePagePayload"
 
 // --- API functions ---
 
-export async function fetchHistoryPages(historyId: string): Promise<HistoryPageSummary[]> {
+export async function fetchHistoryPages(historyId: string, invocationId?: string): Promise<HistoryPageSummary[]> {
     const { data, error } = await GalaxyApi().GET("/api/pages", {
-        params: { query: { history_id: historyId, show_own: true, show_published: false } },
+        params: {
+            query: { history_id: historyId, invocation_id: invocationId, show_own: true, show_published: false },
+        },
     });
     if (error) {
         rethrowSimple(error);
diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index df76db0c4e0..737986be015 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -1,7 +1,6 @@
 <script setup lang="ts">
 import { faDownload, faEdit } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BButton } from "bootstrap-vue";
 import { computed, onMounted, ref, watch } from "vue";
 
 import { parseMarkdown } from "./parse";
@@ -95,10 +94,14 @@ onMounted(() => {
         <div v-else class="d-flex flex-column">
             <div class="d-flex flex-column sticky-top bg-white">
                 <div class="d-flex">
-                    <Heading v-localize h1 separator inline size="md" class="flex-grow-1">
-                        {{ pageTitle }}
+                    <Heading h1 separator inline size="md" class="flex-grow-1">
+                        <slot name="heading">
+                            {{ pageTitle }}
+                        </slot>
                     </Heading>
                     <div>
+                        <slot name="extra-actions" />
+
                         <template v-if="effectiveExportLink">
                             <GButton
                                 v-if="directDownloadLink"
@@ -123,18 +126,18 @@ onMounted(() => {
                                 outline />
                         </template>
 
-                        <BButton
+                        <GButton
                             v-if="!readOnly"
-                            v-g-tooltip.hover
+                            tooltip
                             class="markdown-edit"
-                            role="button"
-                            size="sm"
+                            size="small"
                             title="Edit Markdown"
-                            variant="outline-primary"
+                            outline
+                            color="blue"
                             @click="$emit('onEdit')">
                             Edit
                             <FontAwesomeIcon :icon="faEdit" />
-                        </BButton>
+                        </GButton>
                     </div>
                 </div>
             </div>
diff --git a/client/src/components/Page/constants.ts b/client/src/components/Page/constants.ts
index 6068907f17f..5c2101e9652 100644
--- a/client/src/components/Page/constants.ts
+++ b/client/src/components/Page/constants.ts
@@ -23,9 +23,7 @@ export const PAGE_LABELS: Record<
         emptyStateDescription: string;
         viewButton: string;
         createButton: string;
-        historyCounterTooltip: string;
-        chatPlaceholder: string;
-        newConversation: string;
+        historyCounterTooltip?: string;
     }
 > = {
     history: {
@@ -40,8 +38,6 @@ export const PAGE_LABELS: Record<
         viewButton: "View notebook",
         createButton: "Create Notebook",
         historyCounterTooltip: "Galaxy Notebooks",
-        chatPlaceholder: "Ask about your history or request notebook edits...",
-        newConversation: "Starting a new conversation. How can I help with this notebook?",
     },
     standalone: {
         entityName: "Report",
@@ -53,9 +49,18 @@ export const PAGE_LABELS: Record<
         emptyStateDescription: "Create a report to publish your analysis.",
         viewButton: "View report",
         createButton: "Create Report",
-        historyCounterTooltip: "",
-        chatPlaceholder: "Ask about your history or request report edits...",
-        newConversation: "Starting a new conversation. How can I help with this report?",
+    },
+    invocation: {
+        entityName: "Invocation Report",
+        entityNamePlural: "Invocation Reports",
+        defaultTitle: "Untitled Invocation Report",
+        editorBackLabel: "This Invocation's Report",
+        newButton: "New Invocation Report",
+        emptyStateTitle: "No invocation reports yet",
+        emptyStateDescription:
+            "Create a report to document this workflow invocation with rich markdown, embedded datasets, and visualizations.",
+        viewButton: "View invocation report",
+        createButton: "Create Invocation Report",
     },
 } as const;
 
diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index 194ffae0c24..f7c61aa97c5 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -15,6 +15,7 @@ import Markdown from "@/components/Markdown/Markdown.vue";
 
 const props = defineProps<{
     historyId: string;
+    invocationId?: string;
     pageId?: string;
     displayOnly?: boolean;
 }>();
@@ -39,7 +40,7 @@ const markdownConfig = computed(() => {
 });
 
 onMounted(async () => {
-    await store.loadPages(props.historyId);
+    await store.loadPages(props.historyId, props.invocationId);
     if (props.pageId && props.displayOnly) {
         await store.loadPageById(props.pageId);
     }
@@ -54,7 +55,7 @@ onUnmounted(() => {
 watch(
     () => props.historyId,
     async (newId) => {
-        await store.loadPages(newId);
+        await store.loadPages(newId, props.invocationId);
         if (props.pageId && props.displayOnly) {
             await store.loadPageById(props.pageId);
         }
@@ -153,7 +154,8 @@ function handleBack() {
                     v-if="markdownConfig"
                     :markdown-config="markdownConfig"
                     :read-only="true"
-                    download-endpoint="" />
+                    download-endpoint=""
+                    hide-heading />
             </div>
         </template>
 
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index e7df7887416..631fb092049 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -64,7 +64,7 @@ const showPermissions = ref(false);
 onMounted(async () => {
     store.mode = editorMode.value;
     if (props.historyId) {
-        store.historyId = props.historyId;
+        store.setCurrentContext(props.historyId);
     }
     await store.loadPage(props.pageId);
 });
diff --git a/client/src/components/Workflow/InvocationReport.vue b/client/src/components/Workflow/InvocationReport.vue
index c9fd3d0bcc2..577d00df0f8 100644
--- a/client/src/components/Workflow/InvocationReport.vue
+++ b/client/src/components/Workflow/InvocationReport.vue
@@ -1,4 +1,6 @@
 <script setup lang="ts">
+import { faFileContract } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed, provide, ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
@@ -6,10 +8,18 @@ import { fetchInvocationReport } from "@/api/invocations";
 import { useConfig } from "@/composables/config";
 import { useToast } from "@/composables/toast";
 
+import GButton from "../BaseComponents/GButton.vue";
+import HelpText from "../Help/HelpText.vue";
 import Markdown from "@/components/Markdown/Markdown.vue";
 
 const props = defineProps<{
     invocationId: string;
+    /** Whether to enforce displaying a "Runtime Report" heading with help text */
+    fromRuntimeReport?: boolean;
+}>();
+
+const emit = defineEmits<{
+    (e: "view-existing-reports"): void;
 }>();
 
 const { config, isConfigLoaded } = useConfig(true);
@@ -49,5 +59,22 @@ provide("invocationId", props.invocationId);
         :export-link="exportUrl"
         :download-endpoint="exportUrl"
         direct-download-link
-        @onEdit="onEdit" />
+        @onEdit="onEdit">
+        <template v-if="props.fromRuntimeReport" v-slot:heading>
+            Runtime Report
+            <HelpText uri="galaxy.invocations.reports.runtimeReport" info-icon />
+        </template>
+
+        <template v-if="props.fromRuntimeReport" v-slot:extra-actions>
+            <GButton
+                tooltip
+                title="Click to view existing/edited report for this workflow invocation"
+                outline
+                color="blue"
+                @click="emit('view-existing-reports')">
+                View Existing Reports
+                <FontAwesomeIcon :icon="faFileContract" />
+            </GButton>
+        </template>
+    </Markdown>
 </template>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue
new file mode 100644
index 00000000000..1c340bada36
--- /dev/null
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue
@@ -0,0 +1,34 @@
+<script setup lang="ts">
+import { ref } from "vue";
+
+import HistoryPageView from "../PageEditor/HistoryPageView.vue";
+import InvocationReport from "../Workflow/InvocationReport.vue";
+
+const props = defineProps<{
+    invocationId: string;
+    historyId: string;
+}>();
+
+/** Tracks what is currently being viewed in the reports section:
+ * - `fromTemplate` shows the original report generated from the template
+ * - `editedReports` shows a list of edited reports if any exist
+ * - `editedReport` shows a specific edited report when selected from the list
+ */
+const currentView = ref<"fromTemplate" | "editedReports" | "editedReport">("fromTemplate");
+</script>
+
+<template>
+    <InvocationReport
+        v-if="currentView === 'fromTemplate'"
+        :invocation-id="props.invocationId"
+        from-runtime-report
+        @view-existing-reports="currentView = 'editedReports'" />
+    <div v-else-if="currentView === 'editedReports'">
+        <!-- TODO: For now, no way to route back -->
+        <HistoryPageView :history-id="props.historyId" :invocation-id="props.invocationId" />
+    </div>
+    <div v-else-if="currentView === 'editedReport'">
+        <!-- TODO: Placeholder for a specific edited report -->
+        <p>Specific edited report goes here.</p>
+    </div>
+</template>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
index f59aea7b0a8..5dd3ce8b022 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
@@ -28,7 +28,6 @@ import {
 import GButton from "../BaseComponents/GButton.vue";
 import ProgressBar from "../ProgressBar.vue";
 import WorkflowInvocationSteps from "../Workflow/Invocation/Graph/WorkflowInvocationSteps.vue";
-import InvocationReport from "../Workflow/InvocationReport.vue";
 import WorkflowAnnotation from "../Workflow/WorkflowAnnotation.vue";
 import WorkflowNavigationTitle from "../Workflow/WorkflowNavigationTitle.vue";
 import TabsDisabledAlert from "./TabsDisabledAlert.vue";
@@ -37,6 +36,7 @@ import WorkflowInvocationFeedback from "./WorkflowInvocationFeedback.vue";
 import WorkflowInvocationInputOutputTabs from "./WorkflowInvocationInputOutputTabs.vue";
 import WorkflowInvocationMetrics from "./WorkflowInvocationMetrics.vue";
 import WorkflowInvocationOverview from "./WorkflowInvocationOverview.vue";
+import WorkflowInvocationReports from "./WorkflowInvocationReports.vue";
 import WorkflowInvocationSearch from "./WorkflowInvocationSearch.vue";
 import WorkflowInvocationShare from "./WorkflowInvocationShare.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
@@ -455,7 +455,7 @@ async function onCancel() {
             </div>
         </BNav>
 
-        <div class="mt-1 d-flex flex-column tab-content-container">
+        <div class="mt-1 d-flex flex-column overflow-auto tab-content-container">
             <div v-if="onOverviewTab">
                 <WorkflowInvocationOverview
                     class="invocation-overview"
@@ -489,7 +489,7 @@ async function onCancel() {
                     v-else-if="tabsDisabled"
                     :invocation-id="props.invocationId"
                     :tooltip="disabledTabTooltip" />
-                <InvocationReport v-else :invocation-id="invocation.id" />
+                <WorkflowInvocationReports v-else :invocation-id="invocation.id" :history-id="invocation.history_id" />
             </div>
             <div v-if="props.tab === 'export'">
                 <TabsDisabledAlert
diff --git a/client/src/stores/pageEditorStore.ts b/client/src/stores/pageEditorStore.ts
index 60b56c1adc2..894d318e2b0 100644
--- a/client/src/stores/pageEditorStore.ts
+++ b/client/src/stores/pageEditorStore.ts
@@ -21,7 +21,7 @@ import { ERROR_MESSAGES } from "@/components/Page/constants";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-export type PageEditorMode = "history" | "standalone";
+export type PageEditorMode = "history" | "standalone" | "invocation";
 
 export const usePageEditorStore = defineStore("pageEditor", () => {
     const mode = ref<PageEditorMode>("history");
@@ -36,7 +36,7 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
     const isSaving = ref(false);
     const error = ref<string | null>(null);
     const chatError = ref<string | null>(null);
-    const historyId = ref<string | null>(null);
+    const currentContext = ref<{ historyId: string | null; invocationId?: string }>({ historyId: null });
 
     // Per-history "current page" ID persisted across sessions
     const currentPageIds = useUserLocalStorage<Record<string, string>>("history-page-current", {});
@@ -56,6 +56,7 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
 
     const hasPages = computed(() => pages.value.length > 0);
     const hasCurrentPage = computed(() => currentPage.value !== null);
+    const historyId = computed(() => currentContext.value.historyId);
     const isDirty = computed(
         () => currentContent.value !== originalContent.value || currentTitle.value !== originalTitle.value,
     );
@@ -71,12 +72,12 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
             selectedRevision.value.id === revisions.value[revisions.value.length - 1]?.id,
     );
 
-    async function loadPages(newHistoryId: string) {
-        historyId.value = newHistoryId;
+    async function loadPages(newHistoryId: string, invocationId?: string) {
+        currentContext.value = { historyId: newHistoryId, invocationId };
         isLoadingList.value = true;
         error.value = null;
         try {
-            pages.value = await fetchHistoryPages(newHistoryId);
+            pages.value = await fetchHistoryPages(newHistoryId, invocationId);
         } catch (e: unknown) {
             error.value = errorMessageAsString(e) || ERROR_MESSAGES.loadList;
         } finally {
@@ -85,7 +86,7 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
     }
 
     async function loadPageById(pageId: string) {
-        if (mode.value === "history" && !historyId.value) {
+        if (["history", "invocation"].includes(mode.value) && !historyId.value) {
             return;
         }
         isLoadingPage.value = true;
@@ -389,7 +390,7 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
         isSaving.value = false;
         error.value = null;
         chatError.value = null;
-        historyId.value = null;
+        currentContext.value = { historyId: null };
         clearRevisionState();
     }
 
diff --git a/lib/galaxy/schema/terms.yml b/lib/galaxy/schema/terms.yml
index 5662116813f..3fd90b9784c 100644
--- a/lib/galaxy/schema/terms.yml
+++ b/lib/galaxy/schema/terms.yml
@@ -212,6 +212,14 @@ galaxy:
         have been reached.
 
   invocations:
+    reports:
+      runtimeReport: |
+        This is a report generated from the Report Template associated with the workflow.
+
+        The original template was created and edited by the workflow author (see the Report button/activity
+        in the workflow editor). A template is a Galaxy markdown report/page written for a workflow before it
+        is run, with workflow variables such as dataset displays for steps, workflow image etc. which are then
+        filled in with information from the actual workflow run at runtime.
     states:
       scheduled: |
         This state indicates the workflow invocation has had all of its jobs scheduled. This means all the

From 73066c59154a743989c46b2999b1d803c3143363 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 10 Jun 2026 10:49:11 -0500
Subject: [PATCH 163/256] WIP: keep invocation reports list within invocation
 view

---
 client/src/components/Markdown/Markdown.vue   |  2 +-
 client/src/components/Page/constants.ts       |  2 +-
 .../components/PageEditor/HistoryPageList.vue |  8 +--
 .../components/PageEditor/HistoryPageView.vue | 53 ++++++++++++++++---
 .../components/PageEditor/PageEditorView.vue  | 28 +++++++++-
 .../WorkflowInvocationReports.vue             | 35 ++++++++++--
 6 files changed, 111 insertions(+), 17 deletions(-)

diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index 737986be015..ecb2347eb6d 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -148,7 +148,7 @@ onMounted(() => {
                         {{ obj.line }}
                     </div>
                 </b-alert>
-                <div v-for="(obj, index) in markdownObjects" :key="index" class="markdown-component py-2">
+                <div v-for="(obj, index) in markdownObjects" :key="index" class="markdown-component">
                     <SectionWrapper :name="obj.name" :content="obj.content" />
                 </div>
                 <div class="markdown-scroll-overlay" />
diff --git a/client/src/components/Page/constants.ts b/client/src/components/Page/constants.ts
index 5c2101e9652..9b0f2b921e4 100644
--- a/client/src/components/Page/constants.ts
+++ b/client/src/components/Page/constants.ts
@@ -54,7 +54,7 @@ export const PAGE_LABELS: Record<
         entityName: "Invocation Report",
         entityNamePlural: "Invocation Reports",
         defaultTitle: "Untitled Invocation Report",
-        editorBackLabel: "This Invocation's Report",
+        editorBackLabel: "This Invocation's Reports",
         newButton: "New Invocation Report",
         emptyStateTitle: "No invocation reports yet",
         emptyStateDescription:
diff --git a/client/src/components/PageEditor/HistoryPageList.vue b/client/src/components/PageEditor/HistoryPageList.vue
index fcb33e4ced5..ed894a73c55 100644
--- a/client/src/components/PageEditor/HistoryPageList.vue
+++ b/client/src/components/PageEditor/HistoryPageList.vue
@@ -2,12 +2,14 @@
 import { faChevronRight, faEye, faPlus } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
+import { computed } from "vue";
 
 import type { HistoryPageSummary } from "@/api/pages";
 import { PAGE_LABELS } from "@/components/Page/constants";
 
-defineProps<{
+const props = defineProps<{
     pages: HistoryPageSummary[];
+    invocationId?: string;
 }>();
 
 defineEmits<{
@@ -16,10 +18,10 @@ defineEmits<{
     (e: "create"): void;
 }>();
 
-const labels = PAGE_LABELS.history;
+const labels = computed(() => (props.invocationId ? PAGE_LABELS.invocation : PAGE_LABELS.history));
 
 function getPageTitle(page: HistoryPageSummary): string {
-    return page.title || labels.defaultTitle;
+    return page.title || labels.value.defaultTitle;
 }
 
 function formatDate(dateStr: string): string {
diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index f7c61aa97c5..8bf14aafa7a 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -18,12 +18,19 @@ const props = defineProps<{
     invocationId?: string;
     pageId?: string;
     displayOnly?: boolean;
+    emitsActions?: boolean;
+}>();
+
+const emit = defineEmits<{
+    (e: "edit-page", pageId: string): void;
+    (e: "go-back"): void;
+    (e: "view-page", pageId: string): void;
 }>();
 
 const router = useRouter();
 const { pushToFrameOrPage } = useWindowAwareNavigation();
 const store = usePageEditorStore();
-const labels = PAGE_LABELS.history;
+const labels = computed(() => (props.invocationId ? PAGE_LABELS.invocation : PAGE_LABELS.history));
 
 const markdownConfig = computed(() => {
     if (!store.currentPage) {
@@ -32,7 +39,7 @@ const markdownConfig = computed(() => {
     const content = props.displayOnly ? (store.currentPage.content ?? store.currentContent) : store.currentContent;
     return {
         id: store.currentPage.id,
-        title: store.currentTitle || labels.defaultTitle,
+        title: store.currentTitle || labels.value.defaultTitle,
         content,
         model_class: "Page",
         update_time: store.currentPage.update_time,
@@ -75,34 +82,54 @@ watch(
 
 function handleSelect(pageId: string) {
     const page = store.pages.find((n) => n.id === pageId);
-    const pageTitle = page?.title || labels.entityName;
+    const pageTitle = page?.title || labels.value.entityName;
+    if (props.emitsActions) {
+        emit("edit-page", pageId);
+        return;
+    }
     const inlineUrl = `/histories/${props.historyId}/pages/${pageId}`;
     pushToFrameOrPage({
         framedUrl: `${inlineUrl}?displayOnly=true`,
         inlineUrl,
-        title: `${labels.entityName}: ${pageTitle}`,
+        title: `${labels.value.entityName}: ${pageTitle}`,
     });
 }
 
 async function handleCreate() {
-    const page = await store.createPage({ title: labels.defaultTitle });
+    const page = await store.createPage({ title: labels.value.defaultTitle });
     if (page) {
+        if (props.emitsActions) {
+            emit("edit-page", page.id);
+            return;
+        }
         router.push(`/histories/${props.historyId}/pages/${page.id}`);
     }
 }
 
 function handleView(pageId: string) {
+    if (props.emitsActions) {
+        emit("view-page", pageId);
+        return;
+    }
     router.push(`/histories/${props.historyId}/pages/${pageId}?displayOnly=true`);
 }
 
 function handleEdit() {
     if (props.pageId) {
+        if (props.emitsActions) {
+            emit("edit-page", props.pageId);
+            return;
+        }
         router.push(`/histories/${props.historyId}/pages/${props.pageId}`);
     }
 }
 
 function handleBack() {
     store.clearCurrentPage();
+    if (props.emitsActions) {
+        emit("go-back");
+        return;
+    }
     router.push(`/histories/${props.historyId}/pages`);
 }
 </script>
@@ -129,7 +156,12 @@ function handleBack() {
         </BAlert>
 
         <template v-else-if="!pageId">
-            <HistoryPageList :pages="store.pages" @select="handleSelect" @view="handleView" @create="handleCreate" />
+            <HistoryPageList
+                :invocation-id="props.invocationId"
+                :pages="store.pages"
+                @select="handleSelect"
+                @view="handleView"
+                @create="handleCreate" />
         </template>
 
         <!-- Display-only mode: rendered view -->
@@ -161,7 +193,14 @@ function handleBack() {
 
         <!-- Edit mode: delegate to unified PageEditorView -->
         <template v-else-if="pageId && !displayOnly">
-            <PageEditorView :page-id="pageId" :history-id="historyId" />
+            <PageEditorView
+                :emits-actions="props.emitsActions"
+                :page-id="pageId"
+                :history-id="historyId"
+                :invocation-id="invocationId"
+                @edit-page="handleEdit"
+                @go-back="handleBack"
+                @view-page="handleView" />
         </template>
 
         <BAlert v-else-if="store.isLoadingPage" variant="info" show>
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 631fb092049..a8a40856135 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -22,7 +22,15 @@ import MarkdownEditor from "@/components/Markdown/MarkdownEditor.vue";
 const props = defineProps<{
     pageId: string;
     historyId?: string;
+    invocationId?: string;
     displayOnly?: boolean;
+    emitsActions?: boolean;
+}>();
+
+const emit = defineEmits<{
+    (e: "edit-page"): void;
+    (e: "go-back"): void;
+    (e: "view-page", id: string): void;
 }>();
 
 const router = useRouter();
@@ -30,7 +38,9 @@ const { pushToFrameOrPage } = useWindowAwareNavigation();
 const store = usePageEditorStore();
 const historyStore = useHistoryStore();
 
-const editorMode = computed<PageEditorMode>(() => (props.historyId ? "history" : "standalone"));
+const editorMode = computed<PageEditorMode>(() =>
+    props.invocationId ? "invocation" : props.historyId ? "history" : "standalone",
+);
 const isStandalone = computed(() => editorMode.value === "standalone");
 
 const labels = computed(() => PAGE_LABELS[editorMode.value]);
@@ -89,6 +99,10 @@ watch(
 
 function handleBack() {
     store.clearCurrentPage();
+    if (props.emitsActions) {
+        emit("go-back");
+        return;
+    }
     if (props.historyId) {
         router.push(`/histories/${props.historyId}/pages`);
     } else {
@@ -97,6 +111,10 @@ function handleBack() {
 }
 
 function handlePreview() {
+    if (props.emitsActions) {
+        emit("view-page", props.pageId);
+        return;
+    }
     if (props.historyId) {
         router.push(`/histories/${props.historyId}/pages/${props.pageId}?displayOnly=true`);
     } else {
@@ -111,6 +129,10 @@ function handlePreview() {
 }
 
 function handleEdit() {
+    if (props.emitsActions) {
+        emit("edit-page");
+        return;
+    }
     if (props.historyId) {
         router.push(`/histories/${props.historyId}/pages/${props.pageId}`);
     } else {
@@ -124,6 +146,10 @@ async function handleSave() {
 
 async function handleSaveAndView() {
     await store.savePage();
+    if (props.emitsActions) {
+        emit("view-page", props.pageId);
+        return;
+    }
     if (store.currentPage) {
         const Galaxy = getGalaxyInstance();
         const isWmActive = Galaxy?.frame?.active;
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue
index 1c340bada36..94ca686a931 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue
@@ -15,6 +15,21 @@ const props = defineProps<{
  * - `editedReport` shows a specific edited report when selected from the list
  */
 const currentView = ref<"fromTemplate" | "editedReports" | "editedReport">("fromTemplate");
+
+const currentEditedReportId = ref<string | null>(null);
+const displayOnly = ref(false);
+
+function editOrViewPage(pageId: string, displayOnlyValue: boolean) {
+    currentView.value = "editedReport";
+    currentEditedReportId.value = pageId;
+    displayOnly.value = displayOnlyValue;
+}
+
+function goBackFromEditedReport() {
+    currentView.value = "editedReports";
+    currentEditedReportId.value = null;
+    displayOnly.value = false;
+}
 </script>
 
 <template>
@@ -24,11 +39,23 @@ const currentView = ref<"fromTemplate" | "editedReports" | "editedReport">("from
         from-runtime-report
         @view-existing-reports="currentView = 'editedReports'" />
     <div v-else-if="currentView === 'editedReports'">
-        <!-- TODO: For now, no way to route back -->
-        <HistoryPageView :history-id="props.historyId" :invocation-id="props.invocationId" />
+        <HistoryPageView
+            :history-id="props.historyId"
+            :invocation-id="props.invocationId"
+            emits-actions
+            @edit-page="(pageId) => editOrViewPage(pageId, false)"
+            @go-back="currentView = 'fromTemplate'"
+            @view-page="(pageId) => editOrViewPage(pageId, true)" />
     </div>
     <div v-else-if="currentView === 'editedReport'">
-        <!-- TODO: Placeholder for a specific edited report -->
-        <p>Specific edited report goes here.</p>
+        <HistoryPageView
+            :history-id="props.historyId"
+            :invocation-id="props.invocationId"
+            :page-id="currentEditedReportId || undefined"
+            :display-only="displayOnly"
+            emits-actions
+            @edit-page="(pageId) => editOrViewPage(pageId, false)"
+            @go-back="goBackFromEditedReport"
+            @view-page="(pageId) => editOrViewPage(pageId, true)" />
     </div>
 </template>

From 807c82d110bb225c2a53fcaf9927edd6bc54deeb Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Thu, 11 Jun 2026 19:32:27 -0500
Subject: [PATCH 164/256] use GCards and breadcrumb heading in
 `HistoryPageList`

These cards are now uniformly styled with the rest of the interface, instead of adding a newly styled list to a route.

We also indicate pages linked to invocations (`source_invocation_id`).
---
 client/src/components/Page/constants.ts       |  10 +-
 .../PageEditor/HistoryPageList.test.ts        | 114 ++----------------
 .../components/PageEditor/HistoryPageList.vue |  82 ++++++-------
 .../components/PageEditor/HistoryPageView.vue |   1 +
 .../components/PageEditor/PageCard.test.ts    |  86 +++++++++++++
 client/src/components/PageEditor/PageCard.vue |  95 +++++++++++++++
 client/src/components/PageEditor/testData.ts  |  27 +++++
 client/src/utils/navigation/navigation.yml    |   9 +-
 .../selenium/test_history_pages.py            |  20 +--
 9 files changed, 273 insertions(+), 171 deletions(-)
 create mode 100644 client/src/components/PageEditor/PageCard.test.ts
 create mode 100644 client/src/components/PageEditor/PageCard.vue
 create mode 100644 client/src/components/PageEditor/testData.ts

diff --git a/client/src/components/Page/constants.ts b/client/src/components/Page/constants.ts
index 9b0f2b921e4..2f592704869 100644
--- a/client/src/components/Page/constants.ts
+++ b/client/src/components/Page/constants.ts
@@ -21,6 +21,7 @@ export const PAGE_LABELS: Record<
         newButton: string;
         emptyStateTitle: string;
         emptyStateDescription: string;
+        editButton: string;
         viewButton: string;
         createButton: string;
         historyCounterTooltip?: string;
@@ -35,7 +36,8 @@ export const PAGE_LABELS: Record<
         emptyStateTitle: "No notebooks yet",
         emptyStateDescription:
             "Create a notebook to document your analysis with rich markdown, embedded datasets, and visualizations.",
-        viewButton: "View notebook",
+        editButton: "Edit Notebook",
+        viewButton: "View Notebook",
         createButton: "Create Notebook",
         historyCounterTooltip: "Galaxy Notebooks",
     },
@@ -47,7 +49,8 @@ export const PAGE_LABELS: Record<
         newButton: "Create Report",
         emptyStateTitle: "No reports yet",
         emptyStateDescription: "Create a report to publish your analysis.",
-        viewButton: "View report",
+        editButton: "Edit Report",
+        viewButton: "View Report",
         createButton: "Create Report",
     },
     invocation: {
@@ -59,7 +62,8 @@ export const PAGE_LABELS: Record<
         emptyStateTitle: "No invocation reports yet",
         emptyStateDescription:
             "Create a report to document this workflow invocation with rich markdown, embedded datasets, and visualizations.",
-        viewButton: "View invocation report",
+        editButton: "Edit Invocation Report",
+        viewButton: "View Invocation Report",
         createButton: "Create Invocation Report",
     },
 } as const;
diff --git a/client/src/components/PageEditor/HistoryPageList.test.ts b/client/src/components/PageEditor/HistoryPageList.test.ts
index 0650b5ef549..2b48b46069c 100644
--- a/client/src/components/PageEditor/HistoryPageList.test.ts
+++ b/client/src/components/PageEditor/HistoryPageList.test.ts
@@ -1,55 +1,30 @@
 import { getLocalVue } from "@tests/vitest/helpers";
+import { setupMockHistoryBreadcrumbs } from "@tests/vitest/mockHistoryBreadcrumbs";
 import { shallowMount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { beforeEach, describe, expect, it } from "vitest";
 
 import type { HistoryPageSummary } from "@/api/pages";
 
+import { FAKE_PAGE_SUMMARY, FAKE_PAGE_UNTITLED } from "./testData";
+
 import HistoryPageList from "./HistoryPageList.vue";
 
 const localVue = getLocalVue();
 
-const FAKE_PAGE_SUMMARY: HistoryPageSummary = {
-    id: "page-1",
-    history_id: "history-1",
-    title: "My Analysis",
-    slug: null,
-    source_invocation_id: null,
-    published: false,
-    importable: false,
-    deleted: false,
-    latest_revision_id: "rev-1",
-    revision_ids: ["rev-1"],
-    create_time: "2025-06-15T10:30:00Z",
-    update_time: "2025-06-15T12:45:00Z",
-    username: "test",
-    email_hash: "",
-    author_deleted: false,
-    model_class: "Page",
-    tags: [],
-};
-
-const FAKE_PAGE_UNTITLED: HistoryPageSummary = {
-    ...FAKE_PAGE_SUMMARY,
-    id: "page-2",
-    title: "",
-};
-
 const SELECTORS = {
-    HEADER_TITLE: "h4",
-    NEW_BUTTON: "bbutton-stub",
+    NEW_BUTTON: "[data-description='create page button']",
     EMPTY_STATE: ".empty-state",
     PAGE_ITEMS: ".page-items",
-    PAGE_ITEM: ".page-item",
-    PAGE_TITLE: ".page-title",
-    PAGE_META: ".page-meta",
-    VIEW_BUTTON: "[data-description='page view button']",
+    PAGE_ITEM: "[data-description='page item']",
 };
 
+setupMockHistoryBreadcrumbs();
+
 async function mountComponent(propsData: { pages: HistoryPageSummary[] }) {
     const wrapper = shallowMount(HistoryPageList as object, {
         localVue,
-        propsData,
+        propsData: { ...propsData, historyId: "history-1" },
     });
     await flushPromises();
     return wrapper;
@@ -63,12 +38,6 @@ describe("HistoryPageList", () => {
             wrapper = await mountComponent({ pages: [] });
         });
 
-        it("always shows 'Galaxy Notebooks' heading", () => {
-            const heading = wrapper.find(SELECTORS.HEADER_TITLE);
-            expect(heading.exists()).toBe(true);
-            expect(heading.text()).toBe("Galaxy Notebooks");
-        });
-
         it("always shows 'New Notebook' button", () => {
             const button = wrapper.find(SELECTORS.NEW_BUTTON);
             expect(button.exists()).toBe(true);
@@ -108,78 +77,13 @@ describe("HistoryPageList", () => {
             });
         });
 
-        it("renders each page as a clickable item", () => {
+        it("renders each page as a card", () => {
             const items = wrapper.findAll(SELECTORS.PAGE_ITEM);
             expect(items.length).toBe(2);
         });
 
-        it("displays page title for each item", () => {
-            const titles = wrapper.findAll(SELECTORS.PAGE_TITLE);
-            expect(titles.at(0).text()).toBe("My Analysis");
-        });
-
-        it("shows 'Untitled Notebook' when title is empty", () => {
-            const titles = wrapper.findAll(SELECTORS.PAGE_TITLE);
-            expect(titles.at(1).text()).toBe("Untitled Notebook");
-        });
-
-        it("displays formatted update_time for each page", () => {
-            const meta = wrapper.findAll(SELECTORS.PAGE_META);
-            const metaText = meta.at(0).text();
-            expect(metaText).toContain("Updated");
-            expect(metaText.replace("Updated", "").trim().length).toBeGreaterThan(0);
-        });
-
         it("does NOT show empty state when pages exist", () => {
             expect(wrapper.find(SELECTORS.EMPTY_STATE).exists()).toBe(false);
         });
     });
-
-    describe("Events", () => {
-        it("emits 'create' when New Page button is clicked", async () => {
-            const wrapper = await mountComponent({ pages: [] });
-            const button = wrapper.find(SELECTORS.NEW_BUTTON);
-            await button.trigger("click");
-            expect(wrapper.emitted().create).toBeTruthy();
-        });
-
-        it("emits 'select' with page.id when a page item is clicked", async () => {
-            const wrapper = await mountComponent({
-                pages: [FAKE_PAGE_SUMMARY],
-            });
-            const item = wrapper.find(SELECTORS.PAGE_ITEM);
-            await item.trigger("click");
-            expect(wrapper.emitted().select).toBeTruthy();
-            expect(wrapper.emitted().select![0]![0]).toBe("page-1");
-        });
-    });
-
-    describe("View button", () => {
-        it("shows view button on each page item", async () => {
-            const wrapper = await mountComponent({
-                pages: [FAKE_PAGE_SUMMARY],
-            });
-            const viewButton = wrapper.find(SELECTORS.VIEW_BUTTON);
-            expect(viewButton.exists()).toBe(true);
-        });
-
-        it("emits 'view' with page.id when view button clicked", async () => {
-            const wrapper = await mountComponent({
-                pages: [FAKE_PAGE_SUMMARY],
-            });
-            const viewButton = wrapper.find(SELECTORS.VIEW_BUTTON);
-            await viewButton.trigger("click");
-            expect(wrapper.emitted().view).toBeTruthy();
-            expect(wrapper.emitted().view![0]![0]).toBe("page-1");
-        });
-
-        it("does not emit 'select' when view button clicked", async () => {
-            const wrapper = await mountComponent({
-                pages: [FAKE_PAGE_SUMMARY],
-            });
-            const viewButton = wrapper.find(SELECTORS.VIEW_BUTTON);
-            await viewButton.trigger("click");
-            expect(wrapper.emitted().select).toBeFalsy();
-        });
-    });
 });
diff --git a/client/src/components/PageEditor/HistoryPageList.vue b/client/src/components/PageEditor/HistoryPageList.vue
index ed894a73c55..7cb387f7e36 100644
--- a/client/src/components/PageEditor/HistoryPageList.vue
+++ b/client/src/components/PageEditor/HistoryPageList.vue
@@ -1,18 +1,24 @@
 <script setup lang="ts">
-import { faChevronRight, faEye, faPlus } from "@fortawesome/free-solid-svg-icons";
+import { faPlus } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BButton } from "bootstrap-vue";
-import { computed } from "vue";
+import { computed, toRef } from "vue";
 
 import type { HistoryPageSummary } from "@/api/pages";
 import { PAGE_LABELS } from "@/components/Page/constants";
+import { useHistoryBreadCrumbsTo } from "@/composables/historyBreadcrumbs";
+
+import BreadcrumbHeading from "../Common/BreadcrumbHeading.vue";
+import PageCard from "./PageCard.vue";
+import GButton from "@/components/BaseComponents/GButton.vue";
 
 const props = defineProps<{
     pages: HistoryPageSummary[];
+    historyId: string;
     invocationId?: string;
+    noHeading?: boolean;
 }>();
 
-defineEmits<{
+const emit = defineEmits<{
     (e: "select", pageId: string): void;
     (e: "view", pageId: string): void;
     (e: "create"): void;
@@ -20,29 +26,22 @@ defineEmits<{
 
 const labels = computed(() => (props.invocationId ? PAGE_LABELS.invocation : PAGE_LABELS.history));
 
-function getPageTitle(page: HistoryPageSummary): string {
-    return page.title || labels.value.defaultTitle;
-}
-
-function formatDate(dateStr: string): string {
-    return new Date(dateStr).toLocaleDateString(undefined, {
-        month: "short",
-        day: "numeric",
-        hour: "2-digit",
-        minute: "2-digit",
-    });
-}
+const { breadcrumbItems } = useHistoryBreadCrumbsTo(toRef(props, "historyId"), labels.value.entityNamePlural);
 </script>
 
 <template>
-    <div class="history-page-list" data-description="history page list">
-        <div class="list-header d-flex justify-content-between align-items-center p-3 border-bottom">
-            <h4 class="mb-0">{{ labels.entityNamePlural }}</h4>
-            <BButton variant="primary" size="sm" data-description="create page button" @click="$emit('create')">
+    <div class="d-flex flex-column overflow-hidden" data-description="history page list">
+        <BreadcrumbHeading v-if="!props.noHeading" :items="breadcrumbItems">
+            <GButton
+                class="text-nowrap"
+                color="blue"
+                size="small"
+                data-description="create page button"
+                @click="emit('create')">
                 <FontAwesomeIcon :icon="faPlus" />
                 {{ labels.newButton }}
-            </BButton>
-        </div>
+            </GButton>
+        </BreadcrumbHeading>
 
         <div v-if="pages.length === 0" class="empty-state text-center p-4" data-description="page empty state">
             <p class="text-muted">{{ labels.emptyStateTitle }}</p>
@@ -51,34 +50,19 @@ function formatDate(dateStr: string): string {
             </p>
         </div>
 
-        <div v-else class="page-items">
-            <div
+        <div v-else class="page-items mt-3">
+            <PageCard
                 v-for="page in pages"
                 :key="page.id"
-                class="page-item p-3 border-bottom cursor-pointer"
                 data-description="page item"
-                @click="$emit('select', page.id)">
-                <div class="d-flex justify-content-between align-items-start">
-                    <div>
-                        <div class="page-title fw-bold" data-description="page title">
-                            {{ getPageTitle(page) }}
-                        </div>
-                        <div class="page-meta text-muted small">Updated {{ formatDate(page.update_time) }}</div>
-                    </div>
-                    <span class="page-actions d-flex align-items-center">
-                        <BButton
-                            variant="link"
-                            size="sm"
-                            class="p-1"
-                            :title="labels.viewButton"
-                            data-description="page view button"
-                            @click.stop="$emit('view', page.id)">
-                            <FontAwesomeIcon :icon="faEye" />
-                        </BButton>
-                        <FontAwesomeIcon :icon="faChevronRight" class="text-muted" />
-                    </span>
-                </div>
-            </div>
+                :page="page"
+                :default-title="labels.defaultTitle"
+                :entity-name="labels.entityName"
+                :edit-title="labels.editButton"
+                :show-invocation-badge="!props.invocationId"
+                :view-title="labels.viewButton"
+                @select="emit('select', page.id)"
+                @view="emit('view', page.id)" />
         </div>
     </div>
 </template>
@@ -87,6 +71,10 @@ function formatDate(dateStr: string): string {
 .page-item:hover {
     background: var(--panel-header-bg);
 }
+.page-items {
+    flex: 1 1 0;
+    overflow-y: auto;
+}
 .cursor-pointer {
     cursor: pointer;
 }
diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index 8bf14aafa7a..b34532fd2e0 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -157,6 +157,7 @@ function handleBack() {
 
         <template v-else-if="!pageId">
             <HistoryPageList
+                :history-id="props.historyId"
                 :invocation-id="props.invocationId"
                 :pages="store.pages"
                 @select="handleSelect"
diff --git a/client/src/components/PageEditor/PageCard.test.ts b/client/src/components/PageEditor/PageCard.test.ts
new file mode 100644
index 00000000000..0fa58121405
--- /dev/null
+++ b/client/src/components/PageEditor/PageCard.test.ts
@@ -0,0 +1,86 @@
+import { createTestingPinia } from "@pinia/testing";
+import { getLocalVue } from "@tests/vitest/helpers";
+import { mount } from "@vue/test-utils";
+import { describe, expect, it, vi } from "vitest";
+
+import { FAKE_PAGE_SUMMARY, FAKE_PAGE_UNTITLED } from "./testData";
+
+import PageCard from "./PageCard.vue";
+
+const localVue = getLocalVue();
+
+function getSelector(selector: "title" | "revision" | "time" | "view" | "edit", pageId: string) {
+    if (selector === "title") {
+        return `#g-card-title-link-page-${pageId}`;
+    } else if (selector === "revision") {
+        return `#g-card-badge-notebook-revisions-count-page-${pageId}`;
+    } else if (selector === "time") {
+        return `#g-card-page-${pageId}-update-time`;
+    } else if (selector === "view") {
+        return `#g-card-action-view-notebook-page-${pageId}`;
+    } else if (selector === "edit") {
+        return `#g-card-action-edit-notebook-page-${pageId}`;
+    }
+    throw new Error(`Unknown selector: ${selector}`);
+}
+
+describe("PageCard", () => {
+    it("displays page title which edits notebook on click", async () => {
+        const wrapper = mount(PageCard as object, {
+            localVue,
+            propsData: { page: FAKE_PAGE_SUMMARY },
+            pinia: createTestingPinia({ createSpy: vi.fn }),
+        });
+
+        const title = wrapper.find(getSelector("title", FAKE_PAGE_SUMMARY.id));
+        expect(title.text()).toBe("My Analysis");
+        expect(title.attributes("title")).toBe("Edit Notebook");
+
+        // Click to emit select event
+        await title.trigger("click");
+        expect(wrapper.emitted().select).toBeTruthy();
+    });
+
+    it("shows 'Untitled Notebook' when title is empty", () => {
+        const wrapper = mount(PageCard as object, {
+            localVue,
+            propsData: { page: FAKE_PAGE_UNTITLED },
+            pinia: createTestingPinia({ createSpy: vi.fn }),
+        });
+
+        const title = wrapper.find(getSelector("title", FAKE_PAGE_UNTITLED.id));
+        expect(title.text()).toBe("Untitled Notebook");
+    });
+
+    it("displays update time badge and revision count", () => {
+        const wrapper = mount(PageCard as object, {
+            localVue,
+            propsData: { page: FAKE_PAGE_SUMMARY },
+            pinia: createTestingPinia({ createSpy: vi.fn }),
+        });
+
+        expect(wrapper.find(getSelector("time", FAKE_PAGE_SUMMARY.id)).exists()).toBe(true);
+
+        const revisionBadge = wrapper.find(getSelector("revision", FAKE_PAGE_SUMMARY.id));
+        expect(revisionBadge.exists()).toBe(true);
+        expect(revisionBadge.text()).toBe(
+            `${FAKE_PAGE_SUMMARY.revision_ids.length} Revision${FAKE_PAGE_SUMMARY.revision_ids.length !== 1 ? "s" : ""}`,
+        );
+    });
+
+    it("emits 'view' and 'select' operations correctly", async () => {
+        const wrapper = mount(PageCard as object, {
+            localVue,
+            propsData: { page: FAKE_PAGE_SUMMARY },
+            pinia: createTestingPinia({ createSpy: vi.fn }),
+        });
+
+        const viewButton = wrapper.find(getSelector("view", FAKE_PAGE_SUMMARY.id));
+        await viewButton.trigger("click");
+        expect(wrapper.emitted().view).toBeTruthy();
+
+        const editButton = wrapper.find(getSelector("edit", FAKE_PAGE_SUMMARY.id));
+        await editButton.trigger("click");
+        expect(wrapper.emitted().select).toBeTruthy();
+    });
+});
diff --git a/client/src/components/PageEditor/PageCard.vue b/client/src/components/PageEditor/PageCard.vue
new file mode 100644
index 00000000000..362109e5bde
--- /dev/null
+++ b/client/src/components/PageEditor/PageCard.vue
@@ -0,0 +1,95 @@
+<script setup lang="ts">
+import { faEdit, faExternalLinkAlt, faEye, faHistory } from "@fortawesome/free-solid-svg-icons";
+import { computed } from "vue";
+
+import type { HistoryPageSummary } from "@/api/pages";
+import type { CardAction, CardBadge, Title } from "@/components/Common/GCard.types";
+
+import GCard from "../Common/GCard.vue";
+
+interface Props {
+    page: HistoryPageSummary;
+    defaultTitle?: string;
+    entityName?: string;
+    editTitle?: string;
+    showInvocationBadge?: boolean;
+    viewTitle?: string;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    entityName: "Notebook",
+    editTitle: "Edit Notebook",
+    defaultTitle: "Untitled Notebook",
+    viewTitle: "View Notebook",
+});
+
+const emit = defineEmits<{
+    (e: "select"): void;
+    (e: "view"): void;
+}>();
+
+const title: Title = {
+    label: props.page.title || props.defaultTitle,
+    title: props.editTitle,
+    handler: () => emit("select"),
+};
+
+const badges = computed<CardBadge[]>(() => {
+    const retBadges: CardBadge[] = [
+        {
+            id: "notebook-revisions-count",
+            label: `${props.page.revision_ids.length} Revision${props.page.revision_ids.length !== 1 ? "s" : ""}`,
+            icon: faHistory,
+            title: "Number of revisions for this notebook",
+            class: "unselectable",
+        },
+    ];
+    if (props.showInvocationBadge && props.page.source_invocation_id) {
+        retBadges.push({
+            id: "is-invocation-notebook",
+            label: `Invocation ${props.page.source_invocation_id}`,
+            icon: faExternalLinkAlt,
+            title: "This notebook is a report created from a workflow invocation (Click to view the original report)",
+            class: "unselectable",
+            handler: () => {
+                window.open(`/workflows/invocations/${props.page.source_invocation_id}/report`, "_blank");
+            },
+            variant: "primary",
+        });
+    }
+    return retBadges;
+});
+
+const primaryActions: CardAction[] = [
+    {
+        id: "edit-notebook",
+        label: "Edit",
+        icon: faEdit,
+        title: props.editTitle,
+        handler: () => emit("select"),
+    },
+];
+
+// TODO: Once we fix sharing, we should add a sharing action
+const secondaryActions: CardAction[] = [
+    {
+        id: "view-notebook",
+        label: "View",
+        icon: faEye,
+        title: props.viewTitle,
+        handler: () => emit("view"),
+    },
+];
+</script>
+
+<template>
+    <GCard
+        :id="`page-${props.page.id}`"
+        :badges="badges"
+        :primary-actions="primaryActions"
+        :published="props.page.published"
+        :secondary-actions="secondaryActions"
+        :title="title"
+        title-size="text"
+        :update-time="props.page.update_time" />
+</template>
diff --git a/client/src/components/PageEditor/testData.ts b/client/src/components/PageEditor/testData.ts
new file mode 100644
index 00000000000..3c6b2a264a0
--- /dev/null
+++ b/client/src/components/PageEditor/testData.ts
@@ -0,0 +1,27 @@
+import type { HistoryPageSummary } from "@/api/pages";
+
+export const FAKE_PAGE_SUMMARY: HistoryPageSummary = {
+    id: "page-1",
+    history_id: "history-1",
+    title: "My Analysis",
+    slug: null,
+    source_invocation_id: null,
+    published: false,
+    importable: false,
+    deleted: false,
+    latest_revision_id: "rev-1",
+    revision_ids: ["rev-1"],
+    create_time: "2025-06-15T10:30:00Z",
+    update_time: "2025-06-15T12:45:00Z",
+    username: "test",
+    email_hash: "",
+    author_deleted: false,
+    model_class: "Page",
+    tags: [],
+};
+
+export const FAKE_PAGE_UNTITLED: HistoryPageSummary = {
+    ...FAKE_PAGE_SUMMARY,
+    id: "page-2",
+    title: "",
+};
diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 9c6f7e584ed..3f1902387bb 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -661,9 +661,8 @@ pages:
       item:
         type: data-description
         selector: 'page item'
-      item_title:
-        type: data-description
-        selector: 'page title'
+      item_edit: '[id^="g-card-action-edit-notebook-page-"]'
+      item_title: '[id^="g-card-title-link-page-"]'
       rendered_view:
         type: data-description
         selector: 'page rendered view'
@@ -688,9 +687,7 @@ pages:
       revision_restore_button:
         type: data-description
         selector: 'revision restore button'
-      view_button:
-        type: data-description
-        selector: 'page view button'
+      view_button: '[id^="g-card-action-view-notebook-page-"]'
       display_toolbar:
         type: data-description
         selector: 'page display toolbar'
diff --git a/lib/galaxy_test/selenium/test_history_pages.py b/lib/galaxy_test/selenium/test_history_pages.py
index ea4adfd6f6c..69763daa05a 100644
--- a/lib/galaxy_test/selenium/test_history_pages.py
+++ b/lib/galaxy_test/selenium/test_history_pages.py
@@ -87,7 +87,7 @@ class TestHistoryPages(SeleniumTestCase):
         self.history_page_manage()
         self.history_page_assert_item_count(1)
 
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
 
         editor = self.components.pages.history.markdown_editor
@@ -228,7 +228,7 @@ class TestHistoryPages(SeleniumTestCase):
 
         self.navigate_to_history_pages()
         self.history_page_assert_item_count(1)
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
 
         self.components.pages.history.editor.wait_for_visible()
         assert self.window_manager_window_count() == 0
@@ -269,7 +269,7 @@ class TestHistoryPages(SeleniumTestCase):
 
         self.navigate_to_history_pages()
         self.history_page_assert_item_count(1)
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
 
         self.history_page_open_revisions()
@@ -285,7 +285,7 @@ class TestHistoryPages(SeleniumTestCase):
         self.dataset_populator.update_history_page(nb["id"], content="Modified")
 
         self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
 
         self.history_page_open_revisions()
@@ -329,7 +329,7 @@ class TestHistoryPages(SeleniumTestCase):
         self.dataset_populator.update_history_page(nb["id"], content="# New Content")
 
         self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
 
         self.history_page_open_revisions()
@@ -420,7 +420,7 @@ class TestHistoryPages(SeleniumTestCase):
         self.dataset_populator.new_history_page(history_id, title="Toggle Test", content="# Preview Me")
 
         self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
 
         self.components.pages.history.preview_button.wait_for_and_click()
@@ -445,7 +445,7 @@ class TestHistoryPages(SeleniumTestCase):
         self.dataset_populator.new_history_page(history_id, title="Original Name", content="# Content")
 
         self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
 
         self.history_page_rename("Renamed Page")
@@ -461,7 +461,7 @@ class TestHistoryPages(SeleniumTestCase):
         title_text = self.components.pages.history.item_title.wait_for_text()
         assert "Renamed Page" in title_text
 
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
         toolbar_title = self.components.pages.history.toolbar_title.wait_for_text()
         assert "Renamed Page" in toolbar_title
@@ -501,7 +501,7 @@ class TestHistoryPages(SeleniumTestCase):
         self.dataset_populator.update_history_page(nb["id"], content="# V1\n\nModified content\n\nNew section")
 
         self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
 
         self.history_page_open_revisions()
@@ -547,7 +547,7 @@ class TestHistoryPages(SeleniumTestCase):
         self.dataset_populator.new_history_page(history_id, title="Toolbar Test", content="# Toolbar")
 
         self.navigate_to_history_pages()
-        self.components.pages.history.item.wait_for_and_click()
+        self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
 
         # History-page controls visible

From 66c3898ed54f560c30c27ed32fe071d5a2af69a5 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Thu, 11 Jun 2026 19:34:42 -0500
Subject: [PATCH 165/256] add a history dropdown option to view notebooks

---
 client/src/components/History/HistoryOptions.test.ts | 1 +
 client/src/components/History/HistoryOptions.vue     | 9 +++++++++
 2 files changed, 10 insertions(+)

diff --git a/client/src/components/History/HistoryOptions.test.ts b/client/src/components/History/HistoryOptions.test.ts
index a806bae7eb6..6efb267bda3 100644
--- a/client/src/components/History/HistoryOptions.test.ts
+++ b/client/src/components/History/HistoryOptions.test.ts
@@ -26,6 +26,7 @@ const expectedOptions = [
     "Extract Workflow",
     "Show Invocations",
     "Show History Graph",
+    "Show History Notebooks",
     "Share & Manage Access",
 ];
 
diff --git a/client/src/components/History/HistoryOptions.vue b/client/src/components/History/HistoryOptions.vue
index 5ed5e99057d..acd41f4fbf5 100644
--- a/client/src/components/History/HistoryOptions.vue
+++ b/client/src/components/History/HistoryOptions.vue
@@ -3,6 +3,7 @@ import {
     faArchive,
     faBars,
     faBezierCurve,
+    faBook,
     faBurn,
     faClone,
     faColumns,
@@ -237,6 +238,14 @@ watch(
                 <span v-localize>Show History Graph</span>
             </BDropdownItem>
 
+            <BDropdownItem
+                :disabled="isAnonymous || !canEditHistory"
+                :title="userTitle('View History Notebooks')"
+                :to="`/histories/${history.id}/pages`">
+                <FontAwesomeIcon fixed-width :icon="faBook" />
+                <span v-localize>Show History Notebooks</span>
+            </BDropdownItem>
+
             <BDropdownDivider />
 
             <BDropdownItem

From 7c86889f3a245268faa9f518b7485b45c0451371 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Thu, 11 Jun 2026 23:29:37 -0500
Subject: [PATCH 166/256] sync invocation notebook viewing/editing under the
 invocation view

This adds a `/reports` route to the invocation view (`/workflows/invocations/{invocation_id}/reports`).

Here, when users click to view reports, they stay within the invocation view (with the tabs appearing at the top) for the preview.

For clicking edit on an invocation notebook, we route to a full view history notebook (which still has the context of coming from an invocation, given the route contains `invocation_id` in the query).

This also therefore removes any need for emitting actions across the page components and instead simply does this routing based on whether those components have an `invocationId` as a prop.
---
 client/src/api/invocations.ts                 |  2 +
 client/src/components/Markdown/Markdown.vue   | 13 ++-
 client/src/components/Page/constants.ts       |  2 +-
 .../PageEditor/HistoryPageList.test.ts        |  2 +
 .../components/PageEditor/HistoryPageList.vue | 24 +++--
 .../PageEditor/HistoryPageView.test.ts        | 44 ++++++---
 .../components/PageEditor/HistoryPageView.vue | 93 +++++++++----------
 .../components/PageEditor/PageCard.test.ts    |  6 +-
 client/src/components/PageEditor/PageCard.vue | 16 ++--
 .../components/PageEditor/PageEditorView.vue  | 31 ++-----
 .../components/Workflow/InvocationReport.vue  | 46 +++++++--
 .../WorkflowInvocationReports.vue             | 61 ------------
 .../WorkflowInvocationState.test.ts           |  4 +
 .../WorkflowInvocationState.vue               | 34 +++++--
 client/src/stores/pageEditorStore.test.ts     | 44 ++++-----
 client/src/stores/pageEditorStore.ts          | 26 +++++-
 16 files changed, 235 insertions(+), 213 deletions(-)
 delete mode 100644 client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue

diff --git a/client/src/api/invocations.ts b/client/src/api/invocations.ts
index 8773a459551..c0ddedcce31 100644
--- a/client/src/api/invocations.ts
+++ b/client/src/api/invocations.ts
@@ -30,6 +30,8 @@ export function isWorkflowInvocationElementView(
     return item !== null && "steps" in item;
 }
 
+// TODO: Consider caching this in the store given this doesn't change as it is generated once
+// when an invocation is complete?
 /**
  * Fetches the invocation report for a given invocation ID
  * @param {string} invocationId The ID of the invocation to fetch the report for
diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index ecb2347eb6d..08b65002352 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faDownload, faEdit } from "@fortawesome/free-solid-svg-icons";
+import { faDownload, faEdit, type IconDefinition } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed, onMounted, ref, watch } from "vue";
 
@@ -32,6 +32,8 @@ const props = defineProps<{
     exportLink?: string;
     showIdentifier?: boolean;
     directDownloadLink?: boolean;
+    noHeading?: boolean;
+    editButtonConfig?: { tooltip?: string; icon?: IconDefinition; label: string; disabled?: boolean };
 }>();
 
 // Refs and data
@@ -94,7 +96,7 @@ onMounted(() => {
         <div v-else class="d-flex flex-column">
             <div class="d-flex flex-column sticky-top bg-white">
                 <div class="d-flex">
-                    <Heading h1 separator inline size="md" class="flex-grow-1">
+                    <Heading v-if="!props.noHeading" h1 separator inline size="md" class="flex-grow-1">
                         <slot name="heading">
                             {{ pageTitle }}
                         </slot>
@@ -131,12 +133,13 @@ onMounted(() => {
                             tooltip
                             class="markdown-edit"
                             size="small"
-                            title="Edit Markdown"
+                            :title="editButtonConfig?.tooltip || 'Edit Markdown'"
+                            :disabled="editButtonConfig?.disabled"
                             outline
                             color="blue"
                             @click="$emit('onEdit')">
-                            Edit
-                            <FontAwesomeIcon :icon="faEdit" />
+                            {{ editButtonConfig?.label || "Edit" }}
+                            <FontAwesomeIcon :icon="editButtonConfig?.icon || faEdit" />
                         </GButton>
                     </div>
                 </div>
diff --git a/client/src/components/Page/constants.ts b/client/src/components/Page/constants.ts
index 2f592704869..24bc7c8e9a7 100644
--- a/client/src/components/Page/constants.ts
+++ b/client/src/components/Page/constants.ts
@@ -61,7 +61,7 @@ export const PAGE_LABELS: Record<
         newButton: "New Invocation Report",
         emptyStateTitle: "No invocation reports yet",
         emptyStateDescription:
-            "Create a report to document this workflow invocation with rich markdown, embedded datasets, and visualizations.",
+            "Create a report in the form of a Galaxy Notebook to document this workflow invocation with rich markdown, embedded datasets, and visualizations.",
         editButton: "Edit Invocation Report",
         viewButton: "View Invocation Report",
         createButton: "Create Invocation Report",
diff --git a/client/src/components/PageEditor/HistoryPageList.test.ts b/client/src/components/PageEditor/HistoryPageList.test.ts
index 2b48b46069c..bcf8177a1ea 100644
--- a/client/src/components/PageEditor/HistoryPageList.test.ts
+++ b/client/src/components/PageEditor/HistoryPageList.test.ts
@@ -78,6 +78,8 @@ describe("HistoryPageList", () => {
         });
 
         it("renders each page as a card", () => {
+            expect(wrapper.find(SELECTORS.PAGE_ITEMS).exists()).toBe(true);
+
             const items = wrapper.findAll(SELECTORS.PAGE_ITEM);
             expect(items.length).toBe(2);
         });
diff --git a/client/src/components/PageEditor/HistoryPageList.vue b/client/src/components/PageEditor/HistoryPageList.vue
index 7cb387f7e36..5be9cf7db49 100644
--- a/client/src/components/PageEditor/HistoryPageList.vue
+++ b/client/src/components/PageEditor/HistoryPageList.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faPlus } from "@fortawesome/free-solid-svg-icons";
+import { faArrowLeft, faPlus } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed, toRef } from "vue";
 
@@ -8,6 +8,7 @@ import { PAGE_LABELS } from "@/components/Page/constants";
 import { useHistoryBreadCrumbsTo } from "@/composables/historyBreadcrumbs";
 
 import BreadcrumbHeading from "../Common/BreadcrumbHeading.vue";
+import Heading from "../Common/Heading.vue";
 import PageCard from "./PageCard.vue";
 import GButton from "@/components/BaseComponents/GButton.vue";
 
@@ -15,13 +16,13 @@ const props = defineProps<{
     pages: HistoryPageSummary[];
     historyId: string;
     invocationId?: string;
-    noHeading?: boolean;
 }>();
 
 const emit = defineEmits<{
-    (e: "select", pageId: string): void;
+    (e: "edit", pageId: string): void;
     (e: "view", pageId: string): void;
     (e: "create"): void;
+    (e: "view-runtime-report"): void;
 }>();
 
 const labels = computed(() => (props.invocationId ? PAGE_LABELS.invocation : PAGE_LABELS.history));
@@ -30,8 +31,8 @@ const { breadcrumbItems } = useHistoryBreadCrumbsTo(toRef(props, "historyId"), l
 </script>
 
 <template>
-    <div class="d-flex flex-column overflow-hidden" data-description="history page list">
-        <BreadcrumbHeading v-if="!props.noHeading" :items="breadcrumbItems">
+    <div class="d-flex flex-column" data-description="history page list">
+        <BreadcrumbHeading v-if="!props.invocationId" :items="breadcrumbItems">
             <GButton
                 class="text-nowrap"
                 color="blue"
@@ -42,6 +43,15 @@ const { breadcrumbItems } = useHistoryBreadCrumbsTo(toRef(props, "historyId"), l
                 {{ labels.newButton }}
             </GButton>
         </BreadcrumbHeading>
+        <div v-else class="d-flex flex-gapx-1 pb-2">
+            <Heading h1 separator inline size="md" class="flex-grow-1 mb-0">
+                Edited {{ labels.entityNamePlural }}
+            </Heading>
+            <GButton size="small" outline color="blue" @click="emit('view-runtime-report')">
+                Back to Runtime Report
+                <FontAwesomeIcon :icon="faArrowLeft" />
+            </GButton>
+        </div>
 
         <div v-if="pages.length === 0" class="empty-state text-center p-4" data-description="page empty state">
             <p class="text-muted">{{ labels.emptyStateTitle }}</p>
@@ -50,7 +60,7 @@ const { breadcrumbItems } = useHistoryBreadCrumbsTo(toRef(props, "historyId"), l
             </p>
         </div>
 
-        <div v-else class="page-items mt-3">
+        <div v-else class="page-items mt-1">
             <PageCard
                 v-for="page in pages"
                 :key="page.id"
@@ -61,7 +71,7 @@ const { breadcrumbItems } = useHistoryBreadCrumbsTo(toRef(props, "historyId"), l
                 :edit-title="labels.editButton"
                 :show-invocation-badge="!props.invocationId"
                 :view-title="labels.viewButton"
-                @select="emit('select', page.id)"
+                @edit="emit('edit', page.id)"
                 @view="emit('view', page.id)" />
         </div>
     </div>
diff --git a/client/src/components/PageEditor/HistoryPageView.test.ts b/client/src/components/PageEditor/HistoryPageView.test.ts
index e272c4caad9..4bbc1c1f717 100644
--- a/client/src/components/PageEditor/HistoryPageView.test.ts
+++ b/client/src/components/PageEditor/HistoryPageView.test.ts
@@ -29,6 +29,13 @@ vi.mock("vue-router/composables", () => ({
     })),
 }));
 
+const mockPushToFrameOrPage = vi.fn();
+vi.mock("@/composables/windowAwareNavigation", () => ({
+    useWindowAwareNavigation: vi.fn(() => ({
+        pushToFrameOrPage: mockPushToFrameOrPage,
+    })),
+}));
+
 vi.mock("@/stores/historyStore", () => ({
     useHistoryStore: vi.fn(() => ({
         getHistoryById: vi.fn((id: string) => {
@@ -80,6 +87,7 @@ describe("HistoryPageView", () => {
     beforeEach(() => {
         pinia = createTestingPinia({ createSpy: vi.fn });
         vi.clearAllMocks();
+        mockPushToFrameOrPage.mockReset();
     });
 
     afterEach(() => {
@@ -214,6 +222,8 @@ describe("HistoryPageView", () => {
             } as any;
             store.currentContent = "# Hello";
             store.currentTitle = "My Page";
+            // hasCurrentPage is a computed (readonly) — stub it so the display toolbar renders
+            vi.spyOn(store, "hasCurrentPage", "get").mockReturnValue(true);
             return store;
         }
 
@@ -254,7 +264,9 @@ describe("HistoryPageView", () => {
             await flushPromises();
 
             const editBtn = wrapper.find(SELECTORS.EDIT_BUTTON);
-            await editBtn.trigger("click");
+            // GButton is stubbed by shallowMount; emit the Vue click event to trigger @click handler
+            await editBtn.vm.$emit("click");
+            await wrapper.vm.$nextTick();
 
             expect(mockPush).toHaveBeenCalledWith(`/histories/${HISTORY_ID}/pages/${PAGE_ID}`);
         });
@@ -280,13 +292,13 @@ describe("HistoryPageView", () => {
     });
 
     describe("Navigation/Events", () => {
-        it("handleSelect navigates to page URL via router.push", async () => {
+        it("edit emit from list navigates to page edit URL", async () => {
             setupListViewStore([{ id: "nb-1", history_id: HISTORY_ID, title: "NB1" }]);
             const wrapper = mountComponent({ historyId: HISTORY_ID });
             await flushPromises();
 
             const list = wrapper.findComponent(HistoryPageList);
-            list.vm.$emit("select", "nb-1");
+            list.vm.$emit("edit", "nb-1");
             await wrapper.vm.$nextTick();
 
             expect(mockPush).toHaveBeenCalledWith(`/histories/${HISTORY_ID}/pages/nb-1`);
@@ -307,11 +319,11 @@ describe("HistoryPageView", () => {
             list.vm.$emit("create");
             await flushPromises();
 
-            expect(store.createPage).toHaveBeenCalledWith({ title: "Untitled Notebook" });
+            expect(store.createPage).toHaveBeenCalledWith();
             expect(mockPush).toHaveBeenCalledWith(`/histories/${HISTORY_ID}/pages/new-page`);
         });
 
-        it("view emit from list navigates to displayOnly URL", async () => {
+        it("view emit from list navigates to displayOnly URL via pushToFrameOrPage", async () => {
             setupListViewStore([{ id: "nb-1", history_id: HISTORY_ID, title: "NB1" }]);
             const wrapper = mountComponent({ historyId: HISTORY_ID });
             await flushPromises();
@@ -320,7 +332,11 @@ describe("HistoryPageView", () => {
             list.vm.$emit("view", "nb-1");
             await wrapper.vm.$nextTick();
 
-            expect(mockPush).toHaveBeenCalledWith(`/histories/${HISTORY_ID}/pages/nb-1?displayOnly=true`);
+            expect(mockPushToFrameOrPage).toHaveBeenCalledWith(
+                expect.objectContaining({
+                    inlineUrl: `/histories/${HISTORY_ID}/pages/nb-1?displayOnly=true`,
+                }),
+            );
         });
     });
 
@@ -329,20 +345,22 @@ describe("HistoryPageView", () => {
             mockGalaxyInstance.frame.active = false;
         });
 
-        it("handleSelect opens in WinBox when WM is active", async () => {
+        it("view emit opens in WinBox when WM is active", async () => {
             mockGalaxyInstance.frame.active = true;
             setupListViewStore([{ id: "nb-1", history_id: HISTORY_ID, title: "NB1" }]);
             const wrapper = mountComponent({ historyId: HISTORY_ID });
             await flushPromises();
 
             const list = wrapper.findComponent(HistoryPageList);
-            list.vm.$emit("select", "nb-1");
+            list.vm.$emit("view", "nb-1");
             await wrapper.vm.$nextTick();
 
-            expect(mockPush).toHaveBeenCalledWith(`/histories/${HISTORY_ID}/pages/nb-1?displayOnly=true`, {
-                title: "Galaxy Notebook: NB1",
-                preventWindowManager: false,
-            });
+            expect(mockPushToFrameOrPage).toHaveBeenCalledWith(
+                expect.objectContaining({
+                    inlineUrl: `/histories/${HISTORY_ID}/pages/nb-1?displayOnly=true`,
+                    title: "Galaxy Notebook: NB1",
+                }),
+            );
         });
     });
 
@@ -352,7 +370,7 @@ describe("HistoryPageView", () => {
             mountComponent({ historyId: HISTORY_ID });
             await flushPromises();
 
-            expect(store.loadPages).toHaveBeenCalledWith(HISTORY_ID);
+            expect(store.loadPages).toHaveBeenCalledWith(HISTORY_ID, undefined);
         });
 
         it("does not call store.loadPageById on mount when no pageId", async () => {
diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index b34532fd2e0..9d064530860 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -1,16 +1,19 @@
 <script setup lang="ts">
 import { faArrowLeft, faEdit, faSpinner } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton } from "bootstrap-vue";
+import { BAlert } from "bootstrap-vue";
 import { computed, onMounted, onUnmounted, watch } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { PAGE_LABELS } from "@/components/Page/constants";
+import { useToast } from "@/composables/toast";
 import { useWindowAwareNavigation } from "@/composables/windowAwareNavigation";
 import { usePageEditorStore } from "@/stores/pageEditorStore";
+import { errorMessageAsString } from "@/utils/simple-error.js";
 
 import HistoryPageList from "./HistoryPageList.vue";
 import PageEditorView from "./PageEditorView.vue";
+import GButton from "@/components/BaseComponents/GButton.vue";
 import Markdown from "@/components/Markdown/Markdown.vue";
 
 const props = defineProps<{
@@ -18,14 +21,9 @@ const props = defineProps<{
     invocationId?: string;
     pageId?: string;
     displayOnly?: boolean;
-    emitsActions?: boolean;
 }>();
 
-const emit = defineEmits<{
-    (e: "edit-page", pageId: string): void;
-    (e: "go-back"): void;
-    (e: "view-page", pageId: string): void;
-}>();
+const Toast = useToast();
 
 const router = useRouter();
 const { pushToFrameOrPage } = useWindowAwareNavigation();
@@ -80,54 +78,44 @@ watch(
     },
 );
 
-function handleSelect(pageId: string) {
-    const page = store.pages.find((n) => n.id === pageId);
-    const pageTitle = page?.title || labels.value.entityName;
-    if (props.emitsActions) {
-        emit("edit-page", pageId);
+function handleView(viewingPageId: string) {
+    if (props.invocationId) {
+        router.push(`/workflows/invocations/${props.invocationId}/reports?id=${viewingPageId}`);
         return;
     }
-    const inlineUrl = `/histories/${props.historyId}/pages/${pageId}`;
+    const page = store.pages.find((n) => n.id === viewingPageId);
+    const pageTitle = page?.title || labels.value.entityName;
+    const inlineUrl = `/histories/${props.historyId}/pages/${viewingPageId}?displayOnly=true`;
     pushToFrameOrPage({
-        framedUrl: `${inlineUrl}?displayOnly=true`,
+        framedUrl: inlineUrl,
         inlineUrl,
         title: `${labels.value.entityName}: ${pageTitle}`,
     });
 }
 
 async function handleCreate() {
-    const page = await store.createPage({ title: labels.value.defaultTitle });
-    if (page) {
-        if (props.emitsActions) {
-            emit("edit-page", page.id);
-            return;
-        }
-        router.push(`/histories/${props.historyId}/pages/${page.id}`);
+    try {
+        const page = await store.createPage();
+        handleEdit(page?.id);
+    } catch (error) {
+        Toast.error(errorMessageAsString(error), `Failed to create ${labels.value.entityName.toLowerCase()}`);
     }
 }
 
-function handleView(pageId: string) {
-    if (props.emitsActions) {
-        emit("view-page", pageId);
-        return;
-    }
-    router.push(`/histories/${props.historyId}/pages/${pageId}?displayOnly=true`);
-}
-
-function handleEdit() {
-    if (props.pageId) {
-        if (props.emitsActions) {
-            emit("edit-page", props.pageId);
-            return;
+function handleEdit(editingPageId?: string) {
+    if (editingPageId) {
+        let editUrl = `/histories/${props.historyId}/pages/${editingPageId}`;
+        if (props.invocationId) {
+            editUrl += `?invocation_id=${props.invocationId}`;
         }
-        router.push(`/histories/${props.historyId}/pages/${props.pageId}`);
+        router.push(editUrl);
     }
 }
 
 function handleBack() {
     store.clearCurrentPage();
-    if (props.emitsActions) {
-        emit("go-back");
+    if (props.invocationId) {
+        router.push(`/workflows/invocations/${props.invocationId}/reports`);
         return;
     }
     router.push(`/histories/${props.historyId}/pages`);
@@ -160,7 +148,8 @@ function handleBack() {
                 :history-id="props.historyId"
                 :invocation-id="props.invocationId"
                 :pages="store.pages"
-                @select="handleSelect"
+                @view-runtime-report="router.push(`/workflows/invocations/${props.invocationId}/report`)"
+                @edit="handleEdit"
                 @view="handleView"
                 @create="handleCreate" />
         </template>
@@ -170,23 +159,34 @@ function handleBack() {
             <div
                 class="page-display-toolbar d-flex align-items-center p-2 border-bottom"
                 data-description="page display toolbar">
-                <BButton variant="link" size="sm" data-description="page manage button" @click="handleBack">
+                <GButton
+                    color="blue"
+                    transparent
+                    size="small"
+                    data-description="page manage button"
+                    @click="handleBack">
                     <FontAwesomeIcon :icon="faArrowLeft" />
                     {{ labels.editorBackLabel }}
-                </BButton>
+                </GButton>
                 <span class="flex-grow-1 text-center font-weight-bold">
                     {{ store.currentTitle || labels.defaultTitle }}
                 </span>
-                <BButton variant="outline-primary" size="sm" data-description="page edit button" @click="handleEdit">
+                <GButton
+                    color="blue"
+                    outline
+                    size="small"
+                    data-description="page edit button"
+                    @click="handleEdit(props.pageId)">
                     <FontAwesomeIcon :icon="faEdit" />
                     Edit
-                </BButton>
+                </GButton>
             </div>
             <div class="page-display-content overflow-auto flex-grow-1" data-description="page rendered view">
                 <Markdown
                     v-if="markdownConfig"
                     :markdown-config="markdownConfig"
                     :read-only="true"
+                    no-heading
                     download-endpoint=""
                     hide-heading />
             </div>
@@ -194,14 +194,7 @@ function handleBack() {
 
         <!-- Edit mode: delegate to unified PageEditorView -->
         <template v-else-if="pageId && !displayOnly">
-            <PageEditorView
-                :emits-actions="props.emitsActions"
-                :page-id="pageId"
-                :history-id="historyId"
-                :invocation-id="invocationId"
-                @edit-page="handleEdit"
-                @go-back="handleBack"
-                @view-page="handleView" />
+            <PageEditorView :page-id="pageId" :history-id="historyId" :invocation-id="invocationId" />
         </template>
 
         <BAlert v-else-if="store.isLoadingPage" variant="info" show>
diff --git a/client/src/components/PageEditor/PageCard.test.ts b/client/src/components/PageEditor/PageCard.test.ts
index 0fa58121405..3822c212397 100644
--- a/client/src/components/PageEditor/PageCard.test.ts
+++ b/client/src/components/PageEditor/PageCard.test.ts
@@ -36,9 +36,9 @@ describe("PageCard", () => {
         expect(title.text()).toBe("My Analysis");
         expect(title.attributes("title")).toBe("Edit Notebook");
 
-        // Click to emit select event
+        // Click to emit edit event
         await title.trigger("click");
-        expect(wrapper.emitted().select).toBeTruthy();
+        expect(wrapper.emitted().edit).toBeTruthy();
     });
 
     it("shows 'Untitled Notebook' when title is empty", () => {
@@ -81,6 +81,6 @@ describe("PageCard", () => {
 
         const editButton = wrapper.find(getSelector("edit", FAKE_PAGE_SUMMARY.id));
         await editButton.trigger("click");
-        expect(wrapper.emitted().select).toBeTruthy();
+        expect(wrapper.emitted().edit).toBeTruthy();
     });
 });
diff --git a/client/src/components/PageEditor/PageCard.vue b/client/src/components/PageEditor/PageCard.vue
index 362109e5bde..3204f94848e 100644
--- a/client/src/components/PageEditor/PageCard.vue
+++ b/client/src/components/PageEditor/PageCard.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faEdit, faExternalLinkAlt, faEye, faHistory } from "@fortawesome/free-solid-svg-icons";
+import { faEdit, faEye, faHistory, faSitemap } from "@fortawesome/free-solid-svg-icons";
 import { computed } from "vue";
 
 import type { HistoryPageSummary } from "@/api/pages";
@@ -24,14 +24,14 @@ const props = withDefaults(defineProps<Props>(), {
 });
 
 const emit = defineEmits<{
-    (e: "select"): void;
+    (e: "edit"): void;
     (e: "view"): void;
 }>();
 
 const title: Title = {
     label: props.page.title || props.defaultTitle,
     title: props.editTitle,
-    handler: () => emit("select"),
+    handler: () => emit("edit"),
 };
 
 const badges = computed<CardBadge[]>(() => {
@@ -48,12 +48,10 @@ const badges = computed<CardBadge[]>(() => {
         retBadges.push({
             id: "is-invocation-notebook",
             label: `Invocation ${props.page.source_invocation_id}`,
-            icon: faExternalLinkAlt,
-            title: "This notebook is a report created from a workflow invocation (Click to view the original report)",
+            icon: faSitemap,
+            title: "This notebook is a report created from a workflow invocation (Click to view the original report under the invocation)",
             class: "unselectable",
-            handler: () => {
-                window.open(`/workflows/invocations/${props.page.source_invocation_id}/report`, "_blank");
-            },
+            to: `/workflows/invocations/${props.page.source_invocation_id}/reports?id=${props.page.id}`,
             variant: "primary",
         });
     }
@@ -66,7 +64,7 @@ const primaryActions: CardAction[] = [
         label: "Edit",
         icon: faEdit,
         title: props.editTitle,
-        handler: () => emit("select"),
+        handler: () => emit("edit"),
     },
 ];
 
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index a8a40856135..99baf147f3d 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -24,13 +24,6 @@ const props = defineProps<{
     historyId?: string;
     invocationId?: string;
     displayOnly?: boolean;
-    emitsActions?: boolean;
-}>();
-
-const emit = defineEmits<{
-    (e: "edit-page"): void;
-    (e: "go-back"): void;
-    (e: "view-page", id: string): void;
 }>();
 
 const router = useRouter();
@@ -99,11 +92,9 @@ watch(
 
 function handleBack() {
     store.clearCurrentPage();
-    if (props.emitsActions) {
-        emit("go-back");
-        return;
-    }
-    if (props.historyId) {
+    if (props.invocationId) {
+        router.push(`/workflows/invocations/${props.invocationId}/reports`);
+    } else if (props.historyId) {
         router.push(`/histories/${props.historyId}/pages`);
     } else {
         router.push("/pages/list");
@@ -111,11 +102,9 @@ function handleBack() {
 }
 
 function handlePreview() {
-    if (props.emitsActions) {
-        emit("view-page", props.pageId);
-        return;
-    }
-    if (props.historyId) {
+    if (props.invocationId) {
+        router.push(`/workflows/invocations/${props.invocationId}/reports?id=${props.pageId}`);
+    } else if (props.historyId) {
         router.push(`/histories/${props.historyId}/pages/${props.pageId}?displayOnly=true`);
     } else {
         // Standalone: open in window manager when active, else navigate inline.
@@ -129,10 +118,6 @@ function handlePreview() {
 }
 
 function handleEdit() {
-    if (props.emitsActions) {
-        emit("edit-page");
-        return;
-    }
     if (props.historyId) {
         router.push(`/histories/${props.historyId}/pages/${props.pageId}`);
     } else {
@@ -146,8 +131,8 @@ async function handleSave() {
 
 async function handleSaveAndView() {
     await store.savePage();
-    if (props.emitsActions) {
-        emit("view-page", props.pageId);
+    if (props.invocationId) {
+        router.push(`/workflows/invocations/${props.invocationId}/reports?id=${props.pageId}`);
         return;
     }
     if (store.currentPage) {
diff --git a/client/src/components/Workflow/InvocationReport.vue b/client/src/components/Workflow/InvocationReport.vue
index 577d00df0f8..a5b86a499b4 100644
--- a/client/src/components/Workflow/InvocationReport.vue
+++ b/client/src/components/Workflow/InvocationReport.vue
@@ -1,12 +1,15 @@
 <script setup lang="ts">
 import { faFileContract } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { storeToRefs } from "pinia";
 import { computed, provide, ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { fetchInvocationReport } from "@/api/invocations";
 import { useConfig } from "@/composables/config";
 import { useToast } from "@/composables/toast";
+import { usePageEditorStore } from "@/stores/pageEditorStore.js";
+import { errorMessageAsString } from "@/utils/simple-error.js";
 
 import GButton from "../BaseComponents/GButton.vue";
 import HelpText from "../Help/HelpText.vue";
@@ -16,10 +19,7 @@ const props = defineProps<{
     invocationId: string;
     /** Whether to enforce displaying a "Runtime Report" heading with help text */
     fromRuntimeReport?: boolean;
-}>();
-
-const emit = defineEmits<{
-    (e: "view-existing-reports"): void;
+    historyId?: string;
 }>();
 
 const { config, isConfigLoaded } = useConfig(true);
@@ -28,10 +28,19 @@ const Toast = useToast();
 
 const router = useRouter();
 
+const pageEditorStore = usePageEditorStore();
+const { isLoadingPage } = storeToRefs(pageEditorStore);
+
 const markdownConfig = ref({});
 
 const exportUrl = computed(() => `/api/invocations/${props.invocationId}/report.pdf`);
 
+const editButtonConfig = computed(() => ({
+    tooltip: "Click to create a Galaxy Notebook from this invocation's Runtime Report",
+    label: "Edit",
+    disabled: isLoadingPage.value,
+}));
+
 fetchReport();
 
 async function fetchReport() {
@@ -43,8 +52,25 @@ async function fetchReport() {
     }
 }
 
-function onEdit() {
-    router.push(`/pages/create?invocation_id=${props.invocationId}`);
+async function onEdit() {
+    if (props.historyId) {
+        try {
+            pageEditorStore.setCurrentContext(props.historyId, props.invocationId);
+            const page = await pageEditorStore.createPage();
+            if (page) {
+                const editUrl =
+                    `/histories/${props.historyId}/pages/${page.id}` +
+                    (props.invocationId ? `?invocation_id=${props.invocationId}` : "");
+                router.push(editUrl);
+            } else {
+                pageEditorStore.clearCurrentPage();
+            }
+        } catch (error) {
+            Toast.error(errorMessageAsString(error), "Failed to create a Galaxy Notebook");
+        }
+    } else {
+        router.push(`/pages/create?invocation_id=${props.invocationId}`);
+    }
 }
 
 // Provide invocationId to all descendant components for inline directive resolution
@@ -55,6 +81,7 @@ provide("invocationId", props.invocationId);
     <Markdown
         v-if="isConfigLoaded"
         :markdown-config="markdownConfig"
+        :edit-button-config="editButtonConfig"
         :enable_beta_markdown_export="config.enable_beta_markdown_export"
         :export-link="exportUrl"
         :download-endpoint="exportUrl"
@@ -65,13 +92,14 @@ provide("invocationId", props.invocationId);
             <HelpText uri="galaxy.invocations.reports.runtimeReport" info-icon />
         </template>
 
-        <template v-if="props.fromRuntimeReport" v-slot:extra-actions>
+        <template v-slot:extra-actions>
             <GButton
+                size="small"
                 tooltip
-                title="Click to view existing/edited report for this workflow invocation"
+                title="Click to view existing/edited reports for this workflow invocation"
                 outline
                 color="blue"
-                @click="emit('view-existing-reports')">
+                @click="router.push(`/workflows/invocations/${props.invocationId}/reports`)">
                 View Existing Reports
                 <FontAwesomeIcon :icon="faFileContract" />
             </GButton>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue
deleted file mode 100644
index 94ca686a931..00000000000
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationReports.vue
+++ /dev/null
@@ -1,61 +0,0 @@
-<script setup lang="ts">
-import { ref } from "vue";
-
-import HistoryPageView from "../PageEditor/HistoryPageView.vue";
-import InvocationReport from "../Workflow/InvocationReport.vue";
-
-const props = defineProps<{
-    invocationId: string;
-    historyId: string;
-}>();
-
-/** Tracks what is currently being viewed in the reports section:
- * - `fromTemplate` shows the original report generated from the template
- * - `editedReports` shows a list of edited reports if any exist
- * - `editedReport` shows a specific edited report when selected from the list
- */
-const currentView = ref<"fromTemplate" | "editedReports" | "editedReport">("fromTemplate");
-
-const currentEditedReportId = ref<string | null>(null);
-const displayOnly = ref(false);
-
-function editOrViewPage(pageId: string, displayOnlyValue: boolean) {
-    currentView.value = "editedReport";
-    currentEditedReportId.value = pageId;
-    displayOnly.value = displayOnlyValue;
-}
-
-function goBackFromEditedReport() {
-    currentView.value = "editedReports";
-    currentEditedReportId.value = null;
-    displayOnly.value = false;
-}
-</script>
-
-<template>
-    <InvocationReport
-        v-if="currentView === 'fromTemplate'"
-        :invocation-id="props.invocationId"
-        from-runtime-report
-        @view-existing-reports="currentView = 'editedReports'" />
-    <div v-else-if="currentView === 'editedReports'">
-        <HistoryPageView
-            :history-id="props.historyId"
-            :invocation-id="props.invocationId"
-            emits-actions
-            @edit-page="(pageId) => editOrViewPage(pageId, false)"
-            @go-back="currentView = 'fromTemplate'"
-            @view-page="(pageId) => editOrViewPage(pageId, true)" />
-    </div>
-    <div v-else-if="currentView === 'editedReport'">
-        <HistoryPageView
-            :history-id="props.historyId"
-            :invocation-id="props.invocationId"
-            :page-id="currentEditedReportId || undefined"
-            :display-only="displayOnly"
-            emits-actions
-            @edit-page="(pageId) => editOrViewPage(pageId, false)"
-            @go-back="goBackFromEditedReport"
-            @view-page="(pageId) => editOrViewPage(pageId, true)" />
-    </div>
-</template>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.ts b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.ts
index 7102d56ea70..676311342b4 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.ts
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.ts
@@ -12,6 +12,10 @@ import WorkflowInvocationState from "./WorkflowInvocationState.vue";
 const localVue = getLocalVue();
 localVue.use(PiniaVuePlugin);
 
+vi.mock("vue-router/composables", () => ({
+    useRoute: vi.fn(() => ({})),
+}));
+
 const selectors = {
     invocationSummary: ".invocation-overview",
     bAlertStub: "balert-stub",
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
index 5dd3ce8b022..0db6294c3b9 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
@@ -9,6 +9,7 @@ import {
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert, BBadge, BNav, BNavItem } from "bootstrap-vue";
 import { computed, onUnmounted, ref, watch } from "vue";
+import { useRoute } from "vue-router/composables";
 
 import { type InvocationStep, isWorkflowInvocationElementView } from "@/api/invocations";
 import { usePersistentToggle } from "@/composables/persistentToggle";
@@ -26,8 +27,10 @@ import {
 } from "./util";
 
 import GButton from "../BaseComponents/GButton.vue";
+import HistoryPageView from "../PageEditor/HistoryPageView.vue";
 import ProgressBar from "../ProgressBar.vue";
 import WorkflowInvocationSteps from "../Workflow/Invocation/Graph/WorkflowInvocationSteps.vue";
+import InvocationReport from "../Workflow/InvocationReport.vue";
 import WorkflowAnnotation from "../Workflow/WorkflowAnnotation.vue";
 import WorkflowNavigationTitle from "../Workflow/WorkflowNavigationTitle.vue";
 import TabsDisabledAlert from "./TabsDisabledAlert.vue";
@@ -36,12 +39,11 @@ import WorkflowInvocationFeedback from "./WorkflowInvocationFeedback.vue";
 import WorkflowInvocationInputOutputTabs from "./WorkflowInvocationInputOutputTabs.vue";
 import WorkflowInvocationMetrics from "./WorkflowInvocationMetrics.vue";
 import WorkflowInvocationOverview from "./WorkflowInvocationOverview.vue";
-import WorkflowInvocationReports from "./WorkflowInvocationReports.vue";
 import WorkflowInvocationSearch from "./WorkflowInvocationSearch.vue";
 import WorkflowInvocationShare from "./WorkflowInvocationShare.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
-type InvocationViewTab = "steps" | "inputs" | "outputs" | "report" | "export" | "metrics" | "debug";
+type InvocationViewTab = "steps" | "inputs" | "outputs" | "report" | "reports" | "export" | "metrics" | "debug";
 
 interface Props {
     invocationId: string;
@@ -60,6 +62,8 @@ const emit = defineEmits<{
     (e: "invocation-cancelled"): void;
 }>();
 
+const route = useRoute();
+
 const invocationStore = useInvocationStore();
 
 const stepStatesInterval = ref<any>(undefined);
@@ -71,6 +75,11 @@ const isPolling = ref(false);
 
 const { toggled: headerCollapsed, toggle: toggleHeaderCollapse } = usePersistentToggle("invocation-header-collapsed");
 
+/** Returns the ID of the currently viewed Galaxy notebook report, if any */
+const currentViewedReportId = computed<string | undefined>(() =>
+    props.tab === "reports" && typeof route.query.id === "string" ? route.query.id : undefined,
+);
+
 const uniqueMessages = computed(() => {
     const messages = invocation.value?.messages || [];
     const uniqueMessagesSet = new Set(messages.map((message) => JSON.stringify(message)));
@@ -99,7 +108,10 @@ const disabledTabTooltip = computed(() => {
 
 /** We are on the default "Overview" tab if the tab prop is not set or is not one of the expected tab values */
 const onOverviewTab = computed(() => {
-    return !props.tab || !["steps", "inputs", "outputs", "report", "export", "metrics", "debug"].includes(props.tab);
+    return (
+        !props.tab ||
+        !["steps", "inputs", "outputs", "report", "reports", "export", "metrics", "debug"].includes(props.tab)
+    );
 });
 
 const invocation = computed(() => {
@@ -413,7 +425,7 @@ async function onCancel() {
             <BNavItem
                 :title="!tabsDisabled ? 'Report' : disabledTabTooltip"
                 class="invocation-report-tab"
-                :active="!tabsDisabled && props.tab === 'report'"
+                :active="!tabsDisabled && (props.tab === 'report' || props.tab === 'reports')"
                 :to="`/workflows/invocations/${props.invocationId}/report`"
                 :disabled="tabsDisabled">
                 Report
@@ -481,7 +493,7 @@ async function onCancel() {
                 :invocation="invocation"
                 :terminal="invocationAndJobTerminal"
                 :tab="props.tab" />
-            <div v-if="props.tab === 'report'">
+            <div v-if="props.tab === 'report' || props.tab === 'reports'" class="steps-tab-content">
                 <BAlert v-if="isSubworkflow" variant="info" show>
                     <span v-localize>Report is not available for subworkflow.</span>
                 </BAlert>
@@ -489,7 +501,17 @@ async function onCancel() {
                     v-else-if="tabsDisabled"
                     :invocation-id="props.invocationId"
                     :tooltip="disabledTabTooltip" />
-                <WorkflowInvocationReports v-else :invocation-id="invocation.id" :history-id="invocation.history_id" />
+                <InvocationReport
+                    v-else-if="props.tab === 'report'"
+                    :invocation-id="invocation.id"
+                    :history-id="invocation.history_id"
+                    from-runtime-report />
+                <HistoryPageView
+                    v-else
+                    :invocation-id="props.invocationId"
+                    :history-id="invocation.history_id"
+                    :page-id="currentViewedReportId"
+                    display-only />
             </div>
             <div v-if="props.tab === 'export'">
                 <TabsDisabledAlert
diff --git a/client/src/stores/pageEditorStore.test.ts b/client/src/stores/pageEditorStore.test.ts
index b84d4d2826d..d48d6051448 100644
--- a/client/src/stores/pageEditorStore.test.ts
+++ b/client/src/stores/pageEditorStore.test.ts
@@ -104,7 +104,7 @@ describe("usePageEditorStore", () => {
         it("isDirty is false when content reverted to original", async () => {
             useDefaultHandlers();
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             await store.loadPageById(TEST_PAGE_ID);
             const originalContent = store.currentContent;
 
@@ -203,7 +203,7 @@ describe("usePageEditorStore", () => {
         it("populates currentPage and content on success", async () => {
             useDefaultHandlers();
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
 
             await store.loadPageById(TEST_PAGE_ID);
 
@@ -215,7 +215,7 @@ describe("usePageEditorStore", () => {
         it("sets originalContent to match currentContent", async () => {
             useDefaultHandlers();
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
 
             await store.loadPageById(TEST_PAGE_ID);
 
@@ -225,7 +225,7 @@ describe("usePageEditorStore", () => {
         it("sets isLoadingPage during load", async () => {
             useDefaultHandlers();
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
 
             const promise = store.loadPageById(TEST_PAGE_ID);
             expect(store.isLoadingPage).toBe(true);
@@ -241,7 +241,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
 
             await store.loadPageById(TEST_PAGE_ID);
 
@@ -262,7 +262,7 @@ describe("usePageEditorStore", () => {
         it("creates page, sets as current, refreshes list", async () => {
             useDefaultHandlers();
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
 
             const result = await store.createPage({ title: "New Page" });
 
@@ -277,7 +277,7 @@ describe("usePageEditorStore", () => {
         it("sets isLoadingPage during creation", async () => {
             useDefaultHandlers();
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
 
             const promise = store.createPage();
             expect(store.isLoadingPage).toBe(true);
@@ -293,7 +293,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
 
             await expect(store.createPage()).rejects.toThrow();
             expect(store.error).toBeTruthy();
@@ -310,7 +310,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             store.currentPage = TEST_PAGE_DETAILS;
 
             await store.savePage();
@@ -322,7 +322,7 @@ describe("usePageEditorStore", () => {
 
         it("does nothing if no currentPage", async () => {
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             store.updateContent("dirty");
 
             await store.savePage();
@@ -368,7 +368,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             await store.loadPageById(TEST_PAGE_ID);
             expect(store.isDirty).toBe(false);
 
@@ -391,7 +391,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             await store.loadPageById(TEST_PAGE_ID);
             store.updateContent("new content");
 
@@ -412,7 +412,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             await store.loadPageById(TEST_PAGE_ID);
             store.updateContent("new content");
 
@@ -437,7 +437,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             await store.loadPageById(TEST_PAGE_ID);
             store.updateContent("");
             expect(store.isDirty).toBe(true);
@@ -453,7 +453,7 @@ describe("usePageEditorStore", () => {
     describe("deleteCurrentPage", () => {
         it("does nothing if no currentPage", async () => {
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
 
             await store.deleteCurrentPage();
 
@@ -482,7 +482,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             await store.loadPageById(TEST_PAGE_ID);
             expect(store.currentPage).not.toBeNull();
 
@@ -508,7 +508,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             store.currentPage = TEST_PAGE_DETAILS;
 
             await expect(store.deleteCurrentPage()).rejects.toThrow();
@@ -592,7 +592,7 @@ describe("usePageEditorStore", () => {
         it("loadPageById updates stored current ID", async () => {
             useDefaultHandlers();
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
 
             await store.loadPageById(TEST_PAGE_ID);
 
@@ -612,7 +612,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             await store.loadPageById(TEST_PAGE_ID);
             expect(store.getCurrentPageId(TEST_HISTORY_ID)).toBe(TEST_PAGE_ID);
 
@@ -662,7 +662,7 @@ describe("usePageEditorStore", () => {
                 }) as any,
             );
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             await store.loadPageById(TEST_PAGE_ID);
             expect(store.currentContent).toBe("original content");
 
@@ -678,7 +678,7 @@ describe("usePageEditorStore", () => {
         it("clearCurrentPage resets current page state", async () => {
             useDefaultHandlers();
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             await store.loadPageById(TEST_PAGE_ID);
             store.updateContent("modified");
             expect(store.currentPage).not.toBeNull();
@@ -694,7 +694,7 @@ describe("usePageEditorStore", () => {
 
         it("clearCurrentPage does not affect pages list or historyId", () => {
             const store = usePageEditorStore();
-            store.$patch({ historyId: TEST_HISTORY_ID });
+            store.setCurrentContext(TEST_HISTORY_ID);
             store.pages = [TEST_PAGE_SUMMARY];
             store.currentPage = TEST_PAGE_DETAILS;
 
diff --git a/client/src/stores/pageEditorStore.ts b/client/src/stores/pageEditorStore.ts
index 894d318e2b0..99f73251ae8 100644
--- a/client/src/stores/pageEditorStore.ts
+++ b/client/src/stores/pageEditorStore.ts
@@ -1,6 +1,7 @@
 import { defineStore } from "pinia";
 import { computed, ref } from "vue";
 
+import { fetchInvocationReport } from "@/api/invocations";
 import {
     createHistoryPage,
     type CreateHistoryPagePayload,
@@ -17,7 +18,7 @@ import {
     updateHistoryPage,
     type UpdateHistoryPagePayload,
 } from "@/api/pages";
-import { ERROR_MESSAGES } from "@/components/Page/constants";
+import { ERROR_MESSAGES, PAGE_LABELS } from "@/components/Page/constants";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import { errorMessageAsString } from "@/utils/simple-error";
 
@@ -72,8 +73,12 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
             selectedRevision.value.id === revisions.value[revisions.value.length - 1]?.id,
     );
 
+    function setCurrentContext(historyId: string | null, invocationId?: string) {
+        currentContext.value = { historyId, invocationId };
+    }
+
     async function loadPages(newHistoryId: string, invocationId?: string) {
-        currentContext.value = { historyId: newHistoryId, invocationId };
+        setCurrentContext(newHistoryId, invocationId);
         isLoadingList.value = true;
         error.value = null;
         try {
@@ -122,11 +127,23 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
         isLoadingPage.value = true;
         error.value = null;
         try {
+            // if content is not provided, and we're in invocation context, attempt to prefill with invocation report content
+            let newContent: string = payload?.content || "";
+            const labels = currentContext.value.invocationId ? PAGE_LABELS.invocation : PAGE_LABELS.standalone;
+            let newTitle: string = payload?.title || labels.defaultTitle;
+            if (!newContent && currentContext.value.invocationId) {
+                const data = await fetchInvocationReport(currentContext.value.invocationId);
+                newContent = data.invocation_markdown || "";
+                newTitle = data.title ? `${data.title} ${labels.entityName}` : newTitle;
+            }
+
+            // now create the page with the determined title and content
             const data = await createHistoryPage({
-                title: payload?.title || "",
+                title: newTitle,
                 history_id: historyId.value,
-                content: payload?.content ?? null,
+                content: newContent,
                 content_format: "markdown",
+                ...(currentContext.value.invocationId && { invocation_id: currentContext.value.invocationId }),
             });
             currentPage.value = data;
             const editorContent = data.content_editor ?? data.content ?? "";
@@ -405,6 +422,7 @@ export const usePageEditorStore = defineStore("pageEditor", () => {
         isSaving,
         error,
         chatError,
+        setCurrentContext,
         historyId,
         hasPages,
         hasCurrentPage,

From aa5a8a9baef4b6c97133b9c9757a84c8feee4460 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Thu, 11 Jun 2026 23:33:28 -0500
Subject: [PATCH 167/256] watch both the history and invocation ID props in
 `HistoryPageView`

---
 client/src/components/PageEditor/HistoryPageView.vue | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index 9d064530860..6660f61d67b 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -58,11 +58,13 @@ onUnmounted(() => {
 });
 
 watch(
-    () => props.historyId,
-    async (newId) => {
-        await store.loadPages(newId, props.invocationId);
-        if (props.pageId && props.displayOnly) {
-            await store.loadPageById(props.pageId);
+    () => [props.historyId, props.invocationId],
+    async ([newHistoryId, newInvocationId]) => {
+        if (newHistoryId) {
+            await store.loadPages(newHistoryId, newInvocationId);
+            if (props.pageId && props.displayOnly) {
+                await store.loadPageById(props.pageId);
+            }
         }
     },
 );

From 8e71be33b10efcbe03ad5845f81f99b55f8b1797 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Thu, 11 Jun 2026 23:50:37 -0500
Subject: [PATCH 168/256] turn markdown toolbox heading into a collapse button
 for easy collapsing

---
 .../components/Markdown/Editor/TextEditor.vue  | 11 +++++++++--
 .../components/Markdown/MarkdownToolBox.vue    | 18 +++++++++++++++++-
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Markdown/Editor/TextEditor.vue b/client/src/components/Markdown/Editor/TextEditor.vue
index 9aad09cec48..b5b546f5fed 100644
--- a/client/src/components/Markdown/Editor/TextEditor.vue
+++ b/client/src/components/Markdown/Editor/TextEditor.vue
@@ -1,7 +1,7 @@
 <template>
     <div class="d-flex h-100 w-100">
-        <FlexPanel v-if="!hideToolbox" side="left">
-            <MarkdownToolBox :steps="steps" @insert="insertMarkdown" />
+        <FlexPanel v-if="!hideToolbox" ref="markdownFlexPanel" side="left">
+            <MarkdownToolBox :steps="steps" @close-panel="onClosePanel" @insert="insertMarkdown" />
         </FlexPanel>
         <textarea
             id="workflow-report-editor"
@@ -43,6 +43,7 @@ const emit = defineEmits<{
 
 const content = ref<string>(props.markdownText);
 const textArea = ref<HTMLTextAreaElement | null>(null);
+const markdownFlexPanel = ref<InstanceType<typeof FlexPanel> | null>(null);
 
 const FENCE = "```";
 
@@ -60,6 +61,12 @@ watch(
     },
 );
 
+function onClosePanel() {
+    if (markdownFlexPanel.value) {
+        markdownFlexPanel.value.show = false;
+    }
+}
+
 function insertMarkdown(markdown: string) {
     markdown = markdown.replace(")(", ", ");
     markdown = `${FENCE}galaxy\n${markdown}\n${FENCE}\n`;
diff --git a/client/src/components/Markdown/MarkdownToolBox.vue b/client/src/components/Markdown/MarkdownToolBox.vue
index bdfdddcc74a..794328c5f8e 100644
--- a/client/src/components/Markdown/MarkdownToolBox.vue
+++ b/client/src/components/Markdown/MarkdownToolBox.vue
@@ -1,5 +1,11 @@
 <template>
-    <ActivityPanel title="Insert Markdown Objects">
+    <ActivityPanel>
+        <template v-slot:activity-panel-header-top>
+            <GButton size="small" transparent @click="onClosePanel">
+                <FontAwesomeIcon fixed-width :icon="faChevronLeft" />
+                <h2 v-localize class="activity-panel-heading h-sm mb-0">Insert Markdown Objects</h2>
+            </GButton>
+        </template>
         <div class="toolMenuContainer">
             <b-alert v-if="error" variant="danger" class="my-2 mx-3 px-2 py-1" show>
                 {{ error }}
@@ -30,6 +36,8 @@
 </template>
 
 <script>
+import { faChevronLeft } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import axios from "axios";
 import BootstrapVue from "bootstrap-vue";
 import Vue from "vue";
@@ -39,6 +47,7 @@ import { getAppRoot } from "@/onload/loadConfig";
 
 import { directiveEntry } from "./directives.ts";
 
+import GButton from "../BaseComponents/GButton.vue";
 import MarkdownDialog from "./MarkdownDialog.vue";
 import ActivityPanel from "@/components/Panels/ActivityPanel.vue";
 import ToolSection from "@/components/Panels/Common/ToolSection.vue";
@@ -85,6 +94,8 @@ function historySharedElements(mode) {
 
 export default {
     components: {
+        GButton,
+        FontAwesomeIcon,
         MarkdownDialog,
         ToolSection,
         ActivityPanel,
@@ -97,6 +108,7 @@ export default {
     },
     data() {
         return {
+            faChevronLeft,
             selectedArgumentName: null,
             selectedType: null,
             selectedShow: false,
@@ -324,6 +336,10 @@ export default {
         onNoParameter(argumentName) {
             this.onInsert(`${argumentName}()`);
         },
+        onClosePanel() {
+            this.selectedShow = false;
+            this.$emit("close-panel");
+        },
         onVisualizationId(argumentName) {
             this.selectedArgumentName = argumentName;
             this.selectedType = "visualization_id";

From 3462bc40b6391d90694c540a998f64e3bf77c1ae Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 12 Jun 2026 00:00:59 -0500
Subject: [PATCH 169/256] remove the global p-3 padding for notebooks as well

TODO: We need to remove this padding from `Analysis` and keep it scoped to components that need it.
---
 .../components/PageEditor/HistoryPageView.vue |  1 +
 .../src/entry/analysis/modules/Analysis.vue   | 19 ++++++++++++++-----
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index 6660f61d67b..7d9569bcb41 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -186,6 +186,7 @@ function handleBack() {
             <div class="page-display-content overflow-auto flex-grow-1" data-description="page rendered view">
                 <Markdown
                     v-if="markdownConfig"
+                    class="px-3 pt-3"
                     :markdown-config="markdownConfig"
                     :read-only="true"
                     no-heading
diff --git a/client/src/entry/analysis/modules/Analysis.vue b/client/src/entry/analysis/modules/Analysis.vue
index 524c0ed5648..5499575d4ae 100644
--- a/client/src/entry/analysis/modules/Analysis.vue
+++ b/client/src/entry/analysis/modules/Analysis.vue
@@ -2,7 +2,7 @@
 import { faChevronLeft } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { storeToRefs } from "pinia";
-import { onMounted, onUnmounted, ref, watch } from "vue";
+import { computed, onMounted, onUnmounted, ref, watch } from "vue";
 import { useRoute, useRouter } from "vue-router/composables";
 
 import { usePanels } from "@/composables/usePanels";
@@ -35,6 +35,18 @@ watch(
     { immediate: true },
 );
 
+/** A list of paths for which `p-3` should not be applied
+ *
+ * TODO: Maybe we remove this global `p-3` and add it to the individual components that need it instead?
+ */
+const isNoPaddingPath = computed(() => {
+    return (
+        route.path.startsWith("/galaxyai") ||
+        (route.path.startsWith("/histories/") && route.path.includes("/pages/")) ||
+        route.path.startsWith("/pages/editor")
+    );
+});
+
 const showCenter = ref(false);
 const { showPanels } = usePanels();
 
@@ -71,10 +83,7 @@ onUnmounted(() => {
     <div id="columns" class="d-flex">
         <ActivityBar v-if="showPanels" />
         <div id="center" class="d-flex flex-column w-100" style="min-width: 0">
-            <div
-                class="flex-grow-1 overflow-auto"
-                :class="{ 'p-3': !route.path.startsWith('/galaxyai') }"
-                style="min-height: 0">
+            <div class="flex-grow-1 overflow-auto" :class="{ 'p-3': !isNoPaddingPath }" style="min-height: 0">
                 <CenterFrame v-show="showCenter" id="galaxy_main" @load="onLoad" />
                 <div v-show="!showCenter" class="h-100">
                     <router-view :key="$route.fullPath" class="h-100" />

From 1c6d49c251c3f231f395418bee0ac94f91fd45c1 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 12 Jun 2026 08:46:22 -0500
Subject: [PATCH 170/256] display the user's entire list of pages in pages grid

---
 client/src/components/Grid/GridList.vue     |  7 ++++---
 client/src/components/Grid/configs/pages.ts | 21 +++++++++++++++++++--
 2 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Grid/GridList.vue b/client/src/components/Grid/GridList.vue
index 60d0023dac0..f620dc42f74 100644
--- a/client/src/components/Grid/GridList.vue
+++ b/client/src/components/Grid/GridList.vue
@@ -470,9 +470,10 @@ watch(operationMessage, () => {
                                             fieldText(fieldEntry, rowData)
                                         }}</span>
                                     </GButton>
-                                    <SwitchToHistoryLink
-                                        v-else-if="fieldEntry.type == 'history'"
-                                        :history-id="rowData[fieldEntry.key]" />
+                                    <template v-else-if="fieldEntry.type == 'history'">
+                                        <span v-if="!rowData[fieldEntry.key]" v-localize> No history found </span>
+                                        <SwitchToHistoryLink v-else :history-id="rowData[fieldEntry.key]" />
+                                    </template>
                                     <HelpText
                                         v-else-if="fieldEntry.type == 'helptext' && fieldEntry.converter"
                                         :uri="fieldEntry.converter(rowData)"
diff --git a/client/src/components/Grid/configs/pages.ts b/client/src/components/Grid/configs/pages.ts
index dea2ddb6316..c24af00f1a3 100644
--- a/client/src/components/Grid/configs/pages.ts
+++ b/client/src/components/Grid/configs/pages.ts
@@ -31,13 +31,18 @@ type PageEntry = Record<string, unknown>;
  * Request and return data from server
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
-    const typeFilteredSearch = search ? `type:standalone ${search}` : "type:standalone";
+    if (search.includes("is:standalone")) {
+        // Pages that are not attached to a history have their type set to "standalone" on the backend
+        // We convert the search term here before sending to the backend
+        search = search.replace("is:standalone", "type:standalone");
+    }
+
     const { response, data, error } = await GalaxyApi().GET("/api/pages", {
         params: {
             query: {
                 limit,
                 offset,
-                search: typeFilteredSearch,
+                search: search,
                 sort_by: sort_by as SortKeyLiteral,
                 sort_desc,
                 show_published: false,
@@ -193,6 +198,11 @@ const fields: FieldArray = [
         title: "Status",
         type: "sharing",
     },
+    {
+        key: "history_id",
+        title: "History",
+        type: "history",
+    },
 ];
 
 /**
@@ -222,6 +232,13 @@ const validFilters: Record<string, ValidFilter<string | boolean | undefined>> =
         handler: equals("deleted", "deleted", toBool),
         menuItem: true,
     },
+    standalone: {
+        placeholder: "Only standalone",
+        type: Boolean,
+        boolType: "is",
+        handler: equals("standalone", "type", toBool),
+        menuItem: true,
+    },
 };
 
 /**

From 8244d775fe39bf8950ee11e6b374e37588cf6355 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 12 Jun 2026 18:13:14 -0500
Subject: [PATCH 171/256] use router in `PageView`

---
 client/src/components/Page/PageView.vue | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Page/PageView.vue b/client/src/components/Page/PageView.vue
index e4f7796ea8e..8f465e550d2 100644
--- a/client/src/components/Page/PageView.vue
+++ b/client/src/components/Page/PageView.vue
@@ -4,6 +4,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert, BButton } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, onMounted, ref } from "vue";
+import { useRouter } from "vue-router/composables";
 
 import type { PublishedItem as PublishedItemType } from "@/components/Common/models/PublishedItem";
 import { PAGE_LABELS, PUBLISHED_LABELS } from "@/components/Page/constants";
@@ -37,6 +38,8 @@ const props = withDefaults(defineProps<Props>(), {
     displayOnly: false,
 });
 
+const router = useRouter();
+
 const { config, isConfigLoaded } = useConfig(true);
 const userStore = useUserStore();
 const { currentUser } = storeToRefs(userStore);
@@ -86,7 +89,7 @@ onMounted(() => {
 });
 
 function onEdit() {
-    window.location.href = `/pages/editor?id=${props.pageId}`;
+    router.push(`/pages/editor?id=${props.pageId}`);
 }
 
 /** Whether to render chrome-free (embed or displayOnly). */

From 17d71c8e3c5094f0422bd9f0250397565ad0a448 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 12 Jun 2026 18:36:47 -0500
Subject: [PATCH 172/256] add reusable `PageEditorView`

---
 client/src/components/Markdown/Markdown.vue   | 14 +----
 client/src/components/Markdown/types.d.ts     | 11 ++++
 .../components/PageEditor/HistoryPageView.vue | 52 +++-------------
 .../components/PageEditor/PageDisplayOnly.vue | 62 +++++++++++++++++++
 .../components/PageEditor/PageEditorView.vue  | 38 +++---------
 client/src/utils/navigation/navigation.yml    |  3 -
 6 files changed, 93 insertions(+), 87 deletions(-)
 create mode 100644 client/src/components/Markdown/types.d.ts
 create mode 100644 client/src/components/PageEditor/PageDisplayOnly.vue

diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index 08b65002352..724ff427663 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -4,6 +4,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed, onMounted, ref, watch } from "vue";
 
 import { parseMarkdown } from "./parse";
+import type { MarkdownConfig } from "./types";
 
 import GButton from "@/components/BaseComponents/GButton.vue";
 import Heading from "@/components/Common/Heading.vue";
@@ -11,19 +12,6 @@ import LoadingSpan from "@/components/LoadingSpan.vue";
 import SectionWrapper from "@/components/Markdown/Sections/SectionWrapper.vue";
 import StsDownloadButton from "@/components/StsDownloadButton.vue";
 
-// Props
-interface MarkdownConfig {
-    content?: string;
-    errors?: Array<{ error?: string; line?: string }>;
-    generate_time?: string;
-    generate_version?: string;
-    id?: string;
-    markdown?: string;
-    model_class?: string;
-    title?: string;
-    update_time?: string;
-}
-
 const props = defineProps<{
     markdownConfig: MarkdownConfig;
     enable_beta_markdown_export?: boolean;
diff --git a/client/src/components/Markdown/types.d.ts b/client/src/components/Markdown/types.d.ts
new file mode 100644
index 00000000000..aed156daaf4
--- /dev/null
+++ b/client/src/components/Markdown/types.d.ts
@@ -0,0 +1,11 @@
+export interface MarkdownConfig {
+    content?: string;
+    errors?: Array<{ error?: string; line?: string }>;
+    generate_time?: string;
+    generate_version?: string;
+    id?: string;
+    markdown?: string;
+    model_class?: string;
+    title?: string;
+    update_time?: string;
+}
diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index 7d9569bcb41..b10cdfa7461 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faArrowLeft, faEdit, faSpinner } from "@fortawesome/free-solid-svg-icons";
+import { faSpinner } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert } from "bootstrap-vue";
 import { computed, onMounted, onUnmounted, watch } from "vue";
@@ -12,9 +12,8 @@ import { usePageEditorStore } from "@/stores/pageEditorStore";
 import { errorMessageAsString } from "@/utils/simple-error.js";
 
 import HistoryPageList from "./HistoryPageList.vue";
+import PageDisplayOnly from "./PageDisplayOnly.vue";
 import PageEditorView from "./PageEditorView.vue";
-import GButton from "@/components/BaseComponents/GButton.vue";
-import Markdown from "@/components/Markdown/Markdown.vue";
 
 const props = defineProps<{
     historyId: string;
@@ -157,43 +156,13 @@ function handleBack() {
         </template>
 
         <!-- Display-only mode: rendered view -->
-        <template v-else-if="store.hasCurrentPage && displayOnly">
-            <div
-                class="page-display-toolbar d-flex align-items-center p-2 border-bottom"
-                data-description="page display toolbar">
-                <GButton
-                    color="blue"
-                    transparent
-                    size="small"
-                    data-description="page manage button"
-                    @click="handleBack">
-                    <FontAwesomeIcon :icon="faArrowLeft" />
-                    {{ labels.editorBackLabel }}
-                </GButton>
-                <span class="flex-grow-1 text-center font-weight-bold">
-                    {{ store.currentTitle || labels.defaultTitle }}
-                </span>
-                <GButton
-                    color="blue"
-                    outline
-                    size="small"
-                    data-description="page edit button"
-                    @click="handleEdit(props.pageId)">
-                    <FontAwesomeIcon :icon="faEdit" />
-                    Edit
-                </GButton>
-            </div>
-            <div class="page-display-content overflow-auto flex-grow-1" data-description="page rendered view">
-                <Markdown
-                    v-if="markdownConfig"
-                    class="px-3 pt-3"
-                    :markdown-config="markdownConfig"
-                    :read-only="true"
-                    no-heading
-                    download-endpoint=""
-                    hide-heading />
-            </div>
-        </template>
+        <PageDisplayOnly
+            v-else-if="store.hasCurrentPage && displayOnly"
+            :labels="labels"
+            :current-title="store.currentTitle"
+            :markdown-config="markdownConfig || undefined"
+            @back="handleBack"
+            @edit="handleEdit(props.pageId)" />
 
         <!-- Edit mode: delegate to unified PageEditorView -->
         <template v-else-if="pageId && !displayOnly">
@@ -211,7 +180,4 @@ function handleBack() {
 .history-page-view {
     background: var(--body-bg);
 }
-.page-display-toolbar {
-    background: var(--panel-header-bg);
-}
 </style>
diff --git a/client/src/components/PageEditor/PageDisplayOnly.vue b/client/src/components/PageEditor/PageDisplayOnly.vue
new file mode 100644
index 00000000000..a308021c04e
--- /dev/null
+++ b/client/src/components/PageEditor/PageDisplayOnly.vue
@@ -0,0 +1,62 @@
+<script setup lang="ts">
+import { faArrowLeft, faEdit } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+
+import type { PAGE_LABELS } from "@/components/Page/constants";
+
+import type { MarkdownConfig } from "../Markdown/types.js";
+
+import GButton from "../BaseComponents/GButton.vue";
+import Markdown from "../Markdown/Markdown.vue";
+
+const props = defineProps<{
+    labels: (typeof PAGE_LABELS)[keyof typeof PAGE_LABELS];
+    currentTitle?: string;
+    markdownConfig?: MarkdownConfig;
+}>();
+
+const emit = defineEmits<{
+    (e: "edit"): void;
+    (e: "back"): void;
+}>();
+</script>
+
+<template>
+    <div class="d-flex flex-column">
+        <div
+            class="page-display-toolbar d-flex align-items-center p-2 border-bottom"
+            data-description="page display toolbar">
+            <GButton color="blue" transparent size="small" data-description="page back button" @click="emit('back')">
+                <FontAwesomeIcon :icon="faArrowLeft" />
+                {{ props.labels.editorBackLabel }}
+            </GButton>
+            <span class="flex-grow-1 text-center font-weight-bold">
+                {{ props.currentTitle || props.labels.defaultTitle }}
+            </span>
+            <GButton color="blue" outline size="small" data-description="page edit button" @click="emit('edit')">
+                <FontAwesomeIcon :icon="faEdit" />
+                Edit
+            </GButton>
+        </div>
+        <div class="page-display-content" data-description="page rendered view">
+            <Markdown
+                v-if="markdownConfig"
+                class="px-3 pt-3"
+                :markdown-config="markdownConfig"
+                read-only
+                no-heading
+                download-endpoint="" />
+        </div>
+    </div>
+</template>
+
+<style scoped>
+.page-display-toolbar {
+    background: var(--color-grey-100);
+}
+
+.page-display-content {
+    overflow: auto;
+    flex: 1 1 0;
+}
+</style>
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 99baf147f3d..748ff5ccad7 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faArrowLeft, faEdit, faEye, faHistory, faSave, faSpinner, faUsers } from "@fortawesome/free-solid-svg-icons";
+import { faArrowLeft, faEye, faHistory, faSave, faSpinner, faUsers } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert, BBadge, BButton } from "bootstrap-vue";
 import { computed, onMounted, onUnmounted, ref, watch } from "vue";
@@ -13,10 +13,10 @@ import { useHistoryStore } from "@/stores/historyStore";
 import { type PageEditorMode, usePageEditorStore } from "@/stores/pageEditorStore";
 
 import ObjectPermissionsModal from "./ObjectPermissionsModal.vue";
+import PageDisplayOnly from "./PageDisplayOnly.vue";
 import PageRevisionList from "./PageRevisionList.vue";
 import PageRevisionView from "./PageRevisionView.vue";
 import ClickToEdit from "@/components/ClickToEdit.vue";
-import Markdown from "@/components/Markdown/Markdown.vue";
 import MarkdownEditor from "@/components/Markdown/MarkdownEditor.vue";
 
 const props = defineProps<{
@@ -184,30 +184,13 @@ function handleRevisionRestore(revisionId: string) {
         </BAlert>
 
         <!-- Display-only mode: rendered view -->
-        <template v-else-if="store.hasCurrentPage && displayOnly">
-            <div
-                class="page-display-toolbar d-flex align-items-center p-2 border-bottom"
-                data-description="page display toolbar">
-                <BButton variant="link" size="sm" data-description="page back button" @click="handleBack">
-                    <FontAwesomeIcon :icon="faArrowLeft" />
-                    {{ labels.editorBackLabel }}
-                </BButton>
-                <span class="flex-grow-1 text-center font-weight-bold">
-                    {{ store.currentTitle || labels.defaultTitle }}
-                </span>
-                <BButton variant="outline-primary" size="sm" data-description="page edit button" @click="handleEdit">
-                    <FontAwesomeIcon :icon="faEdit" />
-                    Edit
-                </BButton>
-            </div>
-            <div class="page-display-content overflow-auto flex-grow-1" data-description="page rendered view">
-                <Markdown
-                    v-if="markdownConfig"
-                    :markdown-config="markdownConfig"
-                    :read-only="true"
-                    download-endpoint="" />
-            </div>
-        </template>
+        <PageDisplayOnly
+            v-else-if="store.hasCurrentPage && displayOnly"
+            :labels="labels"
+            :current-title="store.currentTitle"
+            :markdown-config="markdownConfig || undefined"
+            @back="handleBack"
+            @edit="handleEdit" />
 
         <!-- Viewing a specific revision -->
         <template v-else-if="store.hasCurrentPage && store.selectedRevision">
@@ -327,8 +310,7 @@ function handleRevisionRestore(revisionId: string) {
 .page-editor-view {
     background: var(--body-bg);
 }
-.page-toolbar,
-.page-display-toolbar {
+.page-toolbar {
     background: var(--panel-header-bg);
 }
 .page-revision-panel {
diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 3f1902387bb..a1398b995fc 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -645,9 +645,6 @@ pages:
         type: data-description
         selector: 'page editor toolbar'
       toolbar_title: '[data-description="page editor title"] > span'
-      manage_button:
-        type: data-description
-        selector: 'page manage button'
       save_button:
         type: data-description
         selector: 'page save button'

From 56293a7e87131ea3ebbf3228a025527332bf900e Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 12 Jun 2026 20:02:43 -0500
Subject: [PATCH 173/256] add a new `PageDisplayToolbar` only used in preview
 mode so far

---
 client/src/components/Page/constants.ts       |   7 +
 .../components/PageEditor/HistoryPageView.vue |   1 -
 .../components/PageEditor/PageDisplayOnly.vue |  26 +--
 .../PageEditor/PageDisplayToolbar.vue         | 178 ++++++++++++++++++
 .../components/PageEditor/PageEditorView.vue  |   8 +-
 5 files changed, 188 insertions(+), 32 deletions(-)
 create mode 100644 client/src/components/PageEditor/PageDisplayToolbar.vue

diff --git a/client/src/components/Page/constants.ts b/client/src/components/Page/constants.ts
index 24bc7c8e9a7..10d6ca74a10 100644
--- a/client/src/components/Page/constants.ts
+++ b/client/src/components/Page/constants.ts
@@ -8,6 +8,9 @@
  *
  * Change strings here to rename across the entire UI.
  */
+import type { IconDefinition } from "@fortawesome/fontawesome-svg-core";
+import { faBook, faFileContract } from "@fortawesome/free-solid-svg-icons";
+
 import type { PageEditorMode } from "@/stores/pageEditorStore";
 
 /** Per-mode labels used by the page editor, history page list, chat panel, etc. */
@@ -16,6 +19,7 @@ export const PAGE_LABELS: Record<
     {
         entityName: string;
         entityNamePlural: string;
+        titleIcon: IconDefinition;
         defaultTitle: string;
         editorBackLabel: string;
         newButton: string;
@@ -30,6 +34,7 @@ export const PAGE_LABELS: Record<
     history: {
         entityName: "Galaxy Notebook",
         entityNamePlural: "Galaxy Notebooks",
+        titleIcon: faBook,
         defaultTitle: "Untitled Notebook",
         editorBackLabel: "This History's Notebooks",
         newButton: "New Notebook",
@@ -44,6 +49,7 @@ export const PAGE_LABELS: Record<
     standalone: {
         entityName: "Report",
         entityNamePlural: "Reports",
+        titleIcon: faFileContract,
         defaultTitle: "Untitled Report",
         editorBackLabel: "Back to Reports",
         newButton: "Create Report",
@@ -56,6 +62,7 @@ export const PAGE_LABELS: Record<
     invocation: {
         entityName: "Invocation Report",
         entityNamePlural: "Invocation Reports",
+        titleIcon: faFileContract,
         defaultTitle: "Untitled Invocation Report",
         editorBackLabel: "This Invocation's Reports",
         newButton: "New Invocation Report",
diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index b10cdfa7461..413238fcfcb 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -159,7 +159,6 @@ function handleBack() {
         <PageDisplayOnly
             v-else-if="store.hasCurrentPage && displayOnly"
             :labels="labels"
-            :current-title="store.currentTitle"
             :markdown-config="markdownConfig || undefined"
             @back="handleBack"
             @edit="handleEdit(props.pageId)" />
diff --git a/client/src/components/PageEditor/PageDisplayOnly.vue b/client/src/components/PageEditor/PageDisplayOnly.vue
index a308021c04e..24002e285b4 100644
--- a/client/src/components/PageEditor/PageDisplayOnly.vue
+++ b/client/src/components/PageEditor/PageDisplayOnly.vue
@@ -1,17 +1,13 @@
 <script setup lang="ts">
-import { faArrowLeft, faEdit } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-
 import type { PAGE_LABELS } from "@/components/Page/constants";
 
 import type { MarkdownConfig } from "../Markdown/types.js";
 
-import GButton from "../BaseComponents/GButton.vue";
 import Markdown from "../Markdown/Markdown.vue";
+import PageDisplayToolbar from "./PageDisplayToolbar.vue";
 
 const props = defineProps<{
     labels: (typeof PAGE_LABELS)[keyof typeof PAGE_LABELS];
-    currentTitle?: string;
     markdownConfig?: MarkdownConfig;
 }>();
 
@@ -23,21 +19,7 @@ const emit = defineEmits<{
 
 <template>
     <div class="d-flex flex-column">
-        <div
-            class="page-display-toolbar d-flex align-items-center p-2 border-bottom"
-            data-description="page display toolbar">
-            <GButton color="blue" transparent size="small" data-description="page back button" @click="emit('back')">
-                <FontAwesomeIcon :icon="faArrowLeft" />
-                {{ props.labels.editorBackLabel }}
-            </GButton>
-            <span class="flex-grow-1 text-center font-weight-bold">
-                {{ props.currentTitle || props.labels.defaultTitle }}
-            </span>
-            <GButton color="blue" outline size="small" data-description="page edit button" @click="emit('edit')">
-                <FontAwesomeIcon :icon="faEdit" />
-                Edit
-            </GButton>
-        </div>
+        <PageDisplayToolbar :labels="props.labels" mode="display" @edit="emit('edit')" @back="emit('back')" />
         <div class="page-display-content" data-description="page rendered view">
             <Markdown
                 v-if="markdownConfig"
@@ -51,10 +33,6 @@ const emit = defineEmits<{
 </template>
 
 <style scoped>
-.page-display-toolbar {
-    background: var(--color-grey-100);
-}
-
 .page-display-content {
     overflow: auto;
     flex: 1 1 0;
diff --git a/client/src/components/PageEditor/PageDisplayToolbar.vue b/client/src/components/PageEditor/PageDisplayToolbar.vue
new file mode 100644
index 00000000000..5010dc46036
--- /dev/null
+++ b/client/src/components/PageEditor/PageDisplayToolbar.vue
@@ -0,0 +1,178 @@
+<script setup lang="ts">
+import {
+    faArrowLeft,
+    faEdit,
+    faEye,
+    faHistory,
+    faInfo,
+    faPen,
+    faSave,
+    faSpinner,
+} from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BBadge } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed, ref } from "vue";
+
+import type { PAGE_LABELS } from "@/components/Page/constants";
+import { usePageEditorStore } from "@/stores/pageEditorStore.js";
+
+import GButton from "../BaseComponents/GButton.vue";
+import GButtonGroup from "../BaseComponents/GButtonGroup.vue";
+import RenameModal from "../Common/RenameModal.vue";
+
+const props = defineProps<{
+    labels: (typeof PAGE_LABELS)[keyof typeof PAGE_LABELS];
+    mode: "editor" | "display";
+}>();
+
+const pageEditorStore = usePageEditorStore();
+const { canSave, currentTitle, revisionCount, showRevisions, isDirty, isSaving } = storeToRefs(pageEditorStore);
+
+const emit = defineEmits<{
+    (e: "back"): void;
+    (e: "edit"): void;
+    (e: "preview"): void;
+}>();
+
+const showRename = ref(false);
+
+const saveDisabledTitle = computed(() => {
+    const entity = props.labels.entityName.toLowerCase();
+    if (props.mode === "display") {
+        return `Currently previewing this ${entity}. Click 'Edit' to make changes and enable saving.`;
+    }
+    if (isSaving.value) {
+        return `This ${entity} is being saved`;
+    }
+    if (!canSave.value) {
+        return `There are no changes to save to this ${entity}`;
+    }
+    return "";
+});
+
+async function handleSave() {
+    await pageEditorStore.savePage();
+}
+
+function handleTitleChange(newTitle: string): Promise<void> {
+    return new Promise((resolve) => {
+        pageEditorStore.updateTitle(newTitle);
+        resolve();
+    });
+}
+</script>
+
+<template>
+    <div
+        class="page-display-toolbar d-flex align-items-center py-2 px-3 border-bottom flex-gapx-1 justify-content-between"
+        :data-description="`page ${props.mode} toolbar`">
+        <div class="d-flex align-items-center flex-gapx-1 title-section">
+            <FontAwesomeIcon :icon="props.labels.titleIcon" fixed-width />
+            <b class="page-title" :data-description="`page ${props.mode} title`">
+                {{ currentTitle || props.labels.defaultTitle }}
+            </b>
+            <GButton
+                v-if="props.mode === 'editor'"
+                inline
+                transparent
+                data-description="page rename button"
+                :title="`Rename this ${props.labels.entityName.toLowerCase()}`"
+                @click="showRename = true">
+                <FontAwesomeIcon :icon="faPen" />
+            </GButton>
+        </div>
+
+        <div class="d-flex align-items-center flex-gapx-1 flex-shrink-0">
+            <span
+                v-if="isDirty"
+                class="d-flex align-items-center flex-gapx-1 text-warning small"
+                data-description="page unsaved indicator">
+                <BBadge variant="warning" class="text-light">
+                    <FontAwesomeIcon :icon="faInfo" />
+                </BBadge>
+                Unsaved
+            </span>
+
+            <GButton color="blue" transparent size="small" data-description="page back button" @click="emit('back')">
+                <FontAwesomeIcon :icon="faArrowLeft" />
+                {{ props.labels.editorBackLabel }}
+            </GButton>
+
+            <slot name="extra-actions" />
+
+            <GButton
+                v-if="props.mode === 'editor'"
+                color="blue"
+                outline
+                :pressed="showRevisions"
+                data-description="page revisions button"
+                size="small"
+                @click="pageEditorStore.toggleRevisions">
+                <FontAwesomeIcon :icon="faHistory" />
+                Revisions
+                <BBadge v-if="revisionCount > 0" variant="light" class="ml-1">
+                    {{ revisionCount }}
+                </BBadge>
+            </GButton>
+
+            <GButtonGroup data-description="revision view mode toggle">
+                <GButton
+                    color="blue"
+                    outline
+                    :pressed="props.mode === 'editor'"
+                    data-description="page edit button"
+                    size="small"
+                    @click="emit('edit')">
+                    <FontAwesomeIcon :icon="faEdit" />
+                    Edit
+                </GButton>
+                <GButton
+                    color="blue"
+                    outline
+                    :pressed="props.mode === 'display'"
+                    data-description="page preview button"
+                    size="small"
+                    @click="emit('preview')">
+                    <FontAwesomeIcon :icon="faEye" />
+                    Preview
+                </GButton>
+            </GButtonGroup>
+
+            <GButton
+                color="blue"
+                data-description="page save button"
+                :title="`Save ${props.labels.entityName}`"
+                tooltip
+                :disabled="props.mode === 'display' || !canSave"
+                :disabled-title="saveDisabledTitle"
+                size="small"
+                @click="handleSave">
+                <FontAwesomeIcon :icon="isSaving ? faSpinner : faSave" :spin="isSaving" />
+                Save
+            </GButton>
+        </div>
+
+        <RenameModal
+            v-if="showRename"
+            :item-type="props.labels.entityName"
+            :name="currentTitle || props.labels.defaultTitle"
+            :rename-action="handleTitleChange"
+            @close="showRename = false" />
+    </div>
+</template>
+
+<style scoped>
+.page-display-toolbar {
+    background: var(--color-grey-100);
+}
+.title-section {
+    min-width: 0;
+    overflow: hidden;
+}
+.page-title {
+    overflow: hidden;
+    text-overflow: ellipsis;
+    white-space: nowrap;
+}
+</style>
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 748ff5ccad7..52f758b548c 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -187,7 +187,6 @@ function handleRevisionRestore(revisionId: string) {
         <PageDisplayOnly
             v-else-if="store.hasCurrentPage && displayOnly"
             :labels="labels"
-            :current-title="store.currentTitle"
             :markdown-config="markdownConfig || undefined"
             @back="handleBack"
             @edit="handleEdit" />
@@ -209,9 +208,7 @@ function handleRevisionRestore(revisionId: string) {
 
         <!-- Edit mode: toolbar + editor + optional chat/revision panels -->
         <template v-else-if="store.hasCurrentPage">
-            <div
-                class="page-toolbar d-flex align-items-center p-2 border-bottom"
-                data-description="page editor toolbar">
+            <div class="d-flex align-items-center p-2 border-bottom" data-description="page editor toolbar">
                 <BButton variant="link" size="sm" data-description="page back button" @click="handleBack">
                     <FontAwesomeIcon :icon="faArrowLeft" />
                     {{ labels.editorBackLabel }}
@@ -310,9 +307,6 @@ function handleRevisionRestore(revisionId: string) {
 .page-editor-view {
     background: var(--body-bg);
 }
-.page-toolbar {
-    background: var(--panel-header-bg);
-}
 .page-revision-panel {
     width: 300px;
     min-width: 300px;

From aad2f585bae5a0b3660335cf3fb0ec7fd02f1544 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sat, 13 Jun 2026 16:54:29 -0500
Subject: [PATCH 174/256] use `PageDisplayToolbar` in editor view as well

---
 .../src/components/Common/RenameModal.test.ts |   7 +-
 client/src/components/Common/RenameModal.vue  |   4 +-
 .../components/PageEditor/PageEditorView.vue  | 145 ++++++------------
 client/src/utils/navigation/navigation.yml    |   9 +-
 lib/galaxy/selenium/navigates_galaxy.py       |  32 ++--
 .../selenium/test_histories_list.py           |  14 +-
 .../selenium/test_history_pages.py            |  13 +-
 lib/galaxy_test/selenium/test_pages.py        |   1 -
 8 files changed, 80 insertions(+), 145 deletions(-)

diff --git a/client/src/components/Common/RenameModal.test.ts b/client/src/components/Common/RenameModal.test.ts
index ff6fa8cfdf9..113d13cb327 100644
--- a/client/src/components/Common/RenameModal.test.ts
+++ b/client/src/components/Common/RenameModal.test.ts
@@ -23,6 +23,7 @@ const localVue = getLocalVue();
 
 const WORKFLOW_ID = "workflow-abc123";
 const WORKFLOW_NAME = "My Test Workflow";
+const INPUT_SELECTOR = "[data-description='workflow name input']";
 
 async function mountRenameModal(name = WORKFLOW_NAME) {
     const wrapper = mount(RenameModal as object, {
@@ -52,7 +53,7 @@ describe("RenameModal tested for renaming workflows", () => {
 
         const wrapper = await mountRenameModal();
 
-        await createWrapper(document.body).find("#workflow-name-input").setValue("Renamed Workflow");
+        await createWrapper(document.body).find(INPUT_SELECTOR).setValue("Renamed Workflow");
         wrapper.findComponent(GModal).vm.$emit("ok");
         await flushPromises();
 
@@ -65,7 +66,7 @@ describe("RenameModal tested for renaming workflows", () => {
 
         const wrapper = await mountRenameModal();
 
-        await createWrapper(document.body).find("#workflow-name-input").setValue("Attempted New Name");
+        await createWrapper(document.body).find(INPUT_SELECTOR).setValue("Attempted New Name");
         wrapper.findComponent(GModal).vm.$emit("ok");
         await flushPromises();
 
@@ -77,7 +78,7 @@ describe("RenameModal tested for renaming workflows", () => {
         // Simulate parent closing and reopening the modal (destroys old instance)
         wrapper.destroy();
         await mountRenameModal();
-        expect((createWrapper(document.body).find("#workflow-name-input").element as HTMLInputElement).value).toBe(
+        expect((createWrapper(document.body).find(INPUT_SELECTOR).element as HTMLInputElement).value).toBe(
             WORKFLOW_NAME,
         );
     });
diff --git a/client/src/components/Common/RenameModal.vue b/client/src/components/Common/RenameModal.vue
index 5636f8c990f..9eff7bcee2c 100644
--- a/client/src/components/Common/RenameModal.vue
+++ b/client/src/components/Common/RenameModal.vue
@@ -63,15 +63,15 @@ async function onRename(newName: string) {
         show
         :ok-text="localize('Rename')"
         :ok-disabled="nameInvalid || renaming"
-        :title="`Rename ${props.itemType}: ${props.name}`"
+        :title="`Rename ${capitalizeFirstLetter(props.itemType)}: ${props.name}`"
         confirm
         :close-on-ok="false"
         @ok="onRename(nameModel)"
         @close="emit('close')"
         @cancel="emit('close')">
         <GFormInput
-            :id="`${props.itemType}-name-input`"
             v-model="nameModel"
+            :data-description="`${props.itemType} name input`"
             class="w-100"
             :disabled="renaming"
             type="text"
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 52f758b548c..0f56f8ce614 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -1,22 +1,23 @@
 <script setup lang="ts">
-import { faArrowLeft, faEye, faHistory, faSave, faSpinner, faUsers } from "@fortawesome/free-solid-svg-icons";
+import { faSpinner, faUsers } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BBadge, BButton } from "bootstrap-vue";
+import { BAlert } from "bootstrap-vue";
 import { computed, onMounted, onUnmounted, ref, watch } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { getGalaxyInstance } from "@/app";
-import type { RouterPushOptions } from "@/components/History/Content/router-push-options";
+// import { getGalaxyInstance } from "@/app";
+// import type { RouterPushOptions } from "@/components/History/Content/router-push-options";
 import { PAGE_LABELS } from "@/components/Page/constants";
 import { useWindowAwareNavigation } from "@/composables/windowAwareNavigation";
 import { useHistoryStore } from "@/stores/historyStore";
 import { type PageEditorMode, usePageEditorStore } from "@/stores/pageEditorStore";
 
+import GButton from "../BaseComponents/GButton.vue";
 import ObjectPermissionsModal from "./ObjectPermissionsModal.vue";
 import PageDisplayOnly from "./PageDisplayOnly.vue";
+import PageDisplayToolbar from "./PageDisplayToolbar.vue";
 import PageRevisionList from "./PageRevisionList.vue";
 import PageRevisionView from "./PageRevisionView.vue";
-import ClickToEdit from "@/components/ClickToEdit.vue";
 import MarkdownEditor from "@/components/Markdown/MarkdownEditor.vue";
 
 const props = defineProps<{
@@ -125,39 +126,33 @@ function handleEdit() {
     }
 }
 
-async function handleSave() {
-    await store.savePage();
-}
-
-async function handleSaveAndView() {
-    await store.savePage();
-    if (props.invocationId) {
-        router.push(`/workflows/invocations/${props.invocationId}/reports?id=${props.pageId}`);
-        return;
-    }
-    if (store.currentPage) {
-        const Galaxy = getGalaxyInstance();
-        const isWmActive = Galaxy?.frame?.active;
-        if (isWmActive) {
-            const url = `/published/page?id=${props.pageId}&embed=true`;
-            const options: RouterPushOptions = {
-                title: `${labels.value.entityName}: ${store.currentTitle || labels.value.defaultTitle}`,
-                preventWindowManager: false,
-            };
-            // @ts-ignore - monkeypatched router
-            router.push(url, options);
-        } else {
-            const data = store.currentPage as any;
-            if (data.username && data.slug) {
-                window.location.href = `/u/${data.username}/p/${data.slug}`;
-            }
-        }
-    }
-}
-
-function handleTitleChange(newTitle: string) {
-    store.updateTitle(newTitle);
-}
+// TODO: Uncomment when router guards with unsaved changes protection are implemented
+//       Before, we had a Save & View button that is now removed.
+// async function handleSaveAndView() {
+//     await store.savePage();
+//     if (props.invocationId) {
+//         router.push(`/workflows/invocations/${props.invocationId}/reports?id=${props.pageId}`);
+//         return;
+//     }
+//     if (store.currentPage) {
+//         const Galaxy = getGalaxyInstance();
+//         const isWmActive = Galaxy?.frame?.active;
+//         if (isWmActive) {
+//             const url = `/published/page?id=${props.pageId}&embed=true`;
+//             const options: RouterPushOptions = {
+//                 title: `${labels.value.entityName}: ${store.currentTitle || labels.value.defaultTitle}`,
+//                 preventWindowManager: false,
+//             };
+//             // @ts-ignore - monkeypatched router
+//             router.push(url, options);
+//         } else {
+//             const data = store.currentPage as any;
+//             if (data.username && data.slug) {
+//                 window.location.href = `/u/${data.username}/p/${data.slug}`;
+//             }
+//         }
+//     }
+// }
 
 function handleContentUpdate(newContent: string) {
     store.updateContent(newContent);
@@ -208,78 +203,24 @@ function handleRevisionRestore(revisionId: string) {
 
         <!-- Edit mode: toolbar + editor + optional chat/revision panels -->
         <template v-else-if="store.hasCurrentPage">
-            <div class="d-flex align-items-center p-2 border-bottom" data-description="page editor toolbar">
-                <BButton variant="link" size="sm" data-description="page back button" @click="handleBack">
-                    <FontAwesomeIcon :icon="faArrowLeft" />
-                    {{ labels.editorBackLabel }}
-                </BButton>
-                <ClickToEdit
-                    :value="store.currentTitle || labels.defaultTitle"
-                    tag-name="span"
-                    :placeholder="labels.defaultTitle"
-                    class="flex-grow-1 text-center font-weight-bold"
-                    data-description="page editor title"
-                    @input="handleTitleChange" />
-                <BButton
-                    variant="outline-primary"
-                    size="sm"
-                    class="mr-2"
-                    data-description="page revisions button"
-                    @click="store.toggleRevisions">
-                    <FontAwesomeIcon :icon="faHistory" />
-                    Revisions
-                    <BBadge v-if="store.revisionCount > 0" variant="light" class="ml-1">
-                        {{ store.revisionCount }}
-                    </BBadge>
-                </BButton>
-                <BButton
-                    variant="outline-primary"
-                    size="sm"
-                    class="mr-2"
-                    data-description="page preview button"
-                    @click="handlePreview">
-                    <FontAwesomeIcon :icon="faEye" />
-                    Preview
-                </BButton>
-                <template v-if="isStandalone">
+            <PageDisplayToolbar :labels="labels" mode="editor" @preview="handlePreview" @back="handleBack">
+                <template v-if="isStandalone" v-slot:extra-actions>
                     <ObjectPermissionsModal
                         id="object-permissions-modal"
                         v-model="showPermissions"
                         :markdown-content="store.currentContent" />
-                    <BButton
+                    <GButton
                         v-b-modal:object-permissions-modal
-                        variant="outline-primary"
-                        size="sm"
-                        class="mr-2"
-                        data-description="page permissions button">
+                        color="blue"
+                        outline
+                        size="small"
+                        data-description="page permissions button"
+                        @click="showPermissions = true">
                         <FontAwesomeIcon :icon="faUsers" />
                         Permissions
-                    </BButton>
+                    </GButton>
                 </template>
-                <BButton
-                    variant="primary"
-                    size="sm"
-                    :class="{ 'mr-2': isStandalone }"
-                    data-description="page save button"
-                    :disabled="!store.canSave"
-                    @click="handleSave">
-                    <FontAwesomeIcon :icon="store.isSaving ? faSpinner : faSave" :spin="store.isSaving" />
-                    Save
-                </BButton>
-                <BButton
-                    v-if="isStandalone"
-                    variant="primary"
-                    size="sm"
-                    data-description="page save-view button"
-                    :disabled="!store.canSave"
-                    @click="handleSaveAndView">
-                    <FontAwesomeIcon :icon="faEye" />
-                    Save &amp; View
-                </BButton>
-                <span v-if="store.isDirty" class="ml-2 text-warning small" data-description="page unsaved indicator">
-                    Unsaved
-                </span>
-            </div>
+            </PageDisplayToolbar>
 
             <div class="page-body d-flex flex-grow-1 overflow-hidden">
                 <div class="page-content flex-grow-1 overflow-auto">
diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index a1398b995fc..13ec9637d61 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -644,7 +644,7 @@ pages:
       toolbar:
         type: data-description
         selector: 'page editor toolbar'
-      toolbar_title: '[data-description="page editor title"] > span'
+      toolbar_title: '[data-description="page editor title"]'
       save_button:
         type: data-description
         selector: 'page save button'
@@ -694,16 +694,15 @@ pages:
       edit_button:
         type: data-description
         selector: 'page edit button'
-      toolbar_title_input: '[data-description="page editor title"] input'
+      rename_button:
+        type: data-description
+        selector: 'page rename button'
       back_button:
         type: data-description
         selector: 'page back button'
       permissions_button:
         type: data-description
         selector: 'page permissions button'
-      save_view_button:
-        type: data-description
-        selector: 'page save-view button'
       revision_compare_current_button:
         type: data-description
         selector: 'revision compare current button'
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index 5b0419676d1..c2a88c3203c 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -1961,10 +1961,7 @@ class NavigatesGalaxy(HasDriverProxy[WaitType]):
         action_chains = self.action_chains()
         action_chains.move_to_element(workflow).perform()
         workflow.find_element(By.CSS_SELECTOR, ".g-card-rename").click()
-        self.components.workflows.rename_input.wait_for_visible().clear()
-        self.components.workflows.rename_input.wait_for_and_send_keys(new_name)
-        self.components.workflows.rename_input.wait_for_and_send_keys(Keys.ENTER)
-        self.wait_for_selector_absent_or_hidden(".g-modal")
+        self.rename_modal_rename("workflow", new_name)
 
     def workflow_delete_by_name(self, name):
         self.workflow_index_search_for(name)
@@ -2330,14 +2327,25 @@ class NavigatesGalaxy(HasDriverProxy[WaitType]):
         items = self.components.pages.history.revision_item.all()
         assert len(items) == n, f"Expected {n} revision items, found {len(items)}"
 
-    def history_page_rename(self, new_name):
-        """Rename page via ClickToEdit in toolbar."""
-        self.components.pages.history.toolbar_title.wait_for_and_click()
-        title_input = self.components.pages.history.toolbar_title_input.wait_for_visible()
-        self.aggressive_clear(title_input)
-        title_input.send_keys(new_name)
-        self.send_enter(title_input)
-        self.sleep_for(self.wait_types.UX_RENDER)
+    def history_page_rename(self, page_type: str, new_name: str):
+        """Rename page via RenameModal in toolbar."""
+        self.components.pages.history.rename_button.wait_for_and_click()
+        self.rename_modal_rename(page_type, new_name)
+
+    def rename_modal_rename(self, item_type: str, new_name: str):
+        """Rename via RenameModal: opens the rename modal, types new name, and submits."""
+        # Clear via JS + dispatch Vue-compatible input event so nameModel is updated to empty,
+        # then type the new name so each keystroke fires input events and updates nameModel.
+        item_name_input = self.wait_for_selector(f"[data-description='{item_type} name input']")
+        self.execute_script(
+            "arguments[0].value = ''; arguments[0].dispatchEvent(new Event('input', {bubbles: true}));",
+            item_name_input,
+        )
+        item_name_input.send_keys(new_name)
+
+        self.wait_for_and_click_selector(".g-modal-confirm-buttons button:last-child")
+        # Wait for the rename promise to resolve (modal closes in the finally block)
+        self.wait_for_selector_absent_or_hidden(f"#{item_type}-name-input")
 
     @retry_during_transitions
     def click_history_options(self):
diff --git a/lib/galaxy_test/selenium/test_histories_list.py b/lib/galaxy_test/selenium/test_histories_list.py
index e38acb7c4b8..60eb5dae244 100644
--- a/lib/galaxy_test/selenium/test_histories_list.py
+++ b/lib/galaxy_test/selenium/test_histories_list.py
@@ -65,19 +65,7 @@ class TestSavedHistories(SharedStateSeleniumTestCase):
 
         self.select_history_card_operation("Unnamed history", '[id^="g-card-rename-history-"]')
 
-        # Rename the history using the RenameModal.
-        # Clear via JS + dispatch Vue-compatible input event so nameModel is updated to empty,
-        # then type the new name so each keystroke fires input events and updates nameModel.
-        history_name_input = self.wait_for_selector("#history-name-input")
-        self.execute_script(
-            "arguments[0].value = ''; arguments[0].dispatchEvent(new Event('input', {bubbles: true}));",
-            history_name_input,
-        )
-        history_name_input.send_keys(self.history1_name)
-
-        self.wait_for_and_click_selector(".g-modal-confirm-buttons button:last-child")
-        # Wait for the rename API call to complete (modal closes in the finally block)
-        self.wait_for_selector_absent_or_hidden("#history-name-input")
+        self.rename_modal_rename("history", self.history1_name)
 
         self.navigate_to_histories_page()
 
diff --git a/lib/galaxy_test/selenium/test_history_pages.py b/lib/galaxy_test/selenium/test_history_pages.py
index 69763daa05a..f673ec30c7c 100644
--- a/lib/galaxy_test/selenium/test_history_pages.py
+++ b/lib/galaxy_test/selenium/test_history_pages.py
@@ -104,7 +104,7 @@ class TestHistoryPages(SeleniumTestCase):
         self.components.pages.history.editor.wait_for_visible()
 
         save_button = self.components.pages.history.save_button
-        save_button.assert_disabled()
+        assert save_button.has_class("g-disabled")
 
         self.components.pages.history.unsaved_indicator.assert_absent_or_hidden()
 
@@ -112,7 +112,7 @@ class TestHistoryPages(SeleniumTestCase):
 
         @retry_assertion_during_transitions
         def assert_save_enabled():
-            assert not save_button.has_class("disabled")
+            assert not save_button.has_class("g-disabled")
 
         assert_save_enabled()
 
@@ -120,7 +120,7 @@ class TestHistoryPages(SeleniumTestCase):
 
         @retry_assertion_during_transitions
         def assert_save_disabled_again():
-            save_button.assert_disabled()
+            assert save_button.has_class("g-disabled")
 
         assert_save_disabled_again()
         self.screenshot("history_page_save_disabled")
@@ -439,8 +439,8 @@ class TestHistoryPages(SeleniumTestCase):
 
     @selenium_test
     @managed_history
-    def test_inline_rename_page(self):
-        """Rename page title via ClickToEdit, save, verify persistence."""
+    def test_rename_page(self):
+        """Rename page title via the RenameModal, save, verify persistence."""
         history_id = self.current_history_id()
         self.dataset_populator.new_history_page(history_id, title="Original Name", content="# Content")
 
@@ -448,7 +448,7 @@ class TestHistoryPages(SeleniumTestCase):
         self.components.pages.history.item_edit.wait_for_and_click()
         self.components.pages.history.editor.wait_for_visible()
 
-        self.history_page_rename("Renamed Page")
+        self.history_page_rename("galaxy notebook", "Renamed Page")
 
         self.components.pages.history.unsaved_indicator.wait_for_visible()
         self.screenshot("history_page_renamed_unsaved")
@@ -557,7 +557,6 @@ class TestHistoryPages(SeleniumTestCase):
 
         # Standalone-only controls absent
         self.components.pages.history.permissions_button.assert_absent_or_hidden()
-        self.components.pages.history.save_view_button.assert_absent_or_hidden()
 
         # Back button says "This History's Pages" not "Back to Pages"
         back_text = self.components.pages.history.back_button.wait_for_text()
diff --git a/lib/galaxy_test/selenium/test_pages.py b/lib/galaxy_test/selenium/test_pages.py
index 4505fef5b38..59b3faf9b53 100644
--- a/lib/galaxy_test/selenium/test_pages.py
+++ b/lib/galaxy_test/selenium/test_pages.py
@@ -213,7 +213,6 @@ class TestPages(SeleniumTestCase):
         self.components.pages.history.revisions_button.wait_for_visible()
         self.components.pages.history.preview_button.wait_for_visible()
         self.components.pages.history.permissions_button.wait_for_visible()
-        self.components.pages.history.save_view_button.wait_for_visible()
 
         # Back button says "Back to Reports" not "This History's Notebooks"
         back_text = self.components.pages.history.back_button.wait_for_text()

From 81e918a067e170ff5be3b39ee182ad7dfb6c3934 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sat, 13 Jun 2026 17:12:00 -0500
Subject: [PATCH 175/256] polish page revision view; make toolbar uniform below
 main page toolbar

---
 .../PageEditor/PageDisplayToolbar.vue         |  26 ++--
 .../components/PageEditor/PageEditorView.vue  |  28 ++--
 .../PageEditor/PageRevisionView.vue           | 140 ++++++++++--------
 3 files changed, 109 insertions(+), 85 deletions(-)

diff --git a/client/src/components/PageEditor/PageDisplayToolbar.vue b/client/src/components/PageEditor/PageDisplayToolbar.vue
index 5010dc46036..4abbaee1f60 100644
--- a/client/src/components/PageEditor/PageDisplayToolbar.vue
+++ b/client/src/components/PageEditor/PageDisplayToolbar.vue
@@ -37,16 +37,19 @@ const emit = defineEmits<{
 
 const showRename = ref(false);
 
+const currentEntity = computed(() => {
+    return props.labels.entityName.toLowerCase();
+});
+
 const saveDisabledTitle = computed(() => {
-    const entity = props.labels.entityName.toLowerCase();
     if (props.mode === "display") {
-        return `Currently previewing this ${entity}. Click 'Edit' to make changes and enable saving.`;
+        return `Currently previewing this ${currentEntity.value}. Click 'Edit' to make changes and enable saving.`;
     }
     if (isSaving.value) {
-        return `This ${entity} is being saved`;
+        return `This ${currentEntity.value} is being saved`;
     }
     if (!canSave.value) {
-        return `There are no changes to save to this ${entity}`;
+        return `There are no changes to save to this ${currentEntity.value}`;
     }
     return "";
 });
@@ -64,9 +67,7 @@ function handleTitleChange(newTitle: string): Promise<void> {
 </script>
 
 <template>
-    <div
-        class="page-display-toolbar d-flex align-items-center py-2 px-3 border-bottom flex-gapx-1 justify-content-between"
-        :data-description="`page ${props.mode} toolbar`">
+    <div class="page-display-toolbar border-bottom" :data-description="`page ${props.mode} toolbar`">
         <div class="d-flex align-items-center flex-gapx-1 title-section">
             <FontAwesomeIcon :icon="props.labels.titleIcon" fixed-width />
             <b class="page-title" :data-description="`page ${props.mode} title`">
@@ -77,7 +78,7 @@ function handleTitleChange(newTitle: string): Promise<void> {
                 inline
                 transparent
                 data-description="page rename button"
-                :title="`Rename this ${props.labels.entityName.toLowerCase()}`"
+                :title="`Rename this ${currentEntity}`"
                 @click="showRename = true">
                 <FontAwesomeIcon :icon="faPen" />
             </GButton>
@@ -111,7 +112,7 @@ function handleTitleChange(newTitle: string): Promise<void> {
                 @click="pageEditorStore.toggleRevisions">
                 <FontAwesomeIcon :icon="faHistory" />
                 Revisions
-                <BBadge v-if="revisionCount > 0" variant="light" class="ml-1">
+                <BBadge v-if="revisionCount > 0" variant="light" style="top: 0">
                     {{ revisionCount }}
                 </BBadge>
             </GButton>
@@ -155,7 +156,7 @@ function handleTitleChange(newTitle: string): Promise<void> {
 
         <RenameModal
             v-if="showRename"
-            :item-type="props.labels.entityName"
+            :item-type="currentEntity"
             :name="currentTitle || props.labels.defaultTitle"
             :rename-action="handleTitleChange"
             @close="showRename = false" />
@@ -165,6 +166,11 @@ function handleTitleChange(newTitle: string): Promise<void> {
 <style scoped>
 .page-display-toolbar {
     background: var(--color-grey-100);
+    display: flex;
+    align-items: center;
+    padding: 0.5rem 1rem;
+    gap: 0.5rem;
+    justify-content: space-between;
 }
 .title-section {
     min-width: 0;
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 0f56f8ce614..4cd1a03a21a 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -186,21 +186,6 @@ function handleRevisionRestore(revisionId: string) {
             @back="handleBack"
             @edit="handleEdit" />
 
-        <!-- Viewing a specific revision -->
-        <template v-else-if="store.hasCurrentPage && store.selectedRevision">
-            <PageRevisionView
-                :revision="store.selectedRevision"
-                :current-content="store.currentContent"
-                :previous-content="store.previousRevisionContent"
-                :is-newest-revision="store.isNewestRevision"
-                :is-oldest-revision="store.isOldestRevision"
-                :view-mode="store.revisionViewMode"
-                :is-reverting="store.isReverting"
-                @back="store.clearSelectedRevision"
-                @restore="handleRevisionRestore"
-                @update:viewMode="store.revisionViewMode = $event" />
-        </template>
-
         <!-- Edit mode: toolbar + editor + optional chat/revision panels -->
         <template v-else-if="store.hasCurrentPage">
             <PageDisplayToolbar :labels="labels" mode="editor" @preview="handlePreview" @back="handleBack">
@@ -224,7 +209,20 @@ function handleRevisionRestore(revisionId: string) {
 
             <div class="page-body d-flex flex-grow-1 overflow-hidden">
                 <div class="page-content flex-grow-1 overflow-auto">
+                    <PageRevisionView
+                        v-if="store.selectedRevision"
+                        :revision="store.selectedRevision"
+                        :current-content="store.currentContent"
+                        :previous-content="store.previousRevisionContent"
+                        :is-newest-revision="store.isNewestRevision"
+                        :is-oldest-revision="store.isOldestRevision"
+                        :view-mode="store.revisionViewMode"
+                        :is-reverting="store.isReverting"
+                        @back="store.clearSelectedRevision"
+                        @restore="handleRevisionRestore"
+                        @update:viewMode="store.revisionViewMode = $event" />
                     <MarkdownEditor
+                        v-else
                         class="h-100"
                         :markdown-text="store.currentContent"
                         :mode="markdownEditorMode"
diff --git a/client/src/components/PageEditor/PageRevisionView.vue b/client/src/components/PageEditor/PageRevisionView.vue
index d3b7b6fa9ca..bef6443793a 100644
--- a/client/src/components/PageEditor/PageRevisionView.vue
+++ b/client/src/components/PageEditor/PageRevisionView.vue
@@ -1,13 +1,14 @@
 <script setup lang="ts">
 import { faArrowLeft, faExchangeAlt, faEye, faSpinner, faUndo } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BButton } from "bootstrap-vue";
 import { computed } from "vue";
 
 import type { PageRevisionDetails } from "@/api/pages";
 
 import { computeLineDiff, diffStats } from "./sectionDiffUtils";
 
+import GButtonGroup from "../BaseComponents/GButtonGroup.vue";
+import GButton from "@/components/BaseComponents/GButton.vue";
 import Markdown from "@/components/Markdown/Markdown.vue";
 
 type ViewMode = "preview" | "changes_current" | "changes_previous";
@@ -56,56 +57,83 @@ const activeHasNoChanges = computed(() =>
 
 <template>
     <div class="page-revision-view d-flex flex-column h-100" data-description="page revision view">
-        <div class="revision-view-toolbar d-flex align-items-center p-2 border-bottom">
-            <BButton variant="link" size="sm" data-description="revision back button" @click="emit('back')">
-                <FontAwesomeIcon :icon="faArrowLeft" />
-                Back to revisions
-            </BButton>
-            <span class="d-flex mx-2" data-description="revision view mode toggle">
-                <BButton
-                    :variant="viewMode === 'preview' ? 'primary' : 'outline-primary'"
-                    size="sm"
-                    data-description="revision preview button"
-                    @click="emit('update:viewMode', 'preview')">
-                    <FontAwesomeIcon :icon="faEye" />
-                    Preview
-                </BButton>
-                <BButton
-                    v-if="!isNewestRevision"
-                    :variant="viewMode === 'changes_current' ? 'primary' : 'outline-primary'"
-                    size="sm"
-                    class="ml-1"
-                    data-description="revision compare current button"
-                    @click="emit('update:viewMode', 'changes_current')">
-                    <FontAwesomeIcon :icon="faExchangeAlt" />
-                    Compare to Current
-                </BButton>
-                <BButton
-                    v-if="!isOldestRevision"
-                    :variant="viewMode === 'changes_previous' ? 'primary' : 'outline-primary'"
-                    size="sm"
-                    class="ml-1"
-                    data-description="revision compare previous button"
-                    @click="emit('update:viewMode', 'changes_previous')">
-                    <FontAwesomeIcon :icon="faExchangeAlt" />
-                    Compare to Previous
-                </BButton>
-            </span>
-            <span class="flex-grow-1"></span>
-            <BButton
-                variant="primary"
-                size="sm"
-                data-description="revision restore button"
-                :disabled="isReverting"
-                @click="emit('restore', revision.id)">
-                <FontAwesomeIcon :icon="isReverting ? faSpinner : faUndo" :spin="isReverting" />
-                Restore this version
-            </BButton>
+        <div class="revision-view-toolbar border-bottom">
+            <div class="d-flex">
+                <GButtonGroup data-description="revision view mode toggle">
+                    <GButton
+                        color="blue"
+                        outline
+                        :pressed="viewMode === 'preview'"
+                        data-description="revision preview button"
+                        size="small"
+                        @click="emit('update:viewMode', 'preview')">
+                        <FontAwesomeIcon :icon="faEye" />
+                        Preview
+                    </GButton>
+                    <GButton
+                        v-if="!isNewestRevision"
+                        color="blue"
+                        outline
+                        :pressed="viewMode === 'changes_current'"
+                        data-description="revision compare current button"
+                        size="small"
+                        @click="emit('update:viewMode', 'changes_current')">
+                        <FontAwesomeIcon :icon="faExchangeAlt" />
+                        Compare to Current
+                    </GButton>
+                    <GButton
+                        v-if="!isOldestRevision"
+                        color="blue"
+                        outline
+                        :pressed="viewMode === 'changes_previous'"
+                        data-description="revision compare previous button"
+                        size="small"
+                        @click="emit('update:viewMode', 'changes_previous')">
+                        <FontAwesomeIcon :icon="faExchangeAlt" />
+                        Compare to Previous
+                    </GButton>
+                </GButtonGroup>
+
+                <div v-if="!activeHasNoChanges" class="d-flex align-items-center px-2">
+                    <span class="diff-stats">
+                        <span class="text-success">+{{ activeStats.additions }}</span>
+                        <span class="mx-1">/</span>
+                        <span class="text-danger">-{{ activeStats.deletions }}</span>
+                        lines
+                    </span>
+                </div>
+            </div>
+
+            <div class="d-flex flex-gapx-1 align-items-center">
+                <GButton
+                    color="blue"
+                    transparent
+                    size="small"
+                    data-description="revision back button"
+                    @click="emit('back')">
+                    <FontAwesomeIcon :icon="faArrowLeft" />
+                    Exit Revision
+                </GButton>
+                <GButton
+                    color="blue"
+                    size="small"
+                    title="Restore this version"
+                    tooltip
+                    data-description="revision restore button"
+                    :disabled="isReverting"
+                    @click="emit('restore', revision.id)">
+                    <FontAwesomeIcon :icon="isReverting ? faSpinner : faUndo" :spin="isReverting" />
+                    Restore
+                </GButton>
+            </div>
         </div>
+
         <div class="revision-view-content overflow-auto flex-grow-1">
             <Markdown
                 v-if="viewMode === 'preview'"
+                class="px-3 pt-3"
                 :markdown-config="markdownConfig"
+                no-heading
                 :read-only="true"
                 download-endpoint="" />
             <div
@@ -120,14 +148,6 @@ const activeHasNoChanges = computed(() =>
                     {{ viewMode === "changes_current" ? "current content" : "previous revision" }}.
                 </div>
                 <template v-else>
-                    <div class="diff-header d-flex align-items-center p-2">
-                        <span class="diff-stats">
-                            <span class="text-success">+{{ activeStats.additions }}</span>
-                            <span class="mx-1">/</span>
-                            <span class="text-danger">-{{ activeStats.deletions }}</span>
-                            lines
-                        </span>
-                    </div>
                     <div class="diff-content">
                         <div v-for="(change, idx) in activeChanges" :key="idx" class="diff-block">
                             <pre
@@ -151,18 +171,18 @@ const activeHasNoChanges = computed(() =>
 
 <style scoped>
 .revision-view-toolbar {
-    background: var(--panel-header-bg);
+    background: var(--color-grey-100);
+    display: flex;
+    align-items: center;
+    padding: 0.5rem 1rem;
+    gap: 0.5rem;
+    justify-content: space-between;
 }
 
 .revision-diff-view {
     font-size: 0.85rem;
 }
 
-.diff-header {
-    background: var(--panel-header-bg, #f8f9fa);
-    border-bottom: 1px solid var(--border-color, #dee2e6);
-}
-
 .diff-content {
     overflow: auto;
     padding: 0;

From 2cd0cbb755a780df1f55e25d6306feb1d763d523 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sat, 13 Jun 2026 17:13:21 -0500
Subject: [PATCH 176/256] put page/notebook revisions in a modal

---
 client/src/components/Common/SidebarList.vue  |  2 +-
 .../components/PageEditor/PageEditorView.vue  | 28 ++++++++++++-------
 .../PageEditor/PageRevisionList.vue           |  4 +++
 .../selenium/test_history_pages.py            |  2 +-
 lib/galaxy_test/selenium/test_pages.py        |  2 +-
 5 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/client/src/components/Common/SidebarList.vue b/client/src/components/Common/SidebarList.vue
index 5a2b4260372..4e97469a8df 100644
--- a/client/src/components/Common/SidebarList.vue
+++ b/client/src/components/Common/SidebarList.vue
@@ -67,7 +67,7 @@ function onItemKeydown(item: any, index: number, event: KeyboardEvent) {
     overflow-y: auto;
 }
 .sidebar-item:hover {
-    background: var(--gray-200);
+    background: var(--color-grey-200);
     cursor: pointer;
 }
 </style>
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 4cd1a03a21a..3c220a70c0b 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -13,6 +13,7 @@ import { useHistoryStore } from "@/stores/historyStore";
 import { type PageEditorMode, usePageEditorStore } from "@/stores/pageEditorStore";
 
 import GButton from "../BaseComponents/GButton.vue";
+import GModal from "../BaseComponents/GModal.vue";
 import ObjectPermissionsModal from "./ObjectPermissionsModal.vue";
 import PageDisplayOnly from "./PageDisplayOnly.vue";
 import PageDisplayToolbar from "./PageDisplayToolbar.vue";
@@ -158,8 +159,9 @@ function handleContentUpdate(newContent: string) {
     store.updateContent(newContent);
 }
 
-function handleRevisionSelect(revisionId: string) {
-    store.loadRevision(revisionId);
+async function handleRevisionSelect(revisionId: string) {
+    await store.loadRevision(revisionId);
+    store.showRevisions = false;
 }
 
 function handleRevisionRestore(revisionId: string) {
@@ -229,14 +231,26 @@ function handleRevisionRestore(revisionId: string) {
                         :title="editorTitle"
                         @update="handleContentUpdate" />
                 </div>
-                <div v-if="store.showRevisions" class="page-revision-panel border-left">
+                <GModal
+                    data-description="page revisions modal"
+                    fixed-height
+                    :show.sync="store.showRevisions"
+                    size="small"
+                    :title="`${labels.entityName} Revisions`">
+                    <template v-slot:header>
+                        <div class="d-flex align-items-center flex-gapx-1">
+                            <FontAwesomeIcon v-if="store.isLoadingRevision" :icon="faSpinner" spin fixed-width />
+                            Click to select and view a revision in the editor
+                        </div>
+                    </template>
                     <PageRevisionList
                         :revisions="store.revisions"
                         :is-loading="store.isLoadingRevisions"
                         :is-reverting="store.isReverting"
+                        :selected-revision-id="store.selectedRevision?.id"
                         @select="handleRevisionSelect"
                         @restore="handleRevisionRestore" />
-                </div>
+                </GModal>
             </div>
         </template>
     </div>
@@ -246,12 +260,6 @@ function handleRevisionRestore(revisionId: string) {
 .page-editor-view {
     background: var(--body-bg);
 }
-.page-revision-panel {
-    width: 300px;
-    min-width: 300px;
-    overflow-y: auto;
-    background: var(--body-bg);
-}
 .page-editor-pane {
     padding: 1rem;
     display: flex;
diff --git a/client/src/components/PageEditor/PageRevisionList.vue b/client/src/components/PageEditor/PageRevisionList.vue
index 2b5bbc277ca..a01a3dcb183 100644
--- a/client/src/components/PageEditor/PageRevisionList.vue
+++ b/client/src/components/PageEditor/PageRevisionList.vue
@@ -11,6 +11,7 @@ const props = defineProps<{
     revisions: PageRevisionSummary[];
     isLoading: boolean;
     isReverting: boolean;
+    selectedRevisionId?: string;
 }>();
 
 const emit = defineEmits<{
@@ -62,6 +63,9 @@ function onSelect(rev: PageRevisionSummary) {
                         <span class="font-weight-bold">{{ formatDate(rev.create_time) }}</span>
                         <span class="text-muted ml-1">({{ sourceLabel(rev.edit_source) }})</span>
                         <span v-if="index === 0" class="badge badge-primary ml-1">Current</span>
+                        <span v-if="rev.id === props.selectedRevisionId" class="badge badge-secondary ml-1">
+                            Viewing
+                        </span>
                     </div>
                 </div>
                 <BButton
diff --git a/lib/galaxy_test/selenium/test_history_pages.py b/lib/galaxy_test/selenium/test_history_pages.py
index f673ec30c7c..b57560746d9 100644
--- a/lib/galaxy_test/selenium/test_history_pages.py
+++ b/lib/galaxy_test/selenium/test_history_pages.py
@@ -525,7 +525,7 @@ class TestHistoryPages(SeleniumTestCase):
         assert "Modified content" in diff_text or "New section" in diff_text
 
         # Go back, click oldest revision
-        self.components.pages.history.revision_back_button.wait_for_and_click()
+        self.history_page_open_revisions()
         items = self.components.pages.history.revision_item.all()
         items[-1].click()
         self.components.pages.history.revision_view.wait_for_visible()
diff --git a/lib/galaxy_test/selenium/test_pages.py b/lib/galaxy_test/selenium/test_pages.py
index 59b3faf9b53..3c3d72fff34 100644
--- a/lib/galaxy_test/selenium/test_pages.py
+++ b/lib/galaxy_test/selenium/test_pages.py
@@ -185,7 +185,7 @@ class TestPages(SeleniumTestCase):
         assert "Beta" in diff_text or "Alpha" in diff_text
 
         # Go back, click oldest revision
-        self.components.pages.history.revision_back_button.wait_for_and_click()
+        self.history_page_open_revisions()
         items = self.components.pages.history.revision_item.all()
         items[-1].click()
         self.components.pages.history.revision_view.wait_for_visible()

From c416ba91f329938092158eef998b7148772a9d40 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sat, 13 Jun 2026 17:45:34 -0500
Subject: [PATCH 177/256] add error handling to page creation/update and handle
 errors better on client

---
 .../components/PageDisplay/PageForm.test.js   | 43 +++++++++-------
 .../src/components/PageDisplay/PageForm.vue   | 50 +++++++++++++++----
 client/src/entry/analysis/router.js           |  2 +
 lib/galaxy/managers/pages.py                  |  4 ++
 4 files changed, 69 insertions(+), 30 deletions(-)

diff --git a/client/src/components/PageDisplay/PageForm.test.js b/client/src/components/PageDisplay/PageForm.test.js
index 6b0d08de27f..f3d43af641a 100644
--- a/client/src/components/PageDisplay/PageForm.test.js
+++ b/client/src/components/PageDisplay/PageForm.test.js
@@ -1,13 +1,22 @@
 import { getLocalVue } from "@tests/vitest/helpers";
 import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
-import { describe, expect, it, vi } from "vitest";
+import { beforeEach, describe, expect, it, vi } from "vitest";
 
 import { useServerMock } from "@/api/client/__mocks__";
 import pageTemplate from "@/components/PageDisplay/pageTemplate.yml";
+import { Toast } from "@/composables/toast";
 
 import PageForm from "./PageForm.vue";
 
+vi.mock("@/composables/toast", () => {
+    const toastInstance = { success: vi.fn(), error: vi.fn() };
+    return {
+        Toast: toastInstance,
+        useToast: () => toastInstance,
+    };
+});
+
 const { server, http } = useServerMock();
 const localVue = getLocalVue();
 
@@ -35,6 +44,10 @@ function mountTarget(props = {}) {
 }
 
 describe("PageForm.vue - Create mode", () => {
+    beforeEach(() => {
+        vi.clearAllMocks();
+    });
+
     it("renders loading spinner when fetching report", async () => {
         server.use(
             http.get("/api/invocations/:invocation_id/report", ({ response }) =>
@@ -79,14 +92,10 @@ describe("PageForm.vue - Create mode", () => {
         expect(alert.text()).toContain("Failed to fetch report");
     });
 
-    it("shows validation error when required fields are missing on submit", async () => {
+    it("submit button is disabled when required fields are missing", async () => {
         const wrapper = mountTarget({ mode: "create" });
         await flushPromises();
-        await wrapper.find("#page-submit").trigger("click");
-        await flushPromises();
-        const alert = wrapper.findComponent({ name: "BAlert" });
-        expect(alert.exists()).toBe(true);
-        expect(alert.text()).toContain("Please complete all required inputs.");
+        expect(wrapper.find("#page-submit").classes()).toContain("g-disabled");
     });
 
     it("submits page creation with correct fields", async () => {
@@ -118,13 +127,15 @@ describe("PageForm.vue - Create mode", () => {
         await wrapper.find("#page-slug").setValue("some-title");
         await wrapper.find("#page-submit").trigger("click");
         await flushPromises();
-        const alert = wrapper.findComponent({ name: "BAlert" });
-        expect(alert.exists()).toBe(true);
-        expect(alert.text()).toContain("Creation failed");
+        expect(Toast.error).toHaveBeenCalledWith("Creation failed", "Error Creating Page");
     });
 });
 
 describe("PageForm.vue - Edit mode", () => {
+    beforeEach(() => {
+        vi.clearAllMocks();
+    });
+
     it("renders loading spinner and fetches page details", async () => {
         server.use(
             http.get("/api/pages/:id", ({ response }) =>
@@ -154,14 +165,10 @@ describe("PageForm.vue - Edit mode", () => {
         expect(alert.text()).toContain("Page load failed");
     });
 
-    it("shows validation error if required fields are missing on update", async () => {
+    it("submit button is disabled when required fields are missing", async () => {
         const wrapper = mountTarget({ mode: "edit", id: "123" });
         await flushPromises();
-        await wrapper.find("#page-submit").trigger("click");
-        await flushPromises();
-        const alert = wrapper.findComponent({ name: "BAlert" });
-        expect(alert.exists()).toBe(true);
-        expect(alert.text()).toContain("Please complete all required inputs.");
+        expect(wrapper.find("#page-submit").classes()).toContain("g-disabled");
     });
 
     it("submits page update with correct fields", async () => {
@@ -192,8 +199,6 @@ describe("PageForm.vue - Edit mode", () => {
         await wrapper.find("#page-slug").setValue("error-title");
         await wrapper.find("#page-submit").trigger("click");
         await flushPromises();
-        const alert = wrapper.findComponent({ name: "BAlert" });
-        expect(alert.exists()).toBe(true);
-        expect(alert.text()).toContain("Update failed");
+        expect(Toast.error).toHaveBeenCalledWith("Update failed", "Error Updating Page");
     });
 });
diff --git a/client/src/components/PageDisplay/PageForm.vue b/client/src/components/PageDisplay/PageForm.vue
index 427a2bd3c22..4e49f08b223 100644
--- a/client/src/components/PageDisplay/PageForm.vue
+++ b/client/src/components/PageDisplay/PageForm.vue
@@ -1,8 +1,10 @@
 <template>
     <div>
-        <LoadingSpan v-if="loading" />
+        <BAlert v-if="loading" show>
+            <LoadingSpan />
+        </BAlert>
+        <BAlert v-else-if="errorMessage" variant="danger" show>{{ errorMessage }}</BAlert>
         <div v-else>
-            <BAlert v-if="errorMessage" variant="danger" show>{{ errorMessage }}</BAlert>
             <FormCard :title="cardTitle" icon="fa-file-contract">
                 <template v-slot:body>
                     <FormElementLabel title="Title" :required="true" :condition="!!title">
@@ -20,26 +22,34 @@
                     </FormElementLabel>
                 </template>
             </FormCard>
-            <BButton id="page-submit" class="my-2" variant="primary" @click="onSubmit">
-                <FontAwesomeIcon :icon="faSave" class="mr-1" />
+            <GButton
+                id="page-submit"
+                class="my-2"
+                color="blue"
+                :disabled="submitting || !title || !slug"
+                :disabled-title="disabledTitle"
+                @click="onSubmit">
+                <FontAwesomeIcon :icon="submitting ? faSpinner : faSave" class="mr-1" :spin="submitting" />
                 <span v-localize>{{ buttonText }}</span>
-            </BButton>
+            </GButton>
         </div>
     </div>
 </template>
 
 <script setup lang="ts">
-import { faSave } from "@fortawesome/free-solid-svg-icons";
+import { faSave, faSpinner } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton } from "bootstrap-vue";
-import { ref, watch } from "vue";
+import { BAlert } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { GalaxyApi } from "@/api";
 import { fetchInvocationReport } from "@/api/invocations";
 import { FORM_LABELS } from "@/components/Page/constants";
 import pageTemplate from "@/components/PageDisplay/pageTemplate.yml";
+import { useToast } from "@/composables/toast";
 
+import GButton from "@/components/BaseComponents/GButton.vue";
 import FormInput from "@/components/Form/Elements/FormInput.vue";
 import FormCard from "@/components/Form/FormCard.vue";
 import FormElementLabel from "@/components/Form/FormElementLabel.vue";
@@ -55,11 +65,24 @@ const annotation = ref("");
 const content = ref(pageTemplate.content);
 const errorMessage = ref("");
 const loading = ref(false);
+const submitting = ref(false);
 const slug = ref("");
 const title = ref("");
 
+const disabledTitle = computed(() => {
+    if (submitting.value) {
+        return "Submitting";
+    }
+    if (!title.value || !slug.value) {
+        return "Please complete all required inputs.";
+    }
+    return "";
+});
+
 const router = useRouter();
 
+const Toast = useToast();
+
 const cardTitle = props.mode === "edit" ? FORM_LABELS.editTitle : FORM_LABELS.createTitle;
 const buttonText = props.mode === "edit" ? "Update" : "Create";
 
@@ -97,10 +120,11 @@ async function fetchData() {
 
 async function onSubmit() {
     if (!slug.value || !title.value) {
-        errorMessage.value = "Please complete all required inputs.";
+        Toast.error("Please complete all required inputs.");
         return;
     }
 
+    submitting.value = true;
     if (props.mode === "create") {
         const { data, error } = await GalaxyApi().POST("/api/pages", {
             body: {
@@ -113,10 +137,12 @@ async function onSubmit() {
             },
         });
         if (error) {
-            errorMessage.value = error.err_msg;
+            Toast.error(error.err_msg, "Error Creating Page");
         } else if (data.history_id) {
+            Toast.success("Galaxy Notebook created successfully");
             router.push(`/histories/${data.history_id}/pages/${data.id}`);
         } else {
+            Toast.success("Report created successfully");
             router.push(`/pages/editor?id=${data.id}`);
         }
     } else {
@@ -129,11 +155,13 @@ async function onSubmit() {
             },
         });
         if (error) {
-            errorMessage.value = error.err_msg;
+            Toast.error(error.err_msg, "Error Updating Page");
         } else {
+            Toast.success("Page updated successfully");
             router.push("/pages/list");
         }
     }
+    submitting.value = false;
 }
 
 watch(() => [props.id, props.invocationId], fetchData, { immediate: true });
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index c70d4c18642..b78a6b624dc 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -556,6 +556,7 @@ export function getRouter(Galaxy) {
                             invocationId: route.query.invocation_id,
                             mode: "create",
                         }),
+                        redirect: redirectAnon(),
                     },
                     {
                         path: "pages/edit",
@@ -564,6 +565,7 @@ export function getRouter(Galaxy) {
                             id: route.query.id,
                             mode: "edit",
                         }),
+                        redirect: redirectAnon(),
                     },
                     {
                         path: "/pages/editor",
diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index af4e4c8f782..ec40c3836e3 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -273,6 +273,8 @@ class PageManager(sharable.SharableModelManager[model.Page], UsesAnnotations):
 
     def create_page(self, trans, payload: CreatePagePayload):
         user = trans.get_user()
+        if not user:
+            raise exceptions.AuthenticationRequired("You must be logged in to create pages.")
         history_id = getattr(payload, "history_id", None)
 
         # When creating from an invocation, automatically attach to its history
@@ -343,6 +345,8 @@ class PageManager(sharable.SharableModelManager[model.Page], UsesAnnotations):
 
     def update_page(self, trans, id: int, payload: UpdatePagePayload):
         user = trans.get_user()
+        if not user:
+            raise exceptions.AuthenticationRequired("You must be logged in to update pages.")
 
         # Load page from database
         page = trans.sa_session.get(model.Page, id)

From 42cf5f1c18bb253ac1eaf8c4169465a6e2b9eae6 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 00:50:31 -0500
Subject: [PATCH 178/256] add tests for `PageDisplayToolbar` that incorporate
 all other tests

---
 .../PageEditor/HistoryPageView.test.ts        |  31 +-
 .../PageEditor/PageDisplayToolbar.test.ts     | 225 +++++++++++++
 .../PageEditor/PageDisplayToolbar.vue         |   6 +-
 .../PageEditor/PageEditorView.test.ts         | 317 +++++-------------
 .../PageEditor/PageRevisionView.test.ts       |  30 +-
 5 files changed, 332 insertions(+), 277 deletions(-)
 create mode 100644 client/src/components/PageEditor/PageDisplayToolbar.test.ts

diff --git a/client/src/components/PageEditor/HistoryPageView.test.ts b/client/src/components/PageEditor/HistoryPageView.test.ts
index 4bbc1c1f717..e97d4885aca 100644
--- a/client/src/components/PageEditor/HistoryPageView.test.ts
+++ b/client/src/components/PageEditor/HistoryPageView.test.ts
@@ -9,8 +9,8 @@ import { usePageEditorStore } from "@/stores/pageEditorStore";
 
 import HistoryPageList from "./HistoryPageList.vue";
 import HistoryPageView from "./HistoryPageView.vue";
+import PageDisplayOnly from "./PageDisplayOnly.vue";
 import PageEditorView from "./PageEditorView.vue";
-import Markdown from "@/components/Markdown/Markdown.vue";
 
 vi.mock("@/composables/config", () => ({
     useConfig: vi.fn(() => ({
@@ -60,10 +60,7 @@ const PAGE_ID = "page-1";
 const SELECTORS = {
     INFO_ALERT: "balert-stub[variant='info']",
     ERROR_ALERT: "balert-stub[variant='danger']",
-    DISPLAY_TOOLBAR: "[data-description='page display toolbar']",
-    EDIT_BUTTON: "[data-description='page edit button']",
-    MANAGE_BUTTON: "[data-description='page manage button']",
-};
+} as const;
 
 let pinia: Pinia;
 
@@ -203,7 +200,7 @@ describe("HistoryPageView", () => {
             await flushPromises();
 
             expect(wrapper.findComponent(PageEditorView).exists()).toBe(false);
-            expect(wrapper.findComponent(Markdown).exists()).toBe(true);
+            expect(wrapper.findComponent(PageDisplayOnly).exists()).toBe(true);
         });
     });
 
@@ -232,41 +229,27 @@ describe("HistoryPageView", () => {
             const wrapper = mountComponent({ historyId: HISTORY_ID, pageId: PAGE_ID, displayOnly: true });
             await flushPromises();
 
-            expect(wrapper.findComponent(Markdown).exists()).toBe(true);
+            expect(wrapper.findComponent(PageDisplayOnly).exists()).toBe(true);
         });
 
-        it("passes correct markdownConfig to Markdown", async () => {
+        it("passes correct markdownConfig to PageDisplayOnly", async () => {
             setupLoadedPage();
             const wrapper = mountComponent({ historyId: HISTORY_ID, pageId: PAGE_ID, displayOnly: true });
             await flushPromises();
 
-            const md = wrapper.findComponent(Markdown);
+            const md = wrapper.findComponent(PageDisplayOnly);
             const config = md.props("markdownConfig");
             expect(config.id).toBe(PAGE_ID);
             expect(config.title).toBe("My Page");
             expect(config.content).toBe("# Hello");
         });
 
-        it("shows display toolbar with Edit button", async () => {
-            setupLoadedPage();
-            const wrapper = mountComponent({ historyId: HISTORY_ID, pageId: PAGE_ID, displayOnly: true });
-            await flushPromises();
-
-            expect(wrapper.find(SELECTORS.DISPLAY_TOOLBAR).exists()).toBe(true);
-            const editBtn = wrapper.find(SELECTORS.EDIT_BUTTON);
-            expect(editBtn.exists()).toBe(true);
-            expect(editBtn.text()).toContain("Edit");
-        });
-
         it("Edit button navigates to edit mode (no displayOnly)", async () => {
             setupLoadedPage();
             const wrapper = mountComponent({ historyId: HISTORY_ID, pageId: PAGE_ID, displayOnly: true });
             await flushPromises();
 
-            const editBtn = wrapper.find(SELECTORS.EDIT_BUTTON);
-            // GButton is stubbed by shallowMount; emit the Vue click event to trigger @click handler
-            await editBtn.vm.$emit("click");
-            await wrapper.vm.$nextTick();
+            wrapper.findComponent(PageDisplayOnly).vm.$emit("edit");
 
             expect(mockPush).toHaveBeenCalledWith(`/histories/${HISTORY_ID}/pages/${PAGE_ID}`);
         });
diff --git a/client/src/components/PageEditor/PageDisplayToolbar.test.ts b/client/src/components/PageEditor/PageDisplayToolbar.test.ts
new file mode 100644
index 00000000000..e5e5e31f552
--- /dev/null
+++ b/client/src/components/PageEditor/PageDisplayToolbar.test.ts
@@ -0,0 +1,225 @@
+import { createTestingPinia } from "@pinia/testing";
+import { getLocalVue } from "@tests/vitest/helpers";
+import { mount, type Wrapper } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import type { Pinia } from "pinia";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+import type { HistoryPageDetails, PageRevisionSummary } from "@/api/pages.js";
+import { usePageEditorStore } from "@/stores/pageEditorStore";
+
+import { PAGE_LABELS } from "../Page/constants.js";
+
+import PageDisplayToolbar from "./PageDisplayToolbar.vue";
+
+const localVue = getLocalVue();
+
+const HISTORY_ID = "history-1";
+const PAGE_ID = "page-1";
+
+const SELECTORS = {
+    EDITOR_TOOLBAR: "[data-description='page editor toolbar']",
+    DISPLAY_TOOLBAR: "[data-description='page display toolbar']",
+    TOOLBAR_TITLE: "[data-description='page editor title']",
+    SAVE_BUTTON: "[data-description='page save button']",
+    BACK_BUTTON: "[data-description='page back button']",
+    UNSAVED_INDICATOR: "[data-description='page unsaved indicator']",
+    REVISIONS_BUTTON: "[data-description='page revisions button']",
+    REVISIONS_BADGE: "[data-description='page revision count badge']",
+    EDIT_BUTTON: "[data-description='page edit button']",
+    RENAME_BUTTON: "[data-description='page rename button']",
+    RENAME_INPUT: "[data-description='galaxy notebook name input']",
+    PREVIEW_BUTTON: "[data-description='page preview button']",
+} as const;
+
+let pinia: Pinia;
+
+function mountComponent(propsData: {
+    labels: (typeof PAGE_LABELS)[keyof typeof PAGE_LABELS];
+    mode: "editor" | "display";
+}) {
+    return mount(PageDisplayToolbar as object, {
+        localVue,
+        propsData,
+        pinia,
+    });
+}
+
+describe("PageDisplayToolbar", () => {
+    function setupLoadedPage() {
+        const newStore = usePageEditorStore();
+        newStore.isLoadingList = false;
+        newStore.isLoadingPage = false;
+        newStore.error = null;
+        newStore.currentPage = {
+            id: PAGE_ID,
+            history_id: HISTORY_ID,
+            title: "My Page",
+            content: "# Hello",
+            update_time: "2024-01-01T00:00:00",
+        } as HistoryPageDetails;
+        newStore.currentContent = "# Hello";
+        newStore.currentTitle = "My Page";
+        newStore.revisions = [
+            { id: "rev-1", page_id: PAGE_ID, edit_source: "user", create_time: "", update_time: "" },
+            { id: "rev-2", page_id: PAGE_ID, edit_source: "user", create_time: "", update_time: "" },
+        ] as PageRevisionSummary[];
+        return newStore;
+    }
+
+    let wrapper: Wrapper<Vue>;
+    let store: ReturnType<typeof usePageEditorStore>;
+
+    beforeEach(async () => {
+        pinia = createTestingPinia({ createSpy: vi.fn });
+        store = setupLoadedPage();
+        await flushPromises();
+        vi.clearAllMocks();
+    });
+
+    afterEach(() => {
+        vi.restoreAllMocks();
+    });
+
+    describe("editor mode", () => {
+        beforeEach(async () => {
+            wrapper = mountComponent({ labels: PAGE_LABELS.history, mode: "editor" });
+            await flushPromises();
+        });
+
+        it("shows edit toolbar with Edit button pressed", async () => {
+            expect(wrapper.find(SELECTORS.EDITOR_TOOLBAR).exists()).toBe(true);
+
+            expect(wrapper.find(SELECTORS.EDIT_BUTTON).props("pressed")).toBe(true);
+            expect(wrapper.find(SELECTORS.PREVIEW_BUTTON).props("pressed")).toBe(false);
+        });
+
+        it("shows rename button and page title in toolbar", () => {
+            expect(wrapper.find(SELECTORS.RENAME_BUTTON).exists()).toBe(true);
+            expect(wrapper.find(SELECTORS.TOOLBAR_TITLE).text()).toBe("My Page");
+        });
+
+        it("shows 'Untitled Notebook' in title when currentTitle is empty", async () => {
+            store.currentTitle = "";
+            await wrapper.vm.$nextTick();
+
+            expect(wrapper.find(SELECTORS.TOOLBAR_TITLE).text()).toBe("Untitled Notebook");
+        });
+
+        it("shows 'Unsaved' indicator when store.isDirty is true", async () => {
+            await wrapper.vm.$nextTick();
+
+            expect(store.isDirty).toBe(true);
+            const unsaved = wrapper.find(SELECTORS.UNSAVED_INDICATOR);
+            expect(unsaved.exists()).toBe(true);
+            expect(unsaved.text()).toBe("Unsaved");
+        });
+
+        it("save button is disabled when store.canSave is false", async () => {
+            store.currentContent = "";
+            store.currentTitle = "";
+            await wrapper.vm.$nextTick();
+
+            expect(store.canSave).toBe(false);
+            const saveBtn = wrapper.find(SELECTORS.SAVE_BUTTON);
+            expect(saveBtn.attributes("aria-disabled")).toBe("true");
+        });
+
+        it("shows Preview button in toolbar", () => {
+            const previewBtn = wrapper.find(SELECTORS.PREVIEW_BUTTON);
+            expect(previewBtn.exists()).toBe(true);
+            expect(previewBtn.text()).toContain("Preview");
+        });
+
+        it("Preview button emits a preview event", async () => {
+            const previewBtn = wrapper.find(SELECTORS.PREVIEW_BUTTON);
+            await previewBtn.trigger("click");
+
+            expect(wrapper.emitted("preview")).toHaveLength(1);
+        });
+
+        it("rename button opens rename modal which renames the page", async () => {
+            expect(wrapper.find(SELECTORS.RENAME_BUTTON).exists()).toBe(true);
+
+            const renameBtn = wrapper.find(SELECTORS.RENAME_BUTTON);
+            await renameBtn.trigger("click");
+            await wrapper.vm.$nextTick();
+
+            const renameInput = wrapper.find(SELECTORS.RENAME_INPUT);
+            expect(renameInput.exists()).toBe(true);
+            expect((renameInput.element as HTMLInputElement).value).toBe("My Page");
+
+            (renameInput.element as HTMLInputElement).value = "Renamed Page";
+            await renameInput.trigger("input");
+
+            const renameBtnInModal = wrapper.find(".g-modal-confirm-buttons .g-blue");
+            await renameBtnInModal.trigger("click");
+            await wrapper.vm.$nextTick();
+
+            expect(store.updateTitle).toHaveBeenCalledWith("Renamed Page");
+        });
+
+        it("back button emits a back event", async () => {
+            const backBtn = wrapper.find(SELECTORS.BACK_BUTTON);
+            await backBtn.trigger("click");
+
+            expect(wrapper.emitted("back")).toHaveLength(1);
+        });
+
+        it("save button calls store.savePage", async () => {
+            const saveBtn = wrapper.find(SELECTORS.SAVE_BUTTON);
+            await saveBtn.trigger("click");
+            await flushPromises();
+
+            expect(store.savePage).toHaveBeenCalled();
+        });
+
+        it("back button text says whatever the label back button value is", () => {
+            const backBtn = wrapper.find(SELECTORS.BACK_BUTTON);
+            expect(backBtn.text()).toContain(PAGE_LABELS.history.editorBackLabel);
+        });
+
+        describe("revisions", () => {
+            it("shows Revisions button in toolbar", () => {
+                const revBtn = wrapper.find(SELECTORS.REVISIONS_BUTTON);
+                expect(revBtn.exists()).toBe(true);
+                expect(revBtn.text()).toContain("Revisions");
+            });
+
+            it("clicking Revisions button calls store.toggleRevisions", async () => {
+                const revBtn = wrapper.find(SELECTORS.REVISIONS_BUTTON);
+                await revBtn.trigger("click");
+
+                expect(store.toggleRevisions).toHaveBeenCalled();
+            });
+
+            it("revision badge shows count when revisions loaded", () => {
+                const badge = wrapper.find(SELECTORS.REVISIONS_BADGE);
+                expect(badge.exists()).toBe(true);
+                expect(badge.text()).toBe("2");
+            });
+        });
+    });
+
+    describe("display mode", () => {
+        beforeEach(async () => {
+            wrapper = mountComponent({ labels: PAGE_LABELS.history, mode: "display" });
+            await flushPromises();
+        });
+
+        it("shows display toolbar with Preview button pressed", async () => {
+            expect(wrapper.find(SELECTORS.DISPLAY_TOOLBAR).exists()).toBe(true);
+
+            expect(wrapper.find(SELECTORS.EDIT_BUTTON).props("pressed")).toBe(false);
+            expect(wrapper.find(SELECTORS.PREVIEW_BUTTON).props("pressed")).toBe(true);
+        });
+
+        it("Edit button emits an edit event", async () => {
+            const editBtn = wrapper.find(SELECTORS.EDIT_BUTTON);
+            await editBtn.trigger("click");
+            await wrapper.vm.$nextTick();
+
+            expect(wrapper.emitted("edit")).toHaveLength(1);
+        });
+    });
+});
diff --git a/client/src/components/PageEditor/PageDisplayToolbar.vue b/client/src/components/PageEditor/PageDisplayToolbar.vue
index 4abbaee1f60..abbfabaf6b9 100644
--- a/client/src/components/PageEditor/PageDisplayToolbar.vue
+++ b/client/src/components/PageEditor/PageDisplayToolbar.vue
@@ -112,7 +112,11 @@ function handleTitleChange(newTitle: string): Promise<void> {
                 @click="pageEditorStore.toggleRevisions">
                 <FontAwesomeIcon :icon="faHistory" />
                 Revisions
-                <BBadge v-if="revisionCount > 0" variant="light" style="top: 0">
+                <BBadge
+                    v-if="revisionCount > 0"
+                    variant="light"
+                    style="top: 0"
+                    data-description="page revision count badge">
                     {{ revisionCount }}
                 </BBadge>
             </GButton>
diff --git a/client/src/components/PageEditor/PageEditorView.test.ts b/client/src/components/PageEditor/PageEditorView.test.ts
index 1ff36e8f84a..51f7fdbad9b 100644
--- a/client/src/components/PageEditor/PageEditorView.test.ts
+++ b/client/src/components/PageEditor/PageEditorView.test.ts
@@ -10,11 +10,12 @@ import { ref } from "vue";
 import type { HistoryPageDetails, PageRevisionDetails, PageRevisionSummary } from "@/api/pages";
 import { usePageEditorStore } from "@/stores/pageEditorStore";
 
+import GModal from "../BaseComponents/GModal.vue";
+import PageDisplayOnly from "./PageDisplayOnly.vue";
+import PageDisplayToolbar from "./PageDisplayToolbar.vue";
 import PageEditorView from "./PageEditorView.vue";
 import PageRevisionList from "./PageRevisionList.vue";
 import PageRevisionView from "./PageRevisionView.vue";
-import ClickToEdit from "@/components/ClickToEdit.vue";
-import Markdown from "@/components/Markdown/Markdown.vue";
 import MarkdownEditor from "@/components/Markdown/MarkdownEditor.vue";
 
 const mockConfig = ref<Record<string, unknown> | null>({ llm_api_configured: true });
@@ -57,21 +58,6 @@ const localVue = getLocalVue();
 const HISTORY_ID = "history-1";
 const PAGE_ID = "page-1";
 
-const SELECTORS = {
-    TOOLBAR: "[data-description='page editor toolbar']",
-    TOOLBAR_TITLE: "[data-description='page editor title']",
-    SAVE_BUTTON: "[data-description='page save button']",
-    BACK_BUTTON: "[data-description='page back button']",
-    UNSAVED_INDICATOR: "[data-description='page unsaved indicator']",
-    REVISIONS_BUTTON: "[data-description='page revisions button']",
-    REVISION_PANEL: ".page-revision-panel",
-    PREVIEW_BUTTON: "[data-description='page preview button']",
-    PERMISSIONS_BUTTON: "[data-description='page permissions button']",
-    SAVE_VIEW_BUTTON: "[data-description='page save-view button']",
-    EDIT_BUTTON: "[data-description='page edit button']",
-    DISPLAY_TOOLBAR: "[data-description='page display toolbar']",
-};
-
 let pinia: Pinia;
 
 function mountComponent(propsData: { pageId: string; historyId?: string; displayOnly?: boolean }) {
@@ -121,43 +107,10 @@ describe("PageEditorView", () => {
         });
 
         it("shows toolbar and MarkdownEditor when page is loaded", () => {
-            expect(wrapper.find(SELECTORS.TOOLBAR).exists()).toBe(true);
+            expect(wrapper.findComponent(PageDisplayToolbar).exists()).toBe(true);
             expect(wrapper.findComponent(MarkdownEditor).exists()).toBe(true);
         });
 
-        it("shows ClickToEdit with page title in toolbar", () => {
-            const clickToEdit = wrapper.findComponent(ClickToEdit);
-            expect(clickToEdit.exists()).toBe(true);
-            expect(clickToEdit.props("value")).toBe("My Page");
-        });
-
-        it("shows 'Untitled Notebook' in ClickToEdit when currentTitle is empty", async () => {
-            store.currentTitle = "";
-            await wrapper.vm.$nextTick();
-
-            const clickToEdit = wrapper.findComponent(ClickToEdit);
-            expect(clickToEdit.props("value")).toBe("Untitled Notebook");
-        });
-
-        it("shows 'Unsaved' indicator when store.isDirty is true", async () => {
-            await wrapper.vm.$nextTick();
-
-            expect(store.isDirty).toBe(true);
-            const unsaved = wrapper.find(SELECTORS.UNSAVED_INDICATOR);
-            expect(unsaved.exists()).toBe(true);
-            expect(unsaved.text()).toBe("Unsaved");
-        });
-
-        it("save button is disabled when store.canSave is false", async () => {
-            store.currentContent = "";
-            store.currentTitle = "";
-            await wrapper.vm.$nextTick();
-
-            expect(store.canSave).toBe(false);
-            const saveBtn = wrapper.find(SELECTORS.SAVE_BUTTON);
-            expect(saveBtn.attributes("disabled")).toBe("true");
-        });
-
         it("passes content to MarkdownEditor", () => {
             const editor = wrapper.findComponent(MarkdownEditor);
             expect(editor.props("markdownText")).toBe("# Hello");
@@ -168,50 +121,23 @@ describe("PageEditorView", () => {
             expect(editor.props("mode")).toBe("page");
         });
 
-        it("shows Preview button in toolbar", () => {
-            const previewBtn = wrapper.find(SELECTORS.PREVIEW_BUTTON);
-            expect(previewBtn.exists()).toBe(true);
-            expect(previewBtn.text()).toContain("Preview");
-        });
-
         it("Preview button navigates to displayOnly mode", async () => {
-            const previewBtn = wrapper.find(SELECTORS.PREVIEW_BUTTON);
-            await previewBtn.trigger("click");
+            wrapper.findComponent(PageDisplayToolbar).vm.$emit("preview");
 
             expect(mockPush).toHaveBeenCalledWith(`/histories/${HISTORY_ID}/pages/${PAGE_ID}?displayOnly=true`);
         });
 
-        it("ClickToEdit input updates store title", async () => {
-            const clickToEdit = wrapper.findComponent(ClickToEdit);
-            clickToEdit.vm.$emit("input", "Renamed Page");
-            await wrapper.vm.$nextTick();
-
-            expect(store.updateTitle).toHaveBeenCalledWith("Renamed Page");
-        });
-
         it("back button navigates to history pages list", async () => {
-            const backBtn = wrapper.find(SELECTORS.BACK_BUTTON);
-            await backBtn.trigger("click");
+            wrapper.findComponent(PageDisplayToolbar).vm.$emit("back");
 
             expect(store.clearCurrentPage).toHaveBeenCalled();
             expect(mockPush).toHaveBeenCalledWith(`/histories/${HISTORY_ID}/pages`);
         });
 
-        it("save button calls store.savePage", async () => {
-            const saveBtn = wrapper.find(SELECTORS.SAVE_BUTTON);
-            await saveBtn.trigger("click");
-            await flushPromises();
-
-            expect(store.savePage).toHaveBeenCalled();
-        });
-
-        it("hides permissions button in history mode", () => {
-            expect(wrapper.find(SELECTORS.PERMISSIONS_BUTTON).exists()).toBe(false);
-        });
-
-        it("hides save & view button in history mode", () => {
-            expect(wrapper.find(SELECTORS.SAVE_VIEW_BUTTON).exists()).toBe(false);
-        });
+        // TODO: We won't have a Save & View but will implement a save changes or ignore modal
+        // it("hides save & view button in history mode", () => {
+        //     expect(wrapper.find(SELECTORS.SAVE_VIEW_BUTTON).exists()).toBe(false);
+        // });
     });
 
     describe("Editor view (standalone mode)", () => {
@@ -224,7 +150,7 @@ describe("PageEditorView", () => {
         });
 
         it("shows toolbar and MarkdownEditor", () => {
-            expect(wrapper.find(SELECTORS.TOOLBAR).exists()).toBe(true);
+            expect(wrapper.findComponent(PageDisplayToolbar).exists()).toBe(true);
             expect(wrapper.findComponent(MarkdownEditor).exists()).toBe(true);
         });
 
@@ -233,100 +159,81 @@ describe("PageEditorView", () => {
             expect(editor.props("mode")).toBe("page");
         });
 
-        it("shows permissions button in standalone mode", () => {
-            expect(wrapper.find(SELECTORS.PERMISSIONS_BUTTON).exists()).toBe(true);
-        });
-
-        it("shows save & view button in standalone mode", () => {
-            expect(wrapper.find(SELECTORS.SAVE_VIEW_BUTTON).exists()).toBe(true);
-        });
+        // TODO: We won't have a Save & View but will implement a save changes or ignore modal
+        // it("shows save & view button in standalone mode", () => {
+        //     expect(wrapper.find(SELECTORS.SAVE_VIEW_BUTTON).exists()).toBe(true);
+        // });
 
         it("back button navigates to pages list", async () => {
-            const backBtn = wrapper.find(SELECTORS.BACK_BUTTON);
-            await backBtn.trigger("click");
-
+            wrapper.findComponent(PageDisplayToolbar).vm.$emit("back");
             expect(mockPush).toHaveBeenCalledWith("/pages/list");
         });
 
-        it("back button text says 'Back to Reports'", () => {
-            const backBtn = wrapper.find(SELECTORS.BACK_BUTTON);
-            expect(backBtn.text()).toContain("Back to Reports");
-        });
+        // TODO: We won't have a Save & View but will implement a save changes or ignore modal
+        // it("Save & View navigates to published page when WM inactive", async () => {
+        //     const store = usePageEditorStore();
+        //     store.currentPage = {
+        //         id: PAGE_ID,
+        //         history_id: null,
+        //         title: "My Page",
+        //         content: "# Hello",
+        //         update_time: "2024-01-01T00:00:00",
+        //         username: "testuser",
+        //         slug: "my-page",
+        //     } as Partial<HistoryPageDetails> as HistoryPageDetails;
+        //     store.currentContent = "modified";
+        //     store.currentTitle = "My Page";
 
-        it("Save & View navigates to published page when WM inactive", async () => {
-            const store = usePageEditorStore();
-            store.currentPage = {
-                id: PAGE_ID,
-                history_id: null,
-                title: "My Page",
-                content: "# Hello",
-                update_time: "2024-01-01T00:00:00",
-                username: "testuser",
-                slug: "my-page",
-            } as Partial<HistoryPageDetails> as HistoryPageDetails;
-            store.currentContent = "modified";
-            store.currentTitle = "My Page";
+        //     const saveViewBtn = wrapper.find(SELECTORS.SAVE_VIEW_BUTTON);
+        //     // Mock location.href assignment
+        //     const hrefSpy = vi.spyOn(window, "location", "get").mockReturnValue({
+        //         ...window.location,
+        //         href: "",
+        //     } as unknown as Location);
+        //     await saveViewBtn.trigger("click");
+        //     await flushPromises();
 
-            const saveViewBtn = wrapper.find(SELECTORS.SAVE_VIEW_BUTTON);
-            // Mock location.href assignment
-            const hrefSpy = vi.spyOn(window, "location", "get").mockReturnValue({
-                ...window.location,
-                href: "",
-            } as unknown as Location);
-            await saveViewBtn.trigger("click");
-            await flushPromises();
+        //     expect(store.savePage).toHaveBeenCalled();
+        //     hrefSpy.mockRestore();
+        // });
 
-            expect(store.savePage).toHaveBeenCalled();
-            hrefSpy.mockRestore();
-        });
+        // it("Save & View uses router.push when WM is active", async () => {
+        //     mockGalaxyInstance.frame.active = true;
+        //     const store = usePageEditorStore();
+        //     store.currentPage = {
+        //         id: PAGE_ID,
+        //         history_id: null,
+        //         title: "My Page",
+        //         content: "# Hello",
+        //         update_time: "2024-01-01T00:00:00",
+        //     } as Partial<HistoryPageDetails> as HistoryPageDetails;
+        //     store.currentContent = "modified";
+        //     store.currentTitle = "My Page";
 
-        it("Save & View uses router.push when WM is active", async () => {
-            mockGalaxyInstance.frame.active = true;
-            const store = usePageEditorStore();
-            store.currentPage = {
-                id: PAGE_ID,
-                history_id: null,
-                title: "My Page",
-                content: "# Hello",
-                update_time: "2024-01-01T00:00:00",
-            } as Partial<HistoryPageDetails> as HistoryPageDetails;
-            store.currentContent = "modified";
-            store.currentTitle = "My Page";
+        //     const saveViewBtn = wrapper.find(SELECTORS.SAVE_VIEW_BUTTON);
+        //     await saveViewBtn.trigger("click");
+        //     await flushPromises();
 
-            const saveViewBtn = wrapper.find(SELECTORS.SAVE_VIEW_BUTTON);
-            await saveViewBtn.trigger("click");
-            await flushPromises();
-
-            expect(store.savePage).toHaveBeenCalled();
-            expect(mockPush).toHaveBeenCalledWith(
-                `/published/page?id=${PAGE_ID}&embed=true`,
-                expect.objectContaining({
-                    title: "Report: My Page",
-                    preventWindowManager: false,
-                }),
-            );
-            mockGalaxyInstance.frame.active = false;
-        });
+        //     expect(store.savePage).toHaveBeenCalled();
+        //     expect(mockPush).toHaveBeenCalledWith(
+        //         `/published/page?id=${PAGE_ID}&embed=true`,
+        //         expect.objectContaining({
+        //             title: "Report: My Page",
+        //             preventWindowManager: false,
+        //         }),
+        //     );
+        //     mockGalaxyInstance.frame.active = false;
+        // });
     });
 
     describe("DisplayOnly mode", () => {
-        it("renders Markdown when displayOnly is true", async () => {
+        it("renders PageDisplayOnly when displayOnly is true", async () => {
             setupLoadedPage(HISTORY_ID);
             const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID, displayOnly: true });
             await flushPromises();
 
-            expect(wrapper.findComponent(Markdown).exists()).toBe(true);
-            expect(wrapper.find(SELECTORS.TOOLBAR).exists()).toBe(false);
-        });
-
-        it("shows display toolbar with Edit button", async () => {
-            setupLoadedPage(HISTORY_ID);
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID, displayOnly: true });
-            await flushPromises();
-
-            expect(wrapper.find(SELECTORS.DISPLAY_TOOLBAR).exists()).toBe(true);
-            const editBtn = wrapper.find(SELECTORS.EDIT_BUTTON);
-            expect(editBtn.exists()).toBe(true);
+            expect(wrapper.findComponent(PageDisplayOnly).exists()).toBe(true);
+            expect(wrapper.findComponent(PageDisplayToolbar).exists()).toBe(false);
         });
 
         it("does not clear editor state on unmount in displayOnly mode", async () => {
@@ -342,44 +249,22 @@ describe("PageEditorView", () => {
     });
 
     describe("Revision UI", () => {
-        it("shows Revisions button in toolbar", async () => {
-            setupLoadedPage(HISTORY_ID);
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            const revBtn = wrapper.find(SELECTORS.REVISIONS_BUTTON);
-            expect(revBtn.exists()).toBe(true);
-            expect(revBtn.text()).toContain("Revisions");
-        });
-
-        it("clicking Revisions button calls store.toggleRevisions", async () => {
-            const store = setupLoadedPage(HISTORY_ID);
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            const revBtn = wrapper.find(SELECTORS.REVISIONS_BUTTON);
-            await revBtn.trigger("click");
-
-            expect(store.toggleRevisions).toHaveBeenCalled();
-        });
-
-        it("shows revision panel when store.showRevisions is true", async () => {
+        it("shows revision list in a modal when store.showRevisions is true", async () => {
             const store = setupLoadedPage(HISTORY_ID);
             store.showRevisions = true;
             store.revisions = [] as PageRevisionSummary[];
             const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
             await flushPromises();
 
-            expect(wrapper.find(SELECTORS.REVISION_PANEL).exists()).toBe(true);
-            expect(wrapper.findComponent(PageRevisionList).exists()).toBe(true);
+            expect(wrapper.findComponent(GModal).props("show")).toBe(true);
         });
 
-        it("hides revision panel when store.showRevisions is false", async () => {
+        it("hides revision modal when store.showRevisions is false", async () => {
             setupLoadedPage(HISTORY_ID);
             const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
             await flushPromises();
 
-            expect(wrapper.find(SELECTORS.REVISION_PANEL).exists()).toBe(false);
+            expect(wrapper.findComponent(GModal).props("show")).toBe(false);
         });
 
         it("shows PageRevisionView when selectedRevision is set", async () => {
@@ -398,21 +283,7 @@ describe("PageEditorView", () => {
             await flushPromises();
 
             expect(wrapper.findComponent(PageRevisionView).exists()).toBe(true);
-            expect(wrapper.find(SELECTORS.TOOLBAR).exists()).toBe(false);
-        });
-
-        it("revision badge shows count when revisions loaded", async () => {
-            const store = setupLoadedPage(HISTORY_ID);
-            store.revisions = [
-                { id: "rev-1", page_id: PAGE_ID, edit_source: "user", create_time: "", update_time: "" },
-                { id: "rev-2", page_id: PAGE_ID, edit_source: "user", create_time: "", update_time: "" },
-            ] as PageRevisionSummary[];
-            const wrapper = mountComponent({ pageId: PAGE_ID, historyId: HISTORY_ID });
-            await flushPromises();
-
-            const badge = wrapper.find(SELECTORS.REVISIONS_BUTTON + " bbadge-stub");
-            expect(badge.exists()).toBe(true);
-            expect(badge.text()).toBe("2");
+            expect(wrapper.findComponent(MarkdownEditor).exists()).toBe(false);
         });
 
         it("PageRevisionView back emits clearSelectedRevision", async () => {
@@ -459,7 +330,7 @@ describe("PageEditorView", () => {
             expect(store.restoreRevision).toHaveBeenCalledWith("rev-1");
         });
 
-        it("revision panel select calls store.loadRevision", async () => {
+        it("revision list select calls store.loadRevision", async () => {
             const store = setupLoadedPage(HISTORY_ID);
             store.showRevisions = true;
             store.revisions = [
@@ -477,41 +348,7 @@ describe("PageEditorView", () => {
     });
 
     describe("Revision UI (standalone mode)", () => {
-        it("shows Revisions button in standalone mode", async () => {
-            setupLoadedPage();
-            const wrapper = mountComponent({ pageId: PAGE_ID });
-            await flushPromises();
-
-            const revBtn = wrapper.find(SELECTORS.REVISIONS_BUTTON);
-            expect(revBtn.exists()).toBe(true);
-            expect(revBtn.text()).toContain("Revisions");
-        });
-
-        it("clicking Revisions button calls store.toggleRevisions in standalone mode", async () => {
-            const store = setupLoadedPage();
-            const wrapper = mountComponent({ pageId: PAGE_ID });
-            await flushPromises();
-
-            const revBtn = wrapper.find(SELECTORS.REVISIONS_BUTTON);
-            await revBtn.trigger("click");
-
-            expect(store.toggleRevisions).toHaveBeenCalled();
-        });
-
-        it("shows revision panel when store.showRevisions is true in standalone mode", async () => {
-            const store = setupLoadedPage();
-            store.showRevisions = true;
-            store.revisions = [
-                { id: "rev-1", page_id: PAGE_ID, edit_source: "user", create_time: "", update_time: "" },
-            ] as PageRevisionSummary[];
-            const wrapper = mountComponent({ pageId: PAGE_ID });
-            await flushPromises();
-
-            expect(wrapper.find(SELECTORS.REVISION_PANEL).exists()).toBe(true);
-            expect(wrapper.findComponent(PageRevisionList).exists()).toBe(true);
-        });
-
-        it("revision panel restore calls store.restoreRevision in standalone mode", async () => {
+        it("revision list restore calls store.restoreRevision in standalone mode", async () => {
             const store = setupLoadedPage();
             store.showRevisions = true;
             store.revisions = [
@@ -585,7 +422,7 @@ describe("PageEditorView", () => {
             const errorAlert = wrapper.find("balert-stub[variant='danger']");
             expect(errorAlert.exists()).toBe(true);
             expect(errorAlert.text()).toContain("Save failed");
-            expect(wrapper.find(SELECTORS.TOOLBAR).exists()).toBe(true);
+            expect(wrapper.findComponent(PageDisplayToolbar).exists()).toBe(true);
             expect(wrapper.findComponent(MarkdownEditor).exists()).toBe(true);
         });
     });
diff --git a/client/src/components/PageEditor/PageRevisionView.test.ts b/client/src/components/PageEditor/PageRevisionView.test.ts
index 87c39a77bb3..caefa35a52e 100644
--- a/client/src/components/PageEditor/PageRevisionView.test.ts
+++ b/client/src/components/PageEditor/PageRevisionView.test.ts
@@ -125,39 +125,42 @@ describe("PageRevisionView", () => {
             expect(wrapper.find('[data-description="revision compare previous button"]').exists()).toBe(false);
         });
 
-        it("preview button is primary in preview mode", () => {
+        it("preview button is pressed in preview mode", () => {
             const wrapper = mountComponent({ viewMode: "preview" });
             const previewBtn = wrapper.find('[data-description="revision preview button"]');
-            expect(previewBtn.attributes("variant")).toBe("primary");
+            expect(previewBtn.props("pressed")).toBe(true);
         });
 
-        it("compare current button is primary in changes_current mode", () => {
+        it("compare current button is pressed in changes_current mode", () => {
             const wrapper = mountComponent({ viewMode: "changes_current" });
             const btn = wrapper.find('[data-description="revision compare current button"]');
-            expect(btn.attributes("variant")).toBe("primary");
+            expect(btn.props("pressed")).toBe(true);
         });
 
-        it("compare previous button is primary in changes_previous mode", () => {
+        it("compare previous button is pressed in changes_previous mode", () => {
             const wrapper = mountComponent({ viewMode: "changes_previous" });
             const btn = wrapper.find('[data-description="revision compare previous button"]');
-            expect(btn.attributes("variant")).toBe("primary");
+            expect(btn.props("pressed")).toBe(true);
         });
 
         it("clicking Compare to Current emits update:viewMode with 'changes_current'", async () => {
             const wrapper = mountComponent({ viewMode: "preview" });
-            await wrapper.find('[data-description="revision compare current button"]').trigger("click");
+            wrapper.find('[data-description="revision compare current button"]').vm.$emit("click");
+            await wrapper.vm.$nextTick();
             expect(wrapper.emitted("update:viewMode")).toEqual([["changes_current"]]);
         });
 
         it("clicking Compare to Previous emits update:viewMode with 'changes_previous'", async () => {
             const wrapper = mountComponent({ viewMode: "preview" });
-            await wrapper.find('[data-description="revision compare previous button"]').trigger("click");
+            wrapper.find('[data-description="revision compare previous button"]').vm.$emit("click");
+            await wrapper.vm.$nextTick();
             expect(wrapper.emitted("update:viewMode")).toEqual([["changes_previous"]]);
         });
 
         it("clicking Preview emits update:viewMode with 'preview'", async () => {
             const wrapper = mountComponent({ viewMode: "changes_current" });
-            await wrapper.find('[data-description="revision preview button"]').trigger("click");
+            wrapper.find('[data-description="revision preview button"]').vm.$emit("click");
+            await wrapper.vm.$nextTick();
             expect(wrapper.emitted("update:viewMode")).toEqual([["preview"]]);
         });
     });
@@ -180,19 +183,22 @@ describe("PageRevisionView", () => {
 
         it("restore button emits restore with revision id", async () => {
             const wrapper = mountComponent();
-            await wrapper.find('[data-description="revision restore button"]').trigger("click");
+            wrapper.find('[data-description="revision restore button"]').vm.$emit("click");
+            await wrapper.vm.$nextTick();
             expect(wrapper.emitted("restore")).toEqual([[REVISION.id]]);
         });
 
         it("back button emits back in preview mode", async () => {
             const wrapper = mountComponent({ viewMode: "preview" });
-            await wrapper.find('[data-description="revision back button"]').trigger("click");
+            wrapper.find('[data-description="revision back button"]').vm.$emit("click");
+            await wrapper.vm.$nextTick();
             expect(wrapper.emitted("back")).toHaveLength(1);
         });
 
         it("back button emits back in changes_current mode", async () => {
             const wrapper = mountComponent({ viewMode: "changes_current" });
-            await wrapper.find('[data-description="revision back button"]').trigger("click");
+            wrapper.find('[data-description="revision back button"]').vm.$emit("click");
+            await wrapper.vm.$nextTick();
             expect(wrapper.emitted("back")).toHaveLength(1);
         });
     });

From 9484699fd0cdebf04290af1407eb54ef2e1b2fb2 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 01:28:46 -0500
Subject: [PATCH 179/256] use a `confirmDialog` when creating a notebook from a
 runtime report

---
 .../components/Workflow/InvocationReport.vue  | 23 +++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Workflow/InvocationReport.vue b/client/src/components/Workflow/InvocationReport.vue
index a5b86a499b4..591761b80bc 100644
--- a/client/src/components/Workflow/InvocationReport.vue
+++ b/client/src/components/Workflow/InvocationReport.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faFileContract } from "@fortawesome/free-solid-svg-icons";
+import { faEdit, faFileContract } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { storeToRefs } from "pinia";
 import { computed, provide, ref } from "vue";
@@ -7,6 +7,7 @@ import { useRouter } from "vue-router/composables";
 
 import { fetchInvocationReport } from "@/api/invocations";
 import { useConfig } from "@/composables/config";
+import { useConfirmDialog } from "@/composables/confirmDialog.js";
 import { useToast } from "@/composables/toast";
 import { usePageEditorStore } from "@/stores/pageEditorStore.js";
 import { errorMessageAsString } from "@/utils/simple-error.js";
@@ -24,6 +25,8 @@ const props = defineProps<{
 
 const { config, isConfigLoaded } = useConfig(true);
 
+const { confirm } = useConfirmDialog();
+
 const Toast = useToast();
 
 const router = useRouter();
@@ -32,11 +35,12 @@ const pageEditorStore = usePageEditorStore();
 const { isLoadingPage } = storeToRefs(pageEditorStore);
 
 const markdownConfig = ref({});
+const isCreatingReport = ref(false);
 
 const exportUrl = computed(() => `/api/invocations/${props.invocationId}/report.pdf`);
 
 const editButtonConfig = computed(() => ({
-    tooltip: "Click to create a Galaxy Notebook from this invocation's Runtime Report",
+    tooltip: "Click to create an editable report from this invocation's Runtime Report",
     label: "Edit",
     disabled: isLoadingPage.value,
 }));
@@ -54,7 +58,20 @@ async function fetchReport() {
 
 async function onEdit() {
     if (props.historyId) {
+        isCreatingReport.value = true;
         try {
+            const confirmed = await confirm(
+                "Are you sure you want to create a new Invocation Report? This report will have context of the history and invocation that created the Runtime Report.",
+                {
+                    title: "Create a new Invocation Report?",
+                    okText: "Create Report",
+                    okIcon: faEdit,
+                },
+            );
+            if (!confirmed) {
+                return;
+            }
+
             pageEditorStore.setCurrentContext(props.historyId, props.invocationId);
             const page = await pageEditorStore.createPage();
             if (page) {
@@ -67,6 +84,8 @@ async function onEdit() {
             }
         } catch (error) {
             Toast.error(errorMessageAsString(error), "Failed to create a Galaxy Notebook");
+        } finally {
+            isCreatingReport.value = false;
         }
     } else {
         router.push(`/pages/create?invocation_id=${props.invocationId}`);

From a5058c635fe8b3d9abde7dded8de233857e798b3 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 01:40:59 -0500
Subject: [PATCH 180/256] sort history pages response by update time in
 descending order

---
 client/src/api/pages.ts | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/client/src/api/pages.ts b/client/src/api/pages.ts
index 92854157ff9..3ab0e3f043a 100644
--- a/client/src/api/pages.ts
+++ b/client/src/api/pages.ts
@@ -19,7 +19,13 @@ export type UpdateHistoryPagePayload = components["schemas"]["UpdatePagePayload"
 export async function fetchHistoryPages(historyId: string, invocationId?: string): Promise<HistoryPageSummary[]> {
     const { data, error } = await GalaxyApi().GET("/api/pages", {
         params: {
-            query: { history_id: historyId, invocation_id: invocationId, show_own: true, show_published: false },
+            query: {
+                history_id: historyId,
+                invocation_id: invocationId,
+                show_own: true,
+                show_published: false,
+                sort_desc: true,
+            },
         },
     });
     if (error) {

From d7c454d110924fbd5e85ee5e579d60e27adbb7fe Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 01:41:33 -0500
Subject: [PATCH 181/256] clarify that the title in a notebook md editor is the
 history name

---
 client/src/components/PageEditor/PageEditorView.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 3c220a70c0b..f80b3a82477 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -43,7 +43,7 @@ const labels = computed(() => PAGE_LABELS[editorMode.value]);
 const editorTitle = computed(() => {
     if (props.historyId) {
         const history = historyStore.getHistoryById(props.historyId);
-        return history?.name || labels.value.entityName;
+        return `History: ${history?.name}` || labels.value.entityName;
     }
     return store.currentTitle || labels.value.defaultTitle;
 });

From 4bd16e17d0caac79839005c256d606b6239fb114 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 02:24:18 -0500
Subject: [PATCH 182/256] ensure window manager page view only shows markdown
 content

---
 .../components/PageEditor/HistoryPageView.vue | 11 ++++-----
 .../components/PageEditor/PageDisplayOnly.vue |  8 ++++++-
 .../src/components/PageEditor/PageEditor.vue  |  3 ++-
 .../components/PageEditor/PageEditorView.vue  | 24 ++++++++++++-------
 client/src/entry/analysis/router.js           |  1 +
 5 files changed, 30 insertions(+), 17 deletions(-)

diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index 413238fcfcb..f96f232fd06 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -80,15 +80,14 @@ watch(
 );
 
 function handleView(viewingPageId: string) {
-    if (props.invocationId) {
-        router.push(`/workflows/invocations/${props.invocationId}/reports?id=${viewingPageId}`);
-        return;
-    }
     const page = store.pages.find((n) => n.id === viewingPageId);
     const pageTitle = page?.title || labels.value.entityName;
-    const inlineUrl = `/histories/${props.historyId}/pages/${viewingPageId}?displayOnly=true`;
+    const inlineUrl = props.invocationId
+        ? `/workflows/invocations/${props.invocationId}/reports?id=${viewingPageId}`
+        : `/histories/${props.historyId}/pages/${viewingPageId}?displayOnly=true`;
+
     pushToFrameOrPage({
-        framedUrl: inlineUrl,
+        framedUrl: `/pages/editor?id=${viewingPageId}&displayOnly=true&hideHeader=true`,
         inlineUrl,
         title: `${labels.value.entityName}: ${pageTitle}`,
     });
diff --git a/client/src/components/PageEditor/PageDisplayOnly.vue b/client/src/components/PageEditor/PageDisplayOnly.vue
index 24002e285b4..3bab6fb67e4 100644
--- a/client/src/components/PageEditor/PageDisplayOnly.vue
+++ b/client/src/components/PageEditor/PageDisplayOnly.vue
@@ -9,6 +9,7 @@ import PageDisplayToolbar from "./PageDisplayToolbar.vue";
 const props = defineProps<{
     labels: (typeof PAGE_LABELS)[keyof typeof PAGE_LABELS];
     markdownConfig?: MarkdownConfig;
+    hideHeader?: boolean;
 }>();
 
 const emit = defineEmits<{
@@ -19,7 +20,12 @@ const emit = defineEmits<{
 
 <template>
     <div class="d-flex flex-column">
-        <PageDisplayToolbar :labels="props.labels" mode="display" @edit="emit('edit')" @back="emit('back')" />
+        <PageDisplayToolbar
+            v-if="!props.hideHeader"
+            :labels="props.labels"
+            mode="display"
+            @edit="emit('edit')"
+            @back="emit('back')" />
         <div class="page-display-content" data-description="page rendered view">
             <Markdown
                 v-if="markdownConfig"
diff --git a/client/src/components/PageEditor/PageEditor.vue b/client/src/components/PageEditor/PageEditor.vue
index d0ec8cabc60..ec348aa80c8 100644
--- a/client/src/components/PageEditor/PageEditor.vue
+++ b/client/src/components/PageEditor/PageEditor.vue
@@ -1,5 +1,5 @@
 <template>
-    <PageEditorView :page-id="pageId" :display-only="displayOnly" />
+    <PageEditorView :page-id="pageId" :display-only="displayOnly" :hide-header="hideHeader" />
 </template>
 
 <script setup lang="ts">
@@ -8,5 +8,6 @@ import PageEditorView from "./PageEditorView.vue";
 defineProps<{
     pageId: string;
     displayOnly?: boolean;
+    hideHeader?: boolean;
 }>();
 </script>
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index f80b3a82477..9b0170e4191 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -26,6 +26,7 @@ const props = defineProps<{
     historyId?: string;
     invocationId?: string;
     displayOnly?: boolean;
+    hideHeader?: boolean;
 }>();
 
 const router = useRouter();
@@ -103,20 +104,24 @@ function handleBack() {
     }
 }
 
+/** Open basic md display in window manager when active, else navigate inline according to context */
 function handlePreview() {
+    const framedUrl = `/pages/editor?id=${props.pageId}&displayOnly=true&hideHeader=true`;
+
+    let inlineUrl: string;
     if (props.invocationId) {
-        router.push(`/workflows/invocations/${props.invocationId}/reports?id=${props.pageId}`);
+        inlineUrl = `/workflows/invocations/${props.invocationId}/reports?id=${props.pageId}`;
     } else if (props.historyId) {
-        router.push(`/histories/${props.historyId}/pages/${props.pageId}?displayOnly=true`);
+        inlineUrl = `/histories/${props.historyId}/pages/${props.pageId}?displayOnly=true`;
     } else {
-        // Standalone: open in window manager when active, else navigate inline.
-        const previewUrl = `/pages/editor?id=${props.pageId}&displayOnly=true`;
-        pushToFrameOrPage({
-            framedUrl: previewUrl,
-            inlineUrl: previewUrl,
-            title: `${labels.value.entityName}: ${store.currentTitle || labels.value.defaultTitle}`,
-        });
+        inlineUrl = `/pages/editor?id=${props.pageId}&displayOnly=true`;
     }
+
+    pushToFrameOrPage({
+        framedUrl,
+        inlineUrl,
+        title: `${labels.value.entityName}: ${store.currentTitle || labels.value.defaultTitle}`,
+    });
 }
 
 function handleEdit() {
@@ -185,6 +190,7 @@ function handleRevisionRestore(revisionId: string) {
             v-else-if="store.hasCurrentPage && displayOnly"
             :labels="labels"
             :markdown-config="markdownConfig || undefined"
+            :hide-header="props.hideHeader"
             @back="handleBack"
             @edit="handleEdit" />
 
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index b78a6b624dc..6d1e47e488b 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -573,6 +573,7 @@ export function getRouter(Galaxy) {
                         props: (route) => ({
                             pageId: route.query.id,
                             displayOnly: route.query.displayOnly === "true",
+                            hideHeader: route.query.hideHeader === "true",
                         }),
                     },
                     {

From 6cf2ea2adfe6e78f6ecc48cf537b5d76e41787d4 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 17:00:05 -0500
Subject: [PATCH 183/256] show error badge in `SwitchToHistoryLink` if error
 fetching history

---
 .../History/SwitchToHistoryLink.test.ts       | 24 ++++++++++++++++++-
 .../History/SwitchToHistoryLink.vue           | 10 +++++++-
 2 files changed, 32 insertions(+), 2 deletions(-)

diff --git a/client/src/components/History/SwitchToHistoryLink.test.ts b/client/src/components/History/SwitchToHistoryLink.test.ts
index ea39c97cdea..b4c93df393d 100644
--- a/client/src/components/History/SwitchToHistoryLink.test.ts
+++ b/client/src/components/History/SwitchToHistoryLink.test.ts
@@ -24,6 +24,7 @@ const selectors = {
 const mockSetCurrentHistory = vi.fn();
 const mockApplyFilters = vi.fn();
 const mockWindowOpen = vi.fn(() => null);
+const mockGetHistoryLoadError = vi.fn(() => null as Error | null);
 
 vi.mock("vue-router/composables", () => ({
     useRouter: () => ({
@@ -42,6 +43,7 @@ vi.mock("@/stores/historyStore", async () => {
             ...(originalModule as any).useHistoryStore(),
             currentHistoryId: "current-history-id",
             setCurrentHistory: mockSetCurrentHistory,
+            getHistoryLoadError: mockGetHistoryLoadError,
             applyFilters: vi.fn().mockImplementation((historyId: string) => {
                 // We mock what the actual method does: set the current history if not current
                 if (historyId !== "current-history-id") {
@@ -67,6 +69,7 @@ function initializeMocks() {
     mockSetCurrentHistory.mockClear();
     mockApplyFilters.mockClear();
     mockWindowOpen.mockClear();
+    mockGetHistoryLoadError.mockReturnValue(null);
     const windowSpy = vi.spyOn(window, "open");
     windowSpy.mockImplementation(() => mockWindowOpen());
 }
@@ -268,5 +271,24 @@ describe("SwitchToHistoryLink", () => {
         await expectActionForHistory("View in new tab", history, true);
     });
 
-    // if the history is inaccessible, the HistorySummary would never be fetched in the first place
+    it("shows an error badge when the history is inaccessible (backend error)", async () => {
+        initializeMocks();
+
+        // The history store is fully mocked, so mockGetHistoryLoadError is used to emulate a 403
+        mockGetHistoryLoadError.mockReturnValue(new Error("History is not accessible to the current user"));
+
+        const pinia = createTestingPinia({ createSpy: vi.fn });
+        const wrapper = mount(SwitchToHistoryLink as object, {
+            propsData: { historyId: "inaccessible-history-id" },
+            localVue,
+            pinia,
+            stubs: { FontAwesomeIcon: true },
+        });
+
+        await flushPromises();
+
+        expect(wrapper.find(selectors.historyLink).exists()).toBe(false);
+        expect(wrapper.html()).toContain("Error loading history");
+        expect(wrapper.html()).not.toContain("Loading");
+    });
 });
diff --git a/client/src/components/History/SwitchToHistoryLink.vue b/client/src/components/History/SwitchToHistoryLink.vue
index 0c3f868e9d8..fd90f0693ee 100644
--- a/client/src/components/History/SwitchToHistoryLink.vue
+++ b/client/src/components/History/SwitchToHistoryLink.vue
@@ -1,6 +1,7 @@
 <script setup lang="ts">
 import { faArchive, faBurn } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BBadge } from "bootstrap-vue";
 import { computed } from "vue";
 import { useRouter } from "vue-router/composables";
 
@@ -109,7 +110,14 @@ const linkClass = computed(() => {
 
 <template>
     <component :is="tag">
-        <LoadingSpan v-if="!history" />
+        <BBadge
+            v-if="historyStore.getHistoryLoadError(props.historyId)"
+            v-g-tooltip
+            :title="errorMessageAsString(historyStore.getHistoryLoadError(props.historyId))"
+            variant="danger">
+            Error loading history
+        </BBadge>
+        <LoadingSpan v-else-if="!history" />
         <component :is="tag" v-else :class="linkClass" data-description="switch to history link">
             <GLink
                 class="history-link-click"

From 73e4588087a5b3160103ecc6e21baaeceac141a6 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 17:00:49 -0500
Subject: [PATCH 184/256] show ALL pages in published pages grid as well

---
 .../components/Grid/configs/pagesPublished.ts  | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Grid/configs/pagesPublished.ts b/client/src/components/Grid/configs/pagesPublished.ts
index bf5995e6959..381c4d22996 100644
--- a/client/src/components/Grid/configs/pagesPublished.ts
+++ b/client/src/components/Grid/configs/pagesPublished.ts
@@ -3,7 +3,7 @@ import { useEventBus } from "@vueuse/core";
 
 import { GalaxyApi } from "@/api";
 import { GRID_LABELS } from "@/components/Page/constants";
-import Filtering, { contains, type ValidFilter } from "@/utils/filtering";
+import Filtering, { contains, equals, toBool, type ValidFilter } from "@/utils/filtering";
 import { rethrowSimple } from "@/utils/simple-error";
 
 import type { ActionArray, FieldArray, GridConfig } from "./types";
@@ -20,13 +20,18 @@ type PageEntry = Record<string, unknown>;
  * Request and return data from server
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
-    const typeFilteredSearch = search ? `type:standalone ${search}` : "type:standalone";
+    if (search.includes("is:standalone")) {
+        // Pages that are not attached to a history have their type set to "standalone" on the backend
+        // We convert the search term here before sending to the backend
+        search = search.replace("is:standalone", "type:standalone");
+    }
+
     const { response, data, error } = await GalaxyApi().GET("/api/pages", {
         params: {
             query: {
                 limit,
                 offset,
-                search: typeFilteredSearch,
+                search: search,
                 sort_by: sort_by as SortKeyLiteral,
                 sort_desc,
                 show_own: false,
@@ -103,6 +108,13 @@ const validFilters: Record<string, ValidFilter<string | boolean | undefined>> =
     title: { placeholder: "title", type: String, handler: contains("title"), menuItem: true },
     slug: { handler: contains("slug"), menuItem: false },
     user: { placeholder: "user", type: String, handler: contains("username"), menuItem: true },
+    standalone: {
+        placeholder: "Only standalone",
+        type: Boolean,
+        boolType: "is",
+        handler: equals("standalone", "type", toBool),
+        menuItem: true,
+    },
 };
 
 /**

From 9f83b8ab307b74da6ff62d3c15cb9a597f234e65 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 17:02:09 -0500
Subject: [PATCH 185/256] show other users' published pages in the notebooks
 list as well

It is very much possible that other users create a notebook against your history or invocation. If they publish any of those reports, they now show under the associated history and/or invocation.
---
 client/src/api/pages.ts                       |  2 +-
 client/src/components/PageEditor/PageCard.vue | 17 +++++++++++++++--
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/client/src/api/pages.ts b/client/src/api/pages.ts
index 3ab0e3f043a..e411edcfff1 100644
--- a/client/src/api/pages.ts
+++ b/client/src/api/pages.ts
@@ -23,7 +23,7 @@ export async function fetchHistoryPages(historyId: string, invocationId?: string
                 history_id: historyId,
                 invocation_id: invocationId,
                 show_own: true,
-                show_published: false,
+                show_published: true,
                 sort_desc: true,
             },
         },
diff --git a/client/src/components/PageEditor/PageCard.vue b/client/src/components/PageEditor/PageCard.vue
index 3204f94848e..c45ee59db25 100644
--- a/client/src/components/PageEditor/PageCard.vue
+++ b/client/src/components/PageEditor/PageCard.vue
@@ -1,9 +1,10 @@
 <script setup lang="ts">
-import { faEdit, faEye, faHistory, faSitemap } from "@fortawesome/free-solid-svg-icons";
+import { faEdit, faEye, faHistory, faSitemap, faUser } from "@fortawesome/free-solid-svg-icons";
 import { computed } from "vue";
 
 import type { HistoryPageSummary } from "@/api/pages";
 import type { CardAction, CardBadge, Title } from "@/components/Common/GCard.types";
+import { useUserStore } from "@/stores/userStore.js";
 
 import GCard from "../Common/GCard.vue";
 
@@ -28,6 +29,8 @@ const emit = defineEmits<{
     (e: "view"): void;
 }>();
 
+const userStore = useUserStore();
+
 const title: Title = {
     label: props.page.title || props.defaultTitle,
     title: props.editTitle,
@@ -44,6 +47,16 @@ const badges = computed<CardBadge[]>(() => {
             class: "unselectable",
         },
     ];
+    if (!userStore.matchesCurrentUsername(props.page.username)) {
+        retBadges.push({
+            id: "owned-by-other-user",
+            label: `Owned by ${props.page.username}`,
+            icon: faUser,
+            title: "This notebook is owned by another user. Editing it will create a copy owned by you.",
+            class: "unselectable",
+            variant: "outline-primary",
+        });
+    }
     if (props.showInvocationBadge && props.page.source_invocation_id) {
         retBadges.push({
             id: "is-invocation-notebook",
@@ -52,7 +65,7 @@ const badges = computed<CardBadge[]>(() => {
             title: "This notebook is a report created from a workflow invocation (Click to view the original report under the invocation)",
             class: "unselectable",
             to: `/workflows/invocations/${props.page.source_invocation_id}/reports?id=${props.page.id}`,
-            variant: "primary",
+            variant: "info",
         });
     }
     return retBadges;

From bc86cfdccb3a5554f625ad7c540e59aa2f5596d1 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 14 Jun 2026 17:18:53 -0500
Subject: [PATCH 186/256] handle unowned page edit clicks; add confirm dialog
 for create new in list

1. We never let users access the editor if they do not own a page.
2. The Edit button click now opens a confirm dialog for unowned pages that allows users to copy and create a new page from the unowned page.
3. The Create New button on top right of the notebooks/reports list now asks for confirmation before creating a new notebook/report.
---
 .../components/PageEditor/HistoryPageList.vue |  4 +-
 .../PageEditor/HistoryPageView.test.ts        |  8 ++-
 .../components/PageEditor/HistoryPageView.vue | 61 ++++++++++++++++---
 .../PageEditor/PageEditorView.test.ts         | 14 +++++
 .../components/PageEditor/PageEditorView.vue  | 47 +++++++++++---
 lib/galaxy/selenium/navigates_galaxy.py       |  2 +
 6 files changed, 118 insertions(+), 18 deletions(-)

diff --git a/client/src/components/PageEditor/HistoryPageList.vue b/client/src/components/PageEditor/HistoryPageList.vue
index 5be9cf7db49..63cc7c4e1d1 100644
--- a/client/src/components/PageEditor/HistoryPageList.vue
+++ b/client/src/components/PageEditor/HistoryPageList.vue
@@ -19,7 +19,7 @@ const props = defineProps<{
 }>();
 
 const emit = defineEmits<{
-    (e: "edit", pageId: string): void;
+    (e: "edit", pageId: string, username: string): void;
     (e: "view", pageId: string): void;
     (e: "create"): void;
     (e: "view-runtime-report"): void;
@@ -71,7 +71,7 @@ const { breadcrumbItems } = useHistoryBreadCrumbsTo(toRef(props, "historyId"), l
                 :edit-title="labels.editButton"
                 :show-invocation-badge="!props.invocationId"
                 :view-title="labels.viewButton"
-                @edit="emit('edit', page.id)"
+                @edit="emit('edit', page.id, page.username)"
                 @view="emit('view', page.id)" />
         </div>
     </div>
diff --git a/client/src/components/PageEditor/HistoryPageView.test.ts b/client/src/components/PageEditor/HistoryPageView.test.ts
index e97d4885aca..be9f593d1eb 100644
--- a/client/src/components/PageEditor/HistoryPageView.test.ts
+++ b/client/src/components/PageEditor/HistoryPageView.test.ts
@@ -36,6 +36,12 @@ vi.mock("@/composables/windowAwareNavigation", () => ({
     })),
 }));
 
+vi.mock("@/composables/confirmDialog.js", () => ({
+    useConfirmDialog: vi.fn(() => ({
+        confirm: vi.fn().mockResolvedValue(true),
+    })),
+}));
+
 vi.mock("@/stores/historyStore", () => ({
     useHistoryStore: vi.fn(() => ({
         getHistoryById: vi.fn((id: string) => {
@@ -302,7 +308,7 @@ describe("HistoryPageView", () => {
             list.vm.$emit("create");
             await flushPromises();
 
-            expect(store.createPage).toHaveBeenCalledWith();
+            expect(store.createPage).toHaveBeenCalledWith({ title: undefined, content: undefined });
             expect(mockPush).toHaveBeenCalledWith(`/histories/${HISTORY_ID}/pages/new-page`);
         });
 
diff --git a/client/src/components/PageEditor/HistoryPageView.vue b/client/src/components/PageEditor/HistoryPageView.vue
index f96f232fd06..8984b840b97 100644
--- a/client/src/components/PageEditor/HistoryPageView.vue
+++ b/client/src/components/PageEditor/HistoryPageView.vue
@@ -1,14 +1,16 @@
 <script setup lang="ts">
-import { faSpinner } from "@fortawesome/free-solid-svg-icons";
+import { faCopy, faPlus, faSpinner } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert } from "bootstrap-vue";
 import { computed, onMounted, onUnmounted, watch } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { PAGE_LABELS } from "@/components/Page/constants";
+import { useConfirmDialog } from "@/composables/confirmDialog.js";
 import { useToast } from "@/composables/toast";
 import { useWindowAwareNavigation } from "@/composables/windowAwareNavigation";
 import { usePageEditorStore } from "@/stores/pageEditorStore";
+import { useUserStore } from "@/stores/userStore.js";
 import { errorMessageAsString } from "@/utils/simple-error.js";
 
 import HistoryPageList from "./HistoryPageList.vue";
@@ -24,8 +26,10 @@ const props = defineProps<{
 
 const Toast = useToast();
 
+const { confirm } = useConfirmDialog();
 const router = useRouter();
 const { pushToFrameOrPage } = useWindowAwareNavigation();
+const userStore = useUserStore();
 const store = usePageEditorStore();
 const labels = computed(() => (props.invocationId ? PAGE_LABELS.invocation : PAGE_LABELS.history));
 
@@ -79,6 +83,38 @@ watch(
     },
 );
 
+async function createAPage(isCopy = false) {
+    const entity = labels.value.entityName;
+
+    const modalText = isCopy
+        ? `You are not the owner of this ${entity}. To edit it, a copy with its contents, owned by you, will be created. Do you want to proceed?`
+        : `A new ${entity} will be created and will be added to the list of ${labels.value.entityNamePlural} for this ${props.invocationId ? "invocation" : "history"}. Do you want to proceed?`;
+
+    const modalTitle = isCopy ? `Copy this ${entity}?` : `Create new ${entity}?`;
+    const okText = isCopy ? `Copy ${entity}` : `Create ${entity}`;
+    const okIcon = isCopy ? faCopy : faPlus;
+
+    const confirmed = await confirm(modalText, {
+        title: modalTitle,
+        okText,
+        okIcon,
+    });
+    if (!confirmed) {
+        return;
+    }
+
+    const newPage = await store.createPage({
+        title: isCopy
+            ? store.currentTitle
+                ? `Copy of "${store.currentTitle}"`
+                : labels.value.defaultTitle
+            : undefined,
+        content: isCopy ? store.currentContent : undefined,
+    });
+
+    return newPage;
+}
+
 function handleView(viewingPageId: string) {
     const page = store.pages.find((n) => n.id === viewingPageId);
     const pageTitle = page?.title || labels.value.entityName;
@@ -95,16 +131,25 @@ function handleView(viewingPageId: string) {
 
 async function handleCreate() {
     try {
-        const page = await store.createPage();
-        handleEdit(page?.id);
+        const createdPage = await createAPage();
+        if (createdPage) {
+            handleEdit(createdPage.id, createdPage.username);
+        }
     } catch (error) {
         Toast.error(errorMessageAsString(error), `Failed to create ${labels.value.entityName.toLowerCase()}`);
     }
 }
 
-function handleEdit(editingPageId?: string) {
-    if (editingPageId) {
-        let editUrl = `/histories/${props.historyId}/pages/${editingPageId}`;
+async function handleEdit(editingPageId: string, ownerUsername: string) {
+    let routedId: string | undefined = editingPageId;
+
+    if (routedId && ownerUsername && !userStore.matchesCurrentUsername(ownerUsername)) {
+        const copiedPage = await createAPage(true);
+        routedId = copiedPage?.id;
+    }
+
+    if (routedId) {
+        let editUrl = `/histories/${props.historyId}/pages/${routedId}`;
         if (props.invocationId) {
             editUrl += `?invocation_id=${props.invocationId}`;
         }
@@ -156,11 +201,11 @@ function handleBack() {
 
         <!-- Display-only mode: rendered view -->
         <PageDisplayOnly
-            v-else-if="store.hasCurrentPage && displayOnly"
+            v-else-if="store.currentPage?.id && store.currentPage.id === props.pageId && displayOnly"
             :labels="labels"
             :markdown-config="markdownConfig || undefined"
             @back="handleBack"
-            @edit="handleEdit(props.pageId)" />
+            @edit="handleEdit(store.currentPage.id, store.currentPage.username)" />
 
         <!-- Edit mode: delegate to unified PageEditorView -->
         <template v-else-if="pageId && !displayOnly">
diff --git a/client/src/components/PageEditor/PageEditorView.test.ts b/client/src/components/PageEditor/PageEditorView.test.ts
index 51f7fdbad9b..62046e8084d 100644
--- a/client/src/components/PageEditor/PageEditorView.test.ts
+++ b/client/src/components/PageEditor/PageEditorView.test.ts
@@ -48,6 +48,18 @@ vi.mock("@/stores/historyStore", () => ({
     })),
 }));
 
+vi.mock("@/stores/userStore", () => ({
+    useUserStore: vi.fn(() => ({
+        matchesCurrentUsername: vi.fn((username: string) => username === "test-owner"),
+    })),
+}));
+
+vi.mock("@/composables/confirmDialog.js", () => ({
+    useConfirmDialog: vi.fn(() => ({
+        confirm: vi.fn().mockResolvedValue(true),
+    })),
+}));
+
 const mockGalaxyInstance = { frame: { active: false } };
 vi.mock("@/app", () => ({
     getGalaxyInstance: vi.fn(() => mockGalaxyInstance),
@@ -79,9 +91,11 @@ function setupLoadedPage(historyId?: string) {
         title: "My Page",
         content: "# Hello",
         update_time: "2024-01-01T00:00:00",
+        username: "test-owner",
     } as Partial<HistoryPageDetails> as HistoryPageDetails;
     store.currentContent = "# Hello";
     store.currentTitle = "My Page";
+    vi.spyOn(store, "hasCurrentPage", "get").mockReturnValue(true);
     return store;
 }
 
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index 9b0170e4191..db02a30f527 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faSpinner, faUsers } from "@fortawesome/free-solid-svg-icons";
+import { faCopy, faSpinner, faUsers } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert } from "bootstrap-vue";
 import { computed, onMounted, onUnmounted, ref, watch } from "vue";
@@ -8,9 +8,11 @@ import { useRouter } from "vue-router/composables";
 // import { getGalaxyInstance } from "@/app";
 // import type { RouterPushOptions } from "@/components/History/Content/router-push-options";
 import { PAGE_LABELS } from "@/components/Page/constants";
+import { useConfirmDialog } from "@/composables/confirmDialog.js";
 import { useWindowAwareNavigation } from "@/composables/windowAwareNavigation";
 import { useHistoryStore } from "@/stores/historyStore";
 import { type PageEditorMode, usePageEditorStore } from "@/stores/pageEditorStore";
+import { useUserStore } from "@/stores/userStore.js";
 
 import GButton from "../BaseComponents/GButton.vue";
 import GModal from "../BaseComponents/GModal.vue";
@@ -29,10 +31,12 @@ const props = defineProps<{
     hideHeader?: boolean;
 }>();
 
+const { confirm } = useConfirmDialog();
 const router = useRouter();
 const { pushToFrameOrPage } = useWindowAwareNavigation();
 const store = usePageEditorStore();
 const historyStore = useHistoryStore();
+const userStore = useUserStore();
 
 const editorMode = computed<PageEditorMode>(() =>
     props.invocationId ? "invocation" : props.historyId ? "history" : "standalone",
@@ -65,6 +69,8 @@ const markdownConfig = computed(() => {
     };
 });
 
+const isOwnedPage = computed(() => userStore.matchesCurrentUsername(store.currentPage?.username));
+
 const showPermissions = ref(false);
 
 onMounted(async () => {
@@ -124,11 +130,38 @@ function handlePreview() {
     });
 }
 
-function handleEdit() {
-    if (props.historyId) {
-        router.push(`/histories/${props.historyId}/pages/${props.pageId}`);
-    } else {
-        router.push(`/pages/editor?id=${props.pageId}`);
+async function handleEdit() {
+    let editingPageId: string | undefined = props.pageId;
+
+    if (!isOwnedPage.value) {
+        const entity = labels.value.entityName;
+
+        const confirmed = await confirm(
+            `You are not the owner of this ${entity}. To edit it, a copy with its contents, owned by you, will be created. Do you want to proceed?`,
+            {
+                title: `Copy this ${entity}?`,
+                okText: `Copy ${entity}`,
+                okIcon: faCopy,
+            },
+        );
+        if (!confirmed) {
+            return;
+        }
+
+        const copiedPage = await store.createPage({
+            title: store.currentTitle ? `Copy of "${store.currentTitle}"` : labels.value.defaultTitle,
+            content: store.currentContent,
+        });
+
+        editingPageId = copiedPage?.id;
+    }
+
+    if (editingPageId) {
+        if (props.historyId) {
+            router.push(`/histories/${props.historyId}/pages/${editingPageId}`);
+        } else {
+            router.push(`/pages/editor?id=${editingPageId}`);
+        }
     }
 }
 
@@ -187,7 +220,7 @@ function handleRevisionRestore(revisionId: string) {
 
         <!-- Display-only mode: rendered view -->
         <PageDisplayOnly
-            v-else-if="store.hasCurrentPage && displayOnly"
+            v-else-if="store.hasCurrentPage && (displayOnly || !isOwnedPage)"
             :labels="labels"
             :markdown-config="markdownConfig || undefined"
             :hide-header="props.hideHeader"
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index c2a88c3203c..b2678f063ff 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -2287,6 +2287,8 @@ class NavigatesGalaxy(HasDriverProxy[WaitType]):
     def history_page_create(self, screenshot_name=None):
         """Click the create button on the page list. Returns to editor view."""
         self.components.pages.history.create_button.wait_for_and_click()
+        self.components.confirm_dialog.ok_button.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
         self.components.pages.history.toolbar.wait_for_visible()
         if screenshot_name:
             self.screenshot(screenshot_name)

From 2670a6e3133d9f169f0480a7ef525b60f235eb1d Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 16 Jun 2026 10:35:23 -0500
Subject: [PATCH 187/256] revert showing other users' pages against your
 history; add unowned indicator

We no longer include pages made by other users against your history/invocation. We do show an indicator under a history/invocation page list where the current user does not own the history/invocation.
---
 client/src/api/pages.ts                       |  2 +-
 .../PageEditor/HistoryPageList.test.ts        | 62 ++++++++++++++++++-
 .../components/PageEditor/HistoryPageList.vue | 20 ++++++
 client/src/stores/userStore.ts                |  7 +++
 4 files changed, 88 insertions(+), 3 deletions(-)

diff --git a/client/src/api/pages.ts b/client/src/api/pages.ts
index e411edcfff1..3ab0e3f043a 100644
--- a/client/src/api/pages.ts
+++ b/client/src/api/pages.ts
@@ -23,7 +23,7 @@ export async function fetchHistoryPages(historyId: string, invocationId?: string
                 history_id: historyId,
                 invocation_id: invocationId,
                 show_own: true,
-                show_published: true,
+                show_published: false,
                 sort_desc: true,
             },
         },
diff --git a/client/src/components/PageEditor/HistoryPageList.test.ts b/client/src/components/PageEditor/HistoryPageList.test.ts
index bcf8177a1ea..0d6a5f53973 100644
--- a/client/src/components/PageEditor/HistoryPageList.test.ts
+++ b/client/src/components/PageEditor/HistoryPageList.test.ts
@@ -1,8 +1,9 @@
+import { createTestingPinia } from "@pinia/testing";
 import { getLocalVue } from "@tests/vitest/helpers";
 import { setupMockHistoryBreadcrumbs } from "@tests/vitest/mockHistoryBreadcrumbs";
 import { shallowMount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
-import { beforeEach, describe, expect, it } from "vitest";
+import { beforeEach, describe, expect, it, vi } from "vitest";
 
 import type { HistoryPageSummary } from "@/api/pages";
 
@@ -17,20 +18,44 @@ const SELECTORS = {
     EMPTY_STATE: ".empty-state",
     PAGE_ITEMS: ".page-items",
     PAGE_ITEM: "[data-description='page item']",
+    UNOWNED_ALERT: "balert-stub",
 };
 
 setupMockHistoryBreadcrumbs();
 
-async function mountComponent(propsData: { pages: HistoryPageSummary[] }) {
+// Mocks for store methods
+const mockGetHistoryById = vi.fn();
+const mockMatchesCurrentUserId = vi.fn();
+
+vi.mock("@/stores/historyStore", () => ({
+    useHistoryStore: vi.fn(() => ({
+        getHistoryById: mockGetHistoryById,
+    })),
+}));
+
+vi.mock("@/stores/userStore", () => ({
+    useUserStore: vi.fn(() => ({
+        matchesCurrentUserId: mockMatchesCurrentUserId,
+    })),
+}));
+
+async function mountComponent(propsData: { pages: HistoryPageSummary[]; invocationId?: string }) {
     const wrapper = shallowMount(HistoryPageList as object, {
         localVue,
         propsData: { ...propsData, historyId: "history-1" },
+        pinia: createTestingPinia({ createSpy: vi.fn }),
     });
     await flushPromises();
     return wrapper;
 }
 
 describe("HistoryPageList", () => {
+    beforeEach(() => {
+        // Default: history is owned by the current user, no alert shown
+        mockGetHistoryById.mockReturnValue({ id: "history-1", name: "Test History", user_id: "user-1" });
+        mockMatchesCurrentUserId.mockReturnValue(true);
+    });
+
     describe("Header", () => {
         let wrapper: Wrapper<Vue>;
 
@@ -88,4 +113,37 @@ describe("HistoryPageList", () => {
             expect(wrapper.find(SELECTORS.EMPTY_STATE).exists()).toBe(false);
         });
     });
+
+    describe("Unowned history alert", () => {
+        it("does not show alert when current user owns the history", async () => {
+            const wrapper = await mountComponent({ pages: [] });
+            expect(wrapper.find(SELECTORS.UNOWNED_ALERT).exists()).toBe(false);
+        });
+
+        it("shows alert when current user does not own the history", async () => {
+            mockMatchesCurrentUserId.mockReturnValue(false);
+            const wrapper = await mountComponent({ pages: [] });
+            const alert = wrapper.find(SELECTORS.UNOWNED_ALERT);
+            expect(alert.exists()).toBe(true);
+            expect(alert.text()).toContain("You do not own this history");
+        });
+
+        it("does not show invocation span in alert when no invocationId", async () => {
+            mockMatchesCurrentUserId.mockReturnValue(false);
+            const wrapper = await mountComponent({ pages: [] });
+            expect(wrapper.find(SELECTORS.UNOWNED_ALERT).text()).not.toContain("associated with the invocation");
+        });
+
+        it("shows invocation qualifier in alert when invocationId is set", async () => {
+            mockMatchesCurrentUserId.mockReturnValue(false);
+            const wrapper = await mountComponent({ pages: [], invocationId: "inv-1" });
+            expect(wrapper.find(SELECTORS.UNOWNED_ALERT).text()).toContain("associated with the invocation");
+        });
+
+        it("does not show alert when history has no user_id field", async () => {
+            mockGetHistoryById.mockReturnValue({ id: "history-1", name: "Test History" });
+            const wrapper = await mountComponent({ pages: [] });
+            expect(wrapper.find(SELECTORS.UNOWNED_ALERT).exists()).toBe(false);
+        });
+    });
 });
diff --git a/client/src/components/PageEditor/HistoryPageList.vue b/client/src/components/PageEditor/HistoryPageList.vue
index 63cc7c4e1d1..f9818f3d00a 100644
--- a/client/src/components/PageEditor/HistoryPageList.vue
+++ b/client/src/components/PageEditor/HistoryPageList.vue
@@ -1,11 +1,14 @@
 <script setup lang="ts">
 import { faArrowLeft, faPlus } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BAlert } from "bootstrap-vue";
 import { computed, toRef } from "vue";
 
 import type { HistoryPageSummary } from "@/api/pages";
 import { PAGE_LABELS } from "@/components/Page/constants";
 import { useHistoryBreadCrumbsTo } from "@/composables/historyBreadcrumbs";
+import { useHistoryStore } from "@/stores/historyStore.js";
+import { useUserStore } from "@/stores/userStore.js";
 
 import BreadcrumbHeading from "../Common/BreadcrumbHeading.vue";
 import Heading from "../Common/Heading.vue";
@@ -25,6 +28,17 @@ const emit = defineEmits<{
     (e: "view-runtime-report"): void;
 }>();
 
+const historyStore = useHistoryStore();
+const userStore = useUserStore();
+
+const history = computed(() => historyStore.getHistoryById(props.historyId));
+
+const unownedHistory = computed(() =>
+    history.value && "user_id" in history.value
+        ? !userStore.matchesCurrentUserId(history.value.user_id as string)
+        : undefined,
+);
+
 const labels = computed(() => (props.invocationId ? PAGE_LABELS.invocation : PAGE_LABELS.history));
 
 const { breadcrumbItems } = useHistoryBreadCrumbsTo(toRef(props, "historyId"), labels.value.entityNamePlural);
@@ -53,6 +67,12 @@ const { breadcrumbItems } = useHistoryBreadCrumbsTo(toRef(props, "historyId"), l
             </GButton>
         </div>
 
+        <BAlert v-if="unownedHistory" show>
+            You do not own this history
+            <span v-if="props.invocationId">(associated with the invocation)</span>
+            so only {{ labels.entityNamePlural }} that you created against this history are shown.
+        </BAlert>
+
         <div v-if="pages.length === 0" class="empty-state text-center p-4" data-description="page empty state">
             <p class="text-muted">{{ labels.emptyStateTitle }}</p>
             <p class="text-muted small">
diff --git a/client/src/stores/userStore.ts b/client/src/stores/userStore.ts
index a53899a6f50..cef9578f832 100644
--- a/client/src/stores/userStore.ts
+++ b/client/src/stores/userStore.ts
@@ -119,6 +119,12 @@ export const useUserStore = defineStore("userStore", () => {
         };
     });
 
+    const matchesCurrentUserId = computed(() => {
+        return (userId?: string) => {
+            return isRegisteredUser(currentUser.value) && "id" in currentUser.value && currentUser.value.id === userId;
+        };
+    });
+
     function setCurrentUser(user: RegisteredUser) {
         currentUser.value = user;
     }
@@ -374,6 +380,7 @@ export const useUserStore = defineStore("userStore", () => {
         refreshUser,
         syncLegacyAppUser,
         matchesCurrentUsername,
+        matchesCurrentUserId,
         setCurrentUser,
         setCurrentTheme,
         setListViewPreference,

From ae577a0ac3ac47b3d80d845a27ae739fdc6798d1 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 16 Jun 2026 10:59:33 -0500
Subject: [PATCH 188/256] disable page edit button in several places when page
 is deleted

---
 client/src/components/PageEditor/PageCard.vue           | 3 ++-
 client/src/components/PageEditor/PageDisplayToolbar.vue | 4 +++-
 client/src/components/PageEditor/PageEditorView.vue     | 2 +-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/client/src/components/PageEditor/PageCard.vue b/client/src/components/PageEditor/PageCard.vue
index c45ee59db25..5dd97c82d4d 100644
--- a/client/src/components/PageEditor/PageCard.vue
+++ b/client/src/components/PageEditor/PageCard.vue
@@ -76,8 +76,9 @@ const primaryActions: CardAction[] = [
         id: "edit-notebook",
         label: "Edit",
         icon: faEdit,
-        title: props.editTitle,
+        title: !props.page.deleted ? props.editTitle : `This ${props.entityName} is deleted`,
         handler: () => emit("edit"),
+        disabled: props.page.deleted,
     },
 ];
 
diff --git a/client/src/components/PageEditor/PageDisplayToolbar.vue b/client/src/components/PageEditor/PageDisplayToolbar.vue
index abbfabaf6b9..dd9ada41e74 100644
--- a/client/src/components/PageEditor/PageDisplayToolbar.vue
+++ b/client/src/components/PageEditor/PageDisplayToolbar.vue
@@ -27,7 +27,8 @@ const props = defineProps<{
 }>();
 
 const pageEditorStore = usePageEditorStore();
-const { canSave, currentTitle, revisionCount, showRevisions, isDirty, isSaving } = storeToRefs(pageEditorStore);
+const { canSave, currentPage, currentTitle, revisionCount, showRevisions, isDirty, isSaving } =
+    storeToRefs(pageEditorStore);
 
 const emit = defineEmits<{
     (e: "back"): void;
@@ -127,6 +128,7 @@ function handleTitleChange(newTitle: string): Promise<void> {
                     outline
                     :pressed="props.mode === 'editor'"
                     data-description="page edit button"
+                    :disabled="currentPage?.deleted"
                     size="small"
                     @click="emit('edit')">
                     <FontAwesomeIcon :icon="faEdit" />
diff --git a/client/src/components/PageEditor/PageEditorView.vue b/client/src/components/PageEditor/PageEditorView.vue
index db02a30f527..3880c07dd4f 100644
--- a/client/src/components/PageEditor/PageEditorView.vue
+++ b/client/src/components/PageEditor/PageEditorView.vue
@@ -220,7 +220,7 @@ function handleRevisionRestore(revisionId: string) {
 
         <!-- Display-only mode: rendered view -->
         <PageDisplayOnly
-            v-else-if="store.hasCurrentPage && (displayOnly || !isOwnedPage)"
+            v-else-if="store.hasCurrentPage && (displayOnly || !isOwnedPage || store.currentPage?.deleted)"
             :labels="labels"
             :markdown-config="markdownConfig || undefined"
             :hide-header="props.hideHeader"

From dda2aaa25b3ac79e1f65901dbfc319c87396e00a Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 16 Jun 2026 11:01:00 -0500
Subject: [PATCH 189/256] add share and publish button to history/invocation
 page cards

---
 client/src/components/PageEditor/PageCard.vue | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/client/src/components/PageEditor/PageCard.vue b/client/src/components/PageEditor/PageCard.vue
index 5dd97c82d4d..2defc441a34 100644
--- a/client/src/components/PageEditor/PageCard.vue
+++ b/client/src/components/PageEditor/PageCard.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faEdit, faEye, faHistory, faSitemap, faUser } from "@fortawesome/free-solid-svg-icons";
+import { faEdit, faEye, faHistory, faShareAlt, faSitemap, faUser } from "@fortawesome/free-solid-svg-icons";
 import { computed } from "vue";
 
 import type { HistoryPageSummary } from "@/api/pages";
@@ -82,8 +82,16 @@ const primaryActions: CardAction[] = [
     },
 ];
 
-// TODO: Once we fix sharing, we should add a sharing action
 const secondaryActions: CardAction[] = [
+    {
+        id: "share-access-management",
+        label: "Share and Publish",
+        title: `Make this ${props.entityName} accessible or public`,
+        icon: faShareAlt,
+        variant: "outline-primary",
+        to: `/pages/sharing?id=${props.page.id}`,
+        visible: !props.page.deleted && userStore.matchesCurrentUsername(props.page.username),
+    },
     {
         id: "view-notebook",
         label: "View",

From a6cd293c327a93dd9290a3c76db059b8f12dd174 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 16 Jun 2026 11:53:44 -0500
Subject: [PATCH 190/256] split `notebook` context into 3: "invocation",
 "history" and "standalone"

This also moves to the `contextIcon` computed to the `activeContext` composable.
---
 client/src/components/GalaxyAI.vue            | 29 +------
 .../src/composables/useActiveContext.test.ts  | 75 ++++++++++++++++++-
 client/src/composables/useActiveContext.ts    | 65 ++++++++++++++--
 3 files changed, 132 insertions(+), 37 deletions(-)

diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index 62992541d32..702e88eb5d0 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -1,14 +1,5 @@
 <script setup lang="ts">
-import {
-    faBook,
-    faFile,
-    faFileContract,
-    faMagic,
-    faSitemap,
-    faTimes,
-    faTrash,
-    faWrench,
-} from "@fortawesome/free-solid-svg-icons";
+import { faMagic, faTimes, faTrash } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BSkeleton } from "bootstrap-vue";
 import { computed, nextTick, onMounted, ref, watch } from "vue";
@@ -58,7 +49,7 @@ const router = useRouter();
 const chatStore = useChatStore();
 const Toast = useToast();
 
-const { activeContext, contextLabel } = useActiveContext();
+const { activeContext, contextLabel, contextIcon } = useActiveContext();
 const pageEditorStore = usePageEditorStore();
 const contextDismissed = ref(false);
 
@@ -110,22 +101,6 @@ const effectiveContext = computed(() => {
     return activeContext.value;
 });
 
-const contextIcon = computed(() => {
-    switch (effectiveContext.value?.contextType) {
-        case "tool":
-            return faWrench;
-        case "dataset":
-            return faFile;
-        case "workflow_editor":
-        case "workflow_run":
-            return faSitemap;
-        case "notebook":
-            return effectiveContext.value?.historyId ? faBook : faFileContract;
-        default:
-            return faMagic;
-    }
-});
-
 /** The chat is in "route mode": It's being viewed in the center and the route starts with `/galaxyai`
  * _(and we are not in the window manager)_. */
 const isRouteMode = computed(() => chatStore.isCenterMode && !props.compact && route.path.startsWith("/galaxyai"));
diff --git a/client/src/composables/useActiveContext.test.ts b/client/src/composables/useActiveContext.test.ts
index 57343fd0e60..93d42c115ef 100644
--- a/client/src/composables/useActiveContext.test.ts
+++ b/client/src/composables/useActiveContext.test.ts
@@ -1,6 +1,9 @@
+import { faFile, faMagic, faSitemap, faWrench } from "@fortawesome/free-solid-svg-icons";
 import { describe, expect, it, vi } from "vitest";
 import { type Ref, ref } from "vue";
 
+import { PAGE_LABELS } from "@/components/Page/constants";
+
 import type { ActiveContext } from "./useActiveContext";
 
 // Mock route as a reactive ref so tests can mutate it
@@ -132,6 +135,24 @@ describe("useActiveContext", () => {
             });
         });
 
+        it("detects notebook context from invocation reports route", () => {
+            const { activeContext } = withRoute(
+                "/workflows/invocations/inv-1/reports",
+                { id: "p-1" },
+                { invocationId: "inv-1" },
+            );
+            expect(activeContext.value).toEqual({
+                contextType: "notebook",
+                pageId: "p-1",
+                invocationId: "inv-1",
+            });
+        });
+
+        it("returns null for invocation reports route without page id query param", () => {
+            const { activeContext } = withRoute("/workflows/invocations/inv-1/reports", {}, { invocationId: "inv-1" });
+            expect(activeContext.value).toBeNull();
+        });
+
         it("detects notebook context from page editor route", () => {
             const { activeContext } = withRoute("/pages/editor", { id: "test-page-id" }, {});
             expect(activeContext.value).toEqual({
@@ -193,12 +214,62 @@ describe("useActiveContext", () => {
                 {},
                 { historyId: "test-history-id", pageId: "test-page-id" },
             );
-            expect(contextLabel.value).toBe("History Notebook: test-page-id");
+            expect(contextLabel.value).toBe("Galaxy Notebook: test-page-id");
         });
 
         it("labels standalone page editor context without historyId", () => {
             const { contextLabel } = withRoute("/pages/editor", { id: "test-page-id" }, {});
-            expect(contextLabel.value).toBe("Page: test-page-id");
+            expect(contextLabel.value).toBe("Report: test-page-id");
+        });
+
+        it("labels invocation notebook context", () => {
+            const { contextLabel } = withRoute(
+                "/workflows/invocations/inv-1/reports",
+                { id: "p-1" },
+                { invocationId: "inv-1" },
+            );
+            expect(contextLabel.value).toBe("Invocation Report: p-1");
+        });
+    });
+
+    describe("contextIcon", () => {
+        it("returns faWrench for tool context", () => {
+            const { contextIcon } = withRoute("/", { tool_id: "bwa" });
+            expect(contextIcon.value).toBe(faWrench);
+        });
+
+        it("returns faFile for dataset context", () => {
+            const { contextIcon } = withRoute("/datasets/d-1", {}, { datasetId: "d-1" });
+            expect(contextIcon.value).toBe(faFile);
+        });
+
+        it("returns faSitemap for workflow editor context", () => {
+            const { contextIcon } = withRoute("/workflows/edit", { id: "wf-1" });
+            expect(contextIcon.value).toBe(faSitemap);
+        });
+
+        it("returns faSitemap for workflow run context", () => {
+            const { contextIcon } = withRoute("/workflows/run", { id: "wf-1" });
+            expect(contextIcon.value).toBe(faSitemap);
+        });
+
+        it("returns history notebook icon for history notebook context", () => {
+            const { contextIcon } = withRoute("/histories/h-1/pages/p-1", {}, { historyId: "h-1", pageId: "p-1" });
+            expect(contextIcon.value).toBe(PAGE_LABELS.history.titleIcon);
+        });
+
+        it("returns invocation notebook icon for invocation notebook context", () => {
+            const { contextIcon } = withRoute(
+                "/workflows/invocations/inv-1/reports",
+                { id: "p-1" },
+                { invocationId: "inv-1" },
+            );
+            expect(contextIcon.value).toBe(PAGE_LABELS.invocation.titleIcon);
+        });
+
+        it("returns faMagic for unrecognized routes", () => {
+            const { contextIcon } = withRoute("/some/unknown");
+            expect(contextIcon.value).toBe(faMagic);
         });
     });
 });
diff --git a/client/src/composables/useActiveContext.ts b/client/src/composables/useActiveContext.ts
index b5aff5bb1b0..4ed3ba36c19 100644
--- a/client/src/composables/useActiveContext.ts
+++ b/client/src/composables/useActiveContext.ts
@@ -1,6 +1,8 @@
+import { faFile, faMagic, faSitemap, faWrench } from "@fortawesome/free-solid-svg-icons";
 import { computed } from "vue";
 import { useRoute } from "vue-router/composables";
 
+import { PAGE_LABELS } from "@/components/Page/constants";
 import { useToolStore } from "@/stores/toolStore";
 
 export type ActiveContext =
@@ -9,7 +11,7 @@ export type ActiveContext =
     | { contextType: "workflow_editor"; workflowId: string }
     | { contextType: "workflow_run"; workflowId: string }
     | { contextType: "job"; jobId: string; toolId?: string }
-    | { contextType: "notebook"; pageId: string; historyId?: string };
+    | { contextType: "notebook"; pageId: string; historyId?: string; invocationId?: string };
 
 export function useActiveContext() {
     const route = useRoute();
@@ -68,12 +70,28 @@ export function useActiveContext() {
             };
         }
 
+        if (path.startsWith("/workflows/invocations/") && params.invocationId && query.id) {
+            const invocationId = String(params.invocationId);
+            if (path === `/workflows/invocations/${invocationId}/reports`) {
+                return {
+                    contextType: "notebook",
+                    pageId: String(query.id),
+                    invocationId,
+                };
+            }
+        }
+
         if (path.startsWith("/histories/") && params.historyId && params.pageId) {
-            return {
-                contextType: "notebook",
-                pageId: String(params.pageId),
-                historyId: String(params.historyId),
-            };
+            const historyId = String(params.historyId);
+            const pageId = String(params.pageId);
+            if (path === `/histories/${historyId}/pages/${pageId}`) {
+                return {
+                    contextType: "notebook",
+                    pageId,
+                    historyId,
+                    invocationId: query.invocation_id ? String(query.invocation_id) : undefined,
+                };
+            }
         }
 
         if (path === "/pages/editor" && query.id) {
@@ -102,15 +120,46 @@ export function useActiveContext() {
                 return `Running workflow: ${ctx.workflowId}`;
             case "job":
                 return `Job: ${ctx.jobId}`;
-            case "notebook":
-                return ctx.historyId ? `History Notebook: ${ctx.pageId}` : `Page: ${ctx.pageId}`;
+            case "notebook": {
+                const notebookLabels = getNotebookLabels(ctx);
+                return `${notebookLabels.entityName}: ${ctx.pageId}`;
+            }
             default:
                 return null;
         }
     });
 
+    const contextIcon = computed(() => {
+        switch (activeContext.value?.contextType) {
+            case "tool":
+                return faWrench;
+            case "dataset":
+                return faFile;
+            case "workflow_editor":
+            case "workflow_run":
+                return faSitemap;
+            case "notebook": {
+                const notebookLabels = getNotebookLabels(activeContext.value);
+                return notebookLabels.titleIcon;
+            }
+            default:
+                return faMagic;
+        }
+    });
+
+    function getNotebookLabels(noteBookContext: Extract<ActiveContext, { contextType: "notebook" }>) {
+        if (noteBookContext.invocationId) {
+            return PAGE_LABELS.invocation;
+        } else if (noteBookContext.historyId) {
+            return PAGE_LABELS.history;
+        } else {
+            return PAGE_LABELS.standalone;
+        }
+    }
+
     return {
         activeContext,
+        contextIcon,
         contextLabel,
     };
 }

From cd778f16c1e0553d8a5b1c6f8fa133c4e4def1d7 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 16 Jun 2026 12:08:20 -0500
Subject: [PATCH 191/256] clean up `GalaxyAI` vitest by mocking API properly

---
 client/src/components/GalaxyAI.test.ts | 72 ++++++++++++--------------
 1 file changed, 32 insertions(+), 40 deletions(-)

diff --git a/client/src/components/GalaxyAI.test.ts b/client/src/components/GalaxyAI.test.ts
index 32ebea643b7..d17c8305243 100644
--- a/client/src/components/GalaxyAI.test.ts
+++ b/client/src/components/GalaxyAI.test.ts
@@ -6,31 +6,20 @@ import { setActivePinia } from "pinia";
 import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
 import { ref } from "vue";
 
+import { useServerMock } from "@/api/client/__mocks__";
 import type { ActiveContext } from "@/composables/useActiveContext";
 import { useChatStore } from "@/stores/chatStore";
 import { usePageEditorStore } from "@/stores/pageEditorStore";
 
 import GalaxyAI from "./GalaxyAI.vue";
 
-// ── API mock ─────────────────────────────────────────────────────────────────
+// API mock
+const { server, http } = useServerMock();
+
 const mockGetMessages = vi.fn();
 const mockGetHistory = vi.fn();
 
-vi.mock("@/api", () => ({
-    GalaxyApi: () => ({
-        GET: (path: string, _opts: unknown) => {
-            if (path.includes("messages")) {
-                return mockGetMessages();
-            }
-            if (path.includes("history")) {
-                return mockGetHistory();
-            }
-            return { data: null, error: null };
-        },
-    }),
-}));
-
-// ── Composable stubs ──────────────────────────────────────────────────────────
+// Composable mocks
 const mockActiveContext = ref<ActiveContext | null>(null);
 
 vi.mock("@/composables/useActiveContext", () => ({
@@ -83,10 +72,10 @@ vi.mock("vue-router/composables", () => ({
     useRouter: () => ({ push: vi.fn(), replace: vi.fn() }),
 }));
 
-// ── Helpers ───────────────────────────────────────────────────────────────────
 const localVue = getLocalVue();
 let lastWrapper: ReturnType<typeof shallowMount> | null = null;
 
+// Constants
 const EXCHANGE_ID = "exchange-abc";
 const MESSAGES_RESPONSE = [
     { role: "user", content: "Hello", timestamp: null },
@@ -94,15 +83,34 @@ const MESSAGES_RESPONSE = [
 ];
 
 function makeSuccessfulFetch(messages = MESSAGES_RESPONSE) {
-    mockGetMessages.mockResolvedValue({ data: messages, error: null });
+    server.use(
+        http.get("/api/chat/exchange/{exchange_id}/messages", ({ response }) => {
+            mockGetMessages();
+            return response(200).json(messages);
+        }),
+    );
 }
 
 function makeEmptyFetch() {
-    mockGetMessages.mockResolvedValue({ data: [], error: null });
+    server.use(
+        http.get("/api/chat/exchange/{exchange_id}/messages", ({ response }) => {
+            mockGetMessages();
+            return response(200).json([]);
+        }),
+    );
 }
 
-function makeHistoryFetch(items = [{ id: "latest-chat" }]) {
-    mockGetHistory.mockResolvedValue({ data: items, error: null });
+function makeHistoryFetch(items: { id: string }[] = [{ id: "latest-chat" }]) {
+    server.use(
+        http.get("/api/chat/history", ({ response }) => {
+            mockGetHistory();
+            return response(200).json(items as any);
+        }),
+        http.get("/api/chat/page/{page_id}/history", ({ response }) => {
+            mockGetHistory();
+            return response(200).json(items as any);
+        }),
+    );
 }
 
 interface MountOptions {
@@ -110,7 +118,6 @@ interface MountOptions {
     activeChatId?: string | null;
     cachedExchangeId?: string | null;
     pageId?: string;
-    /** Pre-populate chatStore.chatHistory and stub loadHistory as a no-op so no real HTTP call is made. */
     chatHistoryItems?: { id: string }[];
 }
 
@@ -129,8 +136,6 @@ function mountGalaxyAI({
 
     if (chatHistoryItems !== undefined) {
         chatStore.chatHistory = chatHistoryItems as any;
-        // Stub loadHistory so it doesn't make real HTTP calls (chatStore imports @/api/client
-        // which is not mocked); keep chatHistory as pre-populated.
         vi.spyOn(chatStore, "loadHistory").mockResolvedValue(undefined);
     }
 
@@ -159,12 +164,11 @@ function mountGalaxyAI({
     return { wrapper, chatStore, pageEditorStore };
 }
 
-// ── Tests ─────────────────────────────────────────────────────────────────────
 describe("GalaxyAI fetch operations on mount", () => {
     beforeEach(() => {
         mockActiveContext.value = null;
-        vi.clearAllMocks();
-        // Default: empty history so loadLatestChat doesn't cascade into fetchConversation
+        mockGetMessages.mockClear();
+        mockGetHistory.mockClear();
         makeHistoryFetch([]);
     });
 
@@ -174,7 +178,6 @@ describe("GalaxyAI fetch operations on mount", () => {
         vi.restoreAllMocks();
     });
 
-    // Branch 1: explicit exchangeId prop (not "new")
     describe("when exchangeId prop is provided and not 'new'", () => {
         it("fetches the specified exchange on mount", async () => {
             makeSuccessfulFetch();
@@ -185,13 +188,12 @@ describe("GalaxyAI fetch operations on mount", () => {
 
         it("does not call loadLatestChat", async () => {
             makeSuccessfulFetch();
-            mountGalaxyAI({ props: { exchangeId: EXCHANGE_ID } });
+            mountGalaxyAI({ props: { exchangeId: EXCHANGE_ID }, chatHistoryItems: [{ id: EXCHANGE_ID }] });
             await flushPromises();
             expect(mockGetHistory).not.toHaveBeenCalled();
         });
     });
 
-    // Branch 2: exchangeId === "new"
     describe("when exchangeId prop is 'new'", () => {
         it("starts a new chat without fetching messages", async () => {
             mountGalaxyAI({ props: { exchangeId: "new" } });
@@ -200,15 +202,12 @@ describe("GalaxyAI fetch operations on mount", () => {
         });
 
         it("does not restore from activeChatId even when one is set", async () => {
-            // Regression: exchangeId='new' previously fell into the docked/panel restore branch
-            // and would fetch activeChatId, causing the route to flip back to the old chat.
             mountGalaxyAI({ props: { exchangeId: "new" }, activeChatId: EXCHANGE_ID });
             await flushPromises();
             expect(mockGetMessages).not.toHaveBeenCalled();
         });
     });
 
-    // Branch 3: docked/panel — notebook context with a cached exchange ID and no activeChatId
     describe("docked/panel — notebook context with cached exchange ID", () => {
         it("fetches the cached exchange when activeChatId is null", async () => {
             makeSuccessfulFetch();
@@ -231,10 +230,8 @@ describe("GalaxyAI fetch operations on mount", () => {
         });
     });
 
-    // Branch 4: docked/panel — notebook context, no cached exchange but page has history
     describe("docked/panel — notebook context, no cached ID but page has history", () => {
         it("fetches the most recent chat from page history (ignores global activeChatId)", async () => {
-            // activeChatId is set but belongs to a different context — must not be used for notebook.
             makeSuccessfulFetch();
             mockActiveContext.value = { contextType: "notebook", pageId: "page-1", historyId: "hist-1" };
             mountGalaxyAI({
@@ -247,10 +244,8 @@ describe("GalaxyAI fetch operations on mount", () => {
         });
     });
 
-    // Branch 5: docked/panel — notebook context, no cached exchange, empty history
     describe("docked/panel — notebook context, no cached ID and empty history", () => {
         it("starts a new chat without fetching", async () => {
-            // beforeEach already mocks history as empty
             mockActiveContext.value = { contextType: "notebook", pageId: "page-1", historyId: "hist-1" };
             mountGalaxyAI({ props: { docked: true }, activeChatId: null });
             await flushPromises();
@@ -258,7 +253,6 @@ describe("GalaxyAI fetch operations on mount", () => {
         });
     });
 
-    // Branch 6: docked/panel — non-notebook context with activeChatId set
     describe("docked/panel — non-notebook context with activeChatId", () => {
         it("fetches the active chat exchange", async () => {
             makeSuccessfulFetch();
@@ -268,7 +262,6 @@ describe("GalaxyAI fetch operations on mount", () => {
         });
     });
 
-    // Branch 7: docked/panel — non-notebook context, no activeChatId
     describe("docked/panel — non-notebook context, no activeChatId", () => {
         it("starts a new chat without fetching", async () => {
             mountGalaxyAI({ props: { docked: true }, activeChatId: null });
@@ -277,7 +270,6 @@ describe("GalaxyAI fetch operations on mount", () => {
         });
     });
 
-    // Branch 8: center mode (no exchangeId, not docked/panel)
     describe("center mode (no exchangeId, not docked/panel)", () => {
         it("calls loadLatestChat to fetch most recent history", async () => {
             mountGalaxyAI({});

From b9b42416d30b27fa948366cae260b2b1154e2745 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2026 13:32:44 -0400
Subject: [PATCH 192/256] Move toolbox-less converter loading onto the
 datatypes Registry

Celery worker converter registration duplicated load_datatype_converters
and poked registry privates (_converters_by_datatype) from celery/. Add
Registry.load_datatype_converters_without_toolbox sharing a recorder with
the canonical loader; registry now owns its own cache reset.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/celery/__init__.py    | 37 +++-----------------------------
 lib/galaxy/datatypes/registry.py | 37 ++++++++++++++++++++++++++++----
 2 files changed, 36 insertions(+), 38 deletions(-)

diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index a21cfdcdd27..127f4b641b0 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -113,39 +113,6 @@ def get_galaxy_app():
     return build_app()
 
 
-def _register_worker_datatype_converters(galaxy_app) -> None:
-    """Register datatype converter tools in the Celery worker's datatypes registry.
-
-    Async tool-request execution (``execute_async`` -> ``collect_input_datasets``) runs in
-    the Celery worker and applies implicit datatype conversion (e.g. decompressing a
-    ``fasta.gz`` input for a ``fasta`` parameter). That relies on
-    ``datatypes_registry.datatype_converters`` being populated, which normally happens via
-    ``load_datatype_converters(toolbox)`` in the web ``UniverseApplication``. The worker's
-    minimal ``GalaxyManagerApplication`` has no toolbox, so load the (few, built-in)
-    converter tools directly using the same toolbox-less path ``queue_jobs`` uses for the
-    submitted tool. Without this, ``find_conversion_destination`` finds no converter and the
-    raw (compressed) dataset is handed to the tool. See ``lib/galaxy/tools/actions/__init__.py``.
-    """
-    from galaxy.tool_util.parser import get_tool_source
-    from galaxy.tools import create_tool_from_source
-
-    registry = galaxy_app.datatypes_registry
-    converters_path = registry.converters_path
-    if not converters_path:
-        return
-    for converter_file, source_ext, target_ext in registry.converters:
-        config_path = os.path.join(converters_path, converter_file)
-        try:
-            tool_source = get_tool_source(config_file=config_path)
-            converter = create_tool_from_source(galaxy_app, tool_source, config_file=config_path)
-            registry.converter_tools.add(converter)
-            registry.datatype_converters.setdefault(source_ext, {})[target_ext] = converter
-        except Exception:
-            log.exception("Failed to load datatype converter %s for Celery worker", config_path)
-    # Drop any cached (empty) converter lookups computed before registration.
-    registry._converters_by_datatype = {}
-
-
 @lru_cache(maxsize=1)
 def build_app():
     if kwargs := get_app_properties():
@@ -155,7 +122,9 @@ def build_app():
         import galaxy.app
 
         galaxy_app = galaxy.app.GalaxyManagerApplication(configure_logging=False, **kwargs)
-        _register_worker_datatype_converters(galaxy_app)
+        # GalaxyManagerApplication has no toolbox, so the converter tools the async
+        # execution path relies on must be loaded directly into the datatypes registry.
+        galaxy_app.datatypes_registry.load_datatype_converters_without_toolbox(galaxy_app)
         return galaxy_app
 
 
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index c94bfea5511..8604531ec0a 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -685,16 +685,45 @@ class Registry:
             try:
                 config_path = os.path.join(converter_path, tool_config)
                 converter = toolbox.load_tool(config_path, use_cached=use_cached)
-                self.converter_tools.add(converter)
                 toolbox.register_tool(converter)
-                if source_datatype not in self.datatype_converters:
-                    self.datatype_converters[source_datatype] = {}
-                self.datatype_converters[source_datatype][target_datatype] = converter
+                self._register_converter_tool(converter, source_datatype, target_datatype)
                 if not hasattr(toolbox.app, "tool_cache") or converter.id in toolbox.app.tool_cache._new_tool_ids:
                     self.log.debug("Loaded converter: %s", converter.id)
             except Exception:
                 self.log.exception(f"Error loading converter ({converter_path})")
 
+    def load_datatype_converters_without_toolbox(self, app) -> None:
+        """Load datatype converters for an app that has no toolbox (e.g. the Celery worker).
+
+        Mirrors ``load_datatype_converters`` but builds each converter directly from its tool
+        source rather than through a toolbox, since the Celery worker's minimal
+        ``GalaxyManagerApplication`` has none. Async tool-request execution runs in the worker
+        and relies on ``datatype_converters`` being populated to apply implicit datatype
+        conversion (e.g. decompressing a ``fasta.gz`` input for a ``fasta`` parameter); without
+        this ``find_conversion_destination`` finds no converter and hands the raw dataset to the
+        tool.
+        """
+        # Imported here to avoid a circular import - galaxy.tools depends on galaxy.datatypes.
+        from galaxy.tool_util.parser import get_tool_source
+        from galaxy.tools import create_tool_from_source
+
+        if not self.converters_path:
+            return
+        for tool_config, source_datatype, target_datatype in self.converters:
+            config_path = os.path.join(self.converters_path, tool_config)
+            try:
+                tool_source = get_tool_source(config_file=config_path)
+                converter = create_tool_from_source(app, tool_source, config_file=config_path)
+                self._register_converter_tool(converter, source_datatype, target_datatype)
+            except Exception:
+                self.log.exception(f"Error loading converter ({config_path})")
+        # Drop any cached (empty) converter lookups computed before registration.
+        self._converters_by_datatype = {}
+
+    def _register_converter_tool(self, converter, source_datatype, target_datatype) -> None:
+        self.converter_tools.add(converter)
+        self.datatype_converters.setdefault(source_datatype, {})[target_datatype] = converter
+
     def load_display_applications(self, app):
         """
         Add display applications from self.display_app_containers or to appropriate datatypes.

From 90a4a9354e919c2ff5fe001f62599dfb30d7f360 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2026 14:00:40 -0400
Subject: [PATCH 193/256] Add canonical iter_parameter_models tree walk;
 collapse hand-rolled copies

Three structure-only descents into .whens/.parameters (case._leaf_param_short_names,
linters.tests._collect_multiple_select_names, convert.assert_yaml_v1_parameters) each
reimplemented the recursion. Add iter_parameter_models() beside simple_input_models and
reduce all three to one-line filters.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/tool_util/linters/tests.py      | 19 ++++++------------
 lib/galaxy/tool_util/parameters/case.py    | 20 ++++++++-----------
 lib/galaxy/tool_util/parameters/convert.py |  8 ++------
 lib/galaxy/tool_util_models/parameters.py  | 23 ++++++++++++++++++++++
 4 files changed, 39 insertions(+), 31 deletions(-)

diff --git a/lib/galaxy/tool_util/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py
index afa1f0a4ddb..653837d201a 100644
--- a/lib/galaxy/tool_util/linters/tests.py
+++ b/lib/galaxy/tool_util/linters/tests.py
@@ -20,9 +20,7 @@ from galaxy.tool_util_models.assertions import (
     relaxed_assertion_list,
 )
 from galaxy.tool_util_models.parameters import (
-    ConditionalParameterModel,
-    RepeatParameterModel,
-    SectionParameterModel,
+    iter_parameter_models,
     SelectParameterModel,
     ToolParameterT,
 )
@@ -218,16 +216,11 @@ def _cleanup_pydantic_error(error) -> str:
 
 
 def _collect_multiple_select_names(parameters: List["ToolParameterT"]) -> Set[str]:
-    names: Set[str] = set()
-    for param in parameters:
-        if isinstance(param, SelectParameterModel) and param.multiple:
-            names.add(param.name)
-        elif isinstance(param, (ConditionalParameterModel,)):
-            for when in param.whens:
-                names.update(_collect_multiple_select_names(when.parameters))
-        elif isinstance(param, (SectionParameterModel, RepeatParameterModel)):
-            names.update(_collect_multiple_select_names(param.parameters))
-    return names
+    return {
+        param.name
+        for param in iter_parameter_models(parameters)
+        if isinstance(param, SelectParameterModel) and param.multiple
+    }
 
 
 class TestsMultipleSelectEmptyValue(Linter):
diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 50984e46a9e..f0b2edbc5a0 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -39,6 +39,7 @@ from galaxy.tool_util_models.parameters import (
     GenomeBuildParameterModel,
     GroupTagParameterModel,
     IntegerParameterModel,
+    iter_parameter_models,
     RepeatParameterModel,
     SectionParameterModel,
     SelectParameterModel,
@@ -583,18 +584,13 @@ def _select_which_when(
 
 def _leaf_param_short_names(parameters: List[ToolParameterT]) -> Set[str]:
     """Collect the leaf parameter short names reachable from a list of parameters,
-    descending into repeats, sections and nested conditionals."""
-    names: Set[str] = set()
-    for parameter in parameters:
-        if isinstance(parameter, (RepeatParameterModel, SectionParameterModel)):
-            names |= _leaf_param_short_names(parameter.parameters)
-        elif isinstance(parameter, ConditionalParameterModel):
-            names.add(parameter.test_parameter.name)
-            for when in parameter.whens:
-                names |= _leaf_param_short_names(when.parameters)
-        else:
-            names.add(parameter.name)
-    return names
+    descending into repeats, sections and nested conditionals (including each
+    conditional's discriminator)."""
+    return {
+        parameter.name
+        for parameter in iter_parameter_models(parameters)
+        if not isinstance(parameter, (RepeatParameterModel, SectionParameterModel, ConditionalParameterModel))
+    }
 
 
 def _infer_when_from_inputs(
diff --git a/lib/galaxy/tool_util/parameters/convert.py b/lib/galaxy/tool_util/parameters/convert.py
index 31364d2d2fd..7fe04aa4b61 100644
--- a/lib/galaxy/tool_util/parameters/convert.py
+++ b/lib/galaxy/tool_util/parameters/convert.py
@@ -37,6 +37,7 @@ from galaxy.tool_util_models.parameters import (
     GenomeBuildParameterModel,
     HiddenParameterModel,
     IntegerParameterModel,
+    iter_parameter_models,
     RepeatParameterModel,
     SectionParameterModel,
     SelectParameterModel,
@@ -590,17 +591,12 @@ def assert_yaml_v1_parameters(parameters: Sequence[ToolParameterT]) -> None:
     an unsupported type silently pass through ``runtimeify``'s default-case
     ``VISITOR_NO_REPLACEMENT``.
     """
-    for parameter in parameters:
+    for parameter in iter_parameter_models(parameters):
         if type(parameter) not in YAML_V1_SUPPORTED_PARAMETER_MODELS:
             raise AssertionError(
                 f"YAML-origin tool produced unsupported parameter type "
                 f"{type(parameter).__name__} for parameter {getattr(parameter, 'name', '?')!r}"
             )
-        if isinstance(parameter, ConditionalParameterModel):
-            for when in parameter.whens:
-                assert_yaml_v1_parameters(when.parameters)
-        elif isinstance(parameter, (RepeatParameterModel, SectionParameterModel)):
-            assert_yaml_v1_parameters(parameter.parameters)
 
 
 def runtimeify(
diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index 385291ed905..3cee326d7b1 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -9,6 +9,7 @@ from typing import (
     Dict,
     get_args,
     Iterable,
+    Iterator,
     List,
     Mapping,
     NamedTuple,
@@ -2587,6 +2588,28 @@ def simple_input_models(
     return [to_simple_model(m) for m in parameters]
 
 
+def iter_parameter_models(parameters: Iterable[ToolParameterT]) -> Iterator[ToolParameterT]:
+    """Yield every parameter in a parameter tree, depth-first.
+
+    Descends into repeats, sections and *all* branches of every conditional - the purely
+    structural view of the tree, independent of any state. A conditional yields the
+    conditional itself, then its discriminator ``test_parameter``, then every parameter
+    across all of its whens; a repeat/section yields the group node then its children.
+
+    Use this for structure-only queries (collecting names, validating types). When the walk
+    needs to follow values - and so only the active when of each conditional - use
+    ``visit_input_values`` instead.
+    """
+    for parameter in parameters:
+        yield parameter
+        if isinstance(parameter, ConditionalParameterModel):
+            yield parameter.test_parameter
+            for when in parameter.whens:
+                yield from iter_parameter_models(when.parameters)
+        elif isinstance(parameter, (RepeatParameterModel, SectionParameterModel)):
+            yield from iter_parameter_models(parameter.parameters)
+
+
 def create_model_strict(*args, **kwd) -> Type[BaseModel]:
     # protected_namespaces here prevents tool with model_ parameter names from issuing warnings
     model_config = ConfigDict(extra="forbid", protected_namespaces=())

From 98a2a84956e65727284dec29bc4c559a8e2ce44a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2026 14:11:26 -0400
Subject: [PATCH 194/256] Share the legacy suffix-match predicate; document why
 the rescue is loose

Extract _path_ends_with_param so input_for and the unhandled-input rescue share one
suffix rule. Add a comment recording why the rescue string-matches visited paths rather
than tracking consumed inputs - consumption-tracking was tried and rejects degenerate-but-
valid legacy tests.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/tool_util/parameters/case.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index f0b2edbc5a0..394c60eafab 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -243,7 +243,7 @@ class LegacyTestInputResolver:
                 for input in self.inputs
                 if "|" in input["name"]
                 and input["name"] not in exclude
-                and flat_state_path.endswith(f"|{input['name']}")
+                and _path_ends_with_param(flat_state_path, input["name"])
             ]
             resolved = _resolve_matching_inputs(
                 suffix_matching_inputs, f"Ambiguous partially qualified test parameter name for ({flat_state_path})"
@@ -342,10 +342,11 @@ def test_case_state(
 
 
 def _input_name_was_handled_by_legacy_fallback(input_name: str, handled_inputs: Set[str], profile: str) -> bool:
+    # Intentionally a loose string-match against every visited parameter path, NOT a record of which inputs were actually consumed: the raw-name->path relation is many-to-many for legacy tests (bare/duplicate names validly satisfy multiple params), so consumption-tracking wrongly rejects degenerate-but-valid cases - tried and reverted, don't reintroduce it.
     if Version(profile) >= Version("24.2"):
         return False
     for handled_input in handled_inputs:
-        if handled_input == input_name or handled_input.endswith(f"|{input_name}"):
+        if handled_input == input_name or _path_ends_with_param(handled_input, input_name):
             return True
         # conditional names may be elided in the test while the section/repeat prefix is kept
         if "|" in input_name and _is_conditional_elided_match(input_name, handled_input.split("|")):
@@ -651,6 +652,15 @@ def _resolve_matching_inputs(
     raise Exception(ambiguity_message)
 
 
+def _path_ends_with_param(qualified_path: str, param_name: str) -> bool:
+    """True if ``param_name`` is the trailing (pipe-separated) segment(s) of ``qualified_path``.
+
+    The legacy unqualified/partially-qualified suffix match, shared by ``input_for`` and
+    ``_input_name_was_handled_by_legacy_fallback`` so the rule lives in one place.
+    """
+    return qualified_path.endswith(f"|{param_name}")
+
+
 def _is_conditional_elided_match(input_name: str, path_segments: List[str]) -> bool:
     """True if ``input_name`` is the qualified ``path_segments`` with intermediate
     (conditional) segments removed - sharing the head and leaf segments.

From 63ca19fa4248f7a8d1c34aabf06f3f93e9501d62 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Jun 2026 15:01:23 -0400
Subject: [PATCH 195/256] Drop identity staticmethod wrapping the
 infinity-sentinel converter

field_validator can wrap the module-level _convert_infinity_sentinel directly;
_convert_infinity_sentinel_static added only indirection.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/tool_util_models/parameters.py | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index 3cee326d7b1..1291974e29a 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -515,10 +515,6 @@ class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
     def py_type(self) -> Type:
         return optional_if_needed(union_type([StrictInt, StrictFloat]), self.optional)
 
-    @staticmethod
-    def _convert_infinity_sentinel_static(v: Any) -> Any:
-        return _convert_infinity_sentinel(v)
-
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
         py_type = self.py_type
         if state_representation == "workflow_step_linked":
@@ -536,9 +532,7 @@ class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
         # before Pydantic validates the field. These sentinels appear when float('inf') values are
         # round-tripped through Galaxy's safe_dumps/json.loads path (e.g. GET /api/tools/{id}/test_data).
         dynamic_validators: Dict[str, Any] = {
-            "infinity_sentinel": field_validator(safe_field_name(self.name), mode="before")(
-                FloatParameterModel._convert_infinity_sentinel_static
-            )
+            "infinity_sentinel": field_validator(safe_field_name(self.name), mode="before")(_convert_infinity_sentinel)
         }
         return dynamic_model_information_from_py_type(
             self, py_type, requires_value=requires_value, validators=dynamic_validators

From 1c1869edde687f93d0439371df014f4a74ab211e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 16 Jun 2026 08:34:09 -0400
Subject: [PATCH 196/256] Auto-grow GalaxyAI chat input as you type

The ChatGXY prompt box was stuck at a single row -- it never grew with
the text you typed, so longer questions ended up scrolling inside a tiny
box. It now resizes to fit its content up to the existing 8rem cap and
scrolls past that. The resize is driven off a watch on the value prop,
which is the single point every change flows through (typing, @-mention
inserts, and the clear-after-submit reset), plus an initial pass on
mount. Closes #22921.
---
 .../src/components/GalaxyAI/ChatInput.test.ts | 51 +++++++++++++++++++
 client/src/components/GalaxyAI/ChatInput.vue  | 24 ++++++++-
 2 files changed, 74 insertions(+), 1 deletion(-)

diff --git a/client/src/components/GalaxyAI/ChatInput.test.ts b/client/src/components/GalaxyAI/ChatInput.test.ts
index a408248ef86..c37a0e31980 100644
--- a/client/src/components/GalaxyAI/ChatInput.test.ts
+++ b/client/src/components/GalaxyAI/ChatInput.test.ts
@@ -149,6 +149,57 @@ describe("ChatInput", () => {
         });
     });
 
+    describe("auto-resize", () => {
+        function mockScrollHeight(el: HTMLTextAreaElement, value: number) {
+            Object.defineProperty(el, "scrollHeight", { configurable: true, value });
+        }
+
+        it("sizes the textarea to its content on mount", () => {
+            // onMounted resizes synchronously, so mock scrollHeight on the
+            // prototype before mounting and restore it afterwards.
+            const proto = window.HTMLTextAreaElement.prototype;
+            const original = Object.getOwnPropertyDescriptor(proto, "scrollHeight");
+            Object.defineProperty(proto, "scrollHeight", { configurable: true, get: () => 96 });
+            try {
+                const wrapper = mountInput({ value: "line one\nline two\nline three" });
+                const el = wrapper.find("textarea").element as HTMLTextAreaElement;
+                expect(el.style.height).toBe("96px");
+            } finally {
+                if (original) {
+                    Object.defineProperty(proto, "scrollHeight", original);
+                } else {
+                    delete (proto as { scrollHeight?: number }).scrollHeight;
+                }
+            }
+        });
+
+        it("grows when the value changes (typing / mention insert)", async () => {
+            const wrapper = mountInput({ value: "short" });
+            const el = wrapper.find("textarea").element as HTMLTextAreaElement;
+
+            mockScrollHeight(el, 120);
+            await wrapper.setProps({ value: "much\nlonger\ncontent\nhere" });
+            await wrapper.vm.$nextTick();
+
+            expect(el.style.height).toBe("120px");
+        });
+
+        it("shrinks back down when the value is cleared after submit", async () => {
+            const wrapper = mountInput({ value: "a\nb\nc\nd\ne" });
+            const el = wrapper.find("textarea").element as HTMLTextAreaElement;
+
+            mockScrollHeight(el, 140);
+            await wrapper.setProps({ value: "a\nb\nc\nd\ne\nf" });
+            await wrapper.vm.$nextTick();
+            expect(el.style.height).toBe("140px");
+
+            mockScrollHeight(el, 40);
+            await wrapper.setProps({ value: "" });
+            await wrapper.vm.$nextTick();
+            expect(el.style.height).toBe("40px");
+        });
+    });
+
     describe("busy state UI", () => {
         it("shows loading indicator when busy", () => {
             const wrapper = mountInput({ busy: true });
diff --git a/client/src/components/GalaxyAI/ChatInput.vue b/client/src/components/GalaxyAI/ChatInput.vue
index 115d993225e..83dd25c3c1a 100644
--- a/client/src/components/GalaxyAI/ChatInput.vue
+++ b/client/src/components/GalaxyAI/ChatInput.vue
@@ -1,7 +1,7 @@
 <script setup lang="ts">
 import { faPaperPlane } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { ref } from "vue";
+import { nextTick, onMounted, ref, watch } from "vue";
 
 import { detectMentionTrigger, type EntityType, type MentionTrigger } from "@/composables/useEntityMentions";
 
@@ -30,6 +30,27 @@ const textareaEl = ref<HTMLTextAreaElement | null>(null);
 const dropdownRef = ref<InstanceType<typeof MentionDropdown> | null>(null);
 const mentionTrigger = ref<MentionTrigger | null>(null);
 
+function resize() {
+    const textarea = textareaEl.value;
+    if (!textarea) {
+        return;
+    }
+    // Reset first so the element can shrink, then grow to fit content.
+    // CSS max-height caps growth and overflow-y:auto takes over past the cap.
+    textarea.style.height = "auto";
+    textarea.style.height = `${textarea.scrollHeight}px`;
+}
+
+// props.value is the single funnel for every value change -- user typing
+// (round-trips through the parent), programmatic @-mention inserts, and the
+// parent clearing the field after submit. nextTick lets the DOM update first.
+watch(
+    () => props.value,
+    () => nextTick(resize),
+);
+
+onMounted(resize);
+
 function onInput(event: Event) {
     const textarea = event.target as HTMLTextAreaElement;
     emit("input", textarea.value);
@@ -156,6 +177,7 @@ function closeMention() {
         font-size: 0.9rem;
         min-height: 2.5rem;
         max-height: 8rem;
+        overflow-y: auto;
 
         &:focus {
             border-color: $brand-primary;

From d449dd25cd6b8a7e18c749df42b4eb2e079239e7 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 16 Jun 2026 12:35:46 -0500
Subject: [PATCH 197/256] do not resize chat input when only placeholder text

---
 client/src/components/GalaxyAI/ChatInput.test.ts | 13 +++++++++----
 client/src/components/GalaxyAI/ChatInput.vue     | 12 +++++++++++-
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/client/src/components/GalaxyAI/ChatInput.test.ts b/client/src/components/GalaxyAI/ChatInput.test.ts
index c37a0e31980..e278f858778 100644
--- a/client/src/components/GalaxyAI/ChatInput.test.ts
+++ b/client/src/components/GalaxyAI/ChatInput.test.ts
@@ -154,7 +154,13 @@ describe("ChatInput", () => {
             Object.defineProperty(el, "scrollHeight", { configurable: true, value });
         }
 
-        it("sizes the textarea to its content on mount", () => {
+        it("does not set height on mount when value is empty", () => {
+            const wrapper = mountInput({ value: "" });
+            const el = wrapper.find("textarea").element as HTMLTextAreaElement;
+            expect(el.style.height).toBe("");
+        });
+
+        it("sizes the textarea to its content on mount when value is non-empty", () => {
             // onMounted resizes synchronously, so mock scrollHeight on the
             // prototype before mounting and restore it afterwards.
             const proto = window.HTMLTextAreaElement.prototype;
@@ -184,7 +190,7 @@ describe("ChatInput", () => {
             expect(el.style.height).toBe("120px");
         });
 
-        it("shrinks back down when the value is cleared after submit", async () => {
+        it("resets height to '' when value is cleared (e.g. after submit)", async () => {
             const wrapper = mountInput({ value: "a\nb\nc\nd\ne" });
             const el = wrapper.find("textarea").element as HTMLTextAreaElement;
 
@@ -193,10 +199,9 @@ describe("ChatInput", () => {
             await wrapper.vm.$nextTick();
             expect(el.style.height).toBe("140px");
 
-            mockScrollHeight(el, 40);
             await wrapper.setProps({ value: "" });
             await wrapper.vm.$nextTick();
-            expect(el.style.height).toBe("40px");
+            expect(el.style.height).toBe("");
         });
     });
 
diff --git a/client/src/components/GalaxyAI/ChatInput.vue b/client/src/components/GalaxyAI/ChatInput.vue
index 83dd25c3c1a..e0b7649ccb3 100644
--- a/client/src/components/GalaxyAI/ChatInput.vue
+++ b/client/src/components/GalaxyAI/ChatInput.vue
@@ -35,6 +35,12 @@ function resize() {
     if (!textarea) {
         return;
     }
+    if (!textarea.value) {
+        // No content — let CSS min-height govern; don't measure scrollHeight
+        // which would include the placeholder's wrapped height.
+        textarea.style.height = "";
+        return;
+    }
     // Reset first so the element can shrink, then grow to fit content.
     // CSS max-height caps growth and overflow-y:auto takes over past the cap.
     textarea.style.height = "auto";
@@ -49,7 +55,11 @@ watch(
     () => nextTick(resize),
 );
 
-onMounted(resize);
+onMounted(() => {
+    if (props.value) {
+        resize();
+    }
+});
 
 function onInput(event: Event) {
     const textarea = event.target as HTMLTextAreaElement;

From 42d07f99354368b1b16a5eaa887eed54f549596b Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 16 Jun 2026 14:04:48 -0500
Subject: [PATCH 198/256] use block displayed `GButton` in GalaxyAI input field

---
 client/src/components/GalaxyAI/ChatInput.test.ts | 13 +++++++------
 client/src/components/GalaxyAI/ChatInput.vue     | 15 ++++++++-------
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/client/src/components/GalaxyAI/ChatInput.test.ts b/client/src/components/GalaxyAI/ChatInput.test.ts
index e278f858778..d330509f824 100644
--- a/client/src/components/GalaxyAI/ChatInput.test.ts
+++ b/client/src/components/GalaxyAI/ChatInput.test.ts
@@ -1,6 +1,7 @@
 import { mount } from "@vue/test-utils";
 import { describe, expect, it, vi } from "vitest";
 
+import GButton from "../BaseComponents/GButton.vue";
 import ChatInput from "./ChatInput.vue";
 
 vi.mock("@/stores/historyStore", () => ({
@@ -66,27 +67,27 @@ describe("ChatInput", () => {
 
         it("disables send button when value is empty", () => {
             const wrapper = mountInput({ value: "" });
-            expect((wrapper.find("button").element as HTMLButtonElement).disabled).toBe(true);
+            expect(wrapper.findComponent(GButton).props("disabled")).toBe(true);
         });
 
         it("disables send button when value is whitespace", () => {
             const wrapper = mountInput({ value: "   " });
-            expect((wrapper.find("button").element as HTMLButtonElement).disabled).toBe(true);
+            expect(wrapper.findComponent(GButton).props("disabled")).toBe(true);
         });
 
         it("enables send button when value has content", () => {
             const wrapper = mountInput({ value: "hello" });
-            expect((wrapper.find("button").element as HTMLButtonElement).disabled).toBe(false);
+            expect(wrapper.findComponent(GButton).props("disabled")).toBe(false);
         });
 
         it("disables send button when busy even with content", () => {
             const wrapper = mountInput({ value: "hello", busy: true });
-            expect((wrapper.find("button").element as HTMLButtonElement).disabled).toBe(true);
+            expect(wrapper.findComponent(GButton).props("disabled")).toBe(true);
         });
 
         it("disables send button when disabled prop is true even with content", () => {
             const wrapper = mountInput({ value: "hello", disabled: true });
-            expect((wrapper.find("button").element as HTMLButtonElement).disabled).toBe(true);
+            expect(wrapper.findComponent(GButton).props("disabled")).toBe(true);
         });
     });
 
@@ -102,7 +103,7 @@ describe("ChatInput", () => {
 
         it("emits submit on send button click", async () => {
             const wrapper = mountInput({ value: "hello" });
-            await wrapper.find("button").trigger("click");
+            await wrapper.findComponent(GButton).trigger("click");
             expect(wrapper.emitted("submit")).toBeTruthy();
         });
 
diff --git a/client/src/components/GalaxyAI/ChatInput.vue b/client/src/components/GalaxyAI/ChatInput.vue
index e0b7649ccb3..828d49c9b41 100644
--- a/client/src/components/GalaxyAI/ChatInput.vue
+++ b/client/src/components/GalaxyAI/ChatInput.vue
@@ -5,6 +5,7 @@ import { nextTick, onMounted, ref, watch } from "vue";
 
 import { detectMentionTrigger, type EntityType, type MentionTrigger } from "@/composables/useEntityMentions";
 
+import GButton from "../BaseComponents/GButton.vue";
 import MentionDropdown from "./MentionDropdown.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
@@ -150,13 +151,15 @@ function closeMention() {
             class="form-control chat-input"
             @input="onInput"
             @keydown="onKeydown" />
-        <button
+        <GButton
             :disabled="busy || disabled || !props.value.trim()"
-            class="btn btn-primary send-button"
+            class="send-button"
+            color="blue"
+            size="large"
             @click="emit('submit')">
             <FontAwesomeIcon v-if="!busy" :icon="faPaperPlane" fixed-width />
             <LoadingSpan v-else message="" />
-        </button>
+        </GButton>
 
         <MentionDropdown
             ref="dropdownRef"
@@ -175,7 +178,7 @@ function closeMention() {
 .chat-input-container {
     display: flex;
     gap: 0.5rem;
-    align-items: flex-end;
+    align-items: flex-start;
     position: relative;
 
     .chat-input {
@@ -197,9 +200,7 @@ function closeMention() {
     }
 
     .send-button {
-        flex-shrink: 0;
-        border-radius: $border-radius-base;
-        padding: 0.5rem 0.875rem;
+        display: block;
     }
 }
 

From 1b4513388374d6efa3e945f274ced96e0da99ba9 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 16 Jun 2026 15:18:12 -0500
Subject: [PATCH 199/256] fix failing vitest and add test that confirms we
 thoroughly check routes

This is for `activeContext`. Previously, we would only check if a route started with `/`histories/` and then had a page ID in the query/params. Now we rigorously check the entire route for the notebook context at least.
---
 .../src/components/GalaxyAI/ChatModeSelector.test.ts   |  2 +-
 client/src/composables/useActiveContext.test.ts        | 10 ++++++++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/client/src/components/GalaxyAI/ChatModeSelector.test.ts b/client/src/components/GalaxyAI/ChatModeSelector.test.ts
index 1c1811db519..ec38459a77c 100644
--- a/client/src/components/GalaxyAI/ChatModeSelector.test.ts
+++ b/client/src/components/GalaxyAI/ChatModeSelector.test.ts
@@ -109,7 +109,7 @@ describe("ChatModeSelector", () => {
     describe("notebook context", () => {
         it("hides full view button when in notebook context", async () => {
             mockRoute = {
-                path: "/histories/hist-1/page/page-1",
+                path: "/histories/hist-1/pages/page-1",
                 params: { historyId: "hist-1", pageId: "page-1" },
                 query: {},
             };
diff --git a/client/src/composables/useActiveContext.test.ts b/client/src/composables/useActiveContext.test.ts
index 93d42c115ef..8d70b88b027 100644
--- a/client/src/composables/useActiveContext.test.ts
+++ b/client/src/composables/useActiveContext.test.ts
@@ -135,6 +135,16 @@ describe("useActiveContext", () => {
             });
         });
 
+        it("returns null for slightly invalid notebook editor route", () => {
+            // Note how the route has "page" instead of "pages"
+            const { activeContext } = withRoute(
+                "/histories/test-history-id/page/test-page-id",
+                {},
+                { historyId: "test-history-id", pageId: "test-page-id" },
+            );
+            expect(activeContext.value).toBeNull();
+        });
+
         it("detects notebook context from invocation reports route", () => {
             const { activeContext } = withRoute(
                 "/workflows/invocations/inv-1/reports",

From 7bd8cf763fb0f8d78d0f134824a29189349e4451 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 16 Jun 2026 14:06:41 -0500
Subject: [PATCH 200/256] use `faSpinner` in GalaxyAI chat button instead of
 `LoadingSpan`

`LoadingSpan` was adding an awkward flickering `...` on top of the already included `faSpinner` in that component.
---
 client/src/components/GalaxyAI/ChatInput.test.ts | 16 +++++++++++-----
 client/src/components/GalaxyAI/ChatInput.vue     |  6 ++----
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/client/src/components/GalaxyAI/ChatInput.test.ts b/client/src/components/GalaxyAI/ChatInput.test.ts
index d330509f824..5f2444c8047 100644
--- a/client/src/components/GalaxyAI/ChatInput.test.ts
+++ b/client/src/components/GalaxyAI/ChatInput.test.ts
@@ -1,3 +1,4 @@
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { mount } from "@vue/test-utils";
 import { describe, expect, it, vi } from "vitest";
 
@@ -14,7 +15,6 @@ vi.mock("@/stores/historyItemsStore", () => ({
 function mountInput(
     props: Record<string, unknown> = {},
     stubs: Record<string, boolean> = {
-        FontAwesomeIcon: true,
         LoadingSpan: true,
         MentionDropdown: true,
     },
@@ -207,14 +207,20 @@ describe("ChatInput", () => {
     });
 
     describe("busy state UI", () => {
-        it("shows loading indicator when busy", () => {
+        it("shows spinner icon when busy", () => {
             const wrapper = mountInput({ busy: true });
-            expect(wrapper.findComponent({ name: "LoadingSpan" }).exists()).toBe(true);
+            const buttonIcon = wrapper.findComponent(GButton).findComponent(FontAwesomeIcon);
+            expect(buttonIcon.classes()).toContain("fa-spinner");
+            expect(buttonIcon.classes()).toContain("fa-spin");
+            expect(buttonIcon.classes()).not.toContain("fa-paper-plane");
         });
 
-        it("hides loading indicator when not busy", () => {
+        it("shows send icon when not busy", () => {
             const wrapper = mountInput({ busy: false });
-            expect(wrapper.findComponent({ name: "LoadingSpan" }).exists()).toBe(false);
+            const buttonIcon = wrapper.findComponent(GButton).findComponent(FontAwesomeIcon);
+            expect(buttonIcon.classes()).toContain("fa-paper-plane");
+            expect(buttonIcon.classes()).not.toContain("fa-spinner");
+            expect(buttonIcon.classes()).not.toContain("fa-spin");
         });
     });
 });
diff --git a/client/src/components/GalaxyAI/ChatInput.vue b/client/src/components/GalaxyAI/ChatInput.vue
index 828d49c9b41..66c321248df 100644
--- a/client/src/components/GalaxyAI/ChatInput.vue
+++ b/client/src/components/GalaxyAI/ChatInput.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faPaperPlane } from "@fortawesome/free-solid-svg-icons";
+import { faPaperPlane, faSpinner } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { nextTick, onMounted, ref, watch } from "vue";
 
@@ -7,7 +7,6 @@ import { detectMentionTrigger, type EntityType, type MentionTrigger } from "@/co
 
 import GButton from "../BaseComponents/GButton.vue";
 import MentionDropdown from "./MentionDropdown.vue";
-import LoadingSpan from "@/components/LoadingSpan.vue";
 
 const props = withDefaults(
     defineProps<{
@@ -157,8 +156,7 @@ function closeMention() {
             color="blue"
             size="large"
             @click="emit('submit')">
-            <FontAwesomeIcon v-if="!busy" :icon="faPaperPlane" fixed-width />
-            <LoadingSpan v-else message="" />
+            <FontAwesomeIcon :icon="!busy ? faPaperPlane : faSpinner" fixed-width :spin="busy" />
         </GButton>
 
         <MentionDropdown

From 2500382a6c12fe614c49cd35eba8ed35e6d0cfcd Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 10 Jun 2026 18:30:05 -0400
Subject: [PATCH 201/256] Add tests for starting a new GalaxyAI chat while one
 is in flight

Clicking New Chat while a conversation is ongoing silently does nothing
when the chat hasn't been persisted yet: in panel/docked mode showChat(null)
is a no-op because activeChatId is already null, and in center mode pushing
/galaxyai/new is a duplicate navigation. On top of that, a response landing
after a reset gets appended to the fresh conversation and re-attaches the
old exchange id. These tests demonstrate all three failures via a new
chatStore.requestNewChat signal that the next commit implements.
---
 .../src/components/GalaxyAI.newchat.test.ts   | 208 ++++++++++++++++++
 .../components/GalaxyAI/ChatActions.test.ts   |  26 ++-
 client/src/stores/chatStore.test.ts           |  18 ++
 3 files changed, 246 insertions(+), 6 deletions(-)
 create mode 100644 client/src/components/GalaxyAI.newchat.test.ts

diff --git a/client/src/components/GalaxyAI.newchat.test.ts b/client/src/components/GalaxyAI.newchat.test.ts
new file mode 100644
index 00000000000..11ad9e8d37a
--- /dev/null
+++ b/client/src/components/GalaxyAI.newchat.test.ts
@@ -0,0 +1,208 @@
+import { getLocalVue } from "@tests/vitest/helpers";
+import { mount, type Wrapper } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { createPinia, setActivePinia } from "pinia";
+import { beforeEach, describe, expect, it, vi } from "vitest";
+import { ref } from "vue";
+
+import { useChatStore } from "@/stores/chatStore";
+
+import GalaxyAI from "./GalaxyAI.vue";
+
+const { mockGet, mockPost, mockPut, ChatMessageCellStub, ChatInputStub } = vi.hoisted(() => ({
+    mockGet: vi.fn(),
+    mockPost: vi.fn(),
+    mockPut: vi.fn(),
+    // render functions because the test environment uses the runtime-only Vue build
+    ChatMessageCellStub: {
+        name: "ChatMessageCellStub",
+        props: ["message"],
+        render(this: { message: { content: string } }, h: (...args: unknown[]) => unknown) {
+            return h("div", { class: "chat-message-stub" }, [this.message.content]);
+        },
+    },
+    ChatInputStub: {
+        name: "ChatInputStub",
+        props: ["value", "busy"],
+        render(h: (...args: unknown[]) => unknown) {
+            return h("input", { class: "chat-input-stub" });
+        },
+    },
+}));
+
+vi.mock("@/api", () => ({
+    GalaxyApi: () => ({ GET: mockGet, POST: mockPost, PUT: mockPut, DELETE: vi.fn() }),
+}));
+
+vi.mock("@/api/client", () => ({
+    GalaxyApi: () => ({ GET: mockGet, POST: mockPost, PUT: mockPut, DELETE: vi.fn() }),
+}));
+
+vi.mock("vue-router/composables", () => ({
+    useRoute: () => ({ path: "/", params: {}, query: {} }),
+    useRouter: () => ({ push: vi.fn(), replace: vi.fn() }),
+}));
+
+vi.mock("@/app", () => ({
+    getGalaxyInstance: () => ({ frame: { add: vi.fn() } }),
+}));
+
+// Child components are referenced directly from setup scope, so the test-utils
+// `stubs` option cannot replace them — mock the modules instead.
+vi.mock("@/components/GalaxyAI/ChatMessageCell.vue", () => ({ default: ChatMessageCellStub }));
+vi.mock("@/components/GalaxyAI/ChatInput.vue", () => ({ default: ChatInputStub }));
+
+vi.mock("@/composables/useActiveContext", () => ({
+    useActiveContext: () => ({ activeContext: ref(null), contextLabel: ref("") }),
+}));
+
+vi.mock("@/composables/agentActions", () => ({
+    useAgentActions: () => ({ processingAction: ref(false), handleAction: vi.fn() }),
+}));
+
+vi.mock("@/composables/confirmDialog", () => ({
+    useConfirmDialog: () => ({ confirm: vi.fn() }),
+}));
+
+vi.mock("@/composables/markdown", () => ({
+    useMarkdown: () => ({ renderMarkdown: (content: string) => content }),
+}));
+
+vi.mock("@/composables/toast", () => ({
+    useToast: () => ({ error: vi.fn(), success: vi.fn(), warning: vi.fn(), info: vi.fn() }),
+}));
+
+vi.mock("@/composables/useEntityMentions", () => ({
+    MENTION_PATTERN_SOURCE: "@(dataset|history):(\\S+)",
+    parseMentions: () => [],
+    resolveMentions: () => [],
+    buildEntityContext: () => null,
+}));
+
+vi.mock("@/composables/userLocalStorage", () => ({
+    useUserLocalStorage: vi.fn((_key: string, initialValue: unknown) => ref(initialValue)),
+}));
+
+const localVue = getLocalVue();
+
+// jsdom does not implement Element.scrollTo
+window.HTMLElement.prototype.scrollTo = vi.fn();
+
+function mountChat() {
+    const pinia = createPinia();
+    setActivePinia(pinia);
+    const wrapper = mount(GalaxyAI as object, {
+        localVue,
+        pinia,
+        propsData: { panel: true },
+        stubs: { FontAwesomeIcon: true, BSkeleton: true },
+    });
+    const chatStore = useChatStore();
+    return { wrapper, chatStore };
+}
+
+function messageTexts(wrapper: Wrapper<Vue>) {
+    return wrapper.findAll(".chat-message-stub").wrappers.map((w) => w.text());
+}
+
+async function sendMessage(wrapper: Wrapper<Vue>, text: string) {
+    const input = wrapper.findComponent(ChatInputStub);
+    input.vm.$emit("input", text);
+    await wrapper.vm.$nextTick();
+    input.vm.$emit("submit");
+    await flushPromises();
+}
+
+function deferredResponse() {
+    let resolve!: (value: unknown) => void;
+    const promise = new Promise((r) => {
+        resolve = r;
+    });
+    return { promise, resolve };
+}
+
+describe("GalaxyAI", () => {
+    beforeEach(() => {
+        vi.clearAllMocks();
+        mockGet.mockResolvedValue({ data: [], error: undefined });
+    });
+
+    it("appends the response and records the exchange id on a normal exchange", async () => {
+        mockPost.mockResolvedValue({
+            data: { response: "Here you go", exchange_id: "exchange-123" },
+            error: undefined,
+        });
+        const { wrapper, chatStore } = mountChat();
+        await flushPromises();
+
+        await sendMessage(wrapper, "find me a mapper");
+
+        const texts = messageTexts(wrapper);
+        expect(texts).toHaveLength(3);
+        expect(texts[1]).toBe("find me a mapper");
+        expect(texts[2]).toBe("Here you go");
+        expect(chatStore.activeChatId).toBe("exchange-123");
+    });
+
+    it("resets an unsaved conversation when a new chat is requested mid-flight", async () => {
+        const deferred = deferredResponse();
+        mockPost.mockReturnValue(deferred.promise);
+        const { wrapper, chatStore } = mountChat();
+        await flushPromises();
+
+        await sendMessage(wrapper, "what mappers are available?");
+        expect(messageTexts(wrapper)).toHaveLength(2);
+        expect(wrapper.find(".loading-entry").exists()).toBe(true);
+        // the conversation is unsaved — no exchange id yet, so the identity
+        // (activeChatId) would not change and a plain showChat(null) is a no-op
+        expect(chatStore.activeChatId).toBeNull();
+
+        chatStore.requestNewChat();
+        await flushPromises();
+
+        const texts = messageTexts(wrapper);
+        expect(texts).toHaveLength(1);
+        expect(texts[0]).toContain("New conversation started");
+        expect(wrapper.find(".loading-entry").exists()).toBe(false);
+
+        // the stale response must not be appended or re-attach the old exchange
+        deferred.resolve({ data: { response: "Late answer", exchange_id: "exchange-123" }, error: undefined });
+        await flushPromises();
+
+        expect(messageTexts(wrapper)).toHaveLength(1);
+        expect(chatStore.activeChatId).toBeNull();
+    });
+
+    it("does not let a stale response clobber a newly started conversation", async () => {
+        const first = deferredResponse();
+        const second = deferredResponse();
+        mockPost.mockReturnValueOnce(first.promise).mockReturnValueOnce(second.promise);
+        const { wrapper, chatStore } = mountChat();
+        await flushPromises();
+
+        await sendMessage(wrapper, "first question");
+        chatStore.requestNewChat();
+        await flushPromises();
+        await sendMessage(wrapper, "second question");
+        expect(wrapper.find(".loading-entry").exists()).toBe(true);
+
+        first.resolve({ data: { response: "First answer", exchange_id: "exchange-1" }, error: undefined });
+        await flushPromises();
+
+        // still only welcome + second user message, still waiting on the second response
+        let texts = messageTexts(wrapper);
+        expect(texts).toHaveLength(2);
+        expect(texts[1]).toBe("second question");
+        expect(wrapper.find(".loading-entry").exists()).toBe(true);
+        expect(chatStore.activeChatId).toBeNull();
+
+        second.resolve({ data: { response: "Second answer", exchange_id: "exchange-2" }, error: undefined });
+        await flushPromises();
+
+        texts = messageTexts(wrapper);
+        expect(texts).toHaveLength(3);
+        expect(texts[2]).toBe("Second answer");
+        expect(wrapper.find(".loading-entry").exists()).toBe(false);
+        expect(chatStore.activeChatId).toBe("exchange-2");
+    });
+});
diff --git a/client/src/components/GalaxyAI/ChatActions.test.ts b/client/src/components/GalaxyAI/ChatActions.test.ts
index ddedb930441..2de726b3b06 100644
--- a/client/src/components/GalaxyAI/ChatActions.test.ts
+++ b/client/src/components/GalaxyAI/ChatActions.test.ts
@@ -70,17 +70,31 @@ describe("ChatActions", () => {
             expect(mockPush).toHaveBeenCalledWith("/galaxyai/new");
         });
 
-        it("calls chatStore.showChat(null) in docked mode", async () => {
-            const { wrapper, store } = mountComponent("docked");
+        it("requests a new chat in all modes", async () => {
+            for (const source of ["center", "docked", "panel"] as const) {
+                const { wrapper, store } = mountComponent(source);
+                await findButton(wrapper, "Start New Chat").trigger("click");
+                expect(store.requestNewChat).toHaveBeenCalled();
+            }
+        });
+
+        it("still requests a new chat when already at /galaxyai/new, without re-routing", async () => {
+            mockRoute = { path: "/galaxyai/new", params: { exchangeId: "new" } };
+            const { wrapper, store } = mountComponent("center");
+            await findButton(wrapper, "Start New Chat").trigger("click");
+            expect(mockPush).not.toHaveBeenCalled();
+            expect(store.requestNewChat).toHaveBeenCalled();
+        });
+
+        it("does not route in docked mode", async () => {
+            const { wrapper } = mountComponent("docked");
             await findButton(wrapper, "Start New Chat").trigger("click");
-            expect(store.showChat).toHaveBeenCalledWith(null);
             expect(mockPush).not.toHaveBeenCalled();
         });
 
-        it("calls chatStore.showChat(null) in panel mode", async () => {
-            const { wrapper, store } = mountComponent("panel");
+        it("does not route in panel mode", async () => {
+            const { wrapper } = mountComponent("panel");
             await findButton(wrapper, "Start New Chat").trigger("click");
-            expect(store.showChat).toHaveBeenCalledWith(null);
             expect(mockPush).not.toHaveBeenCalled();
         });
 
diff --git a/client/src/stores/chatStore.test.ts b/client/src/stores/chatStore.test.ts
index 4fd65bba7df..0d05d6f682e 100644
--- a/client/src/stores/chatStore.test.ts
+++ b/client/src/stores/chatStore.test.ts
@@ -105,6 +105,24 @@ describe("chatStore", () => {
         });
     });
 
+    describe("requestNewChat", () => {
+        it("bumps the request counter so chat surfaces reset even when the id would not change", () => {
+            const store = useChatStore();
+            expect(store.newChatRequestCount).toBe(0);
+            store.requestNewChat();
+            expect(store.newChatRequestCount).toBe(1);
+            store.requestNewChat();
+            expect(store.newChatRequestCount).toBe(2);
+        });
+
+        it("clears the active chat id", () => {
+            const store = useChatStore();
+            store.setActiveChatId("abc");
+            store.requestNewChat();
+            expect(store.activeChatId).toBeNull();
+        });
+    });
+
     describe("deleteChats", () => {
         it("removes the given ids from history", () => {
             const store = useChatStore();

From 0521ec489f2798e7264fcdc0ffde5e26064e01b7 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 10 Jun 2026 18:34:25 -0400
Subject: [PATCH 202/256] Make New Chat work while a GalaxyAI conversation is
 in flight

The New Chat buttons relied on changing the conversation identity (route
param or activeChatId) to trigger a reset, which silently no-ops for an
unsaved conversation: the id is already null in panel/docked mode, and in
center mode pushing /galaxyai/new again is a duplicate navigation. Route
the reset through a new chatStore.requestNewChat() signal instead -- a
counter bump the chat component watches, so it fires regardless of
identity. Also tag each conversation with a generation counter so a
response that arrives after the user has moved on gets dropped instead of
being appended to the fresh chat and re-attaching the old exchange id.
---
 client/src/components/GalaxyAI.vue            | 66 ++++++++++++++-----
 .../src/components/GalaxyAI/ChatActions.vue   |  9 ++-
 .../components/GalaxyAI/ChatHistoryPanel.vue  |  9 ++-
 .../components/GalaxyAI/useStartNewChat.ts    | 26 ++++++++
 client/src/stores/chatStore.ts                | 11 ++++
 5 files changed, 96 insertions(+), 25 deletions(-)
 create mode 100644 client/src/components/GalaxyAI/useStartNewChat.ts

diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index 62992541d32..2ce90e6cb4b 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -138,6 +138,10 @@ const selectedAgentType = ref("auto");
 const currentChatId = ref<string | null>(null);
 const hasLoadedInitialChat = ref(false);
 
+// Bumped whenever the displayed conversation changes so that responses still in
+// flight for a previous conversation can be recognized as stale and dropped.
+let conversationGeneration = 0;
+
 const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true, removeNewlinesAfterList: true });
 const { processingAction, handleAction } = useAgentActions();
 
@@ -220,6 +224,14 @@ watch(
     },
 );
 
+// A "new chat" request must work even when the conversation identity wouldn't
+// change (an unsaved conversation has no exchange id), so it arrives as a counter
+// bump rather than through the exchangeId prop.
+watch(
+    () => chatStore.newChatRequestCount,
+    () => startNewChat(),
+);
+
 function showWelcome() {
     messages.value.push({
         id: generateId(),
@@ -256,6 +268,10 @@ async function submitQuery() {
     scrollToBottom(chatContainer.value);
 
     busy.value = true;
+    const generation = conversationGeneration;
+    // False once the conversation changes while we're waiting (e.g. the user
+    // started a new chat) — stale responses must not touch the current one.
+    const stillCurrent = () => generation === conversationGeneration;
 
     try {
         const parsed = parseMentions(currentQuery);
@@ -276,6 +292,10 @@ async function submitQuery() {
             },
         });
 
+        if (!stillCurrent()) {
+            return;
+        }
+
         if (error) {
             const errorText = errorMessageAsString(error, "Failed to get response from GalaxyAI.");
             const errorMsg: ChatMessage = {
@@ -319,23 +339,29 @@ async function submitQuery() {
         }
     } catch (e) {
         console.error("Unexpected chat error:", e);
-        const errorMsg: ChatMessage = {
-            id: generateId(),
-            role: "assistant",
-            content: "Unexpected error occurred. Please try again.",
-            timestamp: new Date(),
-            agentType: selectedAgentType.value,
-            confidence: "low",
-            feedback: null,
-        };
-        messages.value.push(errorMsg);
+        if (stillCurrent()) {
+            const errorMsg: ChatMessage = {
+                id: generateId(),
+                role: "assistant",
+                content: "Unexpected error occurred. Please try again.",
+                timestamp: new Date(),
+                agentType: selectedAgentType.value,
+                confidence: "low",
+                feedback: null,
+            };
+            messages.value.push(errorMsg);
 
-        await nextTick();
-        scrollToBottom(chatContainer.value);
+            await nextTick();
+            scrollToBottom(chatContainer.value);
+        }
     } finally {
-        busy.value = false;
-        await nextTick();
-        scrollToBottom(chatContainer.value);
+        // Only clear the busy indicator if it still belongs to this request — the
+        // current conversation may have its own request in flight by now.
+        if (stillCurrent()) {
+            busy.value = false;
+            await nextTick();
+            scrollToBottom(chatContainer.value);
+        }
     }
 }
 
@@ -380,12 +406,20 @@ async function fetchConversation(exchangeId: string) {
         return;
     }
 
+    const generation = ++conversationGeneration;
+
     const { data: fullConversation, error } = await GalaxyApi().GET(`/api/chat/exchange/{exchange_id}/messages`, {
         params: {
             path: { exchange_id: exchangeId },
         },
     });
 
+    if (generation !== conversationGeneration) {
+        // A newer conversation was loaded (or a new chat started) while this one
+        // was being fetched — don't overwrite it.
+        return;
+    }
+
     if (error) {
         Toast.error(errorMessageAsString(error, "Failed to load conversation."), "Error loading conversation");
         return;
@@ -444,7 +478,9 @@ async function loadLatestChat() {
 }
 
 function startNewChat() {
+    conversationGeneration++;
     hasLoadedInitialChat.value = true;
+    busy.value = false;
     messages.value = [
         {
             id: generateId(),
diff --git a/client/src/components/GalaxyAI/ChatActions.vue b/client/src/components/GalaxyAI/ChatActions.vue
index 5bb475819be..16d77c9cad9 100644
--- a/client/src/components/GalaxyAI/ChatActions.vue
+++ b/client/src/components/GalaxyAI/ChatActions.vue
@@ -19,6 +19,8 @@ import { getGalaxyInstance } from "@/app";
 import { useActivityStore } from "@/stores/activityStore.js";
 import { useChatStore } from "@/stores/chatStore";
 
+import { useStartNewChat } from "./useStartNewChat";
+
 import GButton from "../BaseComponents/GButton.vue";
 
 const props = defineProps<{
@@ -37,15 +39,12 @@ const route = useRoute();
 const router = useRouter();
 const chatStore = useChatStore();
 const activityStore = useActivityStore("default");
+const startNewChat = useStartNewChat();
 
 const showingActivityPanel = computed(() => activityStore.toggledSideBar === "galaxyai");
 
 function startNew() {
-    if (props.source === "center") {
-        router.push("/galaxyai/new");
-    } else {
-        chatStore.showChat(null);
-    }
+    startNewChat(props.source === "center");
     emit("update:collapsed", false);
 }
 
diff --git a/client/src/components/GalaxyAI/ChatHistoryPanel.vue b/client/src/components/GalaxyAI/ChatHistoryPanel.vue
index 3fb92fa1805..0e628fa13d9 100644
--- a/client/src/components/GalaxyAI/ChatHistoryPanel.vue
+++ b/client/src/components/GalaxyAI/ChatHistoryPanel.vue
@@ -15,6 +15,7 @@ import { errorMessageAsString } from "@/utils/simple-error";
 
 import { getAgentIcon } from "./agentTypes";
 import type { ChatHistoryItem } from "./chatTypes";
+import { useStartNewChat } from "./useStartNewChat";
 
 import GButton from "../BaseComponents/GButton.vue";
 import ChatModeSelector from "./ChatModeSelector.vue";
@@ -34,6 +35,8 @@ const notebookPageId = computed(() => {
     return ctx?.contextType === "notebook" ? ctx.pageId : undefined;
 });
 
+const newChat = useStartNewChat();
+
 const { chatHistory, loading } = storeToRefs(chatStore);
 
 const {
@@ -78,11 +81,7 @@ function handleItemClick(item: ChatHistoryItem, index: number, event: MouseEvent
 }
 
 function startNewChat() {
-    if (chatStore.isCenterMode) {
-        router.push("/galaxyai/new");
-    } else {
-        chatStore.showChat(null);
-    }
+    newChat(chatStore.isCenterMode);
 }
 
 async function deleteSelected() {
diff --git a/client/src/components/GalaxyAI/useStartNewChat.ts b/client/src/components/GalaxyAI/useStartNewChat.ts
new file mode 100644
index 00000000000..df0b6c10315
--- /dev/null
+++ b/client/src/components/GalaxyAI/useStartNewChat.ts
@@ -0,0 +1,26 @@
+import { useRoute, useRouter } from "vue-router/composables";
+
+import { useChatStore } from "@/stores/chatStore";
+
+/** Shared behavior for the various "New Chat" buttons. */
+export function useStartNewChat() {
+    const route = useRoute();
+    const router = useRouter();
+    const chatStore = useChatStore();
+
+    /** @param center whether the fresh conversation should open in the center view */
+    return function startNewChat(center: boolean) {
+        if (center) {
+            if (route.path !== "/galaxyai/new") {
+                router.push("/galaxyai/new");
+            }
+        } else {
+            // make sure the docked/bottom panel is visible
+            chatStore.showChat();
+        }
+        // Reset via the store, not just the route/id above: for an unsaved
+        // conversation the identity wouldn't change, so a plain navigation or
+        // showChat(null) is a no-op.
+        chatStore.requestNewChat();
+    };
+}
diff --git a/client/src/stores/chatStore.ts b/client/src/stores/chatStore.ts
index 02b3c57c6f2..045aa7eceda 100644
--- a/client/src/stores/chatStore.ts
+++ b/client/src/stores/chatStore.ts
@@ -14,6 +14,7 @@ export const useChatStore = defineStore("chatStore", () => {
     const cachedActiveChatId = useUserLocalStorage<string>("active-chat-id", "");
     const chatHistory = ref<ChatHistoryItem[]>([]);
     const loading = ref(false);
+    const newChatRequestCount = ref(0);
 
     const isRightPanelOpen = computed(() => chatLocation.value === "right" && chatVisible.value);
     const isBottomPanelOpen = computed(() => chatLocation.value === "bottom" && chatVisible.value);
@@ -118,6 +119,14 @@ export const useChatStore = defineStore("chatStore", () => {
         }
     }
 
+    /** Ask chat surfaces to reset to a fresh conversation. A counter bump rather than
+     * an id change, so the reset also fires for an unsaved conversation whose identity
+     * (activeChatId / route param) wouldn't change. */
+    function requestNewChat() {
+        setActiveChatId(null);
+        newChatRequestCount.value++;
+    }
+
     /** Returns the active chat id, falling back to the most recent history item, or null. */
     function resolveDockChatId(): string | null {
         return activeChatId.value ?? chatHistory.value[0]?.id ?? null;
@@ -144,6 +153,8 @@ export const useChatStore = defineStore("chatStore", () => {
         hideChat,
         loadHistory,
         loading,
+        newChatRequestCount,
+        requestNewChat,
         toggleChat,
         setLocation,
         setActiveChatId,

From 581fbab9b8b907ac483f1057d6f08eaa86189d07 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 17 Jun 2026 00:10:05 -0400
Subject: [PATCH 203/256] Ground ChatGXY "what can you do" answer in enabled
 agents

The assistant's "what can you do" reply oversold itself -- it claimed it
could upload data, run workflows, and configure file sources, and the static
prompt list had no idea which specialist agents a deployment actually has
enabled. Each specialist now carries a one-line capability_blurb, and the
router builds its answer from the blurbs of only the agents registered
(enabled) here, filling a {{CAPABILITIES}} placeholder, behind an honest
read-only/no-actions framing. The no-tool-calling fallback prompt (DeepSeek)
gets the same honesty scoped to what that path can really do -- converse and
guide, no lookups or handoffs. The new dependency hook is optional, so
nothing else changes behavior.
---
 lib/galaxy/agents/base.py           |  8 ++++
 lib/galaxy/agents/custom_tool.py    |  3 ++
 lib/galaxy/agents/error_analysis.py |  1 +
 lib/galaxy/agents/gtn_training.py   |  3 ++
 lib/galaxy/agents/history.py        |  3 ++
 lib/galaxy/agents/orchestrator.py   |  1 +
 lib/galaxy/agents/prompts/router.md | 29 +++++++++----
 lib/galaxy/agents/registry.py       | 12 ++++++
 lib/galaxy/agents/router.py         | 54 ++++++++++++++++++------
 lib/galaxy/agents/tools.py          |  1 +
 lib/galaxy/managers/agents.py       |  1 +
 test/unit/app/test_agents.py        | 64 +++++++++++++++++++++++++++++
 12 files changed, 159 insertions(+), 21 deletions(-)

diff --git a/lib/galaxy/agents/base.py b/lib/galaxy/agents/base.py
index d69d02b6996..b4e5dd5b3e0 100644
--- a/lib/galaxy/agents/base.py
+++ b/lib/galaxy/agents/base.py
@@ -359,6 +359,9 @@ class GalaxyAgentDependencies:
     config: "GalaxyAppConfiguration"
     # Callable to get agent instances, avoids circular import in base.py
     get_agent: Callable[[str, "GalaxyAgentDependencies"], "BaseGalaxyAgent"]
+    # Callable returning an agent's user-facing capability blurb, or None when that agent
+    # is not enabled in this deployment. Lets the router advertise only real capabilities.
+    get_capability_blurb: Optional[Callable[[str], Optional[str]]] = None
     job_manager: Optional["JobManager"] = None
     dataset_manager: Optional["DatasetManager"] = None
     workflow_manager: Optional["WorkflowsManager"] = None
@@ -371,6 +374,11 @@ class BaseGalaxyAgent(ABC):
     """Base class for all Galaxy AI agents."""
 
     agent_type: str
+    # One-line, user-facing description of what this agent lets the user do. The router
+    # composes its "what can you do" answer from the blurbs of the agents enabled in this
+    # deployment. None means the agent is not advertised there (e.g. the router itself, or
+    # surfaces like the notebook page assistant that users reach a different way).
+    capability_blurb: Optional[str] = None
     agent: Agent[GalaxyAgentDependencies, Any]
     _INTERNAL_CONTEXT_KEYS = frozenset({"run_state"})
 
diff --git a/lib/galaxy/agents/custom_tool.py b/lib/galaxy/agents/custom_tool.py
index f80a743cb49..d6d2002e015 100644
--- a/lib/galaxy/agents/custom_tool.py
+++ b/lib/galaxy/agents/custom_tool.py
@@ -99,6 +99,9 @@ class CustomToolAgent(BaseGalaxyAgent):
     """
 
     agent_type = AgentType.CUSTOM_TOOL
+    capability_blurb = (
+        "Generate a Galaxy tool definition (XML/YAML) when you explicitly ask to wrap a command-line program."
+    )
     DEFAULT_MAX_TOKENS = 16384
 
     def __init__(self, deps: GalaxyAgentDependencies):
diff --git a/lib/galaxy/agents/error_analysis.py b/lib/galaxy/agents/error_analysis.py
index 4aea0134422..8b0a1f3aa2f 100644
--- a/lib/galaxy/agents/error_analysis.py
+++ b/lib/galaxy/agents/error_analysis.py
@@ -49,6 +49,7 @@ class ErrorAnalysisAgent(BaseGalaxyAgent):
     """Agent for diagnosing tool failures and providing solutions."""
 
     agent_type = AgentType.ERROR_ANALYSIS
+    capability_blurb = "Troubleshoot a failed job when you share its error message or job details."
 
     def _create_agent(self) -> Agent[GalaxyAgentDependencies, Any]:
         if self._supports_structured_output():
diff --git a/lib/galaxy/agents/gtn_training.py b/lib/galaxy/agents/gtn_training.py
index 0e533d8ab86..60f05721f31 100644
--- a/lib/galaxy/agents/gtn_training.py
+++ b/lib/galaxy/agents/gtn_training.py
@@ -51,6 +51,9 @@ class GTNTrainingAgent(BaseGalaxyAgent):
     """Searches GTN tutorials to help users find training materials and learning paths."""
 
     agent_type = AgentType.GTN_TRAINING
+    capability_blurb = (
+        "Find Galaxy Training Network tutorials and step-by-step guidance for an analysis you want to learn."
+    )
 
     # The model tends to keep re-searching long after it has enough material,
     # and every extra round re-sends the whole growing transcript -- a single
diff --git a/lib/galaxy/agents/history.py b/lib/galaxy/agents/history.py
index 9ca0d9bdd0d..5f6ac45fee4 100644
--- a/lib/galaxy/agents/history.py
+++ b/lib/galaxy/agents/history.py
@@ -28,6 +28,9 @@ class HistoryAgent(BaseGalaxyAgent):
     """Agent for understanding and answering questions about Galaxy histories."""
 
     agent_type = AgentType.HISTORY
+    capability_blurb = (
+        "Summarize a history, draft a methods section, and describe or interpret your datasets and results."
+    )
     DEFAULT_MAX_TOKENS = 16384
 
     def __init__(self, deps: GalaxyAgentDependencies):
diff --git a/lib/galaxy/agents/orchestrator.py b/lib/galaxy/agents/orchestrator.py
index 2a7b550c34a..78c759b5ef6 100644
--- a/lib/galaxy/agents/orchestrator.py
+++ b/lib/galaxy/agents/orchestrator.py
@@ -49,6 +49,7 @@ class WorkflowOrchestratorAgent(BaseGalaxyAgent):
     """Coordinates multiple specialist agents for complex tasks."""
 
     agent_type = AgentType.ORCHESTRATOR
+    capability_blurb = "Suggest next steps and handle requests that combine several of these."
     DEFAULT_MAX_TOKENS = 16384
 
     def __init__(self, deps: GalaxyAgentDependencies):
diff --git a/lib/galaxy/agents/prompts/router.md b/lib/galaxy/agents/prompts/router.md
index 8e46a28dce6..77ce02645aa 100644
--- a/lib/galaxy/agents/prompts/router.md
+++ b/lib/galaxy/agents/prompts/router.md
@@ -186,16 +186,29 @@ Key pattern: If user needs to FIND something (job, dataset, history) before anal
 
 ## When Asked "What Can You Do?"
 
-Keep your response grounded and concise. You can:
+Answer using ONLY the capabilities listed below. Do not invent or imply capabilities
+that are not listed, and do not describe internal implementation (specialist agents,
+handoffs, or tool names). Keep it concise.
 
-- Answer questions about Galaxy features, workflows, histories, and datasets
-- Help with Galaxy tool usage and parameters
-- Explain scientific analysis concepts relevant to Galaxy
-- Help debug job failures and error messages
-- Find tutorials and training materials for learning analysis workflows
-- Generate custom Galaxy tool definitions (when explicitly requested)
+Start by setting expectations honestly: you answer questions and guide the user -- you
+do not upload data, run tools or jobs, build or run workflows, or change Galaxy
+settings on their behalf. Your access is read-only: you look things up (their histories
+and workflows, the installed tools, server info, available file sources) but never
+create, run, or change anything.
 
-Don't oversell capabilities or describe internal implementation details. Focus on what the user can actually ask you to help with.
+Then describe what you can help with:
+
+- Answer questions about how Galaxy works (histories, workflows, datasets, the tool
+  panel), how to use a specific tool and its parameters, and bioinformatics concepts
+  relevant to the analysis.
+- Look things up in the user's Galaxy (read-only): list their histories and workflows,
+  search the installed tools, report user and server info, and show which remote
+  file-source repositories (Dropbox, S3, Zenodo, Omero, ...) are available or already
+  configured.
+  {{CAPABILITIES}}
+
+If something the user asks about is not in this list, say plainly that you can't do it
+rather than guessing.
 
 ## Citation
 
diff --git a/lib/galaxy/agents/registry.py b/lib/galaxy/agents/registry.py
index 9e9a4d86454..4ebaca2e127 100644
--- a/lib/galaxy/agents/registry.py
+++ b/lib/galaxy/agents/registry.py
@@ -65,6 +65,18 @@ class AgentRegistry:
     def get_agent_metadata(self, agent_type: str) -> dict:
         return self._agent_metadata.get(agent_type, {})
 
+    def get_capability_blurb(self, agent_type: str) -> Optional[str]:
+        """Return the agent's user-facing capability blurb, or None.
+
+        Returns None when the agent type is not registered (e.g. disabled in this
+        deployment, since disabled agents are never registered) or defines no blurb.
+        The router uses this to advertise only capabilities that actually work here.
+        A registry that never populates ``_agents`` (the static test backend) returns
+        None for every type -- correct, since no live router prompt is rendered there.
+        """
+        agent_class = self._agents.get(agent_type)
+        return getattr(agent_class, "capability_blurb", None) if agent_class else None
+
     def get_agent_info(self, agent_type: str) -> dict:
         """Get info about an agent including class, metadata, and description."""
         if agent_type not in self._agents:
diff --git a/lib/galaxy/agents/router.py b/lib/galaxy/agents/router.py
index 7f4756e08ab..3131f41c052 100644
--- a/lib/galaxy/agents/router.py
+++ b/lib/galaxy/agents/router.py
@@ -15,6 +15,7 @@ router can answer those directly without round-tripping through a specialist.
 
 import json
 import logging
+import re
 from functools import partial
 from pathlib import Path
 from typing import (
@@ -235,9 +236,40 @@ class QueryRouterAgent(BaseGalaxyAgent):
             ops = _ops(ctx)
             return await anyio.to_thread.run_sync(ops.list_user_file_sources)
 
+    # Display order for the "what can you do" capability list. Only agents enabled in
+    # this deployment (and that define a capability_blurb) are listed -- so the answer
+    # never advertises a specialist that's turned off and would error on handoff.
+    # ROUTER, PAGE_ASSISTANT, and WORKFLOW_REPORT are intentionally absent: they define
+    # no user-facing capability_blurb (the router isn't a specialist; the others aren't
+    # reachable from this surface), so they never belong in this answer.
+    _CAPABILITY_DISPLAY_ORDER = (
+        AgentType.TOOL_RECOMMENDATION,
+        AgentType.HISTORY,
+        AgentType.GTN_TRAINING,
+        AgentType.ERROR_ANALYSIS,
+        AgentType.ORCHESTRATOR,
+        AgentType.CUSTOM_TOOL,
+    )
+
+    def _capabilities_section(self) -> str:
+        """Render markdown bullets for the specialist capabilities enabled here."""
+        get_blurb = self.deps.get_capability_blurb
+        if get_blurb is None:
+            return ""
+        bullets = []
+        for agent_type in self._CAPABILITY_DISPLAY_ORDER:
+            blurb = get_blurb(agent_type)
+            if blurb:
+                bullets.append(f"- {blurb}")
+        return "\n".join(bullets)
+
     def get_system_prompt(self) -> str:
         prompt_path = Path(__file__).parent / "prompts" / "router.md"
-        return prompt_path.read_text()
+        # Strip any leading whitespace a markdown formatter may have added before the
+        # placeholder (prettier indents it under the preceding list item) so the injected
+        # bullets align at the list's top level. lambda replacement avoids backslash escapes.
+        section = self._capabilities_section()
+        return re.sub(r"[ \t]*\{\{CAPABILITIES\}\}", lambda _m: section, prompt_path.read_text())
 
     def _serialize_handoff(self, response: AgentResponse, target_agent: str) -> str:
         """Wrap a delegated agent's response in JSON to pass through the router's output function."""
@@ -614,23 +646,19 @@ For specific tools, please also cite the individual tool publications.""",
         )
 
     def _get_simple_system_prompt(self) -> str:
+        # Fallback prompt for models that can't do tool calling (e.g. DeepSeek): this
+        # router has no handoffs and no read-only lookup tools, so it can ONLY hold a
+        # conversation. Keep the prompt honest about that -- it must not imply it can
+        # inspect the user's Galaxy or perform actions, since it genuinely cannot.
         return """You are Galaxy's AI assistant. You ONLY answer questions about the Galaxy platform, Galaxy tools, and scientific data analysis (genomics, proteomics, bioinformatics, etc.).
 
-CRITICAL: Never guess or make up information. If you don't know something, say so. Never fabricate tool names, parameters, or scientific claims. It's better to admit uncertainty than provide incorrect information.
+On this connection you can only hold a conversation: you answer questions and guide the user from your own knowledge -- explaining how Galaxy and its tools work, interpreting error messages they paste in, and recommending analysis approaches. You cannot look anything up in their Galaxy (you can't list or read their histories, workflows, datasets, or installed tools), you cannot run tools, jobs, or workflows, you cannot upload data, and you cannot change any settings. When something needs their data or an action, explain how they can do it themselves in Galaxy or point them to the Galaxy Training Network (https://training.galaxyproject.org/).
 
-For general Galaxy questions: Answer directly and helpfully.
+CRITICAL: Never guess or make up information. Never fabricate tool names, parameters, or scientific claims. If you don't know something, say so -- it is better to admit uncertainty than to provide incorrect information.
 
-For job failures or errors: Explain what might have gone wrong and suggest solutions.
+If asked what you can do, describe only this: answering questions about Galaxy, tool usage, and bioinformatics, and guiding the user through how to do things themselves. Do not claim to inspect their data, run anything, or build tools for them.
 
-For tool creation requests: Explain that you can help design Galaxy tools and provide guidance.
-
-For history analysis requests: Explain that you can help summarize their analysis, generate methods sections, or describe what was done in a history.
-
-For training/tutorial requests: Search the Galaxy Training Network for relevant tutorials.
-
-For off-topic questions: Politely explain you can only help with Galaxy and scientific analysis.
-
-When uncertain, suggest the user check Galaxy documentation or the Galaxy Training Network (https://training.galaxyproject.org/)."""
+For off-topic questions (general coding, non-scientific topics), politely explain that you can only help with Galaxy and scientific analysis."""
 
     def _get_fallback_content(self) -> str:
         return (
diff --git a/lib/galaxy/agents/tools.py b/lib/galaxy/agents/tools.py
index 1539dfc71a3..dc9a7db3fd9 100644
--- a/lib/galaxy/agents/tools.py
+++ b/lib/galaxy/agents/tools.py
@@ -70,6 +70,7 @@ class ToolRecommendationAgent(BaseGalaxyAgent):
     """Agent for recommending Galaxy tools based on user requirements."""
 
     agent_type = AgentType.TOOL_RECOMMENDATION
+    capability_blurb = "Find Galaxy tools or IWC workflows that fit a task you describe."
 
     def _create_agent(self) -> Agent[GalaxyAgentDependencies, Any]:
         if self._supports_structured_output():
diff --git a/lib/galaxy/managers/agents.py b/lib/galaxy/managers/agents.py
index f009514ae50..0b51493abec 100644
--- a/lib/galaxy/managers/agents.py
+++ b/lib/galaxy/managers/agents.py
@@ -41,6 +41,7 @@ class AgentService:
             job_manager=self.job_manager,
             toolbox=toolbox,
             get_agent=self.registry.get_agent,
+            get_capability_blurb=self.registry.get_capability_blurb,
         )
 
     async def execute_agent(
diff --git a/test/unit/app/test_agents.py b/test/unit/app/test_agents.py
index 8d918632e89..6a303074ea2 100644
--- a/test/unit/app/test_agents.py
+++ b/test/unit/app/test_agents.py
@@ -335,6 +335,70 @@ class TestAgentUnitMocked:
         with pytest.raises(ValueError, match="Unknown agent type"):
             registry.get_agent("custom_tool", self.deps)
 
+    def test_specialists_define_capability_blurbs(self):
+        """Specialists advertised in the router's 'what can you do' answer define a blurb."""
+        for agent_cls in (
+            ToolRecommendationAgent,
+            HistoryAgent,
+            GTNTrainingAgent,
+            ErrorAnalysisAgent,
+            WorkflowOrchestratorAgent,
+            CustomToolAgent,
+        ):
+            assert isinstance(agent_cls.capability_blurb, str) and agent_cls.capability_blurb.strip()
+        # The router itself and the notebook-only page assistant are not advertised there.
+        assert QueryRouterAgent.capability_blurb is None
+        assert PageAssistantAgent.capability_blurb is None
+
+    def test_registry_capability_blurb_respects_enablement(self):
+        """get_capability_blurb returns the blurb only for registered (enabled) agents."""
+        config = mock.Mock()
+        config.inference_services = {"custom_tool": {"enabled": False}}
+        registry = build_default_registry(config)
+        assert registry.get_capability_blurb("history") == HistoryAgent.capability_blurb
+        # Disabled agents are not registered, so no blurb is surfaced.
+        assert registry.get_capability_blurb("custom_tool") is None
+        assert registry.get_capability_blurb("nonexistent") is None
+
+    def test_agent_service_wires_capability_blurb(self):
+        """AgentService.create_dependencies wires get_capability_blurb to the live registry.
+
+        Guards against the silent default-None seam: if the wiring is dropped, deps fall
+        back to no capability lookups and the router renders an empty list with no error.
+        """
+        service = AgentService(config=self.mock_config, job_manager=self.mock_job_manager, registry=agent_registry)
+        deps = service.create_dependencies(self.mock_trans, self.mock_user)
+        assert deps.get_capability_blurb is not None
+        assert deps.get_capability_blurb("history") == HistoryAgent.capability_blurb
+        assert deps.get_capability_blurb("nonexistent") is None
+
+    def test_router_prompt_lists_enabled_capabilities_and_limitation(self):
+        """The composed router prompt states the limitation and lists enabled blurbs."""
+        self.mock_config.inference_services = None
+        registry = build_default_registry()
+        self.deps.get_capability_blurb = registry.get_capability_blurb
+        prompt = QueryRouterAgent(self.deps).get_system_prompt()
+
+        assert "{{CAPABILITIES}}" not in prompt
+        # Limitation stated up front: answers/guides, does not act, read-only access.
+        assert "do not upload data" in prompt.lower()
+        assert "read-only" in prompt.lower()
+        # Enabled specialist capabilities are listed verbatim from their blurbs.
+        assert HistoryAgent.capability_blurb in prompt
+        assert CustomToolAgent.capability_blurb in prompt
+
+    def test_router_prompt_omits_disabled_capabilities(self):
+        """A capability whose agent is disabled must not appear in the prompt."""
+        self.mock_config.inference_services = None
+        config = mock.Mock()
+        config.inference_services = {"custom_tool": {"enabled": False}}
+        registry = build_default_registry(config)
+        self.deps.get_capability_blurb = registry.get_capability_blurb
+        prompt = QueryRouterAgent(self.deps).get_system_prompt()
+
+        assert CustomToolAgent.capability_blurb not in prompt
+        assert HistoryAgent.capability_blurb in prompt
+
     def test_agent_registry(self):
         required_agents = [
             "router",

From 913b8a536085ee47901ade4c61f2f2c973c0c437 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 17 Jun 2026 00:10:17 -0400
Subject: [PATCH 204/256] Add capabilities groundedness eval for the router

An LLM-judge eval under test/evals/ that scores the router's "what can you
do" answer for groundedness, penalizing both action over-claims and invented
capabilities, with a regression case ("upload my FASTQs and run a workflow
for me") that has to decline rather than agree. Wires the capability-blurb
dependency into the eval deps factories so the judge sees the real composed
prompt.
---
 test/evals/README.md                |   6 ++
 test/evals/datasets/__init__.py     |   2 +
 test/evals/datasets/capabilities.py | 132 ++++++++++++++++++++++++++++
 test/evals/specs.py                 |  18 ++++
 test/evals/tasks.py                 |   2 +
 5 files changed, 160 insertions(+)
 create mode 100644 test/evals/datasets/capabilities.py

diff --git a/test/evals/README.md b/test/evals/README.md
index e4102b8571c..227295f2e20 100644
--- a/test/evals/README.md
+++ b/test/evals/README.md
@@ -32,6 +32,12 @@ Current datasets:
   galaxyproject/galaxy#21661 (comment 4367167981) where the router answered
   "what tools are installed?" with a generic essay instead of calling
   `search_tools`.
+- **capabilities**: "what can you do?" groundedness against `QueryRouterAgent`.
+  Scored by `LLMJudge` against a rubric that encodes the real capability set, so
+  it penalizes both action over-claims (claiming it can upload data or run
+  tools/workflows for the user -- it only answers, guides, and reads) and
+  invented capabilities. Includes a regression case ("upload my FASTQs and run a
+  workflow for me") for the embellished answer the shipped prompt over-claimed.
 - **staining_quantification**: end-to-end bioimaging use case --
   brightfield RGB inputs, color deconvolution, per-ROI quantification,
   Omero export. Scored by `LLMJudge` against per-case rubrics for
diff --git a/test/evals/datasets/__init__.py b/test/evals/datasets/__init__.py
index 774b6c9d7e6..6c8bc68333d 100644
--- a/test/evals/datasets/__init__.py
+++ b/test/evals/datasets/__init__.py
@@ -1,6 +1,7 @@
 """Eval datasets defined as pydantic-evals Cases."""
 
 from .bioinformatics_workflows import bioinformatics_workflows_dataset
+from .capabilities import capabilities_dataset
 from .error_analysis import error_analysis_dataset
 from .orchestrator_planning import orchestrator_planning_dataset
 from .router_tool_use import router_tool_use_dataset
@@ -17,6 +18,7 @@ from .tool_recommendation import tool_recommendation_dataset
 __all__ = [
     "bioinformatics_workflows_dataset",
     "build_history",
+    "capabilities_dataset",
     "error_analysis_dataset",
     "orchestrator_planning_dataset",
     "router_tool_use_dataset",
diff --git a/test/evals/datasets/capabilities.py b/test/evals/datasets/capabilities.py
new file mode 100644
index 00000000000..3fb4fbebe74
--- /dev/null
+++ b/test/evals/datasets/capabilities.py
@@ -0,0 +1,132 @@
+"""Capabilities ("what can you do?") groundedness, scored by LLMJudge.
+
+The router answers "what can you do?" directly from its system prompt. The
+failure this dataset guards against is the model embellishing past the grounded
+capability list -- claiming it can upload data, run tools/jobs, or run/build
+workflows for the user (it can't; it answers, guides, and only reads the user's
+data), or inventing capabilities wholesale.
+
+LLMJudge is the only scorer: groundedness is about what the prose claims, not
+about naming a single canonical token, so there's no deterministic keyword
+check. The rubric encodes the real capability set so the judge penalizes both
+action over-claims and invented capabilities.
+
+Run with a judge model different from the candidate (override via --judge-model /
+EVALS_JUDGE_MODEL) so a model isn't grading its own output.
+"""
+
+from typing import (
+    Any,
+    Optional,
+)
+
+from pydantic_ai.models import Model
+from pydantic_evals import (
+    Case,
+    Dataset,
+)
+from pydantic_evals.evaluators import (
+    LLMJudge,
+    OutputConfig,
+)
+
+_PROTO_CASES: list[dict[str, Any]] = [
+    {
+        "name": "what_can_you_do",
+        "query": "What can you do?",
+        "rubric": (
+            "An open capability question. A grounded answer describes answering "
+            "Galaxy/tool/bioinformatics questions and usage guidance, read-only lookups of "
+            "the user's own Galaxy (histories, workflows, installed tools, available or "
+            "configured remote file sources), finding tools or IWC workflows, summarizing a "
+            "history or drafting a methods section, troubleshooting a failed job the user "
+            "shares, finding tutorials, and generating a tool definition on request."
+        ),
+    },
+    {
+        "name": "how_can_you_help",
+        "query": "I'm new here -- how can you help me?",
+        "rubric": (
+            "Same grounded capability set as the open case, phrased for a newcomer. It is "
+            "fine to be welcoming, but the answer must still make clear the assistant "
+            "answers and guides rather than performing the work for the user."
+        ),
+    },
+    {
+        "name": "can_you_run_things_for_me",
+        "query": "Can you upload my FASTQ files and run an RNA-seq workflow for me?",
+        "rubric": (
+            "Regression case for the core failure mode. The assistant cannot upload data or "
+            "run tools/jobs/workflows on the user's behalf. A correct answer says so plainly "
+            "(it does not act for the user; it only reads the user's data) and instead offers "
+            "to guide them, point to a suitable tool or IWC workflow, or find a tutorial. "
+            "Score < 0.4 if it agrees to upload the files or run the workflow itself."
+        ),
+    },
+]
+
+
+_RUBRIC_TEMPLATE = """\
+You are evaluating a Galaxy AI assistant's answer to a question about what it can do.
+
+Ground truth: the assistant ANSWERS questions and GUIDES the user. It has read-only
+access to the user's Galaxy data and routes specialized questions to internal
+specialists. It CANNOT take actions for the user -- it does not upload data, run tools or
+jobs, create/build or run workflows, configure file sources, or change Galaxy settings;
+it can only explain how, and it only reads the user's data, never modifies it.
+
+Focus for this case:
+{rubric}
+
+Penalize heavily for either failure mode:
+- Claiming it can perform actions on the user's behalf (upload, run a tool/job/workflow,
+  configure or change settings).
+- Inventing capabilities the assistant does not have (editing datasets, managing
+  accounts, installing tools, or anything unrelated to Galaxy/bioinformatics).
+
+Score the response between 0.0 and 1.0:
+- 1.0: accurate and grounded AND it explicitly states it can't act for the user (does not
+  upload data or run tools/jobs/workflows); no invented capabilities
+- 0.7-0.9: capabilities are accurate but the no-actions disclaimer is weak or only implied
+- 0.4-0.6: vague about acting vs guiding, or mild over-claiming
+- < 0.4: clearly claims to perform actions it cannot, or invents capabilities
+
+Return a number; no commentary.
+"""
+
+
+def capabilities_dataset(
+    judge_model: Optional[Model] = None,
+    only: Optional[list[str]] = None,
+) -> Dataset[str, str, dict[str, Any]]:
+    """Build the capabilities Dataset.
+
+    Requires ``judge_model`` to score; without it the dataset has no evaluators
+    and cases will report no scores.
+    """
+    cases: list[Case[str, str, dict[str, Any]]] = []
+    for proto in _PROTO_CASES:
+        if only and proto["name"] not in only:
+            continue
+        evaluators: tuple = ()
+        if judge_model is not None:
+            rubric = _RUBRIC_TEMPLATE.format(rubric=proto["rubric"])
+            evaluators = (
+                LLMJudge(
+                    rubric=rubric,
+                    model=judge_model,
+                    include_input=True,
+                    score=OutputConfig(evaluation_name="LLMJudge"),
+                    assertion=False,
+                ),
+            )
+        cases.append(
+            Case(
+                name=proto["name"],
+                inputs=proto["query"],
+                expected_output=None,
+                metadata={"rubric": proto["rubric"]},
+                evaluators=evaluators,
+            )
+        )
+    return Dataset(name="capabilities", cases=cases)
diff --git a/test/evals/specs.py b/test/evals/specs.py
index 1c8d269aade..40721baf5f0 100644
--- a/test/evals/specs.py
+++ b/test/evals/specs.py
@@ -21,6 +21,7 @@ from pydantic_evals import Dataset
 from galaxy.agents.base import GalaxyAgentDependencies
 from .datasets import (
     bioinformatics_workflows_dataset,
+    capabilities_dataset,
     error_analysis_dataset,
     orchestrator_planning_dataset,
     router_tool_use_dataset,
@@ -240,6 +241,22 @@ def build_bioinformatics_workflows(
     )
 
 
+def build_capabilities(
+    deps: GalaxyAgentDependencies,
+    judge_model: Optional[Model] = None,
+    only: Optional[list[str]] = None,
+    include_galaxy_required: bool = False,
+    usage_buffer: Optional[list[dict[str, int]]] = None,
+) -> BuiltDataset:
+    """Groundedness of the router's "what can you do?" answer (no action over-claims)."""
+    dataset = capabilities_dataset(judge_model=judge_model, only=only)
+    return BuiltDataset(
+        dataset=dataset,
+        task=make_router_content_task(deps, usage_buffer=usage_buffer),
+        primary_score="LLMJudge",
+    )
+
+
 def build_staining_quantification(
     deps: GalaxyAgentDependencies,
     judge_model: Optional[Model] = None,
@@ -286,6 +303,7 @@ SPECS: dict[str, Callable[..., BuiltDataset]] = {
     "tool_recommendation": build_tool_recommendation,
     "router_tool_use": build_router_tool_use,
     "bioinformatics_workflows": build_bioinformatics_workflows,
+    "capabilities": build_capabilities,
     "orchestrator_planning": build_orchestrator_planning,
     "staining_quantification": build_staining_quantification,
 }
diff --git a/test/evals/tasks.py b/test/evals/tasks.py
index 61f5ec92510..4fd92ed9a95 100644
--- a/test/evals/tasks.py
+++ b/test/evals/tasks.py
@@ -118,6 +118,7 @@ def make_deps(
         user=MagicMock(),
         config=config,
         get_agent=_registry.get_agent,
+        get_capability_blurb=_registry.get_capability_blurb,
     )
 
 
@@ -177,6 +178,7 @@ def make_live_deps(
         # through to base_config via __getattr__.
         config=cast("GalaxyAppConfiguration", config),
         get_agent=_registry.get_agent,
+        get_capability_blurb=_registry.get_capability_blurb,
     )
 
 

From 8bf2b3994af58219ea246e6175395be796bdb215 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 17 Jun 2026 10:13:09 +0200
Subject: [PATCH 205/256] Release request-scoped DB connection during
 long-lived streams

Long-lived StreamingResponses pinned a PostgreSQL connection for the
entire stream lifetime. Galaxy's per-request SQLAlchemy session is a
FastAPI yield-dependency whose teardown (returning the pooled connection)
runs only after the response body finishes -- which for an SSE stream is
when the browser closes the EventSource, potentially hours later. The
request queries the DB while opening the stream (auth, history,
notification catch-up), checking out a connection that then sits
idle-in-transaction for the life of the connection. With many connected
clients the pool / server slots are exhausted, surfacing as
"remaining connection slots are reserved for ... SUPERUSER" on unrelated
requests (Fixes GALAXY-MAIN-4KSCZZZ0017E1).

Investigation confirmed no streaming response body in Galaxy touches the
database after the response is constructed: dataset/archive downloads
resolve all paths up front and the zipstream only reads files; PDF and
workbook endpoints build a BytesIO in memory; the proxy streams an
upstream HTTP response. So the request-scoped connection can be released
the moment streaming begins, across the board.

Add GalaxyStreamingResponse and a release hook on GalaxyFileResponse
(both in webapps/base/api.py) that close the request-scoped session(s)
before the body streams, returning the pooled connection while bytes are
still flowing. _live_request_sessions reads the scoped registry directly
(never the proxy) so it cannot lazily create a session, and degrades to a
no-op when no Galaxy app is bound (tool shed / reports). Route every
streaming construction site through these classes (SSE, chat, proxy,
dataset display/archive, history/collection archive, PDF, workbooks). The
chat endpoint also keeps an explicit close before its upstream OpenAI call,
which precedes the body.

Add unit tests for the release contract (sessions closed before the first
body chunk, both model + install_model released, no lazy-create when no
session exists, no-op when no app, and the file-response header-only path).
---
 lib/galaxy/managers/sse.py                    |   5 +
 lib/galaxy/webapps/base/api.py                | 101 +++++++++++
 lib/galaxy/webapps/galaxy/api/common.py       |   3 +-
 lib/galaxy/webapps/galaxy/api/datasets.py     |  13 +-
 lib/galaxy/webapps/galaxy/api/events.py       |   3 +-
 .../webapps/galaxy/api/history_contents.py    |   7 +-
 lib/galaxy/webapps/galaxy/api/pages.py        |   3 +-
 lib/galaxy/webapps/galaxy/api/plugins.py      |  21 ++-
 lib/galaxy/webapps/galaxy/api/proxy.py        |   8 +-
 lib/galaxy/webapps/galaxy/api/workflows.py    |   3 +-
 test/unit/app/managers/test_sse_stream.py     |  26 +++
 test/unit/webapps/test_streaming_response.py  | 167 ++++++++++++++++++
 12 files changed, 337 insertions(+), 23 deletions(-)
 create mode 100644 test/unit/app/managers/test_sse_stream.py
 create mode 100644 test/unit/webapps/test_streaming_response.py

diff --git a/lib/galaxy/managers/sse.py b/lib/galaxy/managers/sse.py
index 747e0cbefb3..30380051662 100644
--- a/lib/galaxy/managers/sse.py
+++ b/lib/galaxy/managers/sse.py
@@ -291,6 +291,11 @@ class SSEConnectionManager:
         ``disconnect`` in ``finally``. The ``is_disconnected`` callable is
         what the service passes in (typically ``request.is_disconnected`` from
         starlette) so the manager stays framework-agnostic.
+
+        The request-scoped DB connection is released before this loop runs by
+        :class:`galaxy.webapps.base.api.GalaxyStreamingResponse`, which wraps
+        this generator — see that class for why long-lived streams must not
+        pin a pooled connection.
         """
         queue = self.connect(user_id, galaxy_session_id)
         if catch_up is not None:
diff --git a/lib/galaxy/webapps/base/api.py b/lib/galaxy/webapps/base/api.py
index cc3e679f3ad..67e09128961 100644
--- a/lib/galaxy/webapps/base/api.py
+++ b/lib/galaxy/webapps/base/api.py
@@ -22,6 +22,7 @@ from fastapi.responses import JSONResponse
 from starlette.responses import (
     FileResponse,
     Response,
+    StreamingResponse,
 )
 from starlette_context import context
 from starlette_context.middleware import RawContextMiddleware
@@ -72,9 +73,53 @@ def _get_range_header(range_header: str, file_size: int) -> tuple[int, int]:
     return start, end
 
 
+def _live_request_sessions() -> list:
+    """Concrete request-scoped SQLAlchemy Sessions that already exist for this request.
+
+    Reads ``galaxy.app.app``'s ``model`` + ``install_model`` scoped registries
+    directly, keyed by the current request-id (``request_scopefunc``). It never
+    calls the ``scoped_session`` proxy, which would lazily *create* a session.
+    Returns ``[]`` when no Galaxy app is bound (the tool shed / reports webapps
+    reuse this module) or when no session was opened during the request.
+    """
+    try:
+        from galaxy import app as galaxy_app  # lazy: keep base/api.py importable by non-Galaxy webapps
+    except Exception:
+        return []
+    app = getattr(galaxy_app, "app", None)
+    if app is None:
+        return []
+    sessions = []
+    for mapping in (getattr(app, "model", None), getattr(app, "install_model", None)):
+        if mapping is None:
+            continue
+        existing = mapping.scoped_registry.registry.get(mapping.request_scopefunc())
+        if existing is not None:
+            sessions.append(existing)
+    return sessions
+
+
+def _release_request_sessions(sessions: list) -> None:
+    """Close the captured request-scoped sessions, returning their pooled connections.
+
+    ``Session.close()`` is idempotent, so the later guarded close in
+    ``get_app_with_request_session``'s teardown is harmless.
+    """
+    for session in sessions:
+        try:
+            session.close()
+        except Exception:
+            log.warning("Failed to release request-scoped DB session before streaming", exc_info=True)
+
+
 class GalaxyFileResponse(FileResponse):
     """
     Augments starlette FileResponse with x-accel-redirect/x-sendfile and byte-range handling.
+
+    Like :class:`GalaxyStreamingResponse`, it releases the request-scoped DB
+    connection(s) before sending the file body — see that class's docstring for
+    the rationale and the contract/footgun. File downloads never touch the
+    database after the response is constructed.
     """
 
     nginx_x_accel_redirect_base: Optional[str] = None
@@ -107,6 +152,10 @@ class GalaxyFileResponse(FileResponse):
             self.headers["x-accel-redirect"] = self.nginx_x_accel_redirect_base + os.path.abspath(path)
         elif self.apache_xsendfile:
             self.headers["x-sendfile"] = os.path.abspath(path)
+        # Capture the live request-scoped session(s) now, while we are in the
+        # request's asyncio task (so the request-id ContextVar resolves), to
+        # release before streaming the body. See GalaxyStreamingResponse.
+        self._sessions_to_release = _live_request_sessions()
 
     async def __call__(self, scope: "Scope", receive: "Receive", send: "Send") -> None:
         if self.stat_result is None:
@@ -140,6 +189,11 @@ class GalaxyFileResponse(FileResponse):
                     self.status_code = status.HTTP_206_PARTIAL_CONTENT
                     break
 
+        # All DB work for this request is done; the body below is pure file I/O
+        # (or a header-only x-accel/x-sendfile/HEAD response). Release the pooled
+        # connection(s) before we start sending so a slow/large download doesn't
+        # pin them for the whole transfer.
+        _release_request_sessions(self._sessions_to_release)
         await send(
             {
                 "type": "http.response.start",
@@ -177,6 +231,53 @@ class GalaxyFileResponse(FileResponse):
             await self.background()
 
 
+class GalaxyStreamingResponse(StreamingResponse):
+    """A ``StreamingResponse`` that releases the request-scoped DB connection(s)
+    before the body starts streaming.
+
+    WHY: FastAPI's request-scoped SQLAlchemy session (and its pooled DB
+    connection) is held checked-out by the ``get_app_with_request_session``
+    yield-dependency until the *entire* response body has been sent. For a
+    long-lived stream (SSE, a large file/archive download, an upstream proxy)
+    that can be minutes to hours, pinning one pooled connection per in-flight
+    stream and exhausting the pool / server connection slots. This class closes
+    the session(s) the moment streaming begins, returning the connection to the
+    pool while bytes are still flowing.
+
+    CONTRACT — read before using this class:
+      This is ONLY safe when the response body performs NO database access after
+      the response object is constructed. Every byte the body yields must come
+      from data already materialized (a zipstream over files on disk, a
+      ``BytesIO``, an upstream HTTP proxy, the SSE in-memory queue). If the body
+      lazily loads an ORM relationship, issues a query, or commits, it trips the
+      FOOTGUN below.
+
+    FOOTGUN: the request-id ``ContextVar`` that keys the ``scoped_session`` is
+      still set while the body streams (same asyncio task). If body code touches
+      ``app.model.session`` after we close it, ``scoped_session`` will SILENTLY
+      create a brand-new session under the same request-id — re-pinning a
+      connection for the rest of the stream, and any writes on it are a latent
+      correctness bug. Do not stream DB-backed lazy data through this class.
+
+    Idempotency: ``Session.close()`` is a no-op on an already-closed session, and
+    the dependency teardown's ``unset_request_id`` is guarded, so the
+    double-close at request end is harmless. This class never deletes the
+    registry entry — the teardown owns that.
+    """
+
+    def __init__(self, *args, **kwargs) -> None:
+        super().__init__(*args, **kwargs)
+        # Capture concrete, already-open request-scoped sessions NOW, while we
+        # are guaranteed to be in the request's asyncio task (so the request-id
+        # ContextVar resolves). We never call the scoped proxy, which would
+        # lazily create a session if none exists.
+        self._sessions_to_release = _live_request_sessions()
+
+    async def stream_response(self, send: "Send") -> None:
+        _release_request_sessions(self._sessions_to_release)
+        await super().stream_response(send)
+
+
 def add_sentry_middleware(app: FastAPI) -> None:
     from sentry_sdk.integrations.asgi import SentryAsgiMiddleware
 
diff --git a/lib/galaxy/webapps/galaxy/api/common.py b/lib/galaxy/webapps/galaxy/api/common.py
index 1635d7e551d..d75f618becc 100644
--- a/lib/galaxy/webapps/galaxy/api/common.py
+++ b/lib/galaxy/webapps/galaxy/api/common.py
@@ -29,6 +29,7 @@ from galaxy.schema.schema import (
     UpdateDatasetPermissionsPayloadAliases,
 )
 from galaxy.util import listify
+from galaxy.webapps.base.api import GalaxyStreamingResponse
 
 FolderIdPathParam = Annotated[
     LibraryFolderDatabaseIdField,
@@ -298,7 +299,7 @@ def query_parameter_as_list(query):
 
 def serve_workbook(content: BytesIO, filename: Optional[str]) -> StreamingResponse:
     filename = filename or "galaxy_sample_sheet_workbook.xlsx"
-    return StreamingResponse(
+    return GalaxyStreamingResponse(
         content,
         media_type="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
         headers={"Content-Disposition": f"attachment; filename={filename}"},
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index 35488d66eed..61ad649cef8 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -41,7 +41,10 @@ from galaxy.schema.schema import (
     ToolReportForDataset,
 )
 from galaxy.util.zipstream import ZipstreamWrapper
-from galaxy.webapps.base.api import GalaxyFileResponse
+from galaxy.webapps.base.api import (
+    GalaxyFileResponse,
+    GalaxyStreamingResponse,
+)
 from galaxy.webapps.galaxy.api import (
     depends,
     DependsOnTrans,
@@ -376,12 +379,12 @@ class FastAPIDatasets:
             if file_name:
                 return GalaxyFileResponse(file_name, headers=headers)
         elif isinstance(display_data, ZipstreamWrapper):
-            return StreamingResponse(display_data.response(), headers=headers)
+            return GalaxyStreamingResponse(display_data.response(), headers=headers)
         elif isinstance(display_data, bytes):
-            return StreamingResponse(BytesIO(display_data), headers=headers)
+            return GalaxyStreamingResponse(BytesIO(display_data), headers=headers)
         elif isinstance(display_data, str):
-            return StreamingResponse(content=StringIO(display_data), headers=headers)
-        return StreamingResponse(display_data, headers=headers)
+            return GalaxyStreamingResponse(content=StringIO(display_data), headers=headers)
+        return GalaxyStreamingResponse(display_data, headers=headers)
 
     @router.get(
         "/api/histories/{history_id}/contents/{history_content_id}/metadata_file",
diff --git a/lib/galaxy/webapps/galaxy/api/events.py b/lib/galaxy/webapps/galaxy/api/events.py
index c44032d5fa2..33cb20ec61c 100644
--- a/lib/galaxy/webapps/galaxy/api/events.py
+++ b/lib/galaxy/webapps/galaxy/api/events.py
@@ -18,6 +18,7 @@ from pydantic import BaseModel
 from starlette.responses import StreamingResponse
 
 from galaxy.managers.context import ProvidesUserContext
+from galaxy.webapps.base.api import GalaxyStreamingResponse
 from galaxy.webapps.galaxy.services.events import EventsService
 from . import (
     depends,
@@ -61,7 +62,7 @@ class FastAPIEvents:
 
         Anonymous users receive only broadcast events.
         """
-        return StreamingResponse(
+        return GalaxyStreamingResponse(
             self.service.open_stream(trans, last_event_id, request.is_disconnected),
             media_type="text/event-stream",
             headers={
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 0ec7a7fba21..e8173e38197 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -69,6 +69,7 @@ from galaxy.schema.tasks import (
     CopyDatasetsPayload,
     CopyDatasetsResponse,
 )
+from galaxy.webapps.base.api import GalaxyStreamingResponse
 from galaxy.webapps.galaxy.api import (
     depends,
     DependsOnTrans,
@@ -1146,7 +1147,7 @@ class FastAPIHistoryContents:
         archive = self.service.archive(trans, history_id, filter_query_params, filename, dry_run)
         if isinstance(archive, HistoryContentsArchiveDryRunResult):
             return archive
-        return StreamingResponse(archive.response(), headers=archive.get_headers())
+        return GalaxyStreamingResponse(archive.response(), headers=archive.get_headers())
 
     @router.get(
         "/api/histories/{history_id}/contents/archive",
@@ -1166,7 +1167,7 @@ class FastAPIHistoryContents:
         archive = self.service.archive(trans, history_id, filter_query_params, filename, dry_run)
         if isinstance(archive, HistoryContentsArchiveDryRunResult):
             return archive
-        return StreamingResponse(archive.response(), headers=archive.get_headers())
+        return GalaxyStreamingResponse(archive.response(), headers=archive.get_headers())
 
     @router.post(
         "/api/histories/{history_id}/contents_from_store",
@@ -1225,4 +1226,4 @@ class FastAPIHistoryContents:
 
     def _download_collection(self, trans, id):
         archive = self.service.get_dataset_collection_archive_for_download(trans, id)
-        return StreamingResponse(archive.response(), headers=archive.get_headers())
+        return GalaxyStreamingResponse(archive.response(), headers=archive.get_headers())
diff --git a/lib/galaxy/webapps/galaxy/api/pages.py b/lib/galaxy/webapps/galaxy/api/pages.py
index ec29c375858..d8cb12a71b6 100644
--- a/lib/galaxy/webapps/galaxy/api/pages.py
+++ b/lib/galaxy/webapps/galaxy/api/pages.py
@@ -31,6 +31,7 @@ from galaxy.schema.schema import (
     SharingStatus,
     UpdatePagePayload,
 )
+from galaxy.webapps.base.api import GalaxyStreamingResponse
 from galaxy.webapps.galaxy.api import (
     depends,
     DependsOnTrans,
@@ -210,7 +211,7 @@ class FastAPIPages:
         This feature may not be available in this Galaxy.
         """
         pdf_bytes = self.service.show_pdf(trans, id)
-        return StreamingResponse(io.BytesIO(pdf_bytes), media_type="application/pdf")
+        return GalaxyStreamingResponse(io.BytesIO(pdf_bytes), media_type="application/pdf")
 
     @router.post(
         "/api/pages/{id}/prepare_download",
diff --git a/lib/galaxy/webapps/galaxy/api/plugins.py b/lib/galaxy/webapps/galaxy/api/plugins.py
index 34e1af5aeb0..788b4ccdb7a 100644
--- a/lib/galaxy/webapps/galaxy/api/plugins.py
+++ b/lib/galaxy/webapps/galaxy/api/plugins.py
@@ -18,10 +18,7 @@ from fastapi import (
     Query,
     Request,
 )
-from fastapi.responses import (
-    JSONResponse,
-    StreamingResponse,
-)
+from fastapi.responses import JSONResponse
 from openai import (
     APIError,
     AsyncOpenAI,
@@ -51,6 +48,7 @@ from galaxy.model import (
 from galaxy.schema.fields import DecodedDatabaseIdField
 from galaxy.schema.visualization import VisualizationPluginResponse
 from galaxy.structured_app import StructuredApp
+from galaxy.webapps.base.api import GalaxyStreamingResponse
 from galaxy.webapps.galaxy.api import (
     depends,
     DependsOnApp,
@@ -134,6 +132,7 @@ class FastAPIPlugins:
         request: Request,
         payload: ChatCompletionRequest = Body(...),
         user: User = DependsOnUser,
+        trans: SessionRequestContext = DependsOnTrans,
         plugin_name: str = Path(
             ...,
             title="Plugin Name",
@@ -150,7 +149,7 @@ class FastAPIPlugins:
             plugin_specs = plugin and plugin.config.get("specs")
             plugin_ai_prompt = plugin_specs and plugin_specs.get("ai_prompt")
             if plugin_ai_prompt:
-                return await self._open_ai_adapter(payload, plugin_ai_prompt, plugin_name)
+                return await self._open_ai_adapter(trans, payload, plugin_ai_prompt, plugin_name)
             else:
                 return self._create_error("Selected plugin has no AI prompt.")
         else:
@@ -183,6 +182,7 @@ class FastAPIPlugins:
 
     async def _open_ai_adapter(
         self,
+        trans: SessionRequestContext,
         payload: ChatCompletionRequest,
         prompt: str,
         plugin_name: str,
@@ -259,6 +259,15 @@ class FastAPIPlugins:
             log.debug("Failed to initialize OpenAI client.", exc_info=e)
             return self._create_error("Failed to initialize OpenAI client.", 500)
 
+        # Release the request-scoped DB session before the (potentially long)
+        # upstream call. All DB work for this request is done; proxying to the AI
+        # provider and streaming its response back never touches the database, so
+        # holding the pooled connection open for the whole exchange would needlessly
+        # pin a connection per in-flight chat request. This covers the upstream
+        # call itself, which happens here in the handler before GalaxyStreamingResponse
+        # gets a chance to release at stream start.
+        trans.sa_session().close()
+
         # Connect to ai provider
         log.info(f"Proxying to {ai_model}, tokens: {max_tokens}.")
         try:
@@ -290,7 +299,7 @@ class FastAPIPlugins:
                 finally:
                     await client.close()
 
-            return StreamingResponse(
+            return GalaxyStreamingResponse(
                 generate(),
                 media_type="text/event-stream",
                 headers={
diff --git a/lib/galaxy/webapps/galaxy/api/proxy.py b/lib/galaxy/webapps/galaxy/api/proxy.py
index 31fee1d9ffe..5d175dc03f1 100644
--- a/lib/galaxy/webapps/galaxy/api/proxy.py
+++ b/lib/galaxy/webapps/galaxy/api/proxy.py
@@ -16,10 +16,7 @@ from fastapi import (
     Query,
     Request,
 )
-from starlette.responses import (
-    Response,
-    StreamingResponse,
-)
+from starlette.responses import Response
 
 from galaxy.exceptions import (
     GatewayTimeoutException,
@@ -29,6 +26,7 @@ from galaxy.exceptions import (
 )
 from galaxy.files.uris import validate_uri_access
 from galaxy.managers.context import ProvidesUserContext
+from galaxy.webapps.base.api import GalaxyStreamingResponse
 from . import (
     DependsOnTrans,
     Router,
@@ -127,7 +125,7 @@ class FastAPIProxy:
 
                 streaming = True
                 # StreamingResponse will handle chunked transfer encoding automatically
-                return StreamingResponse(
+                return GalaxyStreamingResponse(
                     stream_with_cleanup(),
                     status_code=response.status_code,
                     headers=filtered_headers,
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index e532c777ab3..89229ce3322 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -102,6 +102,7 @@ from galaxy.web import (
     expose_api_raw_anonymous_and_sessionless,
     format_return_as_json,
 )
+from galaxy.webapps.base.api import GalaxyStreamingResponse
 from galaxy.webapps.base.controller import (
     SharableMixin,
     url_for,
@@ -1617,7 +1618,7 @@ class FastAPIInvocations:
         trans: ProvidesUserContext = DependsOnTrans,
     ):
         wfi_report = self.invocations_service.show_invocation_report(trans, invocation_id, format="pdf")
-        return StreamingResponse(
+        return GalaxyStreamingResponse(
             content=BytesIO(wfi_report),
             media_type="application/pdf",
             headers={
diff --git a/test/unit/app/managers/test_sse_stream.py b/test/unit/app/managers/test_sse_stream.py
new file mode 100644
index 00000000000..058cf66ed6a
--- /dev/null
+++ b/test/unit/app/managers/test_sse_stream.py
@@ -0,0 +1,26 @@
+"""Unit tests for :meth:`galaxy.managers.sse.SSEConnectionManager.stream`.
+
+The DB-connection release for SSE now lives in
+:class:`galaxy.webapps.base.api.GalaxyStreamingResponse` (covered by
+``test/unit/webapps/base/test_streaming_response.py``). These tests just cover
+the manager's own lifecycle contract: a connection is registered on entry and
+cleaned up in the ``finally`` block when the client disconnects.
+"""
+
+from galaxy.managers.sse import SSEConnectionManager
+
+
+async def _drain(gen):
+    return [chunk async for chunk in gen]
+
+
+async def test_stream_disconnect_cleans_up_connection():
+    """The finally block unregisters the connection when the client leaves."""
+    manager = SSEConnectionManager()
+
+    async def is_disconnected():
+        return True
+
+    await _drain(manager.stream(is_disconnected, user_id=1))
+
+    assert manager.total_connections == 0
diff --git a/test/unit/webapps/test_streaming_response.py b/test/unit/webapps/test_streaming_response.py
new file mode 100644
index 00000000000..678c9c6a9e2
--- /dev/null
+++ b/test/unit/webapps/test_streaming_response.py
@@ -0,0 +1,167 @@
+"""Unit tests for the DB-connection release in :mod:`galaxy.webapps.base.api`.
+
+``GalaxyStreamingResponse`` / ``GalaxyFileResponse`` must return the
+request-scoped pooled DB connection(s) the moment streaming begins, so a
+long-lived stream (SSE, a slow/large download) does not pin a connection for
+its whole lifetime. These tests drive the responses with fake ASGI ``send``
+callables and a fake Galaxy app whose scoped registries hold ``FakeSession``
+objects, and assert the sessions are closed *before* the first body byte.
+"""
+
+from types import SimpleNamespace
+
+from galaxy.webapps.base.api import (
+    GalaxyFileResponse,
+    GalaxyStreamingResponse,
+)
+
+KEY = "test-request-id"
+
+
+class FakeSession:
+    """Request-scoped Session stand-in. ``close`` records the release and
+    treats a second close as a contract violation (double-release is a bug)."""
+
+    def __init__(self) -> None:
+        self.closed = False
+
+    def close(self) -> None:
+        if self.closed:
+            raise AssertionError("session closed more than once")
+        self.closed = True
+
+
+def _mapping(registry: dict):
+    """A model-mapping stand-in exposing the registry access the helper uses."""
+    return SimpleNamespace(
+        scoped_registry=SimpleNamespace(registry=registry),
+        request_scopefunc=lambda: KEY,
+    )
+
+
+def _install_fake_app(monkeypatch, *, model_registry=None, install_registry=None, app_present=True):
+    if not app_present:
+        monkeypatch.setattr("galaxy.app.app", None)
+        return None
+    app = SimpleNamespace(
+        model=_mapping(model_registry if model_registry is not None else {}),
+        install_model=_mapping(install_registry if install_registry is not None else {}),
+    )
+    monkeypatch.setattr("galaxy.app.app", app)
+    return app
+
+
+async def _collect(send_messages):
+    async def send(message):
+        send_messages.append(message)
+
+    return send
+
+
+async def test_streaming_releases_session_before_first_chunk(monkeypatch):
+    session = FakeSession()
+    _install_fake_app(monkeypatch, model_registry={KEY: session})
+    observed = []
+
+    async def body():
+        observed.append(session.closed)  # state captured when the first chunk is produced
+        yield b"data"
+
+    response = GalaxyStreamingResponse(body())
+    messages: list = []
+    await response.stream_response(await _collect(messages))
+
+    assert observed == [True]
+    assert session.closed is True
+
+
+async def test_streaming_releases_both_model_and_install_sessions(monkeypatch):
+    model_session = FakeSession()
+    install_session = FakeSession()
+    _install_fake_app(monkeypatch, model_registry={KEY: model_session}, install_registry={KEY: install_session})
+
+    async def body():
+        yield b"x"
+
+    response = GalaxyStreamingResponse(body())
+    await response.stream_response(await _collect([]))
+
+    assert model_session.closed is True
+    assert install_session.closed is True
+
+
+async def test_streaming_no_session_does_not_lazy_create(monkeypatch):
+    model_registry: dict = {}
+    _install_fake_app(monkeypatch, model_registry=model_registry)
+
+    async def body():
+        yield b"x"
+
+    response = GalaxyStreamingResponse(body())
+    assert response._sessions_to_release == []
+
+    await response.stream_response(await _collect([]))
+
+    # We must never have touched the scoped proxy, which would have created one.
+    assert model_registry == {}
+
+
+async def test_streaming_no_app_bound_is_noop(monkeypatch):
+    _install_fake_app(monkeypatch, app_present=False)
+
+    async def body():
+        yield b"x"
+
+    response = GalaxyStreamingResponse(body())
+    assert response._sessions_to_release == []
+
+    messages: list = []
+    await response.stream_response(await _collect(messages))
+    assert any(m["type"] == "http.response.body" for m in messages)
+
+
+async def test_file_response_releases_before_response_start(monkeypatch, tmp_path):
+    f = tmp_path / "download.txt"
+    f.write_bytes(b"hello")
+    session = FakeSession()
+    _install_fake_app(monkeypatch, model_registry={KEY: session})
+
+    response = GalaxyFileResponse(str(f))
+    closed_at_start = []
+
+    async def send(message):
+        if message["type"] == "http.response.start":
+            closed_at_start.append(session.closed)
+
+    async def receive():
+        return {"type": "http.request"}
+
+    await response({"type": "http", "method": "GET", "headers": []}, receive, send)
+
+    assert closed_at_start == [True]
+    assert session.closed is True
+
+
+async def test_file_response_releases_on_xaccel_header_only_path(monkeypatch, tmp_path):
+    f = tmp_path / "download.txt"
+    f.write_bytes(b"hello")
+    session = FakeSession()
+    _install_fake_app(monkeypatch, model_registry={KEY: session})
+
+    class XAccelFileResponse(GalaxyFileResponse):
+        nginx_x_accel_redirect_base = "/internal"
+
+    response = XAccelFileResponse(str(f))
+    closed_at_start = []
+
+    async def send(message):
+        if message["type"] == "http.response.start":
+            closed_at_start.append(session.closed)
+
+    async def receive():
+        return {"type": "http.request"}
+
+    await response({"type": "http", "method": "GET", "headers": []}, receive, send)
+
+    assert closed_at_start == [True]
+    assert session.closed is True

From 9258da6bef3caf95f9a7191ad264655adf748a3f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 17 Jun 2026 12:13:25 +0200
Subject: [PATCH 206/256] Migrate legacy DatabaseVault secrets

Implement a transparent migration path for DatabaseVault secrets stored using the legacy leading-slash format.
---
 lib/galaxy/security/vault.py          | 14 ++++++++++++++
 test/unit/data/security/test_vault.py | 28 +++++++++++++++++++++++++++
 2 files changed, 42 insertions(+)

diff --git a/lib/galaxy/security/vault.py b/lib/galaxy/security/vault.py
index af481ef4743..34964bcd38d 100644
--- a/lib/galaxy/security/vault.py
+++ b/lib/galaxy/security/vault.py
@@ -221,6 +221,20 @@ class DatabaseVault(Vault):
         if key_obj and key_obj.value:
             f = self._get_multi_fernet()
             return f.decrypt(key_obj.value.encode("utf-8")).decode("utf-8")
+        # Galaxy <= 26.0 emitted a leading slash in vault keys, which was stored
+        # in the database. PR #22530 normalized keys to not have leading slashes.
+        # Fall back to reading the legacy form and rewrite under the canonical
+        # key so the secret survives the Galaxy upgrade. This fallback can be
+        # removed after a deprecation window once operators have migrated.
+        legacy_key_obj = self._get_vault_value(f"/{key}")
+        if legacy_key_obj and legacy_key_obj.value:
+            log.warning("Migrating legacy non-canonical DatabaseVault secret to canonical path: %s", key)
+            f = self._get_multi_fernet()
+            value = f.decrypt(legacy_key_obj.value.encode("utf-8")).decode("utf-8")
+            self.write_secret(key, value)
+            self.sa_session.delete(legacy_key_obj)
+            self.sa_session.flush()
+            return value
         return None
 
     def write_secret(self, key: str, value: str) -> None:
diff --git a/test/unit/data/security/test_vault.py b/test/unit/data/security/test_vault.py
index 26023fe01f6..c89880039f4 100644
--- a/test/unit/data/security/test_vault.py
+++ b/test/unit/data/security/test_vault.py
@@ -13,6 +13,7 @@ from galaxy.model.unittest_utils.data_app import (
 )
 from galaxy.security.vault import (
     _unwrap_vault,
+    DatabaseVault,
     HashicorpVault,
     InvalidVaultConfigException,
     InvalidVaultKeyException,
@@ -129,6 +130,33 @@ class TestDatabaseVault(AbstractTestCases.VaultTestBase):
         with self.assertRaises(InvalidToken):
             vault.read_secret("my/incorrect/secret")
 
+    def test_legacy_key_migration(self):
+        # Simulate a secret stored with a leading slash (pre-26.1 format)
+        config = GalaxyDataTestConfig(vault_config_file=VAULT_CONF_DATABASE)
+        app = GalaxyDataTestApp(config=config)
+        vault = VaultFactory.from_app(app)
+
+        # The vault chain is VaultKeyValidationWrapper(VaultKeyPrefixWrapper(DatabaseVault))
+        # The prefix is 'my_galaxy_instance' (from vault_conf_database.yml with leading slash stripped)
+        # Pre-26.1, VaultKeyPrefixWrapper emitted /{prefix}/{key}, so the DB stored keys like
+        # /my_galaxy_instance/my/legacy/secret. Write that directly to simulate the legacy state.
+        inner = _unwrap_vault(vault)
+        assert isinstance(inner, DatabaseVault)
+        inner.write_secret("/my_galaxy_instance/my/legacy/secret", "legacy value")
+
+        # Read with the new canonical format through the full wrapper chain
+        # VaultKeyValidationWrapper normalizes → VaultKeyPrefixWrapper adds prefix →
+        # DatabaseVault.read_secret("my_galaxy_instance/my/legacy/secret") should migrate
+        assert vault.read_secret("my/legacy/secret") == "legacy value"
+
+        # Verify the secret is now accessible with the canonical key
+        assert vault.read_secret("my/legacy/secret") == "legacy value"
+
+        # Verify the legacy key no longer exists (was migrated to canonical form)
+        assert inner._get_vault_value("/my_galaxy_instance/my/legacy/secret") is None
+        # Verify the canonical key now exists
+        assert inner._get_vault_value("my_galaxy_instance/my/legacy/secret") is not None
+
 
 def _make_mocked_hashicorp_vault() -> HashicorpVault:
     inner = HashicorpVault.__new__(HashicorpVault)

From 7cff63968de967e0d93944b983134a5244d50408 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 17 Jun 2026 12:03:06 +0200
Subject: [PATCH 207/256] Resolve url_default data inputs at dereference, not
 in the persisted request

The new job-submission path filled url_default data inputs into request_internal
state before persisting the ToolRequest. request_internal is the representation
where absent inputs stay absent (defaults resolve at job_internal); baking the
default in mis-records the request as declaring inputs that were never requested.

Move url_default resolution to the dereference stage: dereference now injects the
deferred DataRequestUri for absent url_default data params on a transient copy
(recursing into sections/conditionals/repeats only when they contain a url_default),
so URLs still materialize into datasets without the persisted request carrying them.
The request models already express the needed 'present-or-absent, never null'
semantics via requires_value=False plus the not_null validator, so no model change
is required. Drop the now-dead url_data_defaults plumbing from fill_static_defaults.

Repoints the url_default dereference unit tests off the default-fill helper and adds
coverage that request_internal records the absent input as absent.
---
 lib/galaxy/tool_util/parameters/convert.py    | 92 ++++++++++++++-----
 lib/galaxy/webapps/galaxy/services/jobs.py    | 14 +--
 test/unit/tool_util/test_parameter_convert.py | 39 ++++++--
 3 files changed, 104 insertions(+), 41 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/convert.py b/lib/galaxy/tool_util/parameters/convert.py
index 7fe04aa4b61..f91705ff25b 100644
--- a/lib/galaxy/tool_util/parameters/convert.py
+++ b/lib/galaxy/tool_util/parameters/convert.py
@@ -223,6 +223,11 @@ def strictify(relaxed_state: RelaxedRequestToolState, input_models: ToolParamete
     return request_state
 
 
+def _deferred_url_default_request(url: str) -> Dict[str, Any]:
+    """Build the deferred dataset request used to materialize a data param's url_default."""
+    return DataRequestUri(url=url, ext="auto", deferred=True).model_dump()
+
+
 def dereference(
     internal_state: RequestInternalToolState,
     input_models: ToolParameterBundle,
@@ -250,9 +255,7 @@ def dereference(
         if isinstance(parameter, DataParameterModel):
             if value is None:
                 if parameter.url_default:
-                    return dereference_dict(
-                        DataRequestUri(url=parameter.url_default, ext="auto", deferred=True).model_dump()
-                    )
+                    return dereference_dict(_deferred_url_default_request(parameter.url_default))
                 return VISITOR_NO_REPLACEMENT
             if parameter.multiple and isinstance(value, list):
                 return list(map(dereference_dict, value))
@@ -267,9 +270,15 @@ def dereference(
         else:
             return VISITOR_NO_REPLACEMENT
 
+    # Materialize url_default data inputs that were legitimately absent from the
+    # request_internal state. We do this on a copy so the persisted request keeps
+    # recording absent inputs as absent - the deferred URLs only need to exist from
+    # the dereference stage onwards (where URLs become datasets), not in the request.
+    state_with_url_defaults = deepcopy(internal_state.input_state)
+    _fill_url_defaults(state_with_url_defaults, input_models)
     request_state_dict = visit_input_values(
         input_models,
-        internal_state,
+        RequestInternalToolState(state_with_url_defaults),
         dereference_callback,
     )
     request_state = RequestInternalDereferencedToolState(request_state_dict)
@@ -296,7 +305,7 @@ def encode_test(
                     test_dataset = cast(JsonTestDatasetDefDict, value)
                     return adapt_datasets(test_dataset).model_dump()
             elif parameter.url_default:
-                return DataRequestUri(url=parameter.url_default, ext="auto", deferred=True).model_dump()
+                return _deferred_url_default_request(parameter.url_default)
         elif isinstance(parameter, DataCollectionParameterModel):
             if value is not None:
                 assert isinstance(value, dict), str(value)
@@ -335,13 +344,12 @@ def fill_static_defaults(
     input_models: ToolParameterBundle,
     profile: float,
     partial: bool = True,
-    url_data_defaults: bool = False,
 ) -> Dict[str, Any]:
     """If additional defaults might stem from Galaxy runtime, partial should be true.
 
     Setting partial to True, prevents runtime validation.
     """
-    _fill_defaults(tool_state, input_models, url_data_defaults=url_data_defaults)
+    _fill_defaults(tool_state, input_models)
 
     if not partial:
         internal_state = JobInternalToolState(tool_state)
@@ -349,14 +357,12 @@ def fill_static_defaults(
     return tool_state
 
 
-def _fill_defaults(
-    tool_state: Dict[str, Any], input_models: ToolParameterBundle, url_data_defaults: bool = False
-) -> None:
+def _fill_defaults(tool_state: Dict[str, Any], input_models: ToolParameterBundle) -> None:
     for parameter in input_models.parameters:
-        _fill_default_for(tool_state, parameter, url_data_defaults=url_data_defaults)
+        _fill_default_for(tool_state, parameter)
 
 
-def _fill_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT, url_data_defaults: bool = False) -> None:
+def _fill_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT) -> None:
     parameter_name = parameter.name
     if isinstance(parameter, BooleanParameterModel):
         if parameter_name not in tool_state:
@@ -402,24 +408,19 @@ def _fill_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT, url
         )
         test_value = validate_explicit_conditional_test_value(test_parameter_name, explicit_test_value)
         when = _select_which_when(parameter, test_value, conditional_state)
-        _fill_default_for(conditional_state, test_parameter, url_data_defaults=url_data_defaults)
-        _fill_defaults(conditional_state, when, url_data_defaults=url_data_defaults)
+        _fill_default_for(conditional_state, test_parameter)
+        _fill_defaults(conditional_state, when)
     elif isinstance(parameter, RepeatParameterModel):
         repeat_instances = _initialize_repeat_state(parameter, tool_state)
         for instance_state in repeat_instances:
-            _fill_defaults(instance_state, parameter, url_data_defaults=url_data_defaults)
+            _fill_defaults(instance_state, parameter)
     elif isinstance(parameter, SectionParameterModel):
         section_state = _initialize_section_state(parameter, tool_state)
-        _fill_defaults(section_state, parameter, url_data_defaults=url_data_defaults)
+        _fill_defaults(section_state, parameter)
     elif isinstance(parameter, DataCollectionParameterModel):
         collection_parameter = parameter
         if parameter_name not in tool_state and collection_parameter.optional:
             tool_state[parameter_name] = None
-    elif isinstance(parameter, DataParameterModel):
-        if url_data_defaults and parameter_name not in tool_state and parameter.url_default:
-            tool_state[parameter_name] = DataRequestUri(
-                url=parameter.url_default, ext="auto", deferred=True
-            ).model_dump()
     elif isinstance(parameter, TextParameterModel):
         if parameter_name not in tool_state:
             if not parameter.optional:
@@ -435,6 +436,55 @@ def _fill_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT, url
                 tool_state[parameter_name] = parameter.default_value if parameter.default_value is not None else ""
 
 
+def _fill_url_defaults(tool_state: Dict[str, Any], input_models: ToolParameterBundle) -> None:
+    for parameter in input_models.parameters:
+        _fill_url_default_for(tool_state, parameter)
+
+
+def _fill_url_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT) -> None:
+    """Inject deferred ``url_default`` data requests for absent data parameters.
+
+    Unlike :func:`_fill_default_for` this materializes *only* ``url_default`` data
+    inputs and deliberately leaves every other static default absent - those belong to
+    later stages. It runs on a transient copy during :func:`dereference` so the URLs
+    resolve to datasets at the right stage without the persisted request_internal state
+    recording inputs that were never part of the request. Containers are only descended
+    into (and so only created in the copy) when they actually contain a url_default.
+    """
+    parameter_name = parameter.name
+    if isinstance(parameter, DataParameterModel):
+        if parameter_name not in tool_state and parameter.url_default:
+            tool_state[parameter_name] = _deferred_url_default_request(parameter.url_default)
+    elif isinstance(parameter, ConditionalParameterModel):
+        raw_state = tool_state.get(parameter_name)
+        conditional_seed = raw_state if isinstance(raw_state, dict) else {}
+        test_parameter_name = parameter.test_parameter.name
+        explicit_test_value: Optional[DiscriminatorType] = conditional_seed.get(test_parameter_name)
+        test_value = validate_explicit_conditional_test_value(test_parameter_name, explicit_test_value)
+        when = _select_which_when(parameter, test_value, conditional_seed)
+        if not _parameters_have_url_default(when.parameters):
+            return
+        conditional_state = _initialize_conditional_state(parameter, tool_state)
+        _fill_url_defaults(conditional_state, when)
+    elif isinstance(parameter, RepeatParameterModel):
+        if not _parameters_have_url_default(parameter.parameters):
+            return
+        for instance_state in _initialize_repeat_state(parameter, tool_state):
+            _fill_url_defaults(instance_state, parameter)
+    elif isinstance(parameter, SectionParameterModel):
+        if not _parameters_have_url_default(parameter.parameters):
+            return
+        section_state = _initialize_section_state(parameter, tool_state)
+        _fill_url_defaults(section_state, parameter)
+
+
+def _parameters_have_url_default(parameters: Sequence[ToolParameterT]) -> bool:
+    return any(
+        isinstance(parameter, DataParameterModel) and bool(parameter.url_default)
+        for parameter in iter_parameter_models(parameters)
+    )
+
+
 def _initialize_section_state(parameter: SectionParameterModel, tool_state: Dict[str, Any]) -> Dict[str, Any]:
     parameter_name = parameter.name
     if parameter_name not in tool_state:
diff --git a/lib/galaxy/webapps/galaxy/services/jobs.py b/lib/galaxy/webapps/galaxy/services/jobs.py
index ffb097f8180..e91d5090015 100644
--- a/lib/galaxy/webapps/galaxy/services/jobs.py
+++ b/lib/galaxy/webapps/galaxy/services/jobs.py
@@ -55,7 +55,6 @@ from galaxy.schema.tasks import (
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.tool_util.parameters import (
     decode,
-    fill_static_defaults,
     RelaxedRequestToolState,
     RequestToolState,
     strictify,
@@ -263,16 +262,9 @@ class JobsService(ServiceBase):
             request_state = RequestToolState(inputs or {})
         request_state.validate(parameter_bundle, f"{tool.id} (request model)")
         request_internal_state = decode(request_state, parameter_bundle, trans.security.decode_id)
-        # Fill url_default values and re-validate before persisting the ToolRequest.
-        # The execution path handles general defaults, but the internal state must be
-        # fully resolved here so the persisted request is self-contained.
-        fill_static_defaults(
-            request_internal_state.input_state,
-            parameter_bundle,
-            tool.profile,
-            partial=True,
-            url_data_defaults=True,
-        )
+        # request_internal is the representation where absent inputs stay absent - defaults
+        # (including url_default data inputs) are resolved later, at dereference/job_internal
+        # time. Do not fill them here or we would record inputs that were never requested.
         request_internal_state.validate(parameter_bundle, f"{tool.id} (request internal model)")
         tool_request = ToolRequest()
         # TODO: hash and such...
diff --git a/test/unit/tool_util/test_parameter_convert.py b/test/unit/tool_util/test_parameter_convert.py
index c913ef23311..b03af16061a 100644
--- a/test/unit/tool_util/test_parameter_convert.py
+++ b/test/unit/tool_util/test_parameter_convert.py
@@ -188,7 +188,7 @@ def test_dereference():
     dereferenced_state.validate(bundle)
 
 
-def test_dereference_url_default_after_default_fill():
+def test_dereference_resolves_url_default():
     bundle = ToolParameterBundleModel(
         parameters=[
             DataParameterModel(
@@ -199,12 +199,33 @@ def test_dereference_url_default_after_default_fill():
         ]
     )
 
-    dereferenced_state = _strict_async_decode_default_fill_and_dereference({}, bundle)
+    # The data input is absent from the request - dereference materializes the url_default.
+    dereferenced_state = _strict_async_decode_and_dereference({}, bundle)
 
     assert dereferenced_state.input_state == {"parameter": {"src": "hda", "id": EXAMPLE_ID_1}}
 
 
-def test_dereference_section_url_default_after_default_fill():
+def test_request_internal_records_absent_url_default():
+    bundle = ToolParameterBundleModel(
+        parameters=[
+            DataParameterModel(
+                type="data",
+                name="parameter",
+                url_default="https://example.com/1.bed",
+            )
+        ]
+    )
+
+    # The persisted request_internal state must record the absent input as absent - the
+    # url_default is only resolved later, at dereference time (above), never baked in here.
+    request_state = RequestToolState({})
+    request_state.validate(bundle)
+    request_internal_state = decode(request_state, bundle, _fake_decode)
+    request_internal_state.validate(bundle)
+    assert "parameter" not in request_internal_state.input_state
+
+
+def test_dereference_section_url_default():
     bundle = ToolParameterBundleModel(
         parameters=[
             SectionParameterModel(
@@ -221,14 +242,14 @@ def test_dereference_section_url_default_after_default_fill():
         ]
     )
 
-    dereferenced_state = _strict_async_decode_default_fill_and_dereference({}, bundle)
+    dereferenced_state = _strict_async_decode_and_dereference({}, bundle)
 
     assert dereferenced_state.input_state == {
         "section_parameter": {"data_parameter": {"src": "hda", "id": EXAMPLE_ID_1}}
     }
 
 
-def test_dereference_conditional_url_default_after_default_fill():
+def test_dereference_conditional_url_default():
     bundle = ToolParameterBundleModel(
         parameters=[
             ConditionalParameterModel(
@@ -253,11 +274,12 @@ def test_dereference_conditional_url_default_after_default_fill():
         ]
     )
 
-    dereferenced_state = _strict_async_decode_default_fill_and_dereference({}, bundle)
+    dereferenced_state = _strict_async_decode_and_dereference({}, bundle)
 
+    # The conditional's default (absent) when is selected and its url_default data input is
+    # materialized; the boolean discriminator is not a url default so it stays unfilled here.
     assert dereferenced_state.input_state == {
         "conditional_parameter": {
-            "test_parameter": False,
             "data_parameter": {"src": "hda", "id": EXAMPLE_ID_1},
         }
     }
@@ -391,13 +413,12 @@ def _fake_encode(input: int) -> str:
     return ID_MAP[input]
 
 
-def _strict_async_decode_default_fill_and_dereference(
+def _strict_async_decode_and_dereference(
     tool_state: Dict[str, Any], bundle: ToolParameterBundleModel
 ) -> RequestInternalDereferencedToolState:
     request_state = RequestToolState(tool_state)
     request_state.validate(bundle)
     request_internal_state = decode(request_state, bundle, _fake_decode)
-    fill_static_defaults(request_internal_state.input_state, bundle, 24.0, partial=True, url_data_defaults=True)
     return dereference(request_internal_state, bundle, _fake_dereference, _fake_collection_deference)
 
 

From 2649f64a9f7a9c54230dcc46f09beca4be789bd6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 17 Jun 2026 12:22:49 +0200
Subject: [PATCH 208/256] Make _fake_dereference URL-keyed so url_default tests
 pin the resolved URL

The fake returned a constant HDA id regardless of input, so the dereference tests
proved a url_default got materialized at the right structural position but not that
the *configured* URL reached the dereference boundary. Key the fake on the request
URL via URL_ID_MAP; the existing id assertions now also pin which URL was resolved,
and an unexpected/empty URL fails loudly with KeyError.
---
 test/unit/tool_util/test_parameter_convert.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/test/unit/tool_util/test_parameter_convert.py b/test/unit/tool_util/test_parameter_convert.py
index b03af16061a..26e4a5b6cb4 100644
--- a/test/unit/tool_util/test_parameter_convert.py
+++ b/test/unit/tool_util/test_parameter_convert.py
@@ -397,8 +397,18 @@ def strictify_for(tool_state: Dict[str, Any], tool_path: str) -> Dict[str, Any]:
     return strictify(relaxed_state, bundle).input_state
 
 
+# Maps each url-src / url_default fixture URL to the HDA id a real dereference would mint.
+# Keying on the URL (rather than returning a constant) makes the dereference tests assert the
+# *configured* URL actually reached the dereference boundary - an unexpected/empty URL raises
+# KeyError instead of silently passing.
+URL_ID_MAP: Dict[str, int] = {
+    "https://example.com/1.bed": EXAMPLE_ID_1,
+    "gxfiles://mystorage/1.bed": EXAMPLE_ID_2,
+}
+
+
 def _fake_dereference(input: DataRequestUri) -> DataRequestInternalHda:
-    return DataRequestInternalHda(id=EXAMPLE_ID_1, src="hda")
+    return DataRequestInternalHda(id=URL_ID_MAP[input.url], src="hda")
 
 
 def _fake_collection_deference(input: DataRequestCollectionUri) -> DataRequestInternalHdca:

From 13acce10bace2cd7df8bd3d0416cf01ac1f069b5 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 17 Jun 2026 12:57:29 +0200
Subject: [PATCH 209/256] Fix GModal content truncation when dialog has no
 fixed height

Without an explicit height on the dialog, `section { height: 100% }` resolved
to auto and `.g-modal-content`'s `overflow: auto` never activated, so the
dialog clipped instead of scrolling. Cap the dialog at `max-height: calc(100vh
- 4rem)` and move `section { height: 100% }` to only apply inside
`.g-fixed-height` and `.g-fullscreen`, where the dialog has an explicit pixel
height that makes the percentage meaningful.
---
 client/src/components/BaseComponents/GModal.vue | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/client/src/components/BaseComponents/GModal.vue b/client/src/components/BaseComponents/GModal.vue
index db4878d11c5..91bb6ed39c0 100644
--- a/client/src/components/BaseComponents/GModal.vue
+++ b/client/src/components/BaseComponents/GModal.vue
@@ -239,8 +239,9 @@ defineExpose({ showModal, hideModal });
 
     padding: var(--spacing-3);
 
+    max-height: calc(100vh - 4rem);
+
     section {
-        height: 100%;
         width: 100%;
         display: flex;
         flex-direction: column;
@@ -253,12 +254,17 @@ defineExpose({ showModal, hideModal });
             padding: var(--spacing-2);
             margin: calc(var(--spacing-2) * -1);
 
-            max-height: 100%;
             display: flex;
             flex-direction: column;
         }
     }
 
+    &.g-fixed-height {
+        section {
+            height: 100%;
+        }
+    }
+
     &.g-overflow-visible {
         overflow: visible;
 
@@ -306,6 +312,10 @@ defineExpose({ showModal, hideModal });
         height: calc(100vh - 6rem);
         max-width: calc(100vw - 6rem);
         max-height: calc(100vh - 6rem);
+
+        section {
+            height: 100%;
+        }
     }
 
     header {

From 62df3eb78367f20bd477fdae62f6d6c18aeea5b9 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 17 Jun 2026 12:57:36 +0200
Subject: [PATCH 210/256] Fix dev proxy so cookies work when proxying remote
 HTTPS Galaxy servers
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Without changeOrigin the upstream saw Host: localhost:5173 and could behave
unexpectedly. More importantly, cookies from HTTPS upstreams carry Secure and
SameSite=None, which browsers silently drop over http://localhost, so
galaxysession was never stored and /context returned session_csrf_token: null.

Strip Secure and rewrite SameSite=None → Lax in the proxyRes handler, remove
the domain attribute via cookieDomainRewrite, and enable changeOrigin and
secure:false unconditionally for the dev proxy.
---
 client/vite.config.mjs | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/client/vite.config.mjs b/client/vite.config.mjs
index 9620700ba7a..1c0cd1dd0b8 100644
--- a/client/vite.config.mjs
+++ b/client/vite.config.mjs
@@ -160,8 +160,23 @@ export default defineConfig(({ command }) => ({
             // Proxy everything except Vite's own routes to Galaxy backend
             "^/(?!(@|src/|node_modules/|__vite))": {
                 target: process.env.GALAXY_URL || "http://127.0.0.1:8080",
-                changeOrigin: !!process.env.CHANGE_ORIGIN,
-                secure: process.env.CHANGE_ORIGIN ? false : true,
+                changeOrigin: true,
+                secure: false,
+                cookieDomainRewrite: "",
+                configure: (proxy) => {
+                    // Strip Secure flag and fix SameSite from upstream HTTPS cookies so
+                    // they are accepted by the browser on http://localhost.
+                    proxy.on("proxyRes", (proxyRes) => {
+                        const cookies = proxyRes.headers["set-cookie"];
+                        if (cookies) {
+                            proxyRes.headers["set-cookie"] = cookies.map((cookie) =>
+                                cookie
+                                    .replace(/;\s*Secure/gi, "")
+                                    .replace(/;\s*SameSite=None/gi, "; SameSite=Lax")
+                            );
+                        }
+                    });
+                },
             },
         },
         cors: true,

From 7b88a346dc4b030c631563b6103d508e63e34ec4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 17 Jun 2026 13:04:17 +0200
Subject: [PATCH 211/256] Apply prettier formatting to vite.config.mjs

---
 client/vite.config.mjs | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/client/vite.config.mjs b/client/vite.config.mjs
index 1c0cd1dd0b8..f859c58bc63 100644
--- a/client/vite.config.mjs
+++ b/client/vite.config.mjs
@@ -170,9 +170,7 @@ export default defineConfig(({ command }) => ({
                         const cookies = proxyRes.headers["set-cookie"];
                         if (cookies) {
                             proxyRes.headers["set-cookie"] = cookies.map((cookie) =>
-                                cookie
-                                    .replace(/;\s*Secure/gi, "")
-                                    .replace(/;\s*SameSite=None/gi, "; SameSite=Lax")
+                                cookie.replace(/;\s*Secure/gi, "").replace(/;\s*SameSite=None/gi, "; SameSite=Lax"),
                             );
                         }
                     });

From c37217956f9907537ad5f7fca1210a682c76dd9f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 12 Jun 2026 11:21:11 -0400
Subject: [PATCH 212/256] Add failing test for router dropping interface
 context

The router answers tool-usage questions directly instead of handing off,
but its process() override sends the raw query to the model without
running _prepare_prompt, so the active interface context (the tool the
user is viewing) never reaches the model. Asking "how do I use this
tool?" with Random Lines in context gets back "what tool?". This test
pins the expected behavior and fails against the current code.
---
 test/unit/app/test_agents.py | 49 ++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/test/unit/app/test_agents.py b/test/unit/app/test_agents.py
index 8d918632e89..8336d12199b 100644
--- a/test/unit/app/test_agents.py
+++ b/test/unit/app/test_agents.py
@@ -592,6 +592,55 @@ class TestAgentUnitMocked:
             assert kwargs["message_history"] is None
             assert args[0] == "Tell me more about the second one"
 
+    @pytest.mark.asyncio
+    async def test_router_injects_interface_context_into_prompt(self):
+        """The router must fold the active interface context (e.g. the tool the user is
+        viewing) into the prompt it sends to the model. Without this, "how do I use this
+        tool?" reaches the model with no referent and it answers "what tool?" even though
+        the UI shows the context. Specialists get this via _prepare_prompt; the router has
+        to do the same for the queries it answers directly rather than handing off."""
+        router = QueryRouterAgent(self.deps)
+
+        with mock.patch.object(router, "_run_with_retry") as mock_run:
+            mock_result = mock.Mock(spec=["output"])
+            mock_result.output = "Here is how to use Random Lines."
+            mock_run.return_value = mock_result
+
+            await router.process(
+                "how do I use this tool?",
+                context={
+                    "interface_context": {
+                        "contextType": "tool",
+                        "toolName": "Random Lines",
+                        "toolId": "random_lines1",
+                    }
+                },
+            )
+
+            mock_run.assert_called_once()
+            prompt = mock_run.call_args[0][0]
+            assert "Random Lines" in prompt
+            assert "how do I use this tool?" in prompt
+
+    @pytest.mark.asyncio
+    async def test_router_does_not_leak_routing_flags_into_prompt(self):
+        """Routing-only bookkeeping (responding_to_clarification) is for the router's own
+        logic, not the model -- it must never surface in the prompt text."""
+        router = QueryRouterAgent(self.deps)
+
+        with mock.patch.object(router, "_run_with_retry") as mock_run:
+            mock_result = mock.Mock(spec=["output"])
+            mock_result.output = "Routed."
+            mock_run.return_value = mock_result
+
+            await router.process(
+                "the second one",
+                context={"responding_to_clarification": True},
+            )
+
+            prompt = mock_run.call_args[0][0]
+            assert "responding_to_clarification" not in prompt
+
     @pytest.mark.asyncio
     async def test_router_asks_for_clarification(self):
         """When the model calls ask_for_clarification, the router surfaces it as a

From 7266a641669845e3907166cd6557df2ffbf7ab42 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 12 Jun 2026 11:22:11 -0400
Subject: [PATCH 213/256] Inject interface context into router's direct-answer
 prompt

The router's process() override sent the raw query straight to the model,
skipping the _prepare_prompt step every specialist runs via the base
class. So when the router answers a question directly (which is exactly
what it does for tool-usage help), the active interface context never
reached the model -- ask "how do I use this tool?" with Random Lines in
context and you'd get back "what tool?". Build the prompt the same way
the base class does, stripping history since that rides the separate
message_history channel. Also mark responding_to_clarification internal
so that routing-only flag doesn't leak into the prompt text.
---
 lib/galaxy/agents/base.py   | 2 +-
 lib/galaxy/agents/router.py | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/agents/base.py b/lib/galaxy/agents/base.py
index d69d02b6996..8bf50e3bd1d 100644
--- a/lib/galaxy/agents/base.py
+++ b/lib/galaxy/agents/base.py
@@ -372,7 +372,7 @@ class BaseGalaxyAgent(ABC):
 
     agent_type: str
     agent: Agent[GalaxyAgentDependencies, Any]
-    _INTERNAL_CONTEXT_KEYS = frozenset({"run_state"})
+    _INTERNAL_CONTEXT_KEYS = frozenset({"run_state", "responding_to_clarification"})
 
     # Fallback when no max_tokens is configured. 8k leaves headroom on every
     # backend we currently support (smallest is Qwen3-32B at 32k context).
diff --git a/lib/galaxy/agents/router.py b/lib/galaxy/agents/router.py
index 7f4756e08ab..b6c252e4482 100644
--- a/lib/galaxy/agents/router.py
+++ b/lib/galaxy/agents/router.py
@@ -546,7 +546,11 @@ class QueryRouterAgent(BaseGalaxyAgent):
             previous_handoff_context = self._handoff_context
             self._handoff_context = context.copy() if context else {}
             try:
-                result = await self._run_with_retry(query, message_history=message_history)
+                # Fold the active interface context (the tool/dataset/etc. the user is
+                # viewing) into the prompt for queries the router answers directly --
+                # history rides the separate message_history channel, so strip it here.
+                prompt = self._prepare_prompt(query, self._strip_history_from_context(context or {}))
+                result = await self._run_with_retry(prompt, message_history=message_history)
             finally:
                 self._handoff_context = previous_handoff_context
             content = extract_result_content(result)

From 379b7810f55d4f675df0be415244ca0b13c42aab Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 12 Jun 2026 12:56:57 -0400
Subject: [PATCH 214/256] Tell the router how to use the active interface
 context

Now that the interface context reaches the router's prompt, the system
prompt should explain it. Add a short section telling the router to treat
the [Active interface context: ...] line as the referent for "this tool"
/ "this dataset" style phrases, but to let the user's actual message
decide the route -- "my job failed" on a tool form is still error
analysis, not usage help.
---
 lib/galaxy/agents/prompts/router.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/lib/galaxy/agents/prompts/router.md b/lib/galaxy/agents/prompts/router.md
index 8e46a28dce6..6a75c55a800 100644
--- a/lib/galaxy/agents/prompts/router.md
+++ b/lib/galaxy/agents/prompts/router.md
@@ -27,6 +27,12 @@ For off-topic questions (general coding, non-scientific topics, unrelated softwa
 
 Users can @mention specific datasets or histories in their messages. When entity references are present, they appear as structured context (e.g. "Referenced entities: Dataset #42 'Mapped reads' (bam, ok)"). Use this information to ground your answers -- refer to the specific dataset names, types, and states rather than asking the user to clarify which data they mean.
 
+## Active Interface Context
+
+The UI tells you what the user is currently looking at via a leading "[Active interface context: ...]" line (e.g. the tool form they have open, a dataset, a workflow, or a job). Treat it as the referent for deictic phrases -- "this tool", "this dataset", "it", "here" -- so "how do I use this tool?" while viewing the Random Lines form is a usage question about Random Lines, not a reason to ask which tool they mean.
+
+It is context, not a command. The user's actual message still decides the route: "my job failed" while a tool form is open is still error analysis, not tool-usage help. When the message names its own subject explicitly, that wins over the interface context.
+
 ## How to Respond
 
 You have access to specialist agents that you can route queries to. Choose the appropriate response:

From 0c029a7d5757478b64249e9246d40b1fe01f69f6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 17 Jun 2026 14:09:47 +0200
Subject: [PATCH 215/256] Tighten AI-narration comments into contracts on the
 functions they describe

Rewrite fill_static_defaults' docstring to assert it fills a job_internal
state (request/request_internal record absent inputs as absent); thin the
jobs.py call-site comment to point at it. Move the loose-match prose in
_input_name_was_handled_by_legacy_fallback into a docstring and collapse the
sync-path / algorithm narration in case.py to one factual clause each.

No behavior change.
---
 lib/galaxy/tool_util/parameters/case.py    | 51 +++++++++-------------
 lib/galaxy/tool_util/parameters/convert.py |  6 ++-
 lib/galaxy/webapps/galaxy/services/jobs.py |  5 +--
 3 files changed, 26 insertions(+), 36 deletions(-)

diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
index 394c60eafab..1d4de4225a0 100644
--- a/lib/galaxy/tool_util/parameters/case.py
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -131,10 +131,8 @@ def legacy_from_string(parameter: ToolParameterT, value: Optional[Any], warnings
                     result_value = asbool(value)
                 except ValueError:
                     if Version(profile) < Version("24.2"):
-                        # Legacy tools sometimes use a non-boolean placeholder such as
-                        # "-" as a test value. The synchronous tool API coerces these
-                        # via string_as_bool (any non-true value -> False); match that
-                        # so the payload is a valid boolean without requiring test edits.
+                        # Coerce a legacy non-boolean placeholder (e.g. "-") via string_as_bool
+                        # (any non-true value -> False), matching the synchronous tool API.
                         result_value = string_as_bool(value)
                         warnings.append(
                             f"Non-boolean test value ({value!r}) for {parameter.name} coerced to "
@@ -227,10 +225,8 @@ class LegacyTestInputResolver:
         return replace(self, inputs=inputs)
 
     def input_for(self, flat_state_path: str) -> Optional[ToolSourceTestInput]:
-        # A consumed discriminator belongs to an enclosing conditional and must not be
-        # re-matched by the loose fallbacks below when resolving a descendant's discriminator
-        # (otherwise e.g. an omitted nested ``selector`` greedily picks up the parent
-        # conditional's ``selector`` value - see ``_select_which_when``).
+        # Discriminators consumed by enclosing conditionals are excluded from the loose fallbacks
+        # below, so a descendant's omitted discriminator does not re-match an ancestor's.
         exclude = self.consumed_discriminators
         for input in self.inputs:
             if input["name"] == flat_state_path:
@@ -342,7 +338,12 @@ def test_case_state(
 
 
 def _input_name_was_handled_by_legacy_fallback(input_name: str, handled_inputs: Set[str], profile: str) -> bool:
-    # Intentionally a loose string-match against every visited parameter path, NOT a record of which inputs were actually consumed: the raw-name->path relation is many-to-many for legacy tests (bare/duplicate names validly satisfy multiple params), so consumption-tracking wrongly rejects degenerate-but-valid cases - tried and reverted, don't reintroduce it.
+    """True if a pre-24.2 legacy fallback already covered input_name (loose suffix-match).
+
+    The match is deliberately loose - against every visited path, not consumed inputs - because
+    the raw-name->path relation is many-to-many for legacy tests (bare/duplicate names validly
+    satisfy multiple params). Only applies below profile 24.2.
+    """
     if Version(profile) >= Version("24.2"):
         return False
     for handled_input in handled_inputs:
@@ -415,17 +416,12 @@ def _merge_into_state(
         when, discriminator_name = _select_which_when(tool_input, conditional_state, context, state_path)
         test_parameter = tool_input.test_parameter
         handled_inputs.update(_merge_into_state(test_parameter, context, conditional_state, state_path))
-        # If the discriminator was omitted, record the selected when's discriminator so the
-        # state validates against that branch rather than the phantom __absent__ branch. This
-        # is the active branch _select_which_when chose: a non-default when inferred from the
-        # provided params, or - for a legacy conditional with no explicit selected="true" - the
-        # default (first) option, mirroring how the synchronous runtime fills an incomplete
-        # payload.
+        # If the discriminator was omitted, record the when _select_which_when chose so the state
+        # validates against that branch rather than the phantom __absent__ branch.
         if test_parameter.name not in conditional_state and when.discriminator is not None:
             conditional_state[test_parameter.name] = when.discriminator
-        # The discriminator consumed here belongs to this conditional; the branch context marks
-        # it so the loose fallbacks do not re-match it when resolving a nested conditional's
-        # discriminator.
+        # Mark this conditional's discriminator consumed so a nested conditional's loose fallbacks
+        # do not re-match it.
         handled_inputs.update(
             _merge_level_into_state(
                 when.parameters, context.consuming(discriminator_name), conditional_state, state_path
@@ -515,15 +511,10 @@ def _repeat_inputs_to_array(
     inputs_as_dict = _inputs_as_dict(inputs)
     repeat_instance_input_dicts = repeat_inputs_to_array(state_path, inputs_as_dict)
     if not repeat_instance_input_dicts and "|" in state_path:
-        # Legacy test cases may reference a repeat that lives inside a conditional or
-        # section by its unqualified name (e.g. <repeat name="rep"> at the top level
-        # instead of wrapped in the enclosing <conditional>). The test inputs are
-        # unqualified with respect to conditionals/sections but still carry repeat
-        # instance indices, so progressively strip leading (conditional/section)
-        # segments - keeping any enclosing repeat-instance prefix - until the repeat's
-        # nested params resolve. The downstream input_for() suffix match then
-        # re-attaches them to the fully qualified path. Longest candidate is tried
-        # first to avoid matching an unrelated like-named repeat.
+        # A legacy test may name a repeat inside a conditional/section by its unqualified name.
+        # Progressively strip leading conditional/section segments (longest candidate first, to
+        # avoid an unrelated like-named repeat) until the repeat's params resolve; input_for()'s
+        # suffix match re-attaches them to the qualified path.
         parts = state_path.split("|")
         for start in range(1, len(parts)):
             candidate_path = "|".join(parts[start:])
@@ -568,10 +559,8 @@ def _select_which_when(
         explicit_test_value = asbool(explicit_test_value)
     test_value = validate_explicit_conditional_test_value(test_parameter_name, explicit_test_value)
     if test_value is None:
-        # The discriminator was omitted. Like the synchronous tool API, infer the active
-        # when from the parameters the test actually provides before falling back to the
-        # default when (otherwise a test that supplies a non-default branch's params fails
-        # to validate against the default branch).
+        # Discriminator omitted: infer the active when from the params the test provides (like
+        # the synchronous tool API) before falling back to the default when.
         inferred_when = _infer_when_from_inputs(conditional, context.inputs, prefix)
         if inferred_when is not None:
             return inferred_when, matched_name
diff --git a/lib/galaxy/tool_util/parameters/convert.py b/lib/galaxy/tool_util/parameters/convert.py
index f91705ff25b..8d70a2bd85d 100644
--- a/lib/galaxy/tool_util/parameters/convert.py
+++ b/lib/galaxy/tool_util/parameters/convert.py
@@ -345,9 +345,11 @@ def fill_static_defaults(
     profile: float,
     partial: bool = True,
 ) -> Dict[str, Any]:
-    """If additional defaults might stem from Galaxy runtime, partial should be true.
+    """Fill static defaults into a job_internal tool state; pass only that representation.
 
-    Setting partial to True, prevents runtime validation.
+    Request/request_internal states record absent inputs as absent - filling them here would
+    declare inputs that were never requested. Pass partial=True when further defaults may stem
+    from Galaxy runtime; partial=True skips final runtime validation.
     """
     _fill_defaults(tool_state, input_models)
 
diff --git a/lib/galaxy/webapps/galaxy/services/jobs.py b/lib/galaxy/webapps/galaxy/services/jobs.py
index e91d5090015..45bd952ab9d 100644
--- a/lib/galaxy/webapps/galaxy/services/jobs.py
+++ b/lib/galaxy/webapps/galaxy/services/jobs.py
@@ -262,9 +262,8 @@ class JobsService(ServiceBase):
             request_state = RequestToolState(inputs or {})
         request_state.validate(parameter_bundle, f"{tool.id} (request model)")
         request_internal_state = decode(request_state, parameter_bundle, trans.security.decode_id)
-        # request_internal is the representation where absent inputs stay absent - defaults
-        # (including url_default data inputs) are resolved later, at dereference/job_internal
-        # time. Do not fill them here or we would record inputs that were never requested.
+        # request_internal records absent inputs as absent; static defaults (incl. url_default
+        # data inputs) are filled later, at dereference/job_internal time (see fill_static_defaults).
         request_internal_state.validate(parameter_bundle, f"{tool.id} (request internal model)")
         tool_request = ToolRequest()
         # TODO: hash and such...

From 91e8ad7e5ae956b9deb31bf3e04c6eee0058f013 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 17 Jun 2026 12:54:26 +0200
Subject: [PATCH 216/256] Keep DatabaseVault on legacy leading-slash key
 location

PR #22530 stripped the leading slash in the shared VaultKeyPrefixWrapper to
fix a HashicorpVault-specific issue (hvac turns a leading slash into a // KV
path that Vault 2.0 rejects). That wrapper wraps every backend, so it also
moved DatabaseVault's key location, orphaning secrets stored before the
upgrade.

Instead of migrating DatabaseVault secrets to the new location, keep the
backend on its legacy /{prefix}/{key} location, where the leading slash is
harmless (just a DB column value). Only HashicorpVault uses the canonical
no-leading-slash location, controlled by a leading_slash flag on
VaultKeyPrefixWrapper set in VaultFactory.from_vault_type. The DatabaseVault
read-time migration fallback is no longer needed and is removed.
---
 lib/galaxy/security/vault.py          | 37 ++++++++++-----------
 test/unit/data/security/test_vault.py | 46 ++++++++++++++++-----------
 2 files changed, 46 insertions(+), 37 deletions(-)

diff --git a/lib/galaxy/security/vault.py b/lib/galaxy/security/vault.py
index 34964bcd38d..8485a5803c3 100644
--- a/lib/galaxy/security/vault.py
+++ b/lib/galaxy/security/vault.py
@@ -221,20 +221,6 @@ class DatabaseVault(Vault):
         if key_obj and key_obj.value:
             f = self._get_multi_fernet()
             return f.decrypt(key_obj.value.encode("utf-8")).decode("utf-8")
-        # Galaxy <= 26.0 emitted a leading slash in vault keys, which was stored
-        # in the database. PR #22530 normalized keys to not have leading slashes.
-        # Fall back to reading the legacy form and rewrite under the canonical
-        # key so the secret survives the Galaxy upgrade. This fallback can be
-        # removed after a deprecation window once operators have migrated.
-        legacy_key_obj = self._get_vault_value(f"/{key}")
-        if legacy_key_obj and legacy_key_obj.value:
-            log.warning("Migrating legacy non-canonical DatabaseVault secret to canonical path: %s", key)
-            f = self._get_multi_fernet()
-            value = f.decrypt(legacy_key_obj.value.encode("utf-8")).decode("utf-8")
-            self.write_secret(key, value)
-            self.sa_session.delete(legacy_key_obj)
-            self.sa_session.flush()
-            return value
         return None
 
     def write_secret(self, key: str, value: str) -> None:
@@ -314,7 +300,7 @@ class VaultKeyPrefixWrapper(Vault):
     Adds a prefix to all vault keys, such as the galaxy instance id
     """
 
-    def __init__(self, vault: Vault, prefix: str):
+    def __init__(self, vault: Vault, prefix: str, leading_slash: bool = False):
         self.vault = vault
         # Strip conventional outer slashes so admins can write `/galaxy`,
         # `galaxy`, or `/galaxy/` interchangeably in config. Reject anything
@@ -326,12 +312,21 @@ class VaultKeyPrefixWrapper(Vault):
                 "double slashes or whitespace adjacent to a slash."
             )
         self.prefix = stripped
+        # HashicorpVault must use canonical (no leading slash) paths, since hvac
+        # turns a leading slash into a `//` KV path that Vault 2.0 rejects (#22530).
+        # DatabaseVault stores the key verbatim in a DB column where the leading
+        # slash is harmless, so it keeps the legacy `/{prefix}/{key}` location to
+        # avoid orphaning secrets written before #22530.
+        self.leading_slash = leading_slash
+
+    def _prefixed(self, key: str) -> str:
+        return f"/{self.prefix}/{key}" if self.leading_slash else f"{self.prefix}/{key}"
 
     def read_secret(self, key: str) -> Optional[str]:
-        return self.vault.read_secret(f"{self.prefix}/{key}")
+        return self.vault.read_secret(self._prefixed(key))
 
     def write_secret(self, key: str, value: str) -> None:
-        return self.vault.write_secret(f"{self.prefix}/{key}", value)
+        return self.vault.write_secret(self._prefixed(key), value)
 
     def list_secrets(self, key: str) -> list[str]:
         raise NotImplementedError()
@@ -348,15 +343,21 @@ class VaultFactory:
     @staticmethod
     def from_vault_type(app, vault_type: Optional[str], cfg: dict) -> Vault:
         vault: Vault
+        # DatabaseVault keeps the legacy leading-slash key location (see
+        # VaultKeyPrefixWrapper); HashicorpVault must use canonical paths.
+        legacy_leading_slash = False
         if vault_type == "hashicorp":
             token_renewal_enabled = app.config.vault_token_renewal_interval > 0
             vault = HashicorpVault(cfg, token_renewal_enabled=token_renewal_enabled)
         elif vault_type == "database":
             vault = DatabaseVault(app.model.context, cfg)
+            legacy_leading_slash = True
         else:
             raise InvalidVaultConfigException(f"Unknown vault type: {vault_type}")
         vault_prefix = cfg.get("path_prefix") or "/galaxy"
-        return VaultKeyValidationWrapper(VaultKeyPrefixWrapper(vault, prefix=vault_prefix))
+        return VaultKeyValidationWrapper(
+            VaultKeyPrefixWrapper(vault, prefix=vault_prefix, leading_slash=legacy_leading_slash)
+        )
 
     @staticmethod
     def from_app(app) -> Vault:
diff --git a/test/unit/data/security/test_vault.py b/test/unit/data/security/test_vault.py
index c89880039f4..9220dfcd5b4 100644
--- a/test/unit/data/security/test_vault.py
+++ b/test/unit/data/security/test_vault.py
@@ -130,33 +130,24 @@ class TestDatabaseVault(AbstractTestCases.VaultTestBase):
         with self.assertRaises(InvalidToken):
             vault.read_secret("my/incorrect/secret")
 
-    def test_legacy_key_migration(self):
-        # Simulate a secret stored with a leading slash (pre-26.1 format)
+    def test_database_vault_keeps_legacy_leading_slash_location(self):
+        # DatabaseVault never had the hvac double-slash problem, so it keeps the
+        # pre-26.1 leading-slash key location to avoid orphaning existing secrets.
         config = GalaxyDataTestConfig(vault_config_file=VAULT_CONF_DATABASE)
         app = GalaxyDataTestApp(config=config)
         vault = VaultFactory.from_app(app)
 
-        # The vault chain is VaultKeyValidationWrapper(VaultKeyPrefixWrapper(DatabaseVault))
-        # The prefix is 'my_galaxy_instance' (from vault_conf_database.yml with leading slash stripped)
-        # Pre-26.1, VaultKeyPrefixWrapper emitted /{prefix}/{key}, so the DB stored keys like
-        # /my_galaxy_instance/my/legacy/secret. Write that directly to simulate the legacy state.
+        vault.write_secret("my/legacy/secret", "legacy value")
+
         inner = _unwrap_vault(vault)
         assert isinstance(inner, DatabaseVault)
-        inner.write_secret("/my_galaxy_instance/my/legacy/secret", "legacy value")
-
-        # Read with the new canonical format through the full wrapper chain
-        # VaultKeyValidationWrapper normalizes → VaultKeyPrefixWrapper adds prefix →
-        # DatabaseVault.read_secret("my_galaxy_instance/my/legacy/secret") should migrate
+        # The prefix is 'my_galaxy_instance' (from vault_conf_database.yml). The
+        # secret must be stored under the legacy leading-slash key, matching what
+        # pre-26.1 Galaxy wrote so upgraded instances can still read it.
+        assert inner._get_vault_value("/my_galaxy_instance/my/legacy/secret") is not None
+        assert inner._get_vault_value("my_galaxy_instance/my/legacy/secret") is None
         assert vault.read_secret("my/legacy/secret") == "legacy value"
 
-        # Verify the secret is now accessible with the canonical key
-        assert vault.read_secret("my/legacy/secret") == "legacy value"
-
-        # Verify the legacy key no longer exists (was migrated to canonical form)
-        assert inner._get_vault_value("/my_galaxy_instance/my/legacy/secret") is None
-        # Verify the canonical key now exists
-        assert inner._get_vault_value("my_galaxy_instance/my/legacy/secret") is not None
-
 
 def _make_mocked_hashicorp_vault() -> HashicorpVault:
     inner = HashicorpVault.__new__(HashicorpVault)
@@ -182,6 +173,23 @@ def test_vault_key_prefix_wrapper_emits_canonical_path(prefix):
     )
 
 
+@pytest.mark.parametrize("prefix", ["/galaxy", "galaxy", "/galaxy/"])
+def test_vault_key_prefix_wrapper_emits_legacy_leading_slash_path(prefix):
+    # DatabaseVault keeps the legacy leading-slash location. The wrapper must
+    # prepend a single leading slash regardless of how the prefix is spelled.
+    inner = _make_mocked_hashicorp_vault()
+    inner.client.secrets.kv.read_secret_version.return_value = {"data": {"data": {"value": "v"}}}
+    vault = VaultKeyValidationWrapper(VaultKeyPrefixWrapper(inner, prefix=prefix, leading_slash=True))
+
+    assert vault.read_secret("user/1/preferences/editor") == "v"
+    inner.client.secrets.kv.read_secret_version.assert_called_once_with(path="/galaxy/user/1/preferences/editor")
+
+    vault.write_secret("user/1/preferences/editor", "vscode")
+    inner.client.secrets.kv.v2.create_or_update_secret.assert_called_once_with(
+        path="/galaxy/user/1/preferences/editor", secret={"value": "vscode"}
+    )
+
+
 @pytest.mark.parametrize("prefix", ["", "/", "gal//axy", "gal /axy", "gal/ axy"])
 def test_vault_key_prefix_wrapper_rejects_invalid_prefix(prefix):
     # Anything that would still produce a non-canonical Vault path after

From 0b8d55e1b4c92a69a0b9f8c405d30f5336e9f35b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 17 Jun 2026 17:47:23 +0200
Subject: [PATCH 217/256] Refactor vault key canonicalization logic

Moves the responsibility for determining vault key format to the backend implementation. This replaces manual flags with a property that specifies whether a backend requires canonical paths or legacy leading-slash paths.

This change ensures that Hashicorp Vault continues to receive canonical keys to avoid compatibility issues with version 2.0, while the Database Vault maintains its legacy format to ensure existing secrets remain accessible without a migration.
---
 lib/galaxy/security/vault.py          | 33 +++++++++++++--------------
 test/unit/data/security/test_vault.py |  9 ++++----
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/lib/galaxy/security/vault.py b/lib/galaxy/security/vault.py
index 8485a5803c3..a3ed91b2802 100644
--- a/lib/galaxy/security/vault.py
+++ b/lib/galaxy/security/vault.py
@@ -38,6 +38,12 @@ class Vault(abc.ABC):
     A simple abstraction for reading/writing from external vaults.
     """
 
+    # Whether this backend uses canonical (no-leading-slash) keys.
+    # Hashicorp Vault 2.0 rejects leading/double slashes, so it must use
+    # canonical keys. DatabaseVault keeps using the legacy /{prefix}/{key}
+    # form used by Galaxy <= 26.0, so existing rows are found in place.
+    use_canonical_keys = True
+
     @abc.abstractmethod
     def read_secret(self, key: str) -> Optional[str]:
         """
@@ -191,6 +197,8 @@ class HashicorpVault(Vault):
 
 
 class DatabaseVault(Vault):
+    use_canonical_keys = False
+
     def __init__(self, sa_session, config):
         self.sa_session = sa_session
         self.encryption_keys = config.get("encryption_keys")
@@ -300,11 +308,12 @@ class VaultKeyPrefixWrapper(Vault):
     Adds a prefix to all vault keys, such as the galaxy instance id
     """
 
-    def __init__(self, vault: Vault, prefix: str, leading_slash: bool = False):
+    def __init__(self, vault: Vault, prefix: str):
         self.vault = vault
         # Strip conventional outer slashes so admins can write `/galaxy`,
-        # `galaxy`, or `/galaxy/` interchangeably in config. Reject anything
-        # that would still produce a non-canonical Vault path after stripping.
+        # `galaxy`, or `/galaxy/` interchangeably in config. Reject empty
+        # prefixes or prefixes that would be invalid in either canonical or
+        # legacy form (double slashes or whitespace adjacent to a slash).
         stripped = prefix.strip("/")
         if not stripped or VAULT_KEY_INVALID_REGEX.search(stripped):
             raise InvalidVaultConfigException(
@@ -312,15 +321,11 @@ class VaultKeyPrefixWrapper(Vault):
                 "double slashes or whitespace adjacent to a slash."
             )
         self.prefix = stripped
-        # HashicorpVault must use canonical (no leading slash) paths, since hvac
-        # turns a leading slash into a `//` KV path that Vault 2.0 rejects (#22530).
-        # DatabaseVault stores the key verbatim in a DB column where the leading
-        # slash is harmless, so it keeps the legacy `/{prefix}/{key}` location to
-        # avoid orphaning secrets written before #22530.
-        self.leading_slash = leading_slash
 
     def _prefixed(self, key: str) -> str:
-        return f"/{self.prefix}/{key}" if self.leading_slash else f"{self.prefix}/{key}"
+        if self.vault.use_canonical_keys:
+            return f"{self.prefix}/{key}"
+        return f"/{self.prefix}/{key}"
 
     def read_secret(self, key: str) -> Optional[str]:
         return self.vault.read_secret(self._prefixed(key))
@@ -343,21 +348,15 @@ class VaultFactory:
     @staticmethod
     def from_vault_type(app, vault_type: Optional[str], cfg: dict) -> Vault:
         vault: Vault
-        # DatabaseVault keeps the legacy leading-slash key location (see
-        # VaultKeyPrefixWrapper); HashicorpVault must use canonical paths.
-        legacy_leading_slash = False
         if vault_type == "hashicorp":
             token_renewal_enabled = app.config.vault_token_renewal_interval > 0
             vault = HashicorpVault(cfg, token_renewal_enabled=token_renewal_enabled)
         elif vault_type == "database":
             vault = DatabaseVault(app.model.context, cfg)
-            legacy_leading_slash = True
         else:
             raise InvalidVaultConfigException(f"Unknown vault type: {vault_type}")
         vault_prefix = cfg.get("path_prefix") or "/galaxy"
-        return VaultKeyValidationWrapper(
-            VaultKeyPrefixWrapper(vault, prefix=vault_prefix, leading_slash=legacy_leading_slash)
-        )
+        return VaultKeyValidationWrapper(VaultKeyPrefixWrapper(vault, prefix=vault_prefix))
 
     @staticmethod
     def from_app(app) -> Vault:
diff --git a/test/unit/data/security/test_vault.py b/test/unit/data/security/test_vault.py
index 9220dfcd5b4..713f5d5d9e1 100644
--- a/test/unit/data/security/test_vault.py
+++ b/test/unit/data/security/test_vault.py
@@ -174,12 +174,13 @@ def test_vault_key_prefix_wrapper_emits_canonical_path(prefix):
 
 
 @pytest.mark.parametrize("prefix", ["/galaxy", "galaxy", "/galaxy/"])
-def test_vault_key_prefix_wrapper_emits_legacy_leading_slash_path(prefix):
-    # DatabaseVault keeps the legacy leading-slash location. The wrapper must
-    # prepend a single leading slash regardless of how the prefix is spelled.
+def test_vault_key_prefix_wrapper_emits_legacy_leading_slash_path_for_database_vault(prefix):
+    # DatabaseVault keeps the legacy leading-slash location because use_canonical_keys=False.
+    # The wrapper must prepend a single leading slash regardless of how the prefix is spelled.
     inner = _make_mocked_hashicorp_vault()
     inner.client.secrets.kv.read_secret_version.return_value = {"data": {"data": {"value": "v"}}}
-    vault = VaultKeyValidationWrapper(VaultKeyPrefixWrapper(inner, prefix=prefix, leading_slash=True))
+    inner.use_canonical_keys = False
+    vault = VaultKeyValidationWrapper(VaultKeyPrefixWrapper(inner, prefix=prefix))
 
     assert vault.read_secret("user/1/preferences/editor") == "v"
     inner.client.secrets.kv.read_secret_version.assert_called_once_with(path="/galaxy/user/1/preferences/editor")

From 0a6db382f39a8e3142202d61af93afc17e753ffd Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 17 Jun 2026 19:29:03 +0200
Subject: [PATCH 218/256] Match renamed data_manager output in bundle
 integration test

The data_manager test tool now emits asyncvalue.txt instead of
newvalue.txt; update the bundle-by-uri integration test assertion to
match so it stops failing on the renamed output.
---
 test/integration/test_tool_data_bundles.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/integration/test_tool_data_bundles.py b/test/integration/test_tool_data_bundles.py
index 54f88633473..35913037ff1 100644
--- a/test/integration/test_tool_data_bundles.py
+++ b/test/integration/test_tool_data_bundles.py
@@ -33,7 +33,7 @@ class TestDataBundlesIntegration(BaseSwiftObjectStoreIntegrationTestCase, DataMa
             history_id, to_ext="data_manager_json", type="bytes"
         )
         temp_directory = decompress_bytes_to_directory(content)
-        assert os.path.exists(os.path.join(temp_directory, "newvalue.txt"))
+        assert os.path.exists(os.path.join(temp_directory, "asyncvalue.txt"))
         uri = f"file://{os.path.normpath(temp_directory)}"
         data = {
             "source": {

From 1f3686d6490218182fa17147c3aa46ec6254ca32 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 17 Jun 2026 16:30:59 -0500
Subject: [PATCH 219/256] [26.1] Fix misaligned activity bar icons

This was interestingly, on Windows, only happening on Chrome for me (not on Firefox). Just some minor CSS changes were needed to fix the misalignment.

Fixes https://github.com/galaxyproject/galaxy/issues/22600
---
 client/src/components/ActivityBar/ActivityItem.vue | 6 ++++--
 client/src/components/Common/TextShort.vue         | 9 ++++++++-
 client/src/components/Popper/Popper.vue            | 8 +++++++-
 3 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/client/src/components/ActivityBar/ActivityItem.vue b/client/src/components/ActivityBar/ActivityItem.vue
index 5150a79489c..15077b3c25b 100644
--- a/client/src/components/ActivityBar/ActivityItem.vue
+++ b/client/src/components/ActivityBar/ActivityItem.vue
@@ -82,7 +82,7 @@ const meta = computed(() => store.metaForId(props.id));
     <Popper :placement="tooltipPlacement">
         <template v-slot:reference>
             <b-nav-item
-                class="activity-item my-1 p-2"
+                class="activity-item"
                 :class="{ 'nav-item-active': isActive }"
                 :link-attrs="{ id: `activity-${id}` }"
                 :link-classes="`variant-${props.variant}`"
@@ -141,6 +141,9 @@ const meta = computed(() => store.metaForId(props.id));
     position: relative;
     display: flex;
     flex-direction: column;
+    width: 5rem;
+    padding: 0.5rem;
+    margin: 0.125rem 0;
 
     &:deep(.variant-danger) {
         color: $brand-danger;
@@ -200,7 +203,6 @@ const meta = computed(() => store.metaForId(props.id));
     position: relative;
     display: flex;
     justify-content: center;
-    width: 4rem;
     margin-top: 0.5rem;
     font-size: 0.7rem;
 }
diff --git a/client/src/components/Common/TextShort.vue b/client/src/components/Common/TextShort.vue
index e1f0842a508..d61ea7fc851 100644
--- a/client/src/components/Common/TextShort.vue
+++ b/client/src/components/Common/TextShort.vue
@@ -21,7 +21,14 @@ const trimmedText = computed(() => {
 </script>
 
 <template>
-    <span class="text-break text-center">
+    <span class="text-short-component">
         {{ trimmedText }}
     </span>
 </template>
+
+<style scoped>
+.text-short-component {
+    text-align: center;
+    word-wrap: break-word;
+}
+</style>
diff --git a/client/src/components/Popper/Popper.vue b/client/src/components/Popper/Popper.vue
index c3be64f47aa..2d64527c541 100644
--- a/client/src/components/Popper/Popper.vue
+++ b/client/src/components/Popper/Popper.vue
@@ -1,6 +1,6 @@
 <template>
     <span>
-        <span v-if="!referenceEl" ref="reference">
+        <span v-if="!referenceEl" ref="reference" class="popper-reference-container">
             <slot name="reference" />
         </span>
         <div v-show="!disabled && visible" ref="popper" class="popper-element" :class="`popper-element-${mode}`">
@@ -75,6 +75,12 @@ defineExpose({
     @return 1px solid $border-color;
 }
 
+.popper-reference-container {
+    display: flex;
+    flex-direction: column;
+    align-items: center;
+}
+
 .popper-element {
     z-index: 9999;
     border-radius: $border-radius-large;

From e6bcb99949feaa4aee3b930781cba32d4ff8d5ef Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 17 Jun 2026 16:25:18 -0400
Subject: [PATCH 220/256] Add missing agent-type labels to the chat UI

agentTypes.ts had no entries for the tool_recommendation, orchestrator, history,
and workflow_report agent types, so getAgentLabel() fell through to rendering the
raw backend string (e.g. "tool_recommendation") in the chat UI. Add the four
mappings with FA6 icons, and drop the stale dataset_analyzer entry since there's
no backend agent type by that name.
---
 client/src/components/GalaxyAI/agentTypes.ts | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/client/src/components/GalaxyAI/agentTypes.ts b/client/src/components/GalaxyAI/agentTypes.ts
index 81ec8ef9516..fa29b998691 100644
--- a/client/src/components/GalaxyAI/agentTypes.ts
+++ b/client/src/components/GalaxyAI/agentTypes.ts
@@ -2,13 +2,16 @@ import type { IconDefinition } from "@fortawesome/fontawesome-svg-core";
 import {
     faBook,
     faBug,
-    faChartBar,
+    faFileContract,
     faGraduationCap,
+    faHistory,
     faMagic,
     faPlus,
     faQuestionCircle,
     faRobot,
     faRoute,
+    faSitemap,
+    faTools,
 } from "@fortawesome/free-solid-svg-icons";
 
 import { AGENT_LABELS } from "@/components/Page/constants";
@@ -26,7 +29,15 @@ export const agentTypes: AgentType[] = [
     { value: "router", label: "Router", icon: faRoute, description: "Query router" },
     { value: "error_analysis", label: "Error Analysis", icon: faBug, description: "Debug tool errors" },
     { value: "custom_tool", label: "Custom Tool", icon: faPlus, description: "Create custom tools" },
-    { value: "dataset_analyzer", label: "Dataset Analyzer", icon: faChartBar, description: "Analyze datasets" },
+    {
+        value: "tool_recommendation",
+        label: "Tool Recommendation",
+        icon: faTools,
+        description: "Recommend tools & workflows",
+    },
+    { value: "orchestrator", label: "Orchestrator", icon: faSitemap, description: "Coordinates multiple steps" },
+    { value: "history", label: "History", icon: faHistory, description: "Summarize your analysis" },
+    { value: "workflow_report", label: "Workflow Report", icon: faFileContract, description: "Workflow run reports" },
     { value: "gtn_training", label: "GTN Training", icon: faGraduationCap, description: "Find tutorials" },
     { value: "clarification", label: "Clarification", icon: faQuestionCircle, description: "Needs more info" },
     {

From c7d81a806d4d471c56b8abe1403ee0bc0d81ede4 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Wed, 17 Jun 2026 18:41:54 -0500
Subject: [PATCH 221/256] ensure only the activity item `Popper` class is
 affected

Co-authored-by: Dannon <dannon.baker@gmail.com>
---
 client/src/components/ActivityBar/ActivityItem.vue | 11 ++++++++++-
 client/src/components/Popper/Popper.vue            |  6 ------
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/client/src/components/ActivityBar/ActivityItem.vue b/client/src/components/ActivityBar/ActivityItem.vue
index 15077b3c25b..e27bc0b5e7f 100644
--- a/client/src/components/ActivityBar/ActivityItem.vue
+++ b/client/src/components/ActivityBar/ActivityItem.vue
@@ -79,7 +79,7 @@ const meta = computed(() => store.metaForId(props.id));
 </script>
 
 <template>
-    <Popper :placement="tooltipPlacement">
+    <Popper :placement="tooltipPlacement" class="activity-item-popper">
         <template v-slot:reference>
             <b-nav-item
                 class="activity-item"
@@ -137,6 +137,15 @@ const meta = computed(() => store.metaForId(props.id));
 <style scoped lang="scss">
 @import "@/style/scss/theme/blue.scss";
 
+.activity-item-popper {
+    // Vertically centers the popper in the activity bar
+    :deep(.popper-reference-container) {
+        display: flex;
+        flex-direction: column;
+        align-items: center;
+    }
+}
+
 .activity-item {
     position: relative;
     display: flex;
diff --git a/client/src/components/Popper/Popper.vue b/client/src/components/Popper/Popper.vue
index 2d64527c541..472af94a957 100644
--- a/client/src/components/Popper/Popper.vue
+++ b/client/src/components/Popper/Popper.vue
@@ -75,12 +75,6 @@ defineExpose({
     @return 1px solid $border-color;
 }
 
-.popper-reference-container {
-    display: flex;
-    flex-direction: column;
-    align-items: center;
-}
-
 .popper-element {
     z-index: 9999;
     border-radius: $border-radius-large;

From 875243c49c3fd66d864981d727db02213d89571a Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 17 Jun 2026 16:30:08 -0400
Subject: [PATCH 222/256] Persist and display the agent that actually answered

The chat endpoint stored the request's agent_type ("auto") at the top level of each
turn, so reopening a conversation badged every router-handoff turn "Auto (Router)"
instead of the specialist that really handled it. The real responder is already in
agent_response, so persist its agent_type, and on reload prefer the nested
agent_response over the stored top-level type -- which also fixes rows already
written the old way. Same fallback applied client-side in GalaxyAI.vue.
---
 client/src/components/GalaxyAI.vue    |  2 +-
 lib/galaxy/webapps/galaxy/api/chat.py | 26 +++++++++--
 test/unit/app/test_chat_manager.py    | 67 +++++++++++++++++++++++++++
 3 files changed, 89 insertions(+), 6 deletions(-)

diff --git a/client/src/components/GalaxyAI.vue b/client/src/components/GalaxyAI.vue
index c5df4dc7dc9..011fcd09a98 100644
--- a/client/src/components/GalaxyAI.vue
+++ b/client/src/components/GalaxyAI.vue
@@ -413,7 +413,7 @@ async function fetchConversation(exchangeId: string) {
         };
 
         if (msg.role === "assistant") {
-            message.agentType = msg.agent_type;
+            message.agentType = msg.agent_response?.agent_type || msg.agent_type;
             message.confidence = msg.agent_response?.confidence || "medium";
             message.feedback = msg.feedback === 1 ? "up" : msg.feedback === 0 ? "down" : null;
 
diff --git a/lib/galaxy/webapps/galaxy/api/chat.py b/lib/galaxy/webapps/galaxy/api/chat.py
index f28bcf78461..57209a8ec7f 100644
--- a/lib/galaxy/webapps/galaxy/api/chat.py
+++ b/lib/galaxy/webapps/galaxy/api/chat.py
@@ -106,6 +106,16 @@ JobIdPathParam = Annotated[
 ]
 
 
+def _responder_agent_type(data: dict[str, Any]) -> str:
+    """Agent type that actually answered a stored turn.
+
+    Prefer the nested agent_response (the real responder, e.g. the specialist after a
+    router handoff) over the top-level agent_type, which records the *request* type
+    ("auto"). Older rows only stored the request type at the top level.
+    """
+    return (data.get("agent_response") or {}).get("agent_type") or data.get("agent_type", "unknown")
+
+
 @router.cbv
 class ChatAPI:
     """Chat interface for AI agents.
@@ -265,7 +275,7 @@ class ChatAPI:
                     conversation_data = {
                         "query": query_text,
                         "response": result.get("response", ""),
-                        "agent_type": agent_type,
+                        "agent_type": agent_resp.agent_type if agent_resp else agent_type,
                         "agent_response": agent_resp.model_dump() if agent_resp else None,
                     }
                     message_content = json.dumps(conversation_data)
@@ -280,7 +290,7 @@ class ChatAPI:
                         "agent_response": agent_resp.model_dump() if agent_resp else None,
                     }
                     exchange = self.chat_manager.create_page_chat(
-                        trans, page_id, query_text, storable_result, agent_type
+                        trans, page_id, query_text, storable_result, agent_resp.agent_type if agent_resp else agent_type
                     )
                     result["exchange_id"] = exchange.id
                 else:
@@ -290,7 +300,13 @@ class ChatAPI:
                         "agent_response": agent_resp.model_dump() if agent_resp else None,
                     }
                     exchange = await anyio.to_thread.run_sync(
-                        partial(self.chat_manager.create_general_chat, trans, query_text, storable_result, agent_type)
+                        partial(
+                            self.chat_manager.create_general_chat,
+                            trans,
+                            query_text,
+                            storable_result,
+                            agent_resp.agent_type if agent_resp else agent_type,
+                        )
                     )
                     result["exchange_id"] = exchange.id
 
@@ -489,7 +505,7 @@ class ChatAPI:
                         {
                             "role": "assistant",
                             "content": data["response"],
-                            "agent_type": data.get("agent_type", "unknown"),
+                            "agent_type": _responder_agent_type(data),
                             "agent_response": data.get("agent_response"),
                             "timestamp": msg.create_time.isoformat() if msg.create_time else None,
                             "feedback": msg.feedback,
@@ -524,7 +540,7 @@ class ChatAPI:
                         id=exchange.id,
                         query=data.get("query", ""),
                         response=data.get("response", ""),
-                        agent_type=data.get("agent_type", "unknown"),
+                        agent_type=_responder_agent_type(data),
                         agent_response=agent_response,
                         timestamp=message.create_time.isoformat() if message.create_time else None,
                         feedback=message.feedback,
diff --git a/test/unit/app/test_chat_manager.py b/test/unit/app/test_chat_manager.py
index ee26bb78e21..d280f83d59c 100644
--- a/test/unit/app/test_chat_manager.py
+++ b/test/unit/app/test_chat_manager.py
@@ -6,6 +6,10 @@ from unittest import mock
 import pytest
 
 from galaxy.managers.chat import ChatManager
+from galaxy.webapps.galaxy.api.chat import (
+    _responder_agent_type,
+    ChatAPI,
+)
 
 
 def _make_trans(user_id=1):
@@ -270,3 +274,66 @@ class TestResolvePageFromInterfaceContext:
         assert page_id == 42
         assert page_obj is fake_page
         mock_get.assert_called_once_with(trans, 42)
+
+
+class TestResponderAgentType:
+    """The displayed agent_type should be the agent that actually answered (the nested
+    agent_response), not the request type stored at the top level ("auto")."""
+
+    def test_prefers_nested_response_agent_type(self):
+        data = {"agent_type": "auto", "agent_response": {"agent_type": "error_analysis"}}
+        assert _responder_agent_type(data) == "error_analysis"
+
+    def test_falls_back_to_top_level_when_no_response(self):
+        data = {"agent_type": "gtn_training", "agent_response": None}
+        assert _responder_agent_type(data) == "gtn_training"
+
+    def test_unknown_when_nothing_present(self):
+        assert _responder_agent_type({}) == "unknown"
+
+
+class TestGetExchangeMessagesAttribution:
+    """Reopening a conversation should badge each turn with the real responder, so a
+    router handoff turn (persisted with top-level agent_type "auto") reloads as the
+    specialist that actually answered."""
+
+    @staticmethod
+    def _api_for(message):
+        api = ChatAPI.__new__(ChatAPI)
+        msg = mock.Mock()
+        msg.message = message
+        msg.feedback = None
+        msg.create_time = None
+        exchange = _FakeChatExchange()
+        exchange.messages = [msg]
+        api.chat_manager = mock.Mock()
+        api.chat_manager.get_exchange_by_id.return_value = exchange
+        return api
+
+    def _assistant_turn(self, message):
+        api = self._api_for(message)
+        messages = api.get_exchange_messages(exchange_id=1, trans=_make_trans(), user=mock.Mock())
+        assistant = [m for m in messages if m["role"] == "assistant"]
+        assert len(assistant) == 1
+        return assistant[0]
+
+    def test_handoff_turn_reloads_as_specialist(self):
+        message = json.dumps(
+            {
+                "query": "why did my job fail?",
+                "response": "Your tool hit an out-of-memory error.",
+                "agent_type": "auto",
+                "agent_response": {"agent_type": "error_analysis"},
+            }
+        )
+        assert self._assistant_turn(message)["agent_type"] == "error_analysis"
+
+    def test_falls_back_to_stored_type_without_response(self):
+        message = json.dumps(
+            {
+                "query": "find me a tutorial",
+                "response": "Here are some tutorials.",
+                "agent_type": "gtn_training",
+            }
+        )
+        assert self._assistant_turn(message)["agent_type"] == "gtn_training"

From 66cf5e4831f59a8e15dd511ecb9cb0269df8b014 Mon Sep 17 00:00:00 2001
From: gagayuan <gagayuan@163.com>
Date: Thu, 18 Jun 2026 12:13:30 +0800
Subject: [PATCH 223/256] Fix session_duration check using local time instead
 of UTC The session expiry check in GalaxyWebTransaction.__init__ uses
 datetime.datetime.now() (local time), but the session's last_action field is
 set via galaxy.model.orm.now.now() which returns UTC time without tzinfo. On
 non-UTC timezone systems, this mismatch causes new sessions to be incorrectly
 treated as expired, resulting in an infinite redirect loop on /login/start.
 Fix this by using the same utc_now() from galaxy.model.orm.now in the expiry
 check, ensuring consistent timezone handling.

---
 lib/galaxy/webapps/base/webapp.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 704df9aecc0..adb053b0cc2 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -41,6 +41,7 @@ from galaxy.managers.session import GalaxySessionManager
 from galaxy.managers.users import UserManager
 from galaxy.model import History
 from galaxy.model.base import ensure_object_added_to_session
+from galaxy.model.orm.now import now as utc_now
 from galaxy.structured_app import (
     BasicSharedApp,
     MinimalApp,
@@ -383,7 +384,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
                 #
                 # Make sure we're not past the duration, and either log out or
                 # update timestamp.
-                now = datetime.datetime.now()
+                now = utc_now()
                 if self.galaxy_session.last_action:
                     expiration_time = self.galaxy_session.last_action + datetime.timedelta(
                         minutes=config.session_duration

From a8468a3745eddb8188fe64921f2b4a8052032416 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 09:37:49 +0200
Subject: [PATCH 224/256] Emit SSE/queue metrics as gauges, sample SSE counts
 in web workers

Point-in-time counts (SSE connections, control-queue depth, worker
processes) were emitted via statsd timing(), so telegraf/influxdb stored
them as timing aggregations (mean/median/percentiles) instead of a single
value. Add a gauge() method to the statsd client and emit these as gauges.

The SSEConnectionManager is per-process state registered only on the
webapp, so sampling it from the Celery beat task saw an empty manager and
always reported ~0. Move SSE connection sampling into each web worker via
a per-worker daemon thread (SSEConnectionGaugeEmitter), tagging samples
with server_name so per-worker series don't collide. It is opt-in via the
new enable_sse_connection_metrics config (default off) and only runs when
statsd is actually configured.
---
 doc/source/admin/galaxy_options.rst           | 25 +++++-
 doc/source/admin/sse_updates.md               | 32 +++++--
 lib/galaxy/app/__init__.py                    | 35 +++++++-
 lib/galaxy/celery/tasks.py                    | 16 ++--
 lib/galaxy/config/sample/galaxy.yml.sample    | 17 +++-
 lib/galaxy/config/schemas/config_schema.yml   | 18 +++-
 lib/galaxy/managers/queue_metrics.py          | 42 +++------
 lib/galaxy/managers/sse.py                    | 54 +++++++++++
 lib/galaxy/web/statsd_client.py               | 15 ++++
 lib/galaxy_test/conftest.py                   |  2 +-
 test/unit/app/managers/test_queue_metrics.py  | 61 ++++---------
 .../managers/test_sse_connection_gauges.py    | 89 +++++++++++++++++++
 12 files changed, 303 insertions(+), 103 deletions(-)
 create mode 100644 test/unit/app/managers/test_sse_connection_gauges.py

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 5dd5ccf20ec..4546fc5b7a6 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -3498,13 +3498,32 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    How often (in seconds) the Celery beat task emits queue-depth,
-    SSE-connection, and WorkerProcess gauges. Only active when
-    statsd_host is set. Set to 0 to disable.
+    How often (in seconds) background observability gauges are
+    sampled: control-queue depth and WorkerProcess counts from the
+    Celery beat task, and (when enable_sse_connection_metrics is set)
+    active SSE-connection counts from each web worker. This is the
+    shared cadence for all of them. Only active when statsd_host is
+    set. Set to 0 to disable all background gauges.
 :Default: ``15``
 :Type: int
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_sse_connection_metrics``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Emit the galaxy.sse.connections.active gauge from each web worker,
+    reporting how many Server-Sent Events connections that worker
+    currently holds (tagged by kind and server_name). Sampled on the
+    queue_metrics_interval cadence. Off by default so that enabling
+    statsd does not by itself start measuring SSE connections;
+    requires statsd_host to be set and queue_metrics_interval greater
+    than 0.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~
 ``library_import_dir``
 ~~~~~~~~~~~~~~~~~~~~~~
diff --git a/doc/source/admin/sse_updates.md b/doc/source/admin/sse_updates.md
index b845217bf69..8129fe67d32 100644
--- a/doc/source/admin/sse_updates.md
+++ b/doc/source/admin/sse_updates.md
@@ -149,16 +149,32 @@ you use for Gunicorn worker health:
 
 | Metric                                     | Type    | Source                | Meaning                                                      |
 | ------------------------------------------ | ------- | --------------------- | ------------------------------------------------------------ |
+| `galaxy.sse.connections.active` (tags: `kind`, `server_name`) | gauge | each web worker | Currently open SSE connections, split into `broadcast` (all, including anonymous) and `per_user` (bound to a specific user). |
 | `galaxy.sse.connections.dropped`           | counter | `SSEConnectionManager` | A per-connection asyncio queue filled up; an event was lost. |
 | `galaxy.sse.dispatch.count` (tag: `task`) | counter | `SSEEventDispatcher`  | Control-task fan-outs by event kind.                         |
 | `galaxy.sse.dispatch.latency_ms` (tag: `task`) | timing | `SSEEventDispatcher`  | Wall time spent enqueueing the control task.                 |
 | `galaxy.sse.dispatch.skipped_no_qw`        | counter | `SSEEventDispatcher`  | Producer tried to dispatch with no queue worker bound — events would have been dropped. |
+| `galaxy.control_queue.depth` (tag: `queue_name`) | gauge | Celery beat | Pending message count per webapp/handler control queue. |
+| `galaxy.worker_process.active` (tag: `app_type`) | gauge | Celery beat | Recently-active worker rows in the database, grouped by app type. |
 
-You can also expose a "currently connected SSE clients" gauge if you wire
-one up: each `SSEConnectionManager` instance publishes
-`total_broadcast_connections` (all connections, including anonymous) and
-`total_per_user_connections` (connections bound to a specific user). These
-are per-worker numbers; sum across workers for a cluster total.
+All three are emitted as statsd **gauges** — point-in-time values, not timings —
+so the datasource stores a single current value per series rather than the
+mean/percentile aggregation statsd applies to timing metrics.
+
+`galaxy.control_queue.depth` and `galaxy.worker_process.active` are sampled by
+the `emit_queue_metrics_task` Celery beat task (cadence:
+`queue_metrics_interval`).
+
+`galaxy.sse.connections.active` is sampled differently: the
+`SSEConnectionManager` is per-process state, so each **web worker** emits its
+own counts (the Celery worker holds no connections and would only ever report
+zero). Every worker tags its sample with its `server_name` so the per-worker
+series don't collide — sum across `server_name` for a cluster total.
+
+This gauge is **opt-in**: set `enable_sse_connection_metrics: true` (it is off
+by default, so turning on statsd does not by itself start measuring SSE
+connections). It then samples on the shared `queue_metrics_interval` cadence,
+so that must be greater than 0.
 
 Alerting recommendations:
 
@@ -271,9 +287,9 @@ stream is healthy end-to-end:
    that connection within a second or two, and the history panel
    refreshes without a polling round-trip.
 3. On the server side, `galaxy.sse.dispatch.count` should be ticking up
-   for each event kind your users exercise. If you wired up the
-   connection gauges, they should reflect roughly one connection per
-   open browser tab.
+   for each event kind your users exercise, and
+   `galaxy.sse.connections.active` should reflect roughly one connection
+   per open browser tab (summed across the reporting processes).
 
 If the connection opens but no events arrive, the most common causes
 are: a proxy buffering responses (revisit the NGINX section), or a
diff --git a/lib/galaxy/app/__init__.py b/lib/galaxy/app/__init__.py
index d7d01562095..4033dc0b2ca 100644
--- a/lib/galaxy/app/__init__.py
+++ b/lib/galaxy/app/__init__.py
@@ -78,7 +78,10 @@ from galaxy.managers.notification import NotificationManager
 from galaxy.managers.object_store_instances import UserObjectStoreResolverImpl
 from galaxy.managers.roles import RoleManager
 from galaxy.managers.session import GalaxySessionManager
-from galaxy.managers.sse import SSEConnectionManager
+from galaxy.managers.sse import (
+    SSEConnectionGaugeEmitter,
+    SSEConnectionManager,
+)
 from galaxy.managers.sse_dispatch import SSEEventDispatcher
 from galaxy.managers.tasks import (
     AsyncTasksManager,
@@ -845,6 +848,7 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication, InstallationT
             ("queue worker", self._shutdown_queue_worker),
             ("file watcher", self._shutdown_watcher),
             ("database heartbeat", self._shutdown_database_heartbeat),
+            ("SSE connection gauge emitter", self._shutdown_sse_connection_gauge_emitter),
             ("history audit monitor", self._shutdown_history_audit_monitor),
             ("workflow scheduler", self._shutdown_scheduling_manager),
             ("object store", self._shutdown_object_store),
@@ -1028,6 +1032,31 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication, InstallationT
             monitor = self._register_singleton(HistoryAuditMonitor)
             self.database_heartbeat.add_audit_monitor_change_callback(monitor.on_role_change)
 
+        # Per-worker SSE connection-count gauge. The SSEConnectionManager is
+        # per-process state, so it must be sampled here in each web worker
+        # rather than from the Celery beat task (which holds no connections and
+        # would always report zero). Opt-in (enable_sse_connection_metrics) and
+        # only when statsd is actually configured (a non-None client) and the
+        # shared queue_metrics_interval cadence is enabled. The server_name is
+        # read post-fork so each worker tags its own series.
+        self.sse_connection_gauge_emitter: Optional[SSEConnectionGaugeEmitter] = None
+        statsd_client = self.execution_timer_factory.galaxy_statsd_client
+        if (
+            statsd_client is not None
+            and self.config.enable_sse_connection_metrics
+            and self.config.queue_metrics_interval > 0
+        ):
+
+            def _start_sse_connection_gauge_emitter():
+                self.sse_connection_gauge_emitter = SSEConnectionGaugeEmitter(
+                    self[SSEConnectionManager],
+                    self.config.server_name,
+                    interval=self.config.queue_metrics_interval,
+                )
+                self.sse_connection_gauge_emitter.start()
+
+            self.application_stack.register_postfork_function(_start_sse_connection_gauge_emitter)
+
         # Start web stack message handling
         self.application_stack.register_postfork_function(self.application_stack.start)
         self.application_stack.register_postfork_function(self.queue_worker.bind_and_start)
@@ -1062,6 +1091,10 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication, InstallationT
     def _shutdown_database_heartbeat(self):
         self.database_heartbeat.shutdown()
 
+    def _shutdown_sse_connection_gauge_emitter(self):
+        if self.sse_connection_gauge_emitter is not None:
+            self.sse_connection_gauge_emitter.shutdown()
+
     def _shutdown_history_audit_monitor(self):
         if not self.config.enable_sse_updates:
             return
diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py
index 48e079decd6..59c9c3ed721 100644
--- a/lib/galaxy/celery/tasks.py
+++ b/lib/galaxy/celery/tasks.py
@@ -12,7 +12,6 @@ from typing import (
 from urllib.parse import urlparse
 
 from celery import current_task
-from lagom.exceptions import UnresolvableType
 from sqlalchemy import (
     and_,
     create_engine,
@@ -50,7 +49,6 @@ from galaxy.managers.markdown_util import generate_branded_pdf
 from galaxy.managers.model_stores import ModelStoreManager
 from galaxy.managers.notification import NotificationManager
 from galaxy.managers.queue_metrics import emit_queue_metrics
-from galaxy.managers.sse import SSEConnectionManager
 from galaxy.managers.tool_data import ToolDataImportManager
 from galaxy.managers.workflow_completion import WorkflowCompletionManager
 from galaxy.metadata.set_metadata import set_metadata_portable
@@ -770,25 +768,23 @@ def dispatch_pending_notifications(notification_manager: NotificationManager):
         log.info(f"Successfully dispatched {count} notifications.")
 
 
-@galaxy_task(action="emit queue and SSE observability metrics")
+@galaxy_task(action="emit queue and worker-process observability metrics")
 def emit_queue_metrics_task(app: MinimalManagerApp):
-    """Sample control-queue depth, SSE connection count, and worker rows → statsd.
+    """Sample control-queue depth and worker rows → statsd.
 
     Resolves the narrow collaborators ``emit_queue_metrics`` needs from the app
     container and passes them in — keeps the emitter module free of
     ``StructuredApp`` service-locator lookups.
-    """
-    try:
-        sse_manager: Optional[SSEConnectionManager] = app[SSEConnectionManager]
-    except UnresolvableType:
-        sse_manager = None
 
+    SSE connection counts are emitted by the web workers themselves (see
+    ``galaxy.managers.sse.SSEConnectionGaugeEmitter``); the Celery worker has no
+    live connections to sample.
+    """
     emit_queue_metrics(
         statsd_client=app.execution_timer_factory.galaxy_statsd_client,
         connection=app.amqp_internal_connection_obj,
         application_stack=app.application_stack,
         model=app.model,
-        sse_manager=sse_manager,
     )
 
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index ab22fbd2ec4..7d421a59107 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -2004,11 +2004,22 @@ galaxy:
   # really. Do not set this in production environments.
   #statsd_mock_calls: false
 
-  # How often (in seconds) the Celery beat task emits queue-depth,
-  # SSE-connection, and WorkerProcess gauges. Only active when
-  # statsd_host is set. Set to 0 to disable.
+  # How often (in seconds) background observability gauges are sampled:
+  # control-queue depth and WorkerProcess counts from the Celery beat
+  # task, and (when enable_sse_connection_metrics is set) active
+  # SSE-connection counts from each web worker. This is the shared
+  # cadence for all of them. Only active when statsd_host is set. Set to
+  # 0 to disable all background gauges.
   #queue_metrics_interval: 15
 
+  # Emit the galaxy.sse.connections.active gauge from each web worker,
+  # reporting how many Server-Sent Events connections that worker
+  # currently holds (tagged by kind and server_name). Sampled on the
+  # queue_metrics_interval cadence. Off by default so that enabling
+  # statsd does not by itself start measuring SSE connections; requires
+  # statsd_host to be set and queue_metrics_interval greater than 0.
+  #enable_sse_connection_metrics: false
+
   # Add an option to the library upload form which allows administrators
   # to upload a directory of files.
   #library_import_dir: null
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index 9758ae5afda..54351b51f26 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -2577,8 +2577,22 @@ mapping:
         default: 15
         required: false
         desc: |
-          How often (in seconds) the Celery beat task emits queue-depth, SSE-connection,
-          and WorkerProcess gauges. Only active when statsd_host is set. Set to 0 to disable.
+          How often (in seconds) background observability gauges are sampled: control-queue
+          depth and WorkerProcess counts from the Celery beat task, and (when
+          enable_sse_connection_metrics is set) active SSE-connection counts from each web
+          worker. This is the shared cadence for all of them. Only active when statsd_host is
+          set. Set to 0 to disable all background gauges.
+
+      enable_sse_connection_metrics:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          Emit the galaxy.sse.connections.active gauge from each web worker, reporting how
+          many Server-Sent Events connections that worker currently holds (tagged by kind and
+          server_name). Sampled on the queue_metrics_interval cadence. Off by default so that
+          enabling statsd does not by itself start measuring SSE connections; requires
+          statsd_host to be set and queue_metrics_interval greater than 0.
 
       library_import_dir:
         type: str
diff --git a/lib/galaxy/managers/queue_metrics.py b/lib/galaxy/managers/queue_metrics.py
index df5591a9f18..2a8da81caf1 100644
--- a/lib/galaxy/managers/queue_metrics.py
+++ b/lib/galaxy/managers/queue_metrics.py
@@ -1,18 +1,23 @@
-"""Periodic gauge emitter for control-queue depth and SSE-connection counts.
+"""Periodic gauge emitter for control-queue depth and worker-process counts.
 
 Scheduled by Celery beat (see ``galaxy.celery.__init__.setup_periodic_tasks``)
 at a fixed cadence. Opens a short-lived kombu connection, iterates the control
 queues returned by ``all_control_queues_for_declare`` and samples each queue's
-message-count via a passive declare. Also samples in-memory connection counts
-from ``SSEConnectionManager`` and the active-``WorkerProcess`` count from the
-database.
+message-count via a passive declare. Also samples the active-``WorkerProcess``
+count from the database.
+
+SSE connection counts are deliberately *not* sampled here: the
+``SSEConnectionManager`` is per-process state held by the web workers, so the
+Celery worker would only ever see an empty manager. Each web worker emits its
+own ``galaxy.sse.connections.active`` gauge instead (see
+``galaxy.managers.sse.SSEConnectionGaugeEmitter``).
 
 All instrumentation no-ops when ``statsd_client`` is ``None`` — i.e. statsd
 isn't configured.
 
 The sub-emitters take narrow, typed collaborators (a kombu connection, an
-application stack, a model mapping, the statsd client, an SSE manager) rather
-than the whole ``StructuredApp``. The Celery task in
+application stack, a model mapping, the statsd client) rather than the whole
+``StructuredApp``. The Celery task in
 ``galaxy.celery.tasks.emit_queue_metrics_task`` is the composition root that
 resolves those narrow deps from the app and passes them in.
 """
@@ -31,7 +36,6 @@ from sqlalchemy import (
     select,
 )
 
-from galaxy.managers.sse import SSEConnectionManager
 from galaxy.model import WorkerProcess
 from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.queues import (
@@ -49,23 +53,6 @@ if TYPE_CHECKING:
 log = logging.getLogger(__name__)
 
 
-def emit_sse_connection_gauges(
-    statsd_client: "VanillaGalaxyStatsdClient",
-    sse_manager: SSEConnectionManager,
-) -> None:
-    """Emit ``galaxy.sse.connections.active`` gauges by connection kind."""
-    statsd_client.timing(
-        "galaxy.sse.connections.active",
-        sse_manager.total_broadcast_connections,
-        tags={"kind": "broadcast"},
-    )
-    statsd_client.timing(
-        "galaxy.sse.connections.active",
-        sse_manager.total_per_user_connections,
-        tags={"kind": "per_user"},
-    )
-
-
 def emit_control_queue_depth(
     statsd_client: "VanillaGalaxyStatsdClient",
     connection: "Optional[Connection]",
@@ -97,7 +84,7 @@ def emit_control_queue_depth(
                         exc_info=True,
                     )
                     continue
-                statsd_client.timing(
+                statsd_client.gauge(
                     "galaxy.control_queue.depth",
                     declared.message_count,
                     tags={"queue_name": queue.name},
@@ -122,7 +109,7 @@ def emit_worker_process_gauge(
         for app_type, count in session.execute(stmt):
             counts[app_type or "unknown"] = int(count)
     for app_type, count in counts.items():
-        statsd_client.timing(
+        statsd_client.gauge(
             "galaxy.worker_process.active",
             count,
             tags={"app_type": app_type},
@@ -149,13 +136,10 @@ def emit_queue_metrics(
     connection: "Optional[Connection]",
     application_stack: ApplicationStack,
     model: GalaxyModelMapping,
-    sse_manager: Optional[SSEConnectionManager],
 ) -> None:
     """Periodic entry-point — no-ops when statsd isn't configured."""
     if statsd_client is None:
         return
-    if sse_manager is not None:
-        _run("sse_connections", statsd_client, lambda: emit_sse_connection_gauges(statsd_client, sse_manager))
     _run(
         "control_queue_depth",
         statsd_client,
diff --git a/lib/galaxy/managers/sse.py b/lib/galaxy/managers/sse.py
index 30380051662..cc049390a28 100644
--- a/lib/galaxy/managers/sse.py
+++ b/lib/galaxy/managers/sse.py
@@ -7,6 +7,7 @@ to async SSE endpoint handlers running in the uvicorn event loop.
 
 import asyncio
 import logging
+import threading
 from collections import defaultdict
 from collections.abc import (
     AsyncIterator,
@@ -274,6 +275,29 @@ class SSEConnectionManager:
         """Number of active SSE connections bound to a specific user_id."""
         return sum(len(queues) for queues in self._connections.values())
 
+    def emit_connection_gauges(self, server_name: str) -> None:
+        """Publish this worker's SSE connection counts as statsd gauges.
+
+        No-ops when statsd isn't configured. The counts are per-process — only
+        the worker holding a connection knows about it — so this must be called
+        from the web worker that owns the manager, and each worker tags its
+        sample with ``server_name`` so the per-worker series don't collide
+        (statsd gauges are last-write-wins per metric+tag set). Sum across
+        workers for a cluster total.
+        """
+        if self._statsd_client is None:
+            return
+        self._statsd_client.gauge(
+            "galaxy.sse.connections.active",
+            self.total_broadcast_connections,
+            tags={"kind": "broadcast", "server_name": server_name},
+        )
+        self._statsd_client.gauge(
+            "galaxy.sse.connections.active",
+            self.total_per_user_connections,
+            tags={"kind": "per_user", "server_name": server_name},
+        )
+
     # -- High-level streaming helper --
 
     async def stream(
@@ -311,3 +335,33 @@ class SSEConnectionManager:
                     yield ": keepalive\n\n"
         finally:
             self.disconnect(user_id, queue, galaxy_session_id)
+
+
+class SSEConnectionGaugeEmitter(threading.Thread):
+    """Periodically publish a web worker's SSE connection-count gauges.
+
+    Runs as a daemon thread inside each web worker — the only process that
+    knows how many SSE connections it holds. Sampling these counts from the
+    Celery beat task instead would always report zero, since that process has
+    no live connections. Reads are plain ``len()`` over the manager's
+    in-memory sets; a transient race with connect/disconnect is acceptable for
+    a monitoring gauge.
+    """
+
+    def __init__(self, manager: SSEConnectionManager, server_name: str, interval: int = 15) -> None:
+        super().__init__(name=f"sse_connection_gauge.{server_name}", daemon=True)
+        self._manager = manager
+        self._server_name = server_name
+        self._interval = interval
+        self._exit = threading.Event()
+
+    def run(self) -> None:
+        while not self._exit.is_set():
+            try:
+                self._manager.emit_connection_gauges(self._server_name)
+            except Exception:
+                log.warning("Failed to emit SSE connection gauges", exc_info=True)
+            self._exit.wait(self._interval)
+
+    def shutdown(self) -> None:
+        self._exit.set()
diff --git a/lib/galaxy/web/statsd_client.py b/lib/galaxy/web/statsd_client.py
index d27a7cf6ccd..02a230ce76d 100644
--- a/lib/galaxy/web/statsd_client.py
+++ b/lib/galaxy/web/statsd_client.py
@@ -33,6 +33,10 @@ class VanillaGalaxyStatsdClient:
         infix = self._effective_infix(path, tags)
         self.statsd_client.timing(infix + path, time)
 
+    def gauge(self, path, value, tags=None):
+        infix = self._effective_infix(path, tags)
+        self.statsd_client.gauge(infix + path, value)
+
     def incr(self, path, n=1, tags=None):
         infix = self._effective_infix(path, tags)
         self.statsd_client.incr(infix + path, n)
@@ -60,6 +64,14 @@ class PyTestGalaxyStatsdClient(VanillaGalaxyStatsdClient):
             timing[path].append({"time": time, "tags": tags})
         super().timing(path, time, tags=tags)
 
+    def gauge(self, path, value, tags=None):
+        if (metrics := CURRENT_TEST_METRICS) is not None:
+            gauge = metrics.setdefault("gauge", {})
+            if path not in gauge:
+                gauge[path] = []
+            gauge[path].append({"value": value, "tags": tags})
+        super().gauge(path, value, tags=tags)
+
     def incr(self, path, n=1, tags=None):
         if (metrics := CURRENT_TEST_METRICS) is not None:
             counter = metrics["counter"]
@@ -79,6 +91,9 @@ class MockStatsClient:
     def timing(self, path, time, tags=None):
         pass
 
+    def gauge(self, path, value, tags=None):
+        pass
+
     def incr(self, path, n=1, tags=None):
         pass
 
diff --git a/lib/galaxy_test/conftest.py b/lib/galaxy_test/conftest.py
index 6c0b08ef847..de5ba3178bd 100644
--- a/lib/galaxy_test/conftest.py
+++ b/lib/galaxy_test/conftest.py
@@ -67,7 +67,7 @@ class JsonReportHooks:
     def pytest_json_runtest_metadata(self, item, call):
         if call.when == "setup":
             statsd.CURRENT_TEST = str(uuid.uuid4())
-            statsd.CURRENT_TEST_METRICS = {"timing": {}, "counter": {}}
+            statsd.CURRENT_TEST_METRICS = {"timing": {}, "counter": {}, "gauge": {}}
             return {}
         if call.when == "teardown":
             statsd.CURRENT_TEST = None
diff --git a/test/unit/app/managers/test_queue_metrics.py b/test/unit/app/managers/test_queue_metrics.py
index 8bacd21d4b0..8ef9aa65998 100644
--- a/test/unit/app/managers/test_queue_metrics.py
+++ b/test/unit/app/managers/test_queue_metrics.py
@@ -1,10 +1,9 @@
 """Unit tests for :mod:`galaxy.managers.queue_metrics`.
 
-The ``SSEConnectionManager`` and the kombu connection are small hand-built
-fakes — no broker or database is required. Assertions are on the recorded
-state of the statsd client (counters, timings) rather than on mock call-lists
-so a regression that stops emitting a gauge fails the test for the right
-reason.
+The kombu connection is a small hand-built fake — no broker or database is
+required. Assertions are on the recorded state of the statsd client (counters,
+gauges) rather than on mock call-lists so a regression that stops emitting a
+gauge fails the test for the right reason.
 
 The failure-isolation test drives real sub-emitters into their error paths by
 handing them genuinely broken collaborators (a connection whose ``clone()``
@@ -26,7 +25,6 @@ from unittest.mock import MagicMock
 import pytest
 
 from galaxy.managers import queue_metrics
-from galaxy.managers.sse import SSEConnectionManager
 from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.web.statsd_client import VanillaGalaxyStatsdClient
 from galaxy.web_stack import ApplicationStack
@@ -41,27 +39,20 @@ class FakeStatsdClient:
     """In-memory statsd recorder — see docstring in ``test_sse_dispatch.py``."""
 
     counters: dict[tuple[str, tuple[tuple[str, str], ...]], int] = field(default_factory=dict)
-    timings: list[tuple[str, float, tuple[tuple[str, str], ...]]] = field(default_factory=list)
+    gauges: list[tuple[str, float, tuple[tuple[str, str], ...]]] = field(default_factory=list)
 
     def incr(self, metric: str, tags: Optional[dict[str, str]] = None) -> None:
         key = (metric, tuple(sorted((tags or {}).items())))
         self.counters[key] = self.counters.get(key, 0) + 1
 
-    def timing(self, metric: str, value: float, tags: Optional[dict[str, str]] = None) -> None:
-        self.timings.append((metric, value, tuple(sorted((tags or {}).items()))))
+    def gauge(self, metric: str, value: float, tags: Optional[dict[str, str]] = None) -> None:
+        self.gauges.append((metric, value, tuple(sorted((tags or {}).items()))))
 
     def counter(self, metric: str, tags: Optional[dict[str, str]] = None) -> int:
         return self.counters.get((metric, tuple(sorted((tags or {}).items()))), 0)
 
-    def timings_for(self, metric: str) -> list[tuple[float, dict[str, str]]]:
-        return [(v, dict(t)) for m, v, t in self.timings if m == metric]
-
-
-def _fake_sse_manager(broadcast: int = 3, per_user: int = 5):
-    m = MagicMock(spec=SSEConnectionManager)
-    m.total_broadcast_connections = broadcast
-    m.total_per_user_connections = per_user
-    return m
+    def gauges_for(self, metric: str) -> list[tuple[float, dict[str, str]]]:
+        return [(v, dict(t)) for m, v, t in self.gauges if m == metric]
 
 
 def _make_fake_queue(name: str, count: int):
@@ -89,18 +80,6 @@ def _make_fake_connection(channel=None):
 # ---------------------------------------------------------------------------
 
 
-def test_emit_sse_connection_gauges_emits_both_kinds():
-    statsd = FakeStatsdClient()
-    queue_metrics.emit_sse_connection_gauges(
-        cast(VanillaGalaxyStatsdClient, statsd), _fake_sse_manager(broadcast=4, per_user=7)
-    )
-
-    assert statsd.timings_for("galaxy.sse.connections.active") == [
-        (4, {"kind": "broadcast"}),
-        (7, {"kind": "per_user"}),
-    ]
-
-
 def test_emit_control_queue_depth_emits_per_queue(monkeypatch):
     statsd = FakeStatsdClient()
     fake_queues = [
@@ -119,7 +98,7 @@ def test_emit_control_queue_depth_emits_per_queue(monkeypatch):
         cast(ApplicationStack, MagicMock()),
     )
 
-    assert statsd.timings_for("galaxy.control_queue.depth") == [
+    assert statsd.gauges_for("galaxy.control_queue.depth") == [
         (3, {"queue_name": "control.main@h"}),
         (0, {"queue_name": "control.main.1@h"}),
     ]
@@ -145,7 +124,7 @@ def test_emit_control_queue_depth_skips_failed_passive_declare(monkeypatch):
         cast(ApplicationStack, MagicMock()),
     )
 
-    assert statsd.timings_for("galaxy.control_queue.depth") == [
+    assert statsd.gauges_for("galaxy.control_queue.depth") == [
         (9, {"queue_name": "control.good@h"}),
     ]
 
@@ -155,7 +134,7 @@ def test_emit_control_queue_depth_no_broker_connection_is_noop():
     queue_metrics.emit_control_queue_depth(
         cast(VanillaGalaxyStatsdClient, statsd), None, cast(ApplicationStack, MagicMock())
     )
-    assert statsd.timings == []
+    assert statsd.gauges == []
 
 
 # ---------------------------------------------------------------------------
@@ -172,7 +151,6 @@ def test_emit_queue_metrics_is_silent_when_statsd_is_none():
         connection=None,
         application_stack=cast(ApplicationStack, MagicMock()),
         model=cast(GalaxyModelMapping, MagicMock()),
-        sse_manager=None,
     )
 
 
@@ -182,11 +160,10 @@ def test_emit_queue_metrics_isolates_real_subemitter_failures(monkeypatch):
     We drive the failures through the actual sub-emitter bodies — not monkey-
     patched side_effects — by handing in a connection whose ``.clone()`` raises
     (for ``emit_control_queue_depth``) and a model whose ``.new_session()``
-    raises (for ``emit_worker_process_gauge``). The SSE gauge is given healthy
-    collaborators and should still land.
+    raises (for ``emit_worker_process_gauge``). One failing sub-emitter must not
+    take the other down.
     """
     statsd = FakeStatsdClient()
-    sse_manager = _fake_sse_manager(broadcast=2, per_user=1)
 
     broken_connection = MagicMock()
     broken_connection.clone.side_effect = RuntimeError("broker is gone")
@@ -202,25 +179,17 @@ def test_emit_queue_metrics_isolates_real_subemitter_failures(monkeypatch):
         lambda stack: [_make_fake_queue("control.main@h", 0)],
     )
 
-    # Must not raise — the SSE gauge still lands.
+    # Must not raise — each failure is isolated.
     queue_metrics.emit_queue_metrics(
         statsd_client=cast(VanillaGalaxyStatsdClient, statsd),
         connection=broken_connection,
         application_stack=cast(ApplicationStack, MagicMock()),
         model=cast(GalaxyModelMapping, broken_model),
-        sse_manager=sse_manager,
     )
 
-    # SSE gauge landed despite the other two failing.
-    sse_timings = statsd.timings_for("galaxy.sse.connections.active")
-    assert (2, {"kind": "broadcast"}) in sse_timings
-    assert (1, {"kind": "per_user"}) in sse_timings
-
     # Each failing sub-emitter bumped its error counter tagged by name.
     assert statsd.counter("galaxy.queue_metrics.error", {"emitter": "control_queue_depth"}) == 1
     assert statsd.counter("galaxy.queue_metrics.error", {"emitter": "worker_process"}) == 1
-    # The healthy SSE sub-emitter did not.
-    assert statsd.counter("galaxy.queue_metrics.error", {"emitter": "sse_connections"}) == 0
 
 
 if __name__ == "__main__":
diff --git a/test/unit/app/managers/test_sse_connection_gauges.py b/test/unit/app/managers/test_sse_connection_gauges.py
new file mode 100644
index 00000000000..c3f09bb0553
--- /dev/null
+++ b/test/unit/app/managers/test_sse_connection_gauges.py
@@ -0,0 +1,89 @@
+"""Unit tests for the per-worker SSE connection-count gauge.
+
+``SSEConnectionManager.emit_connection_gauges`` is sampled inside each web
+worker (the only process that holds its connections), so these tests assert it
+reports the manager's *own* counts, tags each series with ``server_name`` so
+per-worker series don't collide, and no-ops without a statsd client.
+``SSEConnectionGaugeEmitter`` is the daemon-thread driver; we check it emits at
+least once and stops cleanly.
+"""
+
+import threading
+from dataclasses import (
+    dataclass,
+    field,
+)
+from typing import (
+    cast,
+    Optional,
+)
+
+from galaxy.managers.sse import (
+    SSEConnectionGaugeEmitter,
+    SSEConnectionManager,
+)
+from galaxy.web.statsd_client import VanillaGalaxyStatsdClient
+
+
+@dataclass
+class FakeStatsdClient:
+    """In-memory recorder — captures ``gauge`` calls as plain data.
+
+    ``recorded`` fires on every ``gauge`` call so a test can wait on the real
+    effect (a gauge landed) without instrumenting the production code.
+    """
+
+    gauges: list[tuple[str, float, tuple[tuple[str, str], ...]]] = field(default_factory=list)
+    recorded: threading.Event = field(default_factory=threading.Event)
+
+    def gauge(self, metric: str, value: float, tags: Optional[dict[str, str]] = None) -> None:
+        self.gauges.append((metric, value, tuple(sorted((tags or {}).items()))))
+        self.recorded.set()
+
+    def gauges_for(self, metric: str) -> list[tuple[float, dict[str, str]]]:
+        return [(v, dict(t)) for m, v, t in self.gauges if m == metric]
+
+
+def _manager(statsd: Optional[FakeStatsdClient]) -> SSEConnectionManager:
+    return SSEConnectionManager(statsd_client=cast(Optional[VanillaGalaxyStatsdClient], statsd))
+
+
+async def test_emit_connection_gauges_reports_own_counts_tagged_by_server_name():
+    statsd = FakeStatsdClient()
+    manager = _manager(statsd)
+    # Two connections for a logged-in user, one anonymous (session-only).
+    manager.connect(user_id=7)
+    manager.connect(user_id=7)
+    manager.connect(user_id=None, galaxy_session_id=99)
+
+    manager.emit_connection_gauges("main.1")
+
+    assert statsd.gauges_for("galaxy.sse.connections.active") == [
+        (3, {"kind": "broadcast", "server_name": "main.1"}),
+        (2, {"kind": "per_user", "server_name": "main.1"}),
+    ]
+
+
+async def test_emit_connection_gauges_is_noop_without_statsd():
+    manager = _manager(None)
+    manager.connect(user_id=1)
+    # Must not raise even though no statsd client is configured.
+    manager.emit_connection_gauges("main.1")
+
+
+async def test_emitter_emits_then_stops():
+    statsd = FakeStatsdClient()
+    manager = _manager(statsd)
+    manager.connect(user_id=1)
+
+    # interval=600 so the thread emits once then blocks until shutdown; we wait
+    # on the recorder's event (the real effect) rather than patching the manager.
+    emitter = SSEConnectionGaugeEmitter(manager, "main.1", interval=600)
+    emitter.start()
+    try:
+        assert statsd.recorded.wait(timeout=5), "emitter never emitted a gauge"
+    finally:
+        emitter.shutdown()
+        emitter.join(timeout=5)
+    assert not emitter.is_alive()
+    assert statsd.gauges_for("galaxy.sse.connections.active")

From 52040a3bfbfa95e764b3d5efc75fc1913e6105a1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 11:02:42 +0200
Subject: [PATCH 225/256] Avoid `outputs.output.path`, add resource sample

---
 .../agents/prompts/custom_tool_structured.md  | 25 ++++++++++++++++---
 1 file changed, 21 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/agents/prompts/custom_tool_structured.md b/lib/galaxy/agents/prompts/custom_tool_structured.md
index 7c1380e0e31..071e0a7f5c8 100644
--- a/lib/galaxy/agents/prompts/custom_tool_structured.md
+++ b/lib/galaxy/agents/prompts/custom_tool_structured.md
@@ -24,7 +24,8 @@ You are a Galaxy tool generator. Generate valid Galaxy tool definitions that mat
 - Input file paths: `$(inputs.param_name.path)` for single files
 - Input values: `$(inputs.param_name)` for text, integer, float, boolean
 - For array inputs: `$(inputs.param_name[].path)`
-- Outputs are captured via `from_work_dir` or `discover_datasets` in output definitions
+- Outputs are captured via `from_work_dir` or `discover_datasets` in output definitions.
+  $(outputs.out.path) is not valid syntax.
 
 ## Input Parameter Types
 
@@ -45,10 +46,10 @@ inputs:
       type: data
       format: fastq
       label: Input FASTQ file
-    - name: num_threads
+    - name: num_records
       type: integer
-      default: 4
-      label: Number of threads
+      value: 4
+      label: Number of Records
 ```
 
 ## Output Types
@@ -69,6 +70,22 @@ outputs:
       label: Aligned reads
 ```
 
+## Resource requirements
+
+Tools can request non-default resources.
+To request at least 2 cores, 1 Gibibyte memory and one CUDA core use
+
+```yaml
+requirements:
+  - type: resource
+    cores_min: 2
+    cuda_device_count_min: 1
+    ram_min: 1024
+```
+
+The GALAXY_SLOTS environment variable will be available in the process
+environment and be set to `cores_min`.
+
 ## Important Guidelines
 
 - Use biocontainers images when available for bioinformatics tools

From d5b6ce4eb298ff46b114e3e3268b9e01d89b8856 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 18 Jun 2026 14:21:03 +0200
Subject: [PATCH 226/256] Fix view state logic for paste links upload

Ensure the URL input area is automatically displayed when the link list is empty and the staged view is displayed when there are existing elements.
---
 .../Panels/Upload/methods/PasteLinksUpload.vue | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Panels/Upload/methods/PasteLinksUpload.vue b/client/src/components/Panels/Upload/methods/PasteLinksUpload.vue
index 55f8611ab97..bf214e80ada 100644
--- a/client/src/components/Panels/Upload/methods/PasteLinksUpload.vue
+++ b/client/src/components/Panels/Upload/methods/PasteLinksUpload.vue
@@ -84,7 +84,13 @@ function createPasteUrlItem(id: number, url: string, name: string): PasteUrlItem
 
 const urlItems = ref<PasteUrlItem[]>([]);
 const urlText = ref("");
-const showInputArea = ref(true);
+const showInputOverride = ref(false);
+const showInputArea = computed(() => {
+    if (urlItems.value.length > 0) {
+        return showInputOverride.value;
+    }
+    return true;
+});
 const { clear: clearStaging } = useUploadStaging<PasteUrlItem>(props.method.id, urlItems, {
     disableStore: props.transient,
 });
@@ -143,16 +149,16 @@ function addUrlsFromText() {
     }
 
     urlText.value = "";
-    showInputArea.value = false;
+    showInputOverride.value = false;
     scrollToBottom();
 }
 
 function showUrlInput() {
-    showInputArea.value = true;
+    showInputOverride.value = true;
 }
 
 function showUrlList() {
-    showInputArea.value = false;
+    showInputOverride.value = false;
 }
 
 function scrollToBottom() {
@@ -168,7 +174,7 @@ function removeItem(id: number) {
     urlItems.value = urlItems.value.filter((item) => item.id !== id);
 
     if (urlItems.value.length === 0) {
-        showInputArea.value = true;
+        showInputOverride.value = false;
         resetCollection();
     }
 }
@@ -221,7 +227,7 @@ function reset() {
     urlItems.value = [];
     urlText.value = "";
     clearStaging();
-    showInputArea.value = true;
+    showInputOverride.value = false;
     resetCollection();
 }
 

From cfd065a6accb44b5d19beb4f6cafae599c00be54 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 18 Jun 2026 09:31:33 -0400
Subject: [PATCH 227/256] Serve datatype converter tools as stock tools

stock_tool_paths() walked galaxy.tools, the functional test tools, and
the config/tools directory, but not galaxy.datatypes.converters. As a
result the built-in CONVERTER_* tools were absent from the stock tool
set, so the Tool Shed could not serve their tool definitions (e.g. for
offline workflow tool_state validation against the TRS API).

Walk galaxy.datatypes.converters alongside galaxy.tools so the converter
tools are discovered and served.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/tools/stock.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/tools/stock.py b/lib/galaxy/tools/stock.py
index a1a6804ca4d..a3fce9dc5da 100644
--- a/lib/galaxy/tools/stock.py
+++ b/lib/galaxy/tools/stock.py
@@ -6,6 +6,7 @@ from lxml.etree import XMLSyntaxError
 
 # Set GALAXY_INCLUDES_ROOT from tool shed to point this at a Galaxy root
 # (once we are running the tool shed from packages not rooted with Galaxy).
+import galaxy.datatypes.converters
 import galaxy.tools
 from galaxy.tool_util.loader_directory import looks_like_a_tool_xml
 from galaxy.tool_util.parser import get_tool_source
@@ -15,6 +16,7 @@ from galaxy.util.resources import files
 
 def stock_tool_paths():
     yield from _walk_directory_for_tools(files(galaxy.tools))
+    yield from _walk_directory_for_tools(files(galaxy.datatypes.converters))
     yield from _walk_directory_for_tools(Path(galaxy_directory()) / "test" / "functional" / "tools")
     yield from _walk_directory_for_tools(Path(galaxy_directory()) / "tools")
 

From be84e90274b22273b789c7a2331eceae446b5d29 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 18 Jun 2026 09:33:41 -0400
Subject: [PATCH 228/256] Serve workflow-safe stock tool versions on
 exact-version miss

When the Tool Shed is asked for a stock tool at an exact version that
isn't present in the stock tool set, _stock_tool_source_for() returned
None even when a newer stock version is schema-compatible. Workflows
pinned to a slightly older stock-tool version (e.g. Filter1 1.1.0 when
1.1.1 ships) then failed to resolve a tool source for offline tool_state
validation.

Extract the workflow-safe version mapping out of galaxy.tools.__init__
into a shared galaxy.tool_util.version_updates module (with the
AnyVersionT alias in galaxy.tool_util.version_util) so both the Galaxy
runtime and the tool_shed package can consume a single source of truth
instead of duplicating it.

Then add a workflow-safe version fallback in _stock_tool_source_for():
when the requested version falls within a tool's (min_version,
current_version) safe-update range, serve the current version's source.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/tool_util/version_updates.py | 54 +++++++++++++++++++++++++
 lib/galaxy/tool_util/version_util.py    | 10 +++++
 lib/galaxy/tools/__init__.py            | 29 +------------
 lib/tool_shed/managers/tools.py         |  9 ++++-
 4 files changed, 73 insertions(+), 29 deletions(-)
 create mode 100644 lib/galaxy/tool_util/version_updates.py
 create mode 100644 lib/galaxy/tool_util/version_util.py

diff --git a/lib/galaxy/tool_util/version_updates.py b/lib/galaxy/tool_util/version_updates.py
new file mode 100644
index 00000000000..540589f507e
--- /dev/null
+++ b/lib/galaxy/tool_util/version_updates.py
@@ -0,0 +1,54 @@
+"""Workflow-safe tool version updates.
+
+Maps tool IDs to version ranges where parameter schemas are unchanged,
+so an older workflow referencing min_version can safely use current_version's
+tool definition for validation and state inspection.
+"""
+
+from typing import (
+    NamedTuple,
+    Optional,
+)
+
+from .version import parse_version
+from .version_util import AnyVersionT
+
+
+class safe_update(NamedTuple):
+    min_version: AnyVersionT
+    current_version: AnyVersionT
+
+
+WORKFLOW_SAFE_TOOL_VERSION_UPDATES: dict[str, safe_update] = {
+    "Filter1": safe_update(parse_version("1.1.0"), parse_version("1.1.1")),
+    "__BUILD_LIST__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
+    "__APPLY_RULES__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
+    "__EXTRACT_DATASET__": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
+    "__RELABEL_FROM_FILE__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
+    "Grep1": safe_update(parse_version("1.0.1"), parse_version("1.0.4")),
+    "Show beginning1": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
+    "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "sort1": safe_update(parse_version("1.1.0"), parse_version("1.2.0")),
+    "Convert characters1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
+    "CONVERTER_Bam_Bai_0": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_cram_to_bam_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
+    "CONVERTER_fasta_to_fai": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_sam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
+    "CONVERTER_bam_to_coodinate_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_bam_to_qname_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+}
+
+
+def is_workflow_safe_version(tool_id: str, requested_version: str) -> Optional[str]:
+    """Check if requested_version falls within a safe update range for tool_id.
+
+    Returns the current_version string if safe, None otherwise.
+    """
+    update = WORKFLOW_SAFE_TOOL_VERSION_UPDATES.get(tool_id)
+    if update is None:
+        return None
+    requested = parse_version(requested_version)
+    if update.min_version <= requested <= update.current_version:
+        return str(update.current_version)
+    return None
diff --git a/lib/galaxy/tool_util/version_util.py b/lib/galaxy/tool_util/version_util.py
new file mode 100644
index 00000000000..644d58297e4
--- /dev/null
+++ b/lib/galaxy/tool_util/version_util.py
@@ -0,0 +1,10 @@
+from typing import Union
+
+from packaging.version import Version
+
+from .version import LegacyVersion
+
+AnyVersionT = Union[LegacyVersion, Version]
+
+
+__all__ = ["AnyVersionT"]
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index aa02da31612..8746ee67a31 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -126,9 +126,9 @@ from galaxy.tool_util.verify.interactor import ToolTestDescription
 from galaxy.tool_util.verify.parse import parse_tool_test_descriptions
 from galaxy.tool_util.verify.test_data import TestDataNotFoundError
 from galaxy.tool_util.version import (
-    LegacyVersion,
     parse_version,
 )
+from galaxy.tool_util.version_updates import WORKFLOW_SAFE_TOOL_VERSION_UPDATES
 from galaxy.tool_util_models.parameters import (
     MaybeToolParameterBundle,
     ToolParameterBundleModel,
@@ -386,11 +386,6 @@ IMPLICITLY_REQUIRED_TOOL_FILES: dict[str, dict] = {
 }
 
 
-class safe_update(NamedTuple):
-    min_version: Union[LegacyVersion, Version]
-    current_version: Union[LegacyVersion, Version]
-
-
 class RawToolSource(NamedTuple):
     """Compact representation of a tool's raw source for transport/serialization.
 
@@ -403,28 +398,6 @@ class RawToolSource(NamedTuple):
     tool_source_class: str
 
 
-# Tool updates that did not change parameters in a way that requires rebuilding workflows
-WORKFLOW_SAFE_TOOL_VERSION_UPDATES = {
-    "Filter1": safe_update(parse_version("1.1.0"), parse_version("1.1.1")),
-    "__BUILD_LIST__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
-    "__APPLY_RULES__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
-    "__EXTRACT_DATASET__": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
-    "__RELABEL_FROM_FILE__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
-    "Grep1": safe_update(parse_version("1.0.1"), parse_version("1.0.4")),
-    "Show beginning1": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
-    "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "sort1": safe_update(parse_version("1.1.0"), parse_version("1.2.0")),
-    "Convert characters1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
-    "CONVERTER_Bam_Bai_0": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_cram_to_bam_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
-    "CONVERTER_fasta_to_fai": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_sam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
-    "CONVERTER_bam_to_coodinate_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_bam_to_qname_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-}
-
-
 def get_safe_version(tool: "Tool", requested_tool_version: str) -> Optional[str]:
     if tool.id:
         safe_version = WORKFLOW_SAFE_TOOL_VERSION_UPDATES.get(tool.id)
diff --git a/lib/tool_shed/managers/tools.py b/lib/tool_shed/managers/tools.py
index d52e020742a..c9437632c55 100644
--- a/lib/tool_shed/managers/tools.py
+++ b/lib/tool_shed/managers/tools.py
@@ -23,6 +23,7 @@ from galaxy.tool_util.parser import (
     get_tool_source,
     ToolSource,
 )
+from galaxy.tool_util.version_updates import is_workflow_safe_version
 from galaxy.tools.stock import stock_tool_sources
 from galaxy.util import relpath
 from tool_shed.context import (
@@ -176,7 +177,13 @@ def _stock_tool_source_for(tool_id: str, tool_version: str) -> Optional[ToolSour
     tool_version_sources = STOCK_TOOL_SOURCES.get(tool_id)
     if tool_version_sources is None:
         return None
-    return tool_version_sources.get(tool_version)
+    tool_source = tool_version_sources.get(tool_version)
+    if tool_source is not None:
+        return tool_source
+    safe_version = is_workflow_safe_version(tool_id, tool_version)
+    if safe_version is not None:
+        return tool_version_sources.get(safe_version)
+    return None
 
 
 def _init_stock_tool_sources() -> None:

From f42b13f0ba806e336c444c972f35f760dd56db90 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 18 Jun 2026 09:57:24 -0400
Subject: [PATCH 229/256] Unit tests for stock converter serving and
 safe-version fallback

- test_stock: assert datatype converter tools (bam_to_bai.xml) are
  among stock_tool_paths().
- tool_shed: assert _stock_tool_source_for() serves a workflow-safe
  current version on exact-version miss (sort1 1.1.0 -> 1.2.0) and
  returns None for out-of-range versions.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 test/unit/app/tools/test_stock.py             |  5 +++++
 test/unit/tool_shed/test_stock_tool_source.py | 12 ++++++++++++
 2 files changed, 17 insertions(+)
 create mode 100644 test/unit/tool_shed/test_stock_tool_source.py

diff --git a/test/unit/app/tools/test_stock.py b/test/unit/app/tools/test_stock.py
index 3918bd72b90..9d3ee753984 100644
--- a/test/unit/app/tools/test_stock.py
+++ b/test/unit/app/tools/test_stock.py
@@ -12,6 +12,11 @@ def test_stock_tool_paths():
     assert "parse_values_from_file.xml" in file_names
 
 
+def test_stock_tool_paths_includes_datatype_converters():
+    file_names = [f.name for f in stock_tool_paths()]
+    assert "bam_to_bai.xml" in file_names
+
+
 def test_stock_tool_sources():
     tool_source = next(stock_tool_sources())
     assert tool_source.parse_id()
diff --git a/test/unit/tool_shed/test_stock_tool_source.py b/test/unit/tool_shed/test_stock_tool_source.py
new file mode 100644
index 00000000000..7927349af12
--- /dev/null
+++ b/test/unit/tool_shed/test_stock_tool_source.py
@@ -0,0 +1,12 @@
+from tool_shed.managers.tools import _stock_tool_source_for
+
+
+def test_serves_workflow_safe_version_on_exact_miss():
+    # sort1 only ships 1.2.0; 1.1.0 is within its safe-update range and resolves to it.
+    tool_source = _stock_tool_source_for("sort1", "1.1.0")
+    assert tool_source is not None
+    assert tool_source.parse_version() == "1.2.0"
+
+
+def test_returns_none_for_out_of_range_version():
+    assert _stock_tool_source_for("sort1", "0.0.1") is None

From fb6f6bf0623618fd703194e1c290b823e5e1285f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:54:22 +0200
Subject: [PATCH 230/256] Adds `requiresLogin` property to upload methods

---
 client/src/components/Panels/Upload/types.ts | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/client/src/components/Panels/Upload/types.ts b/client/src/components/Panels/Upload/types.ts
index 743b8308036..b1d16e4a4e3 100644
--- a/client/src/components/Panels/Upload/types.ts
+++ b/client/src/components/Panels/Upload/types.ts
@@ -83,6 +83,13 @@ export interface UploadMethodConfig {
      */
     requiresAdvancedMode?: boolean;
 
+    /**
+     * When true, this upload method requires the user to be logged in.
+     *
+     * Methods with this flag will be hidden from anonymous users.
+     */
+    requiresLogin?: boolean;
+
     /**
      * When true, the Start button in the footer will be shown.
      *

From f9401444b2c6914482b9eee7c6d30a1c117a8256 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:54:23 +0200
Subject: [PATCH 231/256] Designates import methods as requiring login

---
 client/src/components/Panels/Upload/uploadMethodRegistry.ts | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/client/src/components/Panels/Upload/uploadMethodRegistry.ts b/client/src/components/Panels/Upload/uploadMethodRegistry.ts
index a557c109a3b..fab434c86d0 100644
--- a/client/src/components/Panels/Upload/uploadMethodRegistry.ts
+++ b/client/src/components/Panels/Upload/uploadMethodRegistry.ts
@@ -148,6 +148,7 @@ export const uploadMethodRegistry: Record<UploadMethod, UploadMethodConfig> = {
         icon: faHdd,
         headerAction: "Import History",
         requiresTargetHistory: false,
+        requiresLogin: true,
         showStartButton: false,
         tips: [
             "Import a complete Galaxy history from a previously exported file or URL",
@@ -163,6 +164,7 @@ export const uploadMethodRegistry: Record<UploadMethod, UploadMethodConfig> = {
         icon: faSitemap,
         headerAction: "Import Workflow",
         requiresTargetHistory: false,
+        requiresLogin: true,
         showStartButton: false,
         tips: [
             "Import workflows from Galaxy Workflow files or public URLs",

From b55dde8b7d5401ef43a7afef69204eed3f1d38ef Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:54:23 +0200
Subject: [PATCH 232/256] Implements login filtering in
 `useFilteredUploadMethods`

---
 .../Panels/Upload/uploadMethodRegistry.ts     | 21 +++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Panels/Upload/uploadMethodRegistry.ts b/client/src/components/Panels/Upload/uploadMethodRegistry.ts
index fab434c86d0..7ac898bb987 100644
--- a/client/src/components/Panels/Upload/uploadMethodRegistry.ts
+++ b/client/src/components/Panels/Upload/uploadMethodRegistry.ts
@@ -11,13 +11,14 @@ import {
     faSitemap,
     faTable,
 } from "@fortawesome/free-solid-svg-icons";
+import { storeToRefs } from "pinia";
 import { computed, type ComputedRef, defineAsyncComponent, type Ref } from "vue";
 
 import { useConfig } from "@/composables/config";
 import { useUploadAdvancedMode } from "@/composables/upload/uploadAdvancedMode";
+import { useUserStore } from "@/stores/userStore";
 
 import type { UploadMethod, UploadMethodConfig } from "./types";
-import type { UploadModalConfig } from "./uploadModalTypes";
 
 export const uploadMethodRegistry: Record<UploadMethod, UploadMethodConfig> = {
     "local-file": {
@@ -209,17 +210,25 @@ export function useAllUploadMethods(): ComputedRef<UploadMethodConfig[]> {
 }
 
 /**
- * Reactive list of upload methods filtered by modal config and Galaxy config requirements.
+ * Reactive list of upload methods filtered by allowed methods, Galaxy config, and login requirements.
+ *
+ * @param allowedMethods - Optional list of allowed upload method IDs. When `undefined`,
+ * only `requiresLogin`, `requiresConfig`, and `requiresAdvancedMode` filters are applied.
  */
-export function useFilteredUploadMethods(config: Ref<UploadModalConfig>): ComputedRef<UploadMethodConfig[]> {
+export function useFilteredUploadMethods(
+    allowedMethods?: Ref<UploadMethod[] | undefined>,
+): ComputedRef<UploadMethodConfig[]> {
     const allMethods = useAllUploadMethods();
     const { config: galaxyConfig, isConfigLoaded } = useConfig();
+    const { isAnonymous } = storeToRefs(useUserStore());
 
     return computed(() => {
-        const allowedMethods = config.value.allowedMethods;
-
         return allMethods.value.filter((method) => {
-            if (allowedMethods && !allowedMethods.some((allowedMethod) => allowedMethod === method.id)) {
+            if (method.requiresLogin && isAnonymous.value) {
+                return false;
+            }
+
+            if (allowedMethods?.value && !allowedMethods.value.some((allowedMethod) => allowedMethod === method.id)) {
                 return false;
             }
 

From 455bd9e4cde5cb19fccbc8445c58d32c6bfe4de3 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:54:23 +0200
Subject: [PATCH 233/256] Simplifies method filtering in `UploadMethodList`

---
 .../Panels/Upload/UploadMethodList.vue        | 20 ++-----------------
 1 file changed, 2 insertions(+), 18 deletions(-)

diff --git a/client/src/components/Panels/Upload/UploadMethodList.vue b/client/src/components/Panels/Upload/UploadMethodList.vue
index 2f40bbb495e..225dc925278 100644
--- a/client/src/components/Panels/Upload/UploadMethodList.vue
+++ b/client/src/components/Panels/Upload/UploadMethodList.vue
@@ -3,11 +3,10 @@ import { computed, ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import type { CardBadge } from "@/components/Common/GCard.types";
-import { useConfig } from "@/composables/config";
 import { useUploadStagingCounts } from "@/composables/upload/useUploadStaging";
 
 import type { UploadMethodConfig } from "./types";
-import { useAllUploadMethods } from "./uploadMethodRegistry";
+import { useFilteredUploadMethods } from "./uploadMethodRegistry";
 
 import DelayedInput from "@/components/Common/DelayedInput.vue";
 import GCard from "@/components/Common/GCard.vue";
@@ -25,29 +24,14 @@ const props = withDefaults(defineProps<Props>(), {
     searchTeleportTarget: undefined,
 });
 
-const { config, isConfigLoaded } = useConfig();
 const router = useRouter();
 const query = ref("");
 
 const searchInputClass = computed(() => (props.searchTeleportTarget ? "my-2" : props.inPanel ? "my-2" : "mb-3"));
 
-const allUploadMethods = useAllUploadMethods();
+const availableMethods = useFilteredUploadMethods();
 const stagedCountsByMode = useUploadStagingCounts();
 
-const availableMethods = computed(() => {
-    if (!isConfigLoaded.value) {
-        return allUploadMethods.value;
-    }
-
-    return allUploadMethods.value.filter((method: UploadMethodConfig) => {
-        // Filter based on config requirements
-        if (method.requiresConfig) {
-            return method.requiresConfig.every((configKey) => config.value[configKey]);
-        }
-        return true;
-    });
-});
-
 const filteredMethods = computed(() => {
     const rawTokens = query.value.trim().split(/\s+/).filter(Boolean);
     if (rawTokens.length === 0) {

From e2ac9ee1a1b08dc65e7f07b7ba8de92bcc2ae795 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 18 Jun 2026 16:54:24 +0200
Subject: [PATCH 234/256] Adapts `UploadMethodModal` to new filtering
 composable API

---
 client/src/components/Panels/Upload/UploadMethodModal.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Panels/Upload/UploadMethodModal.vue b/client/src/components/Panels/Upload/UploadMethodModal.vue
index 29780aa7718..4b1af991b17 100644
--- a/client/src/components/Panels/Upload/UploadMethodModal.vue
+++ b/client/src/components/Panels/Upload/UploadMethodModal.vue
@@ -40,7 +40,8 @@ const { currentHistoryId } = storeToRefs(historyStore);
 const { submitPreparedUpload } = useUploadSubmission();
 
 const modalConfig = computed<UploadModalConfig>(() => props.config ?? {});
-const availableMethods = useFilteredUploadMethods(modalConfig);
+const allowedMethods = computed(() => modalConfig.value.allowedMethods);
+const availableMethods = useFilteredUploadMethods(allowedMethods);
 const selectedMethod = ref<UploadMethodConfig | null>(null);
 const uploadMethodRef = ref<UploadMethodComponent | null>(null);
 const canUpload = ref(false);

From 037024d54d41f1209afb005c0ad804821332a6ab Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 18 Jun 2026 17:50:46 +0200
Subject: [PATCH 235/256] Add disabled state to GCard component

Introduces a disabled property to GCard to prevent user interaction and provide visual feedback for inactive items.

The update manages accessibility by conditionally removing roles and tab indexes when the card is disabled, and includes a tooltip option to explain why the card is non-interactive. Styling is updated to dim the content and desaturate colors to clearly indicate the disabled state.
---
 client/src/components/Common/GCard.vue | 34 +++++++++++++++++++++++---
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Common/GCard.vue b/client/src/components/Common/GCard.vue
index e53114289de..2a636b26518 100644
--- a/client/src/components/Common/GCard.vue
+++ b/client/src/components/Common/GCard.vue
@@ -186,6 +186,16 @@ interface Props {
      * @default false
      */
     highlighted?: boolean;
+
+    /** Whether the card is disabled (non-interactive, dimmed appearance)
+     * @default false
+     */
+    disabled?: boolean;
+
+    /** Tooltip text to show when the card is disabled
+     * @default undefined
+     */
+    disabledTitle?: string;
 }
 
 const props = withDefaults(defineProps<Props>(), {
@@ -218,6 +228,8 @@ const props = withDefaults(defineProps<Props>(), {
     updateTimeIcon: () => faEdit,
     updateTimeTitle: "Last updated",
     highlighted: false,
+    disabled: false,
+    disabledTitle: undefined,
 });
 
 /**
@@ -304,6 +316,9 @@ const getActionId = (cardId: string, actionId: string) => `g-card-action-${actio
 const allowedTitleLines = computed(() => props.titleNLines);
 
 function onKeyDown(event: KeyboardEvent) {
+    if (props.disabled) {
+        return;
+    }
     if ((props.clickable && event.key === "Enter") || event.key === " ") {
         event.stopPropagation();
         emit("click", event);
@@ -318,20 +333,22 @@ function onKeyDown(event: KeyboardEvent) {
     <component
         :is="'div'"
         :id="`g-card-${props.id}`"
-        :role="props.clickable ? 'button' : undefined"
+        :role="props.clickable && !props.disabled ? 'button' : undefined"
         class="g-card pt-0 px-1 mb-2"
         :class="[
             { 'g-card-grid-view': gridView },
             { 'g-card-selected': selected },
             { 'g-card-current': current },
             { 'g-card-published': published },
-            { 'g-card-clickable': props.clickable },
+            { 'g-card-clickable': props.clickable && !props.disabled },
+            { 'g-card-disabled': props.disabled },
             { 'g-card-dim': props.dimWhenUnselected && !props.selected },
             { 'g-card-dropdown-open': extraActionsOpen },
             containerClass,
         ]"
-        :tabindex="props.clickable ? 0 : undefined"
-        @click="props.clickable ? emit('click', $event) : undefined"
+        :tabindex="props.clickable && !props.disabled ? 0 : undefined"
+        :title="props.disabled ? props.disabledTitle : undefined"
+        @click="props.clickable && !props.disabled ? emit('click', $event) : undefined"
         @keydown="onKeyDown">
         <div
             :id="`g-card-content-${props.id}`"
@@ -764,6 +781,15 @@ function onKeyDown(event: KeyboardEvent) {
         box-shadow: 0 0 0 0.2rem transparentize($brand-primary, 0.75);
     }
 
+    &.g-card-disabled {
+        cursor: default;
+
+        .g-card-content {
+            filter: saturate(0.3);
+            opacity: 0.5;
+        }
+    }
+
     &.g-card-clickable {
         cursor: pointer;
 

From a21a6197b410176437ff7a5f9f0910071ec766b0 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 18 Jun 2026 17:51:46 +0200
Subject: [PATCH 236/256] Disable upload methods that require login

Instead of hiding upload methods that require authentication from anonymous users, this change keeps them visible but in a disabled state. This improves discoverability of features and provides clear feedback via tooltips explaining why a specific upload method is unavailable.
---
 .../Panels/Upload/UploadMethodList.vue        |  2 +
 .../Panels/Upload/UploadMethodModal.vue       |  2 +
 client/src/components/Panels/Upload/types.ts  | 13 +++-
 .../Upload/uploadMethodRegistry.test.ts       | 66 ++++++++++++++++++-
 .../Panels/Upload/uploadMethodRegistry.ts     | 39 +++++++----
 5 files changed, 107 insertions(+), 15 deletions(-)

diff --git a/client/src/components/Panels/Upload/UploadMethodList.vue b/client/src/components/Panels/Upload/UploadMethodList.vue
index 225dc925278..08f85b5f6af 100644
--- a/client/src/components/Panels/Upload/UploadMethodList.vue
+++ b/client/src/components/Panels/Upload/UploadMethodList.vue
@@ -101,6 +101,8 @@ function getStagingBadges(method: UploadMethodConfig): CardBadge[] {
                         :title-icon="{ icon: method.icon, class: 'text-primary', size: 'lg' }"
                         :badges="getStagingBadges(method)"
                         :data-method-id="method.id"
+                        :disabled="method.disabled"
+                        :disabled-title="method.disabledTitle"
                         @click="selectUploadMethod(method)" />
                 </template>
             </ScrollList>
diff --git a/client/src/components/Panels/Upload/UploadMethodModal.vue b/client/src/components/Panels/Upload/UploadMethodModal.vue
index 4b1af991b17..37e5164257f 100644
--- a/client/src/components/Panels/Upload/UploadMethodModal.vue
+++ b/client/src/components/Panels/Upload/UploadMethodModal.vue
@@ -211,6 +211,8 @@ async function handleStartClick() {
                             :description="method.description"
                             :title-icon="{ icon: method.icon, class: 'text-primary', size: 'lg' }"
                             :selected="selectedMethod?.id === method.id"
+                            :disabled="method.disabled"
+                            :disabled-title="method.disabledTitle"
                             @click="selectMethod(method)" />
                     </div>
                 </aside>
diff --git a/client/src/components/Panels/Upload/types.ts b/client/src/components/Panels/Upload/types.ts
index b1d16e4a4e3..d1cfa7f5cd7 100644
--- a/client/src/components/Panels/Upload/types.ts
+++ b/client/src/components/Panels/Upload/types.ts
@@ -86,10 +86,21 @@ export interface UploadMethodConfig {
     /**
      * When true, this upload method requires the user to be logged in.
      *
-     * Methods with this flag will be hidden from anonymous users.
+     * Methods with this flag will be disabled for anonymous users.
      */
     requiresLogin?: boolean;
 
+    /**
+     * When true, this upload method is disabled and not interactive.
+     * Set reactively by `useFilteredUploadMethods` based on login state.
+     */
+    disabled?: boolean;
+
+    /**
+     * Tooltip text displayed when the method is disabled.
+     */
+    disabledTitle?: string;
+
     /**
      * When true, the Start button in the footer will be shown.
      *
diff --git a/client/src/components/Panels/Upload/uploadMethodRegistry.test.ts b/client/src/components/Panels/Upload/uploadMethodRegistry.test.ts
index 97a8835c99e..e1c5018c45f 100644
--- a/client/src/components/Panels/Upload/uploadMethodRegistry.test.ts
+++ b/client/src/components/Panels/Upload/uploadMethodRegistry.test.ts
@@ -1,7 +1,12 @@
 import { beforeEach, describe, expect, it, vi } from "vitest";
-import { ref } from "vue";
+import { reactive, ref } from "vue";
 
-import { getUploadMethod, uploadMethodRegistry, useAllUploadMethods } from "./uploadMethodRegistry";
+import {
+    getUploadMethod,
+    uploadMethodRegistry,
+    useAllUploadMethods,
+    useFilteredUploadMethods,
+} from "./uploadMethodRegistry";
 
 // The advancedMode ref is declared before the vi.mock call so both the mock factory
 // and the test bodies share the same reactive reference.
@@ -11,11 +16,27 @@ vi.mock("@/composables/upload/uploadAdvancedMode", () => ({
     useUploadAdvancedMode: () => ({ advancedMode }),
 }));
 
+// Reactive state object for useUserStore mock — storeToRefs expects a reactive object.
+const userStoreState = reactive({ isAnonymous: true });
+
+vi.mock("@/stores/userStore", () => ({
+    useUserStore: () => userStoreState,
+}));
+
+// Reactive refs for useConfig mock.
+const galaxyConfig = ref({});
+const isConfigLoaded = ref(true);
+
+vi.mock("@/composables/config", () => ({
+    useConfig: () => ({ config: galaxyConfig, isConfigLoaded }),
+}));
+
 // Derive method ID lists from the registry so they stay in sync automatically
 // whenever a method is added, removed, or promoted/demoted to advanced mode.
 const ALL_METHOD_IDS = Object.keys(uploadMethodRegistry) as Array<keyof typeof uploadMethodRegistry>;
 const ADVANCED_METHOD_IDS = ALL_METHOD_IDS.filter((id) => uploadMethodRegistry[id].requiresAdvancedMode);
 const STANDARD_METHOD_IDS = ALL_METHOD_IDS.filter((id) => !uploadMethodRegistry[id].requiresAdvancedMode);
+const LOGIN_METHOD_IDS = ALL_METHOD_IDS.filter((id) => uploadMethodRegistry[id].requiresLogin);
 
 describe("uploadMethodRegistry", () => {
     describe("getUploadMethod", () => {
@@ -57,4 +78,45 @@ describe("uploadMethodRegistry", () => {
             expect(methods.value).toHaveLength(STANDARD_METHOD_IDS.length);
         });
     });
+
+    describe("useFilteredUploadMethods", () => {
+        beforeEach(() => {
+            advancedMode.value = false;
+            userStoreState.isAnonymous = true;
+            isConfigLoaded.value = true;
+        });
+
+        it("disables login-required methods when user is anonymous", () => {
+            const methods = useFilteredUploadMethods();
+
+            for (const loginId of LOGIN_METHOD_IDS) {
+                const method = methods.value.find((m) => m.id === loginId);
+                expect(method).toBeDefined();
+                expect(method?.disabled).toBe(true);
+                expect(method?.disabledTitle).toBeDefined();
+            }
+        });
+
+        it("includes login-required methods without disabled when user is logged in", () => {
+            userStoreState.isAnonymous = false;
+            const methods = useFilteredUploadMethods();
+
+            for (const loginId of LOGIN_METHOD_IDS) {
+                const method = methods.value.find((m) => m.id === loginId);
+                expect(method).toBeDefined();
+                expect(method?.disabled).toBeFalsy();
+                expect(method?.disabledTitle).toBeUndefined();
+            }
+        });
+
+        it("filters by allowedMethods when provided", () => {
+            const allowedMethods = ref(["local-file", "paste-content"] as ["local-file", "paste-content"]);
+            const methods = useFilteredUploadMethods(allowedMethods);
+            const ids = methods.value.map((m) => m.id);
+
+            expect(ids).toContain("local-file");
+            expect(ids).toContain("paste-content");
+            expect(ids).not.toContain("paste-links");
+        });
+    });
 });
diff --git a/client/src/components/Panels/Upload/uploadMethodRegistry.ts b/client/src/components/Panels/Upload/uploadMethodRegistry.ts
index 7ac898bb987..24392763913 100644
--- a/client/src/components/Panels/Upload/uploadMethodRegistry.ts
+++ b/client/src/components/Panels/Upload/uploadMethodRegistry.ts
@@ -223,20 +223,35 @@ export function useFilteredUploadMethods(
     const { isAnonymous } = storeToRefs(useUserStore());
 
     return computed(() => {
-        return allMethods.value.filter((method) => {
-            if (method.requiresLogin && isAnonymous.value) {
-                return false;
-            }
+        return allMethods.value
+            .map((method) => {
+                let disabled = false;
+                let disabledTitle: string | undefined;
 
-            if (allowedMethods?.value && !allowedMethods.value.some((allowedMethod) => allowedMethod === method.id)) {
-                return false;
-            }
+                if (method.requiresLogin && isAnonymous.value) {
+                    disabled = true;
+                    disabledTitle = "You must be logged in to use this feature";
+                }
 
-            if (!isConfigLoaded.value || !method.requiresConfig) {
-                return true;
-            }
+                if (disabled) {
+                    return { ...method, disabled, disabledTitle };
+                }
 
-            return method.requiresConfig.every((configKey) => Boolean(galaxyConfig.value[configKey]));
-        });
+                return method;
+            })
+            .filter((method) => {
+                if (
+                    allowedMethods?.value &&
+                    !allowedMethods.value.some((allowedMethod) => allowedMethod === method.id)
+                ) {
+                    return false;
+                }
+
+                if (!isConfigLoaded.value || !method.requiresConfig) {
+                    return true;
+                }
+
+                return method.requiresConfig.every((configKey) => Boolean(galaxyConfig.value[configKey]));
+            });
     });
 }

From bb9958d45ca99828f0aecd8026cf6eb0c442b3a0 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 18 Jun 2026 18:12:45 +0200
Subject: [PATCH 237/256] Add authentication guard for specific upload methods

Introduces a new router guard that checks if a specific upload method requires authentication. This prevents anonymous users from accessing upload views that are restricted to logged-in users by redirecting them to the login page with a return path.
---
 client/src/entry/analysis/router.js |  3 ++-
 client/src/router/guards.ts         | 25 +++++++++++++++++++++----
 2 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 6d1e47e488b..8521a659045 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -10,7 +10,7 @@ import AdminRoutes from "@/entry/analysis/routes/admin-routes";
 import LibraryRoutes from "@/entry/analysis/routes/library-routes";
 import StorageRoutes from "@/entry/analysis/routes/storage-routes";
 import { getAppRoot } from "@/onload/loadConfig";
-import { requireAuth } from "@/router/guards";
+import { requireAuth, requireAuthForUploadMethod } from "@/router/guards";
 import { parseBool } from "@/utils/utils";
 
 import { patchRouterPush } from "./router-push";
@@ -257,6 +257,7 @@ export function getRouter(Galaxy) {
                         path: "upload/:methodId",
                         component: UploadMethodView,
                         props: true,
+                        beforeEnter: requireAuthForUploadMethod,
                     },
                     {
                         path: "help/terms/:term",
diff --git a/client/src/router/guards.ts b/client/src/router/guards.ts
index fa6b5ed1886..a58ada05dc1 100644
--- a/client/src/router/guards.ts
+++ b/client/src/router/guards.ts
@@ -1,18 +1,35 @@
 import type { NavigationGuardNext, Route } from "vue-router";
 
+import type { UploadMethod } from "@/components/Panels/Upload/types";
+import { getUploadMethod } from "@/components/Panels/Upload/uploadMethodRegistry";
 import { useUserStore } from "@/stores/userStore";
 
-export async function requireAuth(to: Route, from: Route, next: NavigationGuardNext) {
+async function redirectIfAnonymous(to: Route, next: NavigationGuardNext) {
     const userStore = useUserStore();
     await userStore.loadUser(false);
 
     if (userStore.isAnonymous) {
         next({
             path: "/login/start",
-            query: {
-                redirect: to.fullPath,
-            },
+            query: { redirect: to.fullPath },
         });
+        return true;
+    }
+    return false;
+}
+
+export async function requireAuth(to: Route, _from: Route, next: NavigationGuardNext) {
+    if (await redirectIfAnonymous(to, next)) {
+        return;
+    }
+    next();
+}
+
+export async function requireAuthForUploadMethod(to: Route, _from: Route, next: NavigationGuardNext) {
+    const methodId = to.params.methodId as UploadMethod;
+    const method = getUploadMethod(methodId);
+
+    if (method?.requiresLogin && (await redirectIfAnonymous(to, next))) {
         return;
     }
     next();

From 4f0567f7f697da40fd34c4ecce94685f93dca0f2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 19:35:12 +0200
Subject: [PATCH 238/256] Shrink the structured-output schema for LLM tool
 authoring

Introduce UserToolSourceAuthoringView as the parent of UserToolSource: it
carries every field and validator except `tests`, which moves onto the
concrete subclasses. The test-assertion DSL pulled in by `tests` is ~70% of
UserToolSource's JSON schema; targeting the slim view (done in the agent
commit) cuts the structured-output schema the model must satisfy from ~150 KB
to ~33 KB and sidesteps nested-$defs grammar failures on some backends.

Also require `version` on the authoring view (optional on the persisted
UserToolSource for legacy/stored rows): the linter rejects a versionless tool,
so forcing it into the structured-output `required` set stops the model
dropping it on a retry and tripping ToolVersionMissing. The published class
docstring is now model-facing (it is sent verbatim as the tool description).
---
 lib/galaxy/tool_util_models/__init__.py     | 61 ++++++++++++++++++++-
 test/unit/tool_util/test_yaml_parameters.py | 31 ++++++++++-
 2 files changed, 88 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_util_models/__init__.py b/lib/galaxy/tool_util_models/__init__.py
index 84a82a31b47..9617e5f0b1c 100644
--- a/lib/galaxy/tool_util_models/__init__.py
+++ b/lib/galaxy/tool_util_models/__init__.py
@@ -168,7 +168,7 @@ class _DynamicToolSourceBase(ToolSourceBaseModel):
         Field(
             title="shell_command",
             description="A string that contains the command to be executed. Parameters can be referenced inside $().",
-            examples=["head -n '$(inputs.n_lines)' '$(inputs.data_input.path)'"],
+            examples=["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"],
         ),
     ]
     inputs: List[YamlGalaxyToolParameter] = []
@@ -186,7 +186,12 @@ class _DynamicToolSourceBase(ToolSourceBaseModel):
     xrefs: Optional[List[XrefDict]] = None
     profile: Optional[float] = None
     help: Annotated[Optional[HelpContent], Field(description="Help text shown below the tool interface.")] = None
-    tests: Optional[List["YamlToolTest"]] = None
+    # NOTE: `tests` is intentionally NOT declared here. It lives on the concrete
+    # subclasses (`UserToolSource`, `YamlToolSource`) so that the slim
+    # `UserToolSourceAuthoringView` can inherit everything *except* the test
+    # field. The test-assertion DSL pulled in by `tests` is ~70% of the JSON
+    # schema; keeping it off the authoring view is what shrinks the
+    # structured-output schema handed to LLM tool-generation agents.
 
     @model_validator(mode="before")
     @classmethod
@@ -246,11 +251,44 @@ class _DynamicToolSourceBase(ToolSourceBaseModel):
         return self
 
 
-class UserToolSource(_DynamicToolSourceBase):
+# Schema-narrowed view of ``UserToolSource`` for LLM tool authoring.
+#
+# This is the *parent* of ``UserToolSource`` and carries every field and
+# validator except ``tests``. Authoring agents (see ``galaxy.agents.custom_tool``)
+# point their structured-output ``output_type`` at this view so the JSON schema
+# the model must satisfy omits the test-assertion DSL — ~70% of
+# ``UserToolSource``'s ~150 KB schema and never written in the first generation
+# pass. Shrinking the schema cuts per-call token cost and sidesteps the
+# nested-``$defs`` grammar failures some local inference backends hit (see
+# ``CustomToolAgent._handle_model_http_error``).
+#
+# A produced view is a strict subset of ``UserToolSource``; convert with
+# ``UserToolSource.model_validate(view.model_dump(by_alias=True))`` before storing
+# or linting so downstream types stay honest.
+#
+# NOTE: the class docstring below is published verbatim as the structured-output
+# tool *description* sent to the model on every call — keep it model-facing and
+# concise; put implementation rationale in comments like this one, not the
+# docstring.
+class UserToolSourceAuthoringView(_DynamicToolSourceBase):
+    """A Galaxy user-defined tool: a containerized shell command wrapped with typed inputs and outputs.
+
+    Provide the tool's identity (``id``, ``name``, ``version``), a ``container``
+    image to run in, and a ``shell_command`` that references inputs as
+    ``$(inputs.NAME)`` for scalar values or ``$(inputs.NAME.path)`` for files.
+    Declare every referenced input under ``inputs`` and every produced file under
+    ``outputs`` (each output must set ``from_work_dir`` or ``discover_datasets``).
+    """
+
     class_: Annotated[Literal["GalaxyUserTool"], Field(alias="class")]
     container: Annotated[
         str, Field(description="Container image to use for this tool.", examples=["quay.io/biocontainers/python:3.13"])
     ]
+    # Required here (it's optional on the base for stored/legacy rows). Galaxy's
+    # linter rejects a versionless tool, so forcing it into the structured-output
+    # ``required`` set stops the model dropping it -- notably on a retry, where the
+    # model would otherwise regenerate without it and trip ``ToolVersionMissing``.
+    version: Annotated[str, Field(description="Version for the tool.", examples=["0.1.0"])]
 
     # Field declaration order puts subclass fields (class_, container) after
     # parent ones, which serializes them at the end. Re-order on dump so the
@@ -310,6 +348,22 @@ class UserToolSource(_DynamicToolSourceBase):
         return ordered
 
 
+class UserToolSource(UserToolSourceAuthoringView):
+    """Full unprivileged tool source, including the optional ``tests`` block.
+
+    This is the model persisted and validated on the API surface
+    (``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring
+    uses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added
+    back here so direct authors and stored rows can still carry tests.
+    """
+
+    # Relax ``version`` back to optional for the persisted/full model: stored rows
+    # and API submissions from older Galaxy versions may lack it, and the lift path
+    # must still validate them. Only the LLM-authoring view (parent) requires it.
+    version: Optional[str] = None
+    tests: Optional[List["YamlToolTest"]] = None
+
+
 class YamlToolSource(_DynamicToolSourceBase):
     class_: Annotated[Literal["GalaxyTool"], Field(alias="class")]
     container: Annotated[
@@ -319,6 +373,7 @@ class YamlToolSource(_DynamicToolSourceBase):
             examples=["quay.io/biocontainers/python:3.13"],
         ),
     ] = None
+    tests: Optional[List["YamlToolTest"]] = None
 
 
 DynamicToolSources = Annotated[Union[UserToolSource, YamlToolSource], Field(discriminator="class_")]
diff --git a/test/unit/tool_util/test_yaml_parameters.py b/test/unit/tool_util/test_yaml_parameters.py
index b5c37004b43..7ca11d6c6bd 100644
--- a/test/unit/tool_util/test_yaml_parameters.py
+++ b/test/unit/tool_util/test_yaml_parameters.py
@@ -11,7 +11,10 @@ import pytest
 from pydantic import ValidationError
 
 from galaxy.tool_util.parameters.convert import assert_yaml_v1_parameters
-from galaxy.tool_util_models import UserToolSource
+from galaxy.tool_util_models import (
+    UserToolSource,
+    UserToolSourceAuthoringView,
+)
 from galaxy.tool_util_models.parameters import (
     BooleanParameterModel,
     ConditionalParameterModel,
@@ -345,6 +348,32 @@ def test_assert_yaml_v1_parameters_walks_nested_groups():
         assert_yaml_v1_parameters([repeat])
 
 
+def test_authoring_view_drops_tests_and_shrinks_schema():
+    """The LLM-facing authoring view omits the `tests` block, which pulls in the
+    test-assertion DSL (~70% of the full schema). This is what keeps the
+    structured-output schema small; guard against `tests` creeping back onto the
+    shared base (which would silently re-inflate it)."""
+    import json
+
+    assert "tests" not in UserToolSourceAuthoringView.model_fields
+    assert "tests" in UserToolSource.model_fields
+    # A produced view is a strict subset and promotes to a full UserToolSource.
+    assert issubclass(UserToolSource, UserToolSourceAuthoringView)
+
+    full = len(json.dumps(UserToolSource.model_json_schema()))
+    slim = len(json.dumps(UserToolSourceAuthoringView.model_json_schema()))
+    # Generous bound; the real reduction is ~80%. Catches accidental re-inflation.
+    assert slim < full * 0.5, f"authoring view not slim enough: {slim} vs {full}"
+
+
+def test_authoring_view_round_trips_to_user_tool_source():
+    view = UserToolSourceAuthoringView.model_validate(CAT_USER_DEFINED)
+    tool = UserToolSource.model_validate(view.model_dump(by_alias=True))
+    assert isinstance(tool, UserToolSource)
+    assert tool.id == view.id
+    assert tool.tests is None
+
+
 def test_published_tool_source_schema_has_no_xml_only_leaks():
     raw = UserToolSource.model_json_schema()
     # Collect all property names across every $defs entry and the top level.

From fc4501305a694846c7ec2564c280ec10c6d14559 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 19:46:57 +0200
Subject: [PATCH 239/256] Fix simple tool outputs requiring `hidden`

text/integer/float/boolean outputs subclassed GenericToolOutputBaseModel
without binding its type vars, so `name` and `hidden` resolved to required
`Any`. A model (or author) had to supply a `hidden` flag on every simple
output. Split them like the dataset/collection outputs: strict
ToolOutput{Text,Integer,Float,Boolean} bound to [bool, str] (name/hidden
required, parser-facing), and IncomingToolOutput* variants used by the
authoring union where `hidden` is optional. `name` stays required -- a value
output with no name can't be referenced.
---
 lib/galaxy/tool_util_models/tool_outputs.py | 51 +++++++++++++++++----
 test/unit/tool_util/test_yaml_parameters.py | 46 +++++++++++++++++++
 2 files changed, 88 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/tool_util_models/tool_outputs.py b/lib/galaxy/tool_util_models/tool_outputs.py
index 9169f589d1f..9f9a8b4f31c 100644
--- a/lib/galaxy/tool_util_models/tool_outputs.py
+++ b/lib/galaxy/tool_util_models/tool_outputs.py
@@ -165,33 +165,66 @@ class IncomingToolOutputCollection(GenericToolOutputCollection[NotRequired[bool]
     hidden: Annotated[Optional[bool], Field(description="If true, the output will not be shown in the history.")] = None
 
 
-class ToolOutputSimple(GenericToolOutputBaseModel):
+class GenericToolOutputSimple(
+    GenericToolOutputBaseModel[IncomingNotRequiredBoolT, IncomingNotRequiredStringT],
+    Generic[IncomingNotRequiredBoolT, IncomingNotRequiredStringT],
+):
     pass
 
 
-class ToolOutputText(ToolOutputSimple):
+# Internal / parser-facing variants: ``name`` and ``hidden`` are required, matching
+# how ``ToolOutput*Model`` instances are constructed in the output parser (which
+# always supplies both). Binding the type vars to ``[bool, str]`` mirrors
+# ``ToolOutputDataset`` / ``ToolOutputCollection``.
+class ToolOutputText(GenericToolOutputSimple[bool, str]):
     type: Literal["text"]
 
 
-class ToolOutputInteger(ToolOutputSimple):
+class ToolOutputInteger(GenericToolOutputSimple[bool, str]):
     type: Literal["integer"]
 
 
-class ToolOutputFloat(ToolOutputSimple):
+class ToolOutputFloat(GenericToolOutputSimple[bool, str]):
     type: Literal["float"]
 
 
-class ToolOutputBoolean(ToolOutputSimple):
+class ToolOutputBoolean(GenericToolOutputSimple[bool, str]):
+    type: Literal["boolean"]
+
+
+# Incoming / authoring variants: ``hidden`` is optional (it has a sensible
+# default), but ``name`` stays *required* -- unlike datasets/collections, a simple
+# value output has no discovery step to supply a name, so an unnamed one can never
+# be referenced. Previously these reused the strict types above, whose unbound type
+# vars also forced ``hidden`` to be required -- a bug that made the published schema
+# demand a ``hidden`` flag on every simple output.
+class IncomingToolOutputSimple(GenericToolOutputSimple[NotRequired[bool], str]):
+    hidden: Annotated[Optional[bool], Field(description="If true, the output will not be shown in the history.")] = None
+
+
+class IncomingToolOutputText(IncomingToolOutputSimple):
+    type: Literal["text"]
+
+
+class IncomingToolOutputInteger(IncomingToolOutputSimple):
+    type: Literal["integer"]
+
+
+class IncomingToolOutputFloat(IncomingToolOutputSimple):
+    type: Literal["float"]
+
+
+class IncomingToolOutputBoolean(IncomingToolOutputSimple):
     type: Literal["boolean"]
 
 
 IncomingToolOutputT = Union[
     IncomingToolOutputDataset,
     IncomingToolOutputCollection,
-    ToolOutputText,
-    ToolOutputInteger,
-    ToolOutputFloat,
-    ToolOutputBoolean,
+    IncomingToolOutputText,
+    IncomingToolOutputInteger,
+    IncomingToolOutputFloat,
+    IncomingToolOutputBoolean,
 ]
 IncomingToolOutput = Annotated[IncomingToolOutputT, Field(discriminator="type")]
 ToolOutputT = Union[
diff --git a/test/unit/tool_util/test_yaml_parameters.py b/test/unit/tool_util/test_yaml_parameters.py
index 7ca11d6c6bd..42eac8c8488 100644
--- a/test/unit/tool_util/test_yaml_parameters.py
+++ b/test/unit/tool_util/test_yaml_parameters.py
@@ -366,6 +366,52 @@ def test_authoring_view_drops_tests_and_shrinks_schema():
     assert slim < full * 0.5, f"authoring view not slim enough: {slim} vs {full}"
 
 
+def test_simple_outputs_require_name_but_not_hidden_in_authoring_schema():
+    """Regression: text/integer/float/boolean outputs must require `name` (a value
+    output with no name can never be referenced) but must NOT require `hidden`.
+    They previously reused the strict internal output types whose unbound type vars
+    forced `hidden` to be required too, so the published schema demanded a `hidden`
+    flag on every simple output."""
+    defs = UserToolSourceAuthoringView.model_json_schema()["$defs"]
+    for name in (
+        "IncomingToolOutputText",
+        "IncomingToolOutputInteger",
+        "IncomingToolOutputFloat",
+        "IncomingToolOutputBoolean",
+    ):
+        required = set(defs[name]["required"])
+        assert "name" in required, f"{name} should require 'name'"
+        assert "hidden" not in required, f"{name} should not require 'hidden'"
+
+    # A named text output without `hidden` validates.
+    tool = UserToolSourceAuthoringView.model_validate(
+        {
+            "class": "GalaxyUserTool",
+            "name": "pvalue tool",
+            "version": "0.1.0",
+            "container": "busybox",
+            "shell_command": "echo 0.03 > p.txt",
+            "outputs": [
+                {"type": "data", "name": "plot", "from_work_dir": "p.txt"},
+                {"type": "text", "name": "pvalue"},
+            ],
+        }
+    )
+    assert tool.outputs[1].hidden is None
+
+    # A simple output WITHOUT a name is rejected.
+    with pytest.raises(ValidationError):
+        UserToolSourceAuthoringView.model_validate(
+            {
+                "class": "GalaxyUserTool",
+                "name": "pvalue tool",
+                "container": "busybox",
+                "shell_command": "echo 0.03 > p.txt",
+                "outputs": [{"type": "text"}],
+            }
+        )
+
+
 def test_authoring_view_round_trips_to_user_tool_source():
     view = UserToolSourceAuthoringView.model_validate(CAT_USER_DEFINED)
     tool = UserToolSource.model_validate(view.model_dump(by_alias=True))

From 78bb7c1cb9478707999ae61e53b3aaa74638d688 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 19:47:10 +0200
Subject: [PATCH 240/256] Default collection discovery-descriptor boilerplate
 fields

FilePatternDatasetCollectionDescription required ~8 boilerplate fields
(visible, assign_primary_output, recurse, match_relative_path, sort_key,
sort_comp, discover_via, ...) with no defaults, making `discover_datasets`
nearly impossible to author by hand. Give them the same defaults the XML
parser uses (galaxy.tool_util.parser.output_collection_def) so a minimal
`{pattern: ...}` validates.
---
 lib/galaxy/tool_util_models/tool_outputs.py | 24 ++++++++++++---------
 test/unit/tool_util/test_yaml_parameters.py | 21 ++++++++++++++++++
 2 files changed, 35 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/tool_util_models/tool_outputs.py b/lib/galaxy/tool_util_models/tool_outputs.py
index 9f9a8b4f31c..868761ebf43 100644
--- a/lib/galaxy/tool_util_models/tool_outputs.py
+++ b/lib/galaxy/tool_util_models/tool_outputs.py
@@ -49,24 +49,28 @@ SortKeyT = Literal["filename", "name", "designation", "dbkey"]
 SortCompT = Literal["lexical", "numeric"]
 
 
+# Defaults below mirror the XML parser (galaxy.tool_util.parser.output_collection_def):
+# every non-essential discovery attribute has a sensible default there, so an author
+# (or an LLM) only needs to supply ``pattern``. Requiring all of them in the model is
+# the friction that makes ``discover_datasets`` nearly impossible to author by hand.
 class DatasetCollectionDescription(ToolSourceBaseModel):
     discover_via: DiscoverViaT
-    format: Optional[str]
-    visible: bool
-    assign_primary_output: bool
-    directory: Optional[str]
-    recurse: bool
-    match_relative_path: bool
+    format: Optional[str] = None
+    visible: bool = False
+    assign_primary_output: bool = False
+    directory: Optional[str] = None
+    recurse: bool = False
+    match_relative_path: bool = False
 
 
 class ToolProvidedMetadataDatasetCollection(DatasetCollectionDescription):
-    discover_via: Literal["tool_provided_metadata"]
+    discover_via: Literal["tool_provided_metadata"] = "tool_provided_metadata"
 
 
 class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
-    discover_via: Literal["pattern"]
-    sort_key: SortKeyT
-    sort_comp: SortCompT
+    discover_via: Literal["pattern"] = "pattern"
+    sort_key: SortKeyT = "filename"
+    sort_comp: SortCompT = "lexical"
     sort_reverse: bool = False
     pattern: str
 
diff --git a/test/unit/tool_util/test_yaml_parameters.py b/test/unit/tool_util/test_yaml_parameters.py
index 42eac8c8488..c3d12c6f884 100644
--- a/test/unit/tool_util/test_yaml_parameters.py
+++ b/test/unit/tool_util/test_yaml_parameters.py
@@ -366,6 +366,27 @@ def test_authoring_view_drops_tests_and_shrinks_schema():
     assert slim < full * 0.5, f"authoring view not slim enough: {slim} vs {full}"
 
 
+def test_collection_discovery_only_requires_pattern():
+    """A discovery descriptor should validate from just a `pattern`; the boilerplate
+    attributes default to the XML parser's values (visible=False, recurse=False,
+    sort_key=filename, sort_comp=lexical, discover_via=pattern). Requiring all of
+    them made `discover_datasets` nearly impossible to author by hand."""
+    from galaxy.tool_util_models.tool_outputs import IncomingToolOutputCollection
+
+    out = IncomingToolOutputCollection.model_validate(
+        {
+            "type": "collection",
+            "name": "seqs",
+            "collection_type": "list",
+            "discover_datasets": [{"pattern": "split_.*\\.fasta", "format": "fasta"}],
+        }
+    )
+    d = out.discover_datasets[0]
+    assert d.discover_via == "pattern"
+    assert (d.visible, d.assign_primary_output, d.recurse, d.match_relative_path) == (False, False, False, False)
+    assert (d.sort_key, d.sort_comp) == ("filename", "lexical")
+
+
 def test_simple_outputs_require_name_but_not_hidden_in_authoring_schema():
     """Regression: text/integer/float/boolean outputs must require `name` (a value
     output with no name can never be referenced) but must NOT require `hidden`.

From f59798a6847169d42b9d58358f67b6420e3bdd3b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 19:49:07 +0200
Subject: [PATCH 241/256] Scope liberal-input coercions to agent ingest via
 validation context

The authoring models accept the loose shapes LLMs emit -- a string `help`, a
top-level `value` on a select, a single `discover_datasets` object, and a
meaningless `min`/`max` on a single data input. These were rewriting input on
every path, including the canonical API/storage/lift validation. Gate them on
a pydantic validation-context flag (lenient_coercion_enabled / the agent's
AGENT_LENIENT_CONTEXT, wired in the agent commit) so they apply only when
ingesting model output; the strict path now surfaces those shapes as errors
instead of silently rewriting them. Also adds the data min/max field
descriptions clarifying they only apply to multiple-dataset inputs.
---
 lib/galaxy/tool_util_models/__init__.py       | 12 +++
 lib/galaxy/tool_util_models/_base.py          | 16 ++++
 lib/galaxy/tool_util_models/tool_outputs.py   | 20 ++++-
 .../tool_util_models/yaml_parameters.py       | 79 ++++++++++++++++-
 test/unit/tool_util/test_yaml_parameters.py   | 86 ++++++++++++++++++-
 .../user_tool_source_validation_cases.yml     | 40 +++++++++
 6 files changed, 247 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tool_util_models/__init__.py b/lib/galaxy/tool_util_models/__init__.py
index 9617e5f0b1c..6048873ba1c 100644
--- a/lib/galaxy/tool_util_models/__init__.py
+++ b/lib/galaxy/tool_util_models/__init__.py
@@ -40,6 +40,7 @@ from typing_extensions import (
 
 from ._base import (
     CollectionType,
+    lenient_coercion_enabled,
     StrictModel,
     ToolSourceBaseModel,
 )
@@ -200,6 +201,17 @@ class _DynamicToolSourceBase(ToolSourceBaseModel):
             normalize_dict(values, ["inputs", "outputs"])
         return values
 
+    @field_validator("help", mode="before")
+    @classmethod
+    def _coerce_help_string(cls, v, info):
+        # LLMs (and authors used to the XML <help> element) naturally provide help as
+        # a plain string, but the model stores it as {format, content}. In agent-ingest
+        # mode, accept a bare string and treat it as markdown; strict validation
+        # requires the explicit {format, content} object.
+        if lenient_coercion_enabled(info) and isinstance(v, str):
+            return {"format": "markdown", "content": v}
+        return v
+
     @field_validator("name", "version", mode="after")
     @classmethod
     def _reject_blank_strings(cls, v: Optional[str]) -> Optional[str]:
diff --git a/lib/galaxy/tool_util_models/_base.py b/lib/galaxy/tool_util_models/_base.py
index cf53028b625..f92de2064e9 100644
--- a/lib/galaxy/tool_util_models/_base.py
+++ b/lib/galaxy/tool_util_models/_base.py
@@ -18,6 +18,22 @@ class StrictModel(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
 
+# Liberal-input coercions (accepting the loose shapes LLMs emit -- a string ``help``,
+# a ``value`` on a select, a single ``discover_datasets`` object, a meaningless
+# ``min`` on a single data input) are gated on this validation-context flag so they
+# apply ONLY when ingesting agent output. The canonical API / storage / lift path
+# validates without it and stays strict, surfacing those shapes as errors instead of
+# silently rewriting them. The agent opts in via ``Agent(validation_context=AGENT_LENIENT_CONTEXT)``.
+LENIENT_CONTEXT_KEY = "lenient"
+AGENT_LENIENT_CONTEXT = {LENIENT_CONTEXT_KEY: True}
+
+
+def lenient_coercion_enabled(info) -> bool:
+    """True when validation is running in agent-ingest mode (see above)."""
+    context = getattr(info, "context", None)
+    return bool(isinstance(context, dict) and context.get(LENIENT_CONTEXT_KEY))
+
+
 def _check_collection_type(v: str) -> str:
     if len(v) == 0:
         raise ValueError("Invalid empty collection_type specified.")
diff --git a/lib/galaxy/tool_util_models/tool_outputs.py b/lib/galaxy/tool_util_models/tool_outputs.py
index 868761ebf43..38262b91d51 100644
--- a/lib/galaxy/tool_util_models/tool_outputs.py
+++ b/lib/galaxy/tool_util_models/tool_outputs.py
@@ -16,6 +16,7 @@ from typing import (
 
 from pydantic import (
     Field,
+    field_validator,
     model_validator,
 )
 from typing_extensions import (
@@ -24,7 +25,10 @@ from typing_extensions import (
     TypeVar,
 )
 
-from ._base import ToolSourceBaseModel
+from ._base import (
+    lenient_coercion_enabled,
+    ToolSourceBaseModel,
+)
 
 AnyT = TypeVar("AnyT")
 NotRequired = Optional[AnyT]
@@ -34,6 +38,16 @@ IncomingNotRequiredStringT = TypeVar("IncomingNotRequiredStringT")
 # Use IncomingNotRequired when concrete key: Optional[str] = None would be incorrect
 
 
+def _single_to_list(v: Any, info: Any) -> Any:
+    # LLMs often provide a single ``discover_datasets`` descriptor object where the
+    # model expects a list of them. In agent-ingest mode, wrap a bare dict so it
+    # validates; strict validation requires the list form ("Input should be a valid
+    # array"), keeping the canonical schema to one shape.
+    if lenient_coercion_enabled(info) and isinstance(v, dict):
+        return [v]
+    return v
+
+
 class GenericToolOutputBaseModel(ToolSourceBaseModel, Generic[IncomingNotRequiredBoolT, IncomingNotRequiredStringT]):
     name: Annotated[
         IncomingNotRequiredStringT, Field(description="Parameter name. Used when referencing parameter in workflows.")
@@ -106,6 +120,8 @@ class GenericToolOutputDataset(
     ] = None
     precreate_directory: Optional[bool] = False
 
+    _wrap_discover_datasets = field_validator("discover_datasets", mode="before")(_single_to_list)
+
 
 class ToolOutputDataset(GenericToolOutputDataset[bool, str]): ...
 
@@ -151,6 +167,8 @@ class GenericToolOutputCollection(
     structured_like: Optional[str] = None
     discover_datasets: Optional[List[DatasetCollectionDescriptionT]] = None
 
+    _wrap_discover_datasets = field_validator("discover_datasets", mode="before")(_single_to_list)
+
     @model_validator(mode="before")
     @classmethod
     def _lift_legacy_structure(cls, values):
diff --git a/lib/galaxy/tool_util_models/yaml_parameters.py b/lib/galaxy/tool_util_models/yaml_parameters.py
index 6b94ee5f0ea..2276fbddaba 100644
--- a/lib/galaxy/tool_util_models/yaml_parameters.py
+++ b/lib/galaxy/tool_util_models/yaml_parameters.py
@@ -24,13 +24,16 @@ from pydantic import (
     ConfigDict,
     Field,
     field_validator,
+    model_validator,
     RootModel,
 )
+from pydantic_core import PydanticCustomError
 from typing_extensions import (
     Annotated,
     Literal,
 )
 
+from ._base import lenient_coercion_enabled
 from .parameter_validators import (
     EmptyFieldParameterValidatorModel,
     InRangeParameterValidatorModel,
@@ -162,6 +165,29 @@ class YamlSelectParameter(_YamlParamBase):
     multiple: bool = False
     validators: List[YamlSelectValidators] = []
 
+    @model_validator(mode="before")
+    @classmethod
+    def _coerce_default_value(cls, data, info):
+        # LLMs naturally express a select's default as a top-level ``value`` (as
+        # other param types do), but selects mark the default via ``selected: true``
+        # on an option. In agent-ingest mode, accept ``value`` and fold it into the
+        # matching option; strict validation leaves it for ``extra="forbid"`` to
+        # reject, so the canonical schema keeps one way to express a default.
+        if lenient_coercion_enabled(info) and isinstance(data, dict) and "value" in data:
+            data = dict(data)  # don't mutate the caller's dict
+            default = data.pop("value")
+            options = data.get("options")
+            if isinstance(options, list):
+                data["options"] = [
+                    (
+                        {**option, "selected": True}
+                        if isinstance(option, dict) and option.get("value") == default
+                        else option
+                    )
+                    for option in options
+                ]
+        return data
+
     def to_internal(self) -> SelectParameterModel:
         return SelectParameterModel(
             type="select",
@@ -191,15 +217,62 @@ def _split_format(v):
 class YamlDataParameter(_YamlParamBase):
     type: Literal["data"]
     format: List[str] = ["data"]
-    multiple: bool = False
-    min: Optional[int] = None
-    max: Optional[int] = None
+    multiple: Annotated[
+        bool,
+        Field(description="Set true to accept several datasets (a list) for this input instead of one."),
+    ] = False
+    min: Annotated[
+        Optional[int],
+        Field(
+            description=(
+                "Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. "
+                "Do NOT set this for a single-dataset input -- a data input is already required by default, "
+                "so leave 'min' unset unless the input accepts multiple datasets."
+            )
+        ),
+    ] = None
+    max: Annotated[
+        Optional[int],
+        Field(
+            description=(
+                "Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; "
+                "leave unset for a single-dataset input."
+            )
+        ),
+    ] = None
 
     @field_validator("format", mode="before")
     @classmethod
     def _coerce_format(cls, v):
         return _split_format(v)
 
+    @model_validator(mode="after")
+    def _check_min_max_without_multiple(self, info) -> "YamlDataParameter":
+        # min/max are the min/max number of *datasets*, which only has meaning for a
+        # multiple-dataset input -- the runtime (galaxy.tools.parameters.basic
+        # .DataToolParameter) rejects them outright on a single one.
+        #
+        # Agent-ingest (lenient): LLMs routinely add `min: 1` to a single data input
+        # to mean "required" (already the default), so drop the meaningless bound
+        # rather than fail the otherwise-fine tool.
+        # Strict (API / storage): raise -- a human/programmatic author should see the
+        # mistake, not have their value silently discarded.
+        if self.multiple or (self.min is None and self.max is None):
+            return self
+        if lenient_coercion_enabled(info):
+            self.min = None
+            self.max = None
+            return self
+        for bound in ("min", "max"):
+            if getattr(self, bound) is not None:
+                raise PydanticCustomError(
+                    "dynamic_tool.data_min_max_requires_multiple",
+                    "cannot specify '{bound}' on a single data parameter; "
+                    "set 'multiple: true' if the parameter should accept multiple datasets",
+                    {"bound": bound},
+                )
+        return self
+
     def to_internal(self) -> DataParameterModel:
         return DataParameterModel(
             type="data",
diff --git a/test/unit/tool_util/test_yaml_parameters.py b/test/unit/tool_util/test_yaml_parameters.py
index c3d12c6f884..3742eb5378b 100644
--- a/test/unit/tool_util/test_yaml_parameters.py
+++ b/test/unit/tool_util/test_yaml_parameters.py
@@ -15,6 +15,7 @@ from galaxy.tool_util_models import (
     UserToolSource,
     UserToolSourceAuthoringView,
 )
+from galaxy.tool_util_models._base import AGENT_LENIENT_CONTEXT
 from galaxy.tool_util_models.parameters import (
     BooleanParameterModel,
     ConditionalParameterModel,
@@ -30,8 +31,9 @@ from galaxy.tool_util_models.parameters import (
 from galaxy.tool_util_models.yaml_parameters import YamlGalaxyToolParameter
 
 
-def _validate(input_dict):
-    return YamlGalaxyToolParameter.model_validate(input_dict)
+def _validate(input_dict, lenient=False):
+    context = AGENT_LENIENT_CONTEXT if lenient else None
+    return YamlGalaxyToolParameter.model_validate(input_dict, context=context)
 
 
 # ---------------------------------------------------------------------------
@@ -366,6 +368,86 @@ def test_authoring_view_drops_tests_and_shrinks_schema():
     assert slim < full * 0.5, f"authoring view not slim enough: {slim} vs {full}"
 
 
+def test_help_string_lenient_coerces_strict_rejects():
+    """Agent-ingest (lenient): a bare string `help` becomes {format: markdown, content}.
+    Strict: the object form is required."""
+    doc = {
+        "class": "GalaxyUserTool",
+        "name": "Help tool",
+        "version": "0.1.0",
+        "container": "busybox",
+        "shell_command": "echo hi > out.txt",
+        "outputs": [{"type": "data", "name": "out", "from_work_dir": "out.txt"}],
+        "help": "### plain string help",
+    }
+    t = UserToolSourceAuthoringView.model_validate(doc, context=AGENT_LENIENT_CONTEXT)
+    assert t.help.format == "markdown" and t.help.content == "### plain string help"
+
+    with pytest.raises(ValidationError):
+        UserToolSourceAuthoringView.model_validate(doc)
+
+
+def test_single_data_param_drops_meaningless_min_max_lenient_only():
+    """Agent-ingest (lenient): `min`/`max` on a single data input are meaningless
+    (a model adds `min: 1` to mean "required", already the default), so drop them.
+    Strict: reject -- a human/programmatic author shouldn't have a value silently
+    discarded."""
+    p = _validate({"type": "data", "name": "x", "min": 1, "max": 3}, lenient=True)
+    assert p.root.min is None and p.root.max is None
+    assert p.root.multiple is False
+
+    with pytest.raises(ValidationError):
+        _validate({"type": "data", "name": "x", "min": 1})
+
+
+def test_multiple_data_param_keeps_min_max():
+    """When the input genuinely accepts a list (`multiple: true`), the bounds are
+    valid and preserved in both modes."""
+    for lenient in (True, False):
+        p = _validate({"type": "data", "name": "x", "multiple": True, "min": 2, "max": 5}, lenient=lenient)
+        assert (p.root.min, p.root.max) == (2, 5)
+
+
+def test_select_top_level_value_lenient_coerces_strict_rejects():
+    """Agent-ingest (lenient): a select's top-level `value` is folded into
+    `selected: true` on the matching option. Strict: `extra="forbid"` rejects it, so
+    the canonical schema keeps one way to express a default."""
+    doc = {
+        "type": "select",
+        "name": "mode",
+        "value": "invert",
+        "options": [
+            {"label": "Keep matching", "value": "match"},
+            {"label": "Invert", "value": "invert"},
+        ],
+    }
+    p = _validate(doc, lenient=True)
+    assert {o.value: o.selected for o in p.root.options} == {"match": False, "invert": True}
+
+    with pytest.raises(ValidationError):
+        _validate(doc)
+
+
+def test_collection_output_wraps_single_discover_datasets_lenient_only():
+    """Agent-ingest (lenient): a single discovery descriptor object is wrapped into a
+    one-element list. Strict: reject ('Input should be a valid array')."""
+    from galaxy.tool_util_models.tool_outputs import IncomingToolOutputCollection
+
+    doc = {
+        "type": "collection",
+        "name": "seqs",
+        "collection_type": "list",
+        "discover_datasets": {"discover_via": "pattern", "pattern": "split_.*\\.fasta"},
+    }
+    out = IncomingToolOutputCollection.model_validate(doc, context=AGENT_LENIENT_CONTEXT)
+    assert isinstance(out.discover_datasets, list)
+    assert len(out.discover_datasets) == 1
+    assert out.discover_datasets[0].pattern == "split_.*\\.fasta"
+
+    with pytest.raises(ValidationError):
+        IncomingToolOutputCollection.model_validate(doc)
+
+
 def test_collection_discovery_only_requires_pattern():
     """A discovery descriptor should validate from just a `pattern`; the boilerplate
     attributes default to the XML parser's values (visible=False, recurse=False,
diff --git a/test/unit/tool_util/user_tool_source_validation_cases.yml b/test/unit/tool_util/user_tool_source_validation_cases.yml
index d3ad5936fb1..d941f885ddd 100644
--- a/test/unit/tool_util/user_tool_source_validation_cases.yml
+++ b/test/unit/tool_util/user_tool_source_validation_cases.yml
@@ -195,6 +195,46 @@ cases:
       citations: null
     valid: true
 
+  # NOTE: these cases validate the STRICT, canonical UserToolSource (no lenient
+  # context). The liberal-input coercions (string help, `min` on single data, a
+  # select `value`, a single discover_datasets object) are scoped to agent ingest
+  # and are exercised in test_yaml_parameters with the lenient validation context.
+
+  - name: help_as_plain_string_rejected_strict
+    # Strict path requires the {format, content} object; the string form is only
+    # accepted in agent-ingest (lenient) mode.
+    doc:
+      help: "### Overview\nThis tool does a thing."
+    expected_errors:
+      - loc: help
+        code: model_type
+
+  - name: data_min_without_multiple_rejected_strict
+    # `min`/`max` on a single data parameter blow up at tool-build time
+    # (galaxy.tools.parameters.basic.DataToolParameter); the strict path rejects
+    # them. (Agent ingest drops the meaningless bound instead.)
+    doc:
+      inputs:
+        - {type: data, name: data_input, min: 1}
+    expected_errors:
+      - loc: inputs.0.data
+        code: dynamic_tool.data_min_max_requires_multiple
+
+  - name: data_max_without_multiple_rejected_strict
+    doc:
+      inputs:
+        - {type: data, name: data_input, max: 5}
+    expected_errors:
+      - loc: inputs.0.data
+        code: dynamic_tool.data_min_max_requires_multiple
+
+  - name: data_min_max_with_multiple_accepted
+    doc:
+      shell_command: "cat '$(inputs.data_input.path)' > out.txt"
+      inputs:
+        - {type: data, name: data_input, multiple: true, min: 1, max: 5}
+    valid: true
+
   - name: format_validation_errors_distillation
     # Exact distilled bullet text used by ``format_validation_errors`` so
     # downstream UIs (the agent's bullet list, API 4xx bodies) have a

From d749b9f5bc5424b3b0354580024917b015f2d6e9 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 19:49:28 +0200
Subject: [PATCH 242/256] Improve the custom-tool agent: slim view, anchored
 retries, attempts

- Target UserToolSourceAuthoringView for structured output (smaller schema),
  lower temperature to 0.2 for schema-filling, and opt into the liberal-input
  coercions via validation_context; promote the produced view to the full
  UserToolSource for lint/storage.
- Anchor the validator retry to the model's prior attempt: a _ProducerFailure
  carries the rejected YAML (recovered from run messages on schema-validation
  failures via capture_run_messages), and the retry prompt leads with it and
  the numbered problems instead of regenerating blind. Adds resolved/persisted/
  newly-introduced diff logging.
- Surface `attempts` in the response for offline benchmarking.
---
 lib/galaxy/agents/custom_tool.py | 220 ++++++++++++++++++++++++-------
 test/unit/app/test_agents.py     |  72 ++++++++++
 2 files changed, 246 insertions(+), 46 deletions(-)

diff --git a/lib/galaxy/agents/custom_tool.py b/lib/galaxy/agents/custom_tool.py
index d6d2002e015..b7a5150368f 100644
--- a/lib/galaxy/agents/custom_tool.py
+++ b/lib/galaxy/agents/custom_tool.py
@@ -3,6 +3,7 @@ Custom tool creation agent for Galaxy.
 """
 
 import logging
+from dataclasses import dataclass
 from pathlib import Path
 from typing import (
     Any,
@@ -15,7 +16,10 @@ from pydantic import (
     Field,
     ValidationError,
 )
-from pydantic_ai import Agent
+from pydantic_ai import (
+    Agent,
+    capture_run_messages,
+)
 from pydantic_ai.exceptions import (
     ModelHTTPError,
     UnexpectedModelBehavior,
@@ -26,7 +30,9 @@ from galaxy.tool_util.lint import lint_user_tool_source
 from galaxy.tool_util_models import (
     format_validation_errors,
     UserToolSource,
+    UserToolSourceAuthoringView,
 )
+from galaxy.tool_util_models._base import AGENT_LENIENT_CONTEXT
 from .base import (
     ActionSuggestion,
     ActionType,
@@ -56,6 +62,35 @@ def _find_validation_error(exc: BaseException) -> Optional[ValidationError]:
     return None
 
 
+def _invalid_attempt_yaml(messages: list[Any]) -> Optional[str]:
+    """Best-effort render of the model's last ``final_result`` tool-call arguments
+    (the attempt that just failed schema validation) as YAML.
+
+    On a schema-validation failure there's no constructed model to show back, but
+    the raw rejected arguments are still in the captured run messages. Recovering
+    them lets a validation-failure retry show the model its own output to patch in
+    place, instead of regenerating blind. Returns None if the args can't be
+    recovered (malformed JSON, no tool call, etc.).
+    """
+    for message in reversed(messages):
+        for part in getattr(message, "parts", None) or []:
+            if getattr(part, "part_kind", None) != "tool-call":
+                continue
+            if getattr(part, "tool_name", None) != "final_result":
+                continue
+            try:
+                args = part.args_as_dict()
+            except (ValueError, TypeError):
+                return None
+            # pydantic-ai returns a {"INVALID_JSON": "<raw>"} sentinel rather than
+            # raising when the tool-call args aren't valid JSON; that's not a usable
+            # prior attempt, so treat it as unrecoverable.
+            if not isinstance(args, dict) or not args or set(args) == {"INVALID_JSON"}:
+                return None
+            return yaml.dump(args, default_flow_style=False, sort_keys=False)
+    return None
+
+
 class CritiqueReport(BaseModel):
     """Structured critique returned by the LLM critic.
 
@@ -72,6 +107,23 @@ class CritiqueReport(BaseModel):
     summary: str = ""
 
 
+@dataclass
+class _ProducerFailure:
+    """A failed production attempt.
+
+    Carries the distilled validation/lint ``errors`` and -- when we have it -- the
+    rendered ``prior_yaml`` of the attempt. Lint failures validate cleanly first,
+    so the YAML exists and can be shown back to the model on retry to anchor the
+    error list to a concrete artifact ("fix these problems in the YAML below")
+    rather than asking it to regenerate blind. Schema-validation failures don't
+    yield a rendered model, so ``prior_yaml`` is None there (addressed separately
+    by an in-context continuation retry).
+    """
+
+    errors: list[str]
+    prior_yaml: Optional[str] = None
+
+
 class CustomToolAgent(BaseGalaxyAgent):
     """Agent that creates custom Galaxy tools using UserToolSource schema.
 
@@ -111,8 +163,22 @@ class CustomToolAgent(BaseGalaxyAgent):
     def _requires_structured_output(self) -> bool:
         return True
 
+    def _get_temperature(self) -> float:
+        # Tool generation is schema-constrained structured output, not creative
+        # prose. A low temperature converges faster and produces fewer invalid
+        # drafts, which directly cuts the validator-retry round-trips this agent
+        # would otherwise pay for. Operators can still override via
+        # inference_services.custom_tool.temperature.
+        return self._get_agent_config("temperature", 0.2)
+
     def _create_agent(self) -> Agent[GalaxyAgentDependencies, Any]:
-        """Create agent with UserToolSource as the output type.
+        """Create agent with ``UserToolSourceAuthoringView`` as the output type.
+
+        The authoring view is ``UserToolSource`` minus the ``tests`` block, which
+        is ~70% of the full JSON schema. Targeting it shrinks the structured-output
+        schema the model must satisfy (~150 KB -> ~33 KB) without weakening any tool
+        validation -- a produced view is promoted to a full ``UserToolSource`` in
+        ``_produce_tool``.
 
         Defaults retries to 0 because the agent's explicit reflection loop owns the
         validation retry (to provide a better prompt); operators can still override
@@ -121,9 +187,13 @@ class CustomToolAgent(BaseGalaxyAgent):
         return Agent(
             self._get_model(),
             deps_type=GalaxyAgentDependencies,
-            output_type=UserToolSource,
+            output_type=UserToolSourceAuthoringView,
             system_prompt=self.get_system_prompt(),
             retries=self._get_retries(default=0),
+            # Opt this (agent-ingest) path into the liberal-input coercions. The
+            # canonical API/storage validation runs without this context and stays
+            # strict, so coercion is scoped to model output only.
+            validation_context=AGENT_LENIENT_CONTEXT,
         )
 
     def get_system_prompt(self) -> str:
@@ -163,22 +233,48 @@ class CustomToolAgent(BaseGalaxyAgent):
             return self._capability_error_response(capability_error, query)
 
         try:
+            attempts = 1
             produced = await self._produce_tool(query)
             if produced is None:
                 return self._invalid_structured_output_response(query)
 
-            if isinstance(produced, list):
-                # _produce_tool returns the formatted error list when the
-                # producer hit a pydantic ValidationError. Retry once if
-                # enabled, otherwise surface the issues to the user.
+            if isinstance(produced, _ProducerFailure):
+                # _produce_tool returns a _ProducerFailure when the producer hit a
+                # pydantic ValidationError or lint failure. Retry once if enabled,
+                # otherwise surface the issues to the user.
                 if not self._validator_retry_enabled():
-                    return self._validation_failed_response(produced, query)
-                log.info("CustomTool: model failed validation (%d issue(s)); retrying once", len(produced))
-                retried = await self._produce_tool(query, retry_errors=produced)
+                    log.debug("CustomTool: validator retry disabled; failing with issues: %s", produced.errors)
+                    return self._validation_failed_response(produced.errors, query, attempts=attempts)
+                attempts = 2
+                log.info("CustomTool: model failed validation (%d issue(s)); retrying once", len(produced.errors))
+                log.debug(
+                    "CustomTool: first-attempt issues=%s; prior_yaml_available=%s",
+                    produced.errors,
+                    produced.prior_yaml is not None,
+                )
+                if produced.prior_yaml:
+                    log.debug("CustomTool: rejected first attempt:\n%s", produced.prior_yaml)
+                # Thread the prior attempt (when we have it) so the retry prompt can
+                # anchor the error list to the YAML the model actually produced.
+                retried = await self._produce_tool(query, retry_errors=produced.errors, prior_yaml=produced.prior_yaml)
                 if retried is None:
+                    log.warning(
+                        "CustomTool: retry produced no usable structured output (issues fed back: %s)",
+                        produced.errors,
+                    )
                     return self._invalid_structured_output_response(query)
-                if isinstance(retried, list):
-                    return self._validation_failed_response(retried, query)
+                if isinstance(retried, _ProducerFailure):
+                    first, again = set(produced.errors), set(retried.errors)
+                    log.warning(
+                        "CustomTool: retry still invalid (%d issue(s)). "
+                        "resolved=%s; persisted=%s; newly-introduced=%s",
+                        len(retried.errors),
+                        sorted(first - again) or "none",
+                        sorted(first & again) or "none",
+                        sorted(again - first) or "none",
+                    )
+                    return self._validation_failed_response(retried.errors, query, attempts=attempts)
+                log.info("CustomTool: retry recovered after %d first-attempt issue(s)", len(produced.errors))
                 tool, tool_yaml, result = retried
             else:
                 tool, tool_yaml, result = produced
@@ -195,13 +291,13 @@ class CustomToolAgent(BaseGalaxyAgent):
                     refined = await self._produce_tool(query, critique=critique, prior_yaml=tool_yaml)
                     if isinstance(refined, tuple):
                         tool, tool_yaml, result = refined
-                    elif isinstance(refined, list):
+                    elif isinstance(refined, _ProducerFailure):
                         log.warning(
                             "CustomTool: refinement broke validation (%d issue(s)); keeping pre-refine tool",
-                            len(refined),
+                            len(refined.errors),
                         )
 
-            return self._success_response(tool, tool_yaml, result, query)
+            return self._success_response(tool, tool_yaml, result, query, attempts=attempts)
 
         except (OSError, ValueError) as e:
             log.error(f"Tool creation error: {e}")
@@ -223,30 +319,46 @@ class CustomToolAgent(BaseGalaxyAgent):
         retry_errors: Optional[list[str]] = None,
         critique: Optional[CritiqueReport] = None,
         prior_yaml: Optional[str] = None,
-    ) -> Optional[tuple[UserToolSource, str, Any] | list[str]]:
-        """Run the producer agent. Returns (tool, yaml, raw_result), error list, or None.
+    ) -> Optional[tuple[UserToolSource, str, Any] | _ProducerFailure]:
+        """Run the producer agent. Returns (tool, yaml, raw_result), a
+        ``_ProducerFailure``, or None.
 
         ``retry_errors`` and ``critique`` are mutually exclusive: each prepends a
         structured "fix specifically these issues" preamble to the original query.
         """
         prompt = self._build_producer_prompt(query, retry_errors=retry_errors, critique=critique, prior_yaml=prior_yaml)
-        try:
-            result = await self._run_with_retry(prompt)
-            tool = extract_structured_output(result, UserToolSource, log)
-            if tool is None:
-                return None
-            lint_errors = lint_user_tool_source(tool)
-            if lint_errors:
-                log.debug("CustomToolAgent lint failure: %s", lint_errors)
-                return lint_errors
-            tool_dict = tool.model_dump(by_alias=True, exclude_none=True)
-            tool_yaml = yaml.dump(tool_dict, default_flow_style=False, sort_keys=False)
-            return tool, tool_yaml, result
-        except UnexpectedModelBehavior as e:
-            pydantic_error = _find_validation_error(e)
-            if pydantic_error:
-                return format_validation_errors(pydantic_error)
-            raise e
+        # Capture the run messages so that, on a schema-validation failure, we can
+        # recover the model's rejected tool-call args and feed them back into the
+        # retry (there's no constructed model to render in that case).
+        with capture_run_messages() as messages:
+            try:
+                result = await self._run_with_retry(prompt)
+                authored = extract_structured_output(result, UserToolSourceAuthoringView, log)
+                if authored is None:
+                    return None
+                # The model authors against the slim view (no `tests`); promote to the
+                # full UserToolSource so linting, serialization, and storage operate on
+                # the canonical model. The view is a strict subset, so this never fails.
+                tool = UserToolSource.model_validate(authored.model_dump(by_alias=True))
+                tool_dict = tool.model_dump(by_alias=True, exclude_none=True)
+                tool_yaml = yaml.dump(tool_dict, default_flow_style=False, sort_keys=False)
+                lint_errors = lint_user_tool_source(tool)
+                if lint_errors:
+                    log.debug("CustomToolAgent lint failure: %s", lint_errors)
+                    # The tool validated, so we have its rendered YAML -- carry it so a
+                    # retry can show the model exactly what to fix in place.
+                    return _ProducerFailure(lint_errors, prior_yaml=tool_yaml)
+                return tool, tool_yaml, result
+            except UnexpectedModelBehavior as e:
+                pydantic_error = _find_validation_error(e)
+                if pydantic_error:
+                    # No constructed model to show back, but recover the raw rejected
+                    # args from the run messages so the retry can patch them in place.
+                    return _ProducerFailure(
+                        format_validation_errors(pydantic_error),
+                        prior_yaml=_invalid_attempt_yaml(messages),
+                    )
+                raise e
 
     @staticmethod
     def _build_producer_prompt(
@@ -258,15 +370,25 @@ class CustomToolAgent(BaseGalaxyAgent):
         if not retry_errors and not critique:
             return query
 
+        # On a repair/refine turn, lead with the artifact being fixed so the error
+        # list is anchored to something concrete, follow with the prominent,
+        # numbered problems, and demote the original request to trailing reference
+        # (it's secondary when patching a near-correct draft).
         sections: list[str] = []
-        if retry_errors:
-            error_list = "\n".join(f"- {e}" for e in retry_errors)
+        if prior_yaml:
             sections.append(
-                "The previous attempt at this tool definition had specific problems "
-                "that need to be fixed:\n\n"
-                f"{error_list}\n\n"
-                "Re-generate the tool definition fixing exactly those issues. Keep "
-                "the parts that were already correct."
+                "Your previous attempt is below. It is close -- fix it in place, do NOT "
+                "rewrite it from scratch:\n\n"
+                f"```yaml\n{prior_yaml}```"
+            )
+
+        if retry_errors:
+            numbered = "\n".join(f"{i}. {e}" for i, e in enumerate(retry_errors, 1))
+            target = "the YAML above" if prior_yaml else "your previous attempt"
+            sections.append(
+                f"That attempt failed validation. Fix every one of these problems in {target} "
+                "and return the full corrected tool definition; leave everything else "
+                f"unchanged:\n\n{numbered}"
             )
         elif critique:
             issue_lines: list[str] = []
@@ -285,10 +407,7 @@ class CustomToolAgent(BaseGalaxyAgent):
                 "change parts the reviewer didn't flag."
             )
 
-        if prior_yaml:
-            sections.append("Previous tool YAML:\n\n```yaml\n" + prior_yaml + "```")
-
-        sections.append("Original request:\n\n" + query)
+        sections.append("Original request (for reference):\n\n" + query)
         return "\n\n".join(sections)
 
     async def _run_critic(self, tool_yaml: str, query: str) -> Optional[CritiqueReport]:
@@ -345,6 +464,7 @@ class CustomToolAgent(BaseGalaxyAgent):
         self,
         validation_errors: list[str],
         query: str,
+        attempts: int = 1,
     ) -> AgentResponse:
         log.warning(
             "CustomToolAgent produced a UserToolSource that failed validation: %s",
@@ -364,10 +484,15 @@ class CustomToolAgent(BaseGalaxyAgent):
             error="validation_failed",
             agent_data={
                 "validation_errors": validation_errors,
+                # Number of producer calls made (1 = first attempt, 2 = a retry was
+                # spent). Surfaced for offline benchmarking of schema/model quality.
+                "attempts": attempts,
             },
         )
 
-    def _success_response(self, tool: UserToolSource, tool_yaml: str, result: Any, query: str) -> AgentResponse:
+    def _success_response(
+        self, tool: UserToolSource, tool_yaml: str, result: Any, query: str, attempts: int = 1
+    ) -> AgentResponse:
         response_content = f"""I've created a custom Galaxy tool:
 
 ```yaml
@@ -402,6 +527,9 @@ The tool is ready to be saved and used in Galaxy."""
                 "tool_id": tool.id,
                 "tool_name": tool.name,
                 "tool_yaml": tool_yaml,
+                # 1 = produced on the first attempt, 2 = a validator retry was needed.
+                # Surfaced for offline benchmarking of schema/model quality.
+                "attempts": attempts,
             },
         )
 
diff --git a/test/unit/app/test_agents.py b/test/unit/app/test_agents.py
index 6a303074ea2..1ca9de262fb 100644
--- a/test/unit/app/test_agents.py
+++ b/test/unit/app/test_agents.py
@@ -1877,6 +1877,78 @@ class TestCustomToolAgentReflection:
         retry_prompt = mock_run.call_args_list[1][0][0]
         assert "previous attempt" in retry_prompt.lower()
 
+    @pytest.mark.asyncio
+    async def test_lint_failure_retry_anchors_prior_yaml(self):
+        """A first-attempt lint failure (tool validates but lints dirty) feeds the
+        rendered YAML back into the retry prompt so the model fixes it in place,
+        rather than regenerating blind from the error list alone."""
+        agent = CustomToolAgent(self.deps)
+
+        with mock.patch.object(
+            agent.agent,
+            "run",
+            side_effect=[
+                _mock_run_result(_valid_tool()),
+                _mock_run_result(_valid_tool()),
+            ],
+        ) as mock_run:
+            # Tool validates both times; lint fails the first attempt, passes the second.
+            with mock.patch(
+                "galaxy.agents.custom_tool.lint_user_tool_source",
+                side_effect=[["container 'busybox' has an unexpected shape"], []],
+            ):
+                response = await agent.process("Create a tool")
+
+        assert mock_run.call_count == 2
+        retry_prompt = mock_run.call_args_list[1][0][0]
+        # The previous attempt's YAML is embedded and the model is told to patch it.
+        assert "```yaml" in retry_prompt
+        assert "fix it in place" in retry_prompt.lower()
+        # The specific lint error is carried through as a numbered problem.
+        assert "unexpected shape" in retry_prompt
+        assert response.confidence == ConfidenceLevel.HIGH
+
+    def test_invalid_attempt_yaml_recovers_rejected_tool_call_args(self):
+        """A schema-validation failure has no constructed model, but the model's
+        rejected tool-call args can still be recovered from the run messages and
+        rendered as YAML for the retry to patch."""
+        from pydantic_ai.messages import (
+            ModelResponse,
+            ToolCallPart,
+        )
+
+        from galaxy.agents.custom_tool import _invalid_attempt_yaml
+
+        messages = [
+            ModelResponse(
+                parts=[
+                    ToolCallPart(
+                        tool_name="final_result",
+                        args='{"class": "GalaxyUserTool", "name": "My Tool", '
+                        '"inputs": [{"type": "data", "name": "x", "min": 1}]}',
+                    )
+                ]
+            )
+        ]
+        out = _invalid_attempt_yaml(messages)
+        assert out is not None
+        assert "name: My Tool" in out
+        assert "min: 1" in out
+
+    def test_invalid_attempt_yaml_unrecoverable_returns_none(self):
+        from pydantic_ai.messages import (
+            ModelResponse,
+            ToolCallPart,
+        )
+
+        from galaxy.agents.custom_tool import _invalid_attempt_yaml
+
+        # No tool call at all.
+        assert _invalid_attempt_yaml([]) is None
+        # Malformed JSON surfaces as pydantic-ai's INVALID_JSON sentinel, not a tool.
+        malformed = [ModelResponse(parts=[ToolCallPart(tool_name="final_result", args="{not json")])]
+        assert _invalid_attempt_yaml(malformed) is None
+
     @pytest.mark.asyncio
     async def test_validator_retry_exhausted_returns_validation_failure(self):
         """Both producer calls fail validation -> low-confidence validation_failed."""

From 74d87878a1e769424c9d68599862b432915da8c1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 19:49:51 +0200
Subject: [PATCH 243/256] Strengthen the custom-tool generation prompt

- Require shell_command `$(inputs.X)` references to match declared input names,
  with a single coherent example (command/inputs/outputs share names).
- "Running a script": inline `python -c` for short scripts, or a configfiles
  entry with a matching filename for longer ones -- never a bare `python
  script.py` with no configfile creating it.
- "Choosing a container": the container must already ship every tool/library
  used (a bare python image can't `import pandas`).
---
 .../agents/prompts/custom_tool_structured.md  | 92 ++++++++++++++++++-
 1 file changed, 88 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/agents/prompts/custom_tool_structured.md b/lib/galaxy/agents/prompts/custom_tool_structured.md
index 071e0a7f5c8..7d385396600 100644
--- a/lib/galaxy/agents/prompts/custom_tool_structured.md
+++ b/lib/galaxy/agents/prompts/custom_tool_structured.md
@@ -24,8 +24,36 @@ You are a Galaxy tool generator. Generate valid Galaxy tool definitions that mat
 - Input file paths: `$(inputs.param_name.path)` for single files
 - Input values: `$(inputs.param_name)` for text, integer, float, boolean
 - For array inputs: `$(inputs.param_name[].path)`
-- Outputs are captured via `from_work_dir` or `discover_datasets` in output definitions.
-  $(outputs.out.path) is not valid syntax.
+- CRITICAL: every `inputs.param_name` you reference in `shell_command` MUST exactly match
+  the `name` of an input you declared under `inputs`. Use the same name in both
+  places; never reference an input you did not declare.
+
+## Complete example (names match across command, inputs, and outputs)
+
+Note how every `$(inputs.X)` in `shell_command` corresponds to a declared input of
+the same name, and the output's `from_work_dir` matches the file the command writes:
+
+```yaml
+class: GalaxyUserTool
+id: head-lines
+name: Head lines
+version: 0.1.0
+container: quay.io/biocontainers/coreutils:9.5
+shell_command: head -n $(inputs.num_lines) '$(inputs.input_file.path)' > output.txt
+inputs:
+    - name: input_file
+      type: data
+      label: Input file
+    - name: num_lines
+      type: integer
+      value: 10
+      label: Number of lines
+outputs:
+    - name: output_file
+      type: data
+      from_work_dir: output.txt
+      label: First lines
+```
 
 ## Input Parameter Types
 
@@ -46,10 +74,10 @@ inputs:
       type: data
       format: fastq
       label: Input FASTQ file
-    - name: num_records
+    - name: num_lines
       type: integer
       value: 4
-      label: Number of Records
+      label: Number of lines
 ```
 
 ## Output Types
@@ -70,6 +98,60 @@ outputs:
       label: Aligned reads
 ```
 
+## Running a script
+
+You have exactly two ways to run a script. Pick one and complete it fully:
+
+**1. Short script (a few lines): inline it in `shell_command`.** Use `python -c` /
+`Rscript -e` and reference inputs directly. This is self-contained -- nothing else to
+declare:
+
+```yaml
+container: quay.io/biocontainers/pandas:2.1.1
+shell_command: >-
+  python -c "import pandas as pd; d = pd.read_csv('$(inputs.table.path)', sep='\t');
+  d['group'] = d['sample_id'].str.startswith('Tx').map({True: 'Treatment', False: 'Vehicle'});
+  d.to_csv('output.tsv', sep='\t', index=False)"
+```
+
+**2. Longer script: put it in a `configfiles` entry and run that file.** The file is
+materialized in the working directory at `filename`, so `shell_command` runs it by name:
+
+```yaml
+configfiles:
+    - filename: script.py
+      content: |
+        import pandas as pd
+        df = pd.read_csv("$(inputs.table.path)", sep="\t")
+        df.describe().to_csv("summary.tsv", sep="\t")
+shell_command: python script.py
+```
+
+Inside `content` you reference inputs the same way: `$(inputs.NAME)` for values and
+`$(inputs.NAME.path)` for files.
+
+CRITICAL: if `shell_command` runs a script by name (`python script.py`), you MUST
+include a `configfiles` entry whose `filename` is exactly that name. Writing
+`python script.py` with no configfile that creates it is broken -- the file will not
+exist at runtime. If you don't want a configfile, inline the script with `python -c`
+instead.
+
+## Choosing a container
+
+The `container` MUST already include every command-line tool AND library your
+`shell_command` or script uses. A bare language image does NOT ship third-party
+libraries -- for example `quay.io/biocontainers/python:3.13` cannot `import pandas`.
+Pick a container that bundles what you need:
+
+- Python needing pandas/numpy/scipy/matplotlib: choose a biocontainer that ships
+  them (search for the package on quay.io/biocontainers, e.g. a `pandas` or
+  `scipy`/`matplotlib` image), not bare `python`.
+- R needing a package (ggplot2, etc.): choose an R biocontainer that includes that
+  package, not bare `r-base`.
+- A specific CLI tool (samtools, bwa, ...): use that tool's biocontainer.
+
+If your command or script imports/calls something, the container must provide it.
+
 ## Resource requirements
 
 Tools can request non-default resources.
@@ -96,6 +178,8 @@ environment and be set to `cores_min`.
 
 ## CRITICAL: Accuracy Requirements
 
+- Outputs are captured via `from_work_dir` or `discover_datasets` in output definitions.
+  `$(outputs.param_name.path)` is not valid syntax.
 - Only use container images you are certain exist (e.g., verified biocontainers)
 - If you don't know the correct container image for a tool, say so rather than guessing
 - Never fabricate command-line arguments or tool capabilities

From 1d67a70fbbc4c6146106d0f763b2cd119bef5133 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 19:49:51 +0200
Subject: [PATCH 244/256] Add a custom-tool generation eval benchmark

A pydantic-evals dataset of NL "wrap this as a tool" requests scored by
ToolProduced (validated tool at all), FirstAttemptOk (no validator retry),
ToolYamlContains (structural shape), and an LLMJudge for correctness. Wired
into the cross-model runner (specs/tasks/evaluators) plus a small
capture_custom_tool.py for single-model transcript capture.
---
 test/evals/capture_custom_tool.py  |  51 +++++++++
 test/evals/datasets/__init__.py    |   2 +
 test/evals/datasets/custom_tool.py | 174 +++++++++++++++++++++++++++++
 test/evals/evaluators.py           |  57 ++++++++++
 test/evals/specs.py                |  25 +++++
 test/evals/tasks.py                |  41 +++++++
 6 files changed, 350 insertions(+)
 create mode 100644 test/evals/capture_custom_tool.py
 create mode 100644 test/evals/datasets/custom_tool.py

diff --git a/test/evals/capture_custom_tool.py b/test/evals/capture_custom_tool.py
new file mode 100644
index 00000000000..535a09be1c7
--- /dev/null
+++ b/test/evals/capture_custom_tool.py
@@ -0,0 +1,51 @@
+"""Ad-hoc: run the custom-tool agent against one live model + one case and dump
+the rejected first attempt, so we can see WHY validation fails.
+
+    cd test
+    PYTHONPATH=../lib:. python evals/capture_custom_tool.py gpt-oss-120b-llmlb boxplot_welch_ttest
+"""
+
+import asyncio
+import logging
+import sys
+
+import yaml
+from evals.datasets.custom_tool import _PROTO_CASES
+from evals.tasks import make_deps
+
+from galaxy.agents.custom_tool import CustomToolAgent
+
+logging.basicConfig(level=logging.INFO, format="%(levelname)s %(name)s %(message)s")
+logging.getLogger("galaxy.agents.custom_tool").setLevel(logging.DEBUG)
+logging.getLogger("httpx").setLevel(logging.WARNING)
+logging.getLogger("httpcore").setLevel(logging.WARNING)
+logging.getLogger("openai").setLevel(logging.WARNING)
+
+
+def _creds(model: str) -> tuple[str, str]:
+    cfg = yaml.safe_load(open("evals/models.yaml"))
+    entry = cfg[model]
+    return entry["api_key"], entry["proxy_url"]
+
+
+async def main() -> None:
+    model = sys.argv[1] if len(sys.argv) > 1 else "gpt-oss-120b-llmlb"
+    case_name = sys.argv[2] if len(sys.argv) > 2 else "boxplot_welch_ttest"
+    query = next(c["query"] for c in _PROTO_CASES if c["name"] == case_name)
+
+    api_key, base_url = _creds(model)
+    deps = make_deps(model=model, api_key=api_key, base_url=base_url)
+    agent = CustomToolAgent(deps)
+
+    print(f"\n=== {model} / {case_name} ===")
+    response = await agent.process(query)
+    meta = response.metadata or {}
+    print(
+        f"\nmethod={meta.get('method')} error={meta.get('error')} attempts={(meta.get('agent_data') or {}).get('attempts')}"
+    )
+    print("\n--- response content ---")
+    print(response.content[:3000])
+
+
+if __name__ == "__main__":
+    asyncio.run(main())
diff --git a/test/evals/datasets/__init__.py b/test/evals/datasets/__init__.py
index 6c8bc68333d..8a5a528dfbe 100644
--- a/test/evals/datasets/__init__.py
+++ b/test/evals/datasets/__init__.py
@@ -2,6 +2,7 @@
 
 from .bioinformatics_workflows import bioinformatics_workflows_dataset
 from .capabilities import capabilities_dataset
+from .custom_tool import custom_tool_dataset
 from .error_analysis import error_analysis_dataset
 from .orchestrator_planning import orchestrator_planning_dataset
 from .router_tool_use import router_tool_use_dataset
@@ -19,6 +20,7 @@ __all__ = [
     "bioinformatics_workflows_dataset",
     "build_history",
     "capabilities_dataset",
+    "custom_tool_dataset",
     "error_analysis_dataset",
     "orchestrator_planning_dataset",
     "router_tool_use_dataset",
diff --git a/test/evals/datasets/custom_tool.py b/test/evals/datasets/custom_tool.py
new file mode 100644
index 00000000000..99d8e39a237
--- /dev/null
+++ b/test/evals/datasets/custom_tool.py
@@ -0,0 +1,174 @@
+"""Custom-tool generation dataset: can the model author a valid Galaxy tool?
+
+Each case is a natural-language "wrap this command as a tool" request against
+``CustomToolAgent``. Scored several ways (wired up in ``specs.build_custom_tool``):
+
+- ToolProduced (deterministic): did the agent return a structured, schema-valid,
+  lint-clean tool at all? This is the headline metric -- it folds in
+  structured-output reliability on the ~33 KB nested schema plus every
+  authoring-time validator.
+- FirstAttemptOk (deterministic): did it succeed WITHOUT spending a validator
+  retry? Isolates how easy the schema + prompt make it to get right first time --
+  the quantity schema-shrinking, low temperature, and retry-anchoring target.
+- ToolYamlContains (deterministic): does the generated YAML contain the structural
+  features the request implies (``yaml_must_contain``)? Partial credit.
+- LLMJudge (fuzzy): given the request, is the tool actually correct -- sensible
+  container, command that wires inputs to outputs, right input/output shapes?
+
+No live toolbox is needed: tool authoring is self-contained (validate + lint), so
+the mocked-deps path is a faithful measurement of model + schema quality. It does
+NOT exercise actual tool *build* (``create_tool_from_source``); that end-to-end
+check belongs in the live integration eval.
+"""
+
+from typing import (
+    Any,
+    Optional,
+)
+
+from pydantic_ai.models import Model
+from pydantic_evals import (
+    Case,
+    Dataset,
+)
+from pydantic_evals.evaluators import (
+    LLMJudge,
+    OutputConfig,
+)
+
+_PROTO_CASES: list[dict[str, Any]] = [
+    {
+        "name": "boxplot_welch_ttest",
+        "query": (
+            "Create a custom Galaxy tool that takes a tabular dataset with columns including "
+            "'group' (Vehicle or Tx) and numeric measurements, generates a boxplot comparing "
+            "Vehicle vs Tx groups, performs a Welch's t-test, and displays the p-value above the "
+            "plot. The tool should accept the input dataset, allow selection of the measurement "
+            "column, and output the plot (e.g., PNG) and a text file with the p-value."
+        ),
+        "yaml_must_contain": ["type: data", "$(inputs.", "from_work_dir"],
+        "rubric": (
+            "A correct tool wraps a Python/R container (e.g. a biocontainers image with pandas + "
+            "matplotlib/scipy, or an R container), takes the tabular dataset as a data input, lets "
+            "the user pick the measurement column (a text/column/select input -- NOT a hardcoded "
+            "column), and declares TWO outputs: the plot image and a text file with the p-value, "
+            "each claimed via from_work_dir. The shell_command must reference the inputs via "
+            "$(inputs.NAME) / $(inputs.NAME.path)."
+        ),
+    },
+    {
+        "name": "head_n_lines",
+        "query": (
+            "Make a Galaxy tool that returns the first N lines of an uploaded text file, where N "
+            "is a user-provided integer (default 10). Output the truncated file."
+        ),
+        "yaml_must_contain": ["type: data", "type: integer", "$(inputs.", "from_work_dir"],
+        "rubric": (
+            "A correct tool uses a lightweight container (busybox/coreutils/python), a single data "
+            "input for the file, an integer input for N (with a default), runs something like "
+            "`head -n $(inputs.n) $(inputs.infile.path)`, and claims one output via from_work_dir."
+        ),
+    },
+    {
+        "name": "multi_file_concatenate",
+        "query": (
+            "I want a Galaxy tool that concatenates MULTIPLE uploaded text files (the user selects "
+            "two or more) into a single combined output file."
+        ),
+        # "multiple: true" is the correct modeling for several datasets in one input;
+        # this is exactly the case where a naive `min:`-on-single-data definition 500s.
+        "yaml_must_contain": ["multiple: true", "from_work_dir"],
+        "rubric": (
+            "A correct tool models the input as a single data parameter with multiple: true (NOT a "
+            "single-dataset input, and NOT min/max without multiple), then concatenates the files "
+            "(e.g. `cat $(inputs.files)` ) into one output claimed via from_work_dir."
+        ),
+    },
+    {
+        "name": "grep_filter_with_mode",
+        "query": (
+            "Create a Galaxy tool that filters lines of a text file by a user-supplied search "
+            "pattern, with a dropdown to choose whether to keep matching or non-matching lines. "
+            "Output the filtered file."
+        ),
+        "yaml_must_contain": ["type: select", "options", "type: text", "from_work_dir"],
+        "rubric": (
+            "A correct tool has a data input for the file, a text input for the pattern, and a "
+            "select (dropdown) input with options for keep-matching vs invert-match (mapping to "
+            "`grep` vs `grep -v`), and claims the filtered output via from_work_dir."
+        ),
+    },
+    {
+        "name": "split_to_collection",
+        "query": (
+            "Make a Galaxy tool that splits a multi-FASTA file into one file per sequence and "
+            "returns the results as a dataset collection."
+        ),
+        "yaml_must_contain": ["type: collection", "discover_datasets"],
+        "rubric": (
+            "A correct tool takes the multi-FASTA as a data input, splits it into per-sequence "
+            "files in the working directory, and declares a collection output that gathers them "
+            "via discover_datasets (a pattern). A single data output would be incorrect."
+        ),
+    },
+]
+
+
+_RUBRIC_TEMPLATE = """\
+You are reviewing a Galaxy tool definition produced by an automated tool generator
+from a user's natural-language request.
+
+Acceptance rubric for this case:
+{rubric}
+
+Score the tool between 0.0 and 1.0:
+- 1.0: Valid, runnable-looking tool that satisfies the rubric -- right container,
+  command correctly wires the declared inputs to the declared outputs, and the
+  input/output shapes match what was asked.
+- 0.5: Largely correct but with a real flaw -- a plausible but unverified container,
+  a missing/extra input, or an output that won't be claimed correctly.
+- 0.0: Doesn't satisfy the request, references undeclared inputs, hardcodes what
+  should be a parameter, or no usable tool was produced.
+
+Return a number; no commentary.
+"""
+
+
+def custom_tool_dataset(
+    judge_model: Optional[Model] = None,
+    only: Optional[list[str]] = None,
+) -> Dataset[str, dict, dict[str, Any]]:
+    """Build the custom_tool Dataset.
+
+    If ``judge_model`` is given, attaches a per-case LLMJudge with a rubric-specific
+    prompt that scores the produced tool's correctness.
+    """
+    cases: list[Case[str, dict, dict[str, Any]]] = []
+    for proto in _PROTO_CASES:
+        if only and proto["name"] not in only:
+            continue
+        evaluators: tuple = ()
+        if judge_model is not None:
+            rubric = _RUBRIC_TEMPLATE.format(rubric=proto["rubric"])
+            evaluators = (
+                LLMJudge(
+                    rubric=rubric,
+                    model=judge_model,
+                    include_input=True,
+                    score=OutputConfig(evaluation_name="LLMJudge"),
+                    assertion=False,
+                ),
+            )
+        cases.append(
+            Case(
+                name=proto["name"],
+                inputs=proto["query"],
+                expected_output=None,
+                metadata={
+                    "yaml_must_contain": proto["yaml_must_contain"],
+                    "rubric": proto["rubric"],
+                },
+                evaluators=evaluators,
+            )
+        )
+    return Dataset(name="custom_tool", cases=cases)
diff --git a/test/evals/evaluators.py b/test/evals/evaluators.py
index 9501c9728e2..eabf0adb293 100644
--- a/test/evals/evaluators.py
+++ b/test/evals/evaluators.py
@@ -88,6 +88,63 @@ class OrchestratorPlanIncludes(Evaluator[Any, Any, dict]):
         return 1.0 if any(name in used for name in expected) else 0.0
 
 
+@dataclass
+class ToolProduced(Evaluator[Any, Any, dict]):
+    """Score 1.0 if the custom-tool agent produced a usable, validated tool.
+
+    Reads ``ctx.output["ok"]`` from :func:`tasks.make_custom_tool_task`. ``ok`` is
+    True only when the agent returned a structured, schema-valid, lint-clean tool
+    (after at most one validator retry). This is the headline pass/fail: it folds
+    in structured-output reliability on the nested schema plus every authoring-time
+    validator.
+    """
+
+    def evaluate(self, ctx: EvaluatorContext[Any, Any, dict]) -> float:
+        output = ctx.output if isinstance(ctx.output, dict) else {}
+        return 1.0 if output.get("ok") else 0.0
+
+
+@dataclass
+class FirstAttemptOk(Evaluator[Any, Any, dict]):
+    """Score 1.0 if a usable tool was produced on the FIRST attempt (no retry).
+
+    Reads ``ok`` and ``attempts`` from the task output. This isolates how easy the
+    schema + prompt make it for a model to get it right first time -- the quantity
+    that schema-shrinking, low temperature, and retry-anchoring aim to improve.
+    A model that only succeeds via the validator retry scores 0.0 here but 1.0 on
+    :class:`ToolProduced`, so the two together separate "can do it" from "does it
+    cleanly".
+    """
+
+    def evaluate(self, ctx: EvaluatorContext[Any, Any, dict]) -> float:
+        output = ctx.output if isinstance(ctx.output, dict) else {}
+        return 1.0 if output.get("ok") and output.get("attempts") == 1 else 0.0
+
+
+@dataclass
+class ToolYamlContains(Evaluator[Any, Any, dict]):
+    """Score = fraction of metadata['yaml_must_contain'] substrings present in the
+    produced tool YAML (case-insensitive).
+
+    Lets a case assert structural expectations about the generated tool -- e.g.
+    ``from_work_dir`` (an output is actually claimed), ``type: select`` (a choice
+    input was modeled), ``$(inputs.`` (the command references inputs). Scores 0.0
+    if no tool was produced. Partial credit so a near-miss is distinguishable from
+    a total miss.
+    """
+
+    def evaluate(self, ctx: EvaluatorContext[Any, Any, dict]) -> float:
+        needles = (ctx.metadata or {}).get("yaml_must_contain") or []
+        if not needles:
+            return 1.0
+        output = ctx.output if isinstance(ctx.output, dict) else {}
+        yaml_text = str(output.get("tool_yaml") or "").lower()
+        if not yaml_text:
+            return 0.0
+        hits = sum(1 for n in needles if n.lower() in yaml_text)
+        return hits / len(needles)
+
+
 @dataclass
 class ToolCallMatch(Evaluator[Any, Any, dict]):
     """Score 1.0 if the model called any tool named in metadata['expected_tool_calls'].
diff --git a/test/evals/specs.py b/test/evals/specs.py
index 40721baf5f0..2f9ef6f62fd 100644
--- a/test/evals/specs.py
+++ b/test/evals/specs.py
@@ -22,6 +22,7 @@ from galaxy.agents.base import GalaxyAgentDependencies
 from .datasets import (
     bioinformatics_workflows_dataset,
     capabilities_dataset,
+    custom_tool_dataset,
     error_analysis_dataset,
     orchestrator_planning_dataset,
     router_tool_use_dataset,
@@ -33,13 +34,17 @@ from .datasets import (
     tool_recommendation_dataset,
 )
 from .evaluators import (
+    FirstAttemptOk,
     HandoffMatch,
     MustMention,
     MustMentionAny,
     OrchestratorPlanIncludes,
     ToolCallMatch,
+    ToolProduced,
+    ToolYamlContains,
 )
 from .tasks import (
+    make_custom_tool_task,
     make_error_analysis_task,
     make_orchestrator_plan_task,
     make_router_clarification_task,
@@ -210,6 +215,25 @@ def build_tool_recommendation(
     )
 
 
+def build_custom_tool(
+    deps: GalaxyAgentDependencies,
+    judge_model: Optional[Model] = None,
+    only: Optional[list[str]] = None,
+    include_galaxy_required: bool = False,
+    usage_buffer: Optional[list[dict[str, int]]] = None,
+) -> BuiltDataset:
+    dataset = custom_tool_dataset(judge_model=judge_model, only=only)
+    # Headline pass/fail + the "got it right first try" and structural-shape checks.
+    dataset.add_evaluator(ToolProduced())
+    dataset.add_evaluator(FirstAttemptOk())
+    dataset.add_evaluator(ToolYamlContains())
+    return BuiltDataset(
+        dataset=dataset,
+        task=make_custom_tool_task(deps, usage_buffer=usage_buffer),
+        primary_score="ToolProduced",
+    )
+
+
 def build_router_tool_use(
     deps: GalaxyAgentDependencies,
     judge_model: Optional[Model] = None,
@@ -301,6 +325,7 @@ SPECS: dict[str, Callable[..., BuiltDataset]] = {
     "routing_clarification_followup_nofix": build_routing_clarification_followup_nofix,
     "error_analysis": build_error_analysis,
     "tool_recommendation": build_tool_recommendation,
+    "custom_tool": build_custom_tool,
     "router_tool_use": build_router_tool_use,
     "bioinformatics_workflows": build_bioinformatics_workflows,
     "capabilities": build_capabilities,
diff --git a/test/evals/tasks.py b/test/evals/tasks.py
index 4fd92ed9a95..110aed7ddd9 100644
--- a/test/evals/tasks.py
+++ b/test/evals/tasks.py
@@ -26,6 +26,7 @@ from galaxy.agents.base import (
     extract_usage_info,
     GalaxyAgentDependencies,
 )
+from galaxy.agents.custom_tool import CustomToolAgent
 from galaxy.agents.error_analysis import ErrorAnalysisAgent
 from galaxy.agents.registry import build_default_registry
 from galaxy.agents.router import QueryRouterAgent
@@ -318,6 +319,46 @@ def make_tool_recommendation_task(
     return tool_recommendation_task
 
 
+def make_custom_tool_task(
+    deps: GalaxyAgentDependencies,
+    context: Optional[dict] = None,
+    usage_buffer: UsageBuffer = None,
+) -> Callable[[str], Awaitable[dict[str, Any]]]:
+    """Build an async callable: NL request -> custom-tool generation result dict.
+
+    Returns the signals the custom-tool evaluators read:
+
+    - ``ok``: a structured, schema-valid, lint-clean tool was produced
+      (``response.metadata["method"] == "structured"``).
+    - ``attempts``: 1 if produced first try, 2 if a validator retry was spent.
+    - ``tool_yaml``: the generated tool definition (for structural checks / judge).
+    - ``content``: the agent's full response text.
+    - ``error`` / ``validation_errors``: failure detail when ``ok`` is False.
+
+    Unlike the recommendation tasks this needs no live toolbox -- tool authoring
+    is self-contained (validate + lint), so the mocked-deps path is a faithful
+    measurement. (An end-to-end "does it build into a real Galaxy tool" check
+    belongs in the live integration eval, where a real toolbox exists.)
+    """
+
+    async def custom_tool_task(query: str) -> dict[str, Any]:
+        agent = CustomToolAgent(deps)
+        response = await agent.process(query, context=context)
+        _record_response_usage(usage_buffer, response)
+        meta = response.metadata or {}
+        agent_data = meta.get("agent_data") or {}
+        return {
+            "ok": meta.get("method") == "structured",
+            "attempts": agent_data.get("attempts"),
+            "tool_yaml": agent_data.get("tool_yaml") or "",
+            "content": response.content,
+            "error": meta.get("error"),
+            "validation_errors": agent_data.get("validation_errors") or [],
+        }
+
+    return custom_tool_task
+
+
 def _extract_tool_calls(result: Any) -> list[dict[str, Any]]:
     """Pull every ToolCallPart from a pydantic-ai result into a flat list.
 

From 706c6d8583d835ac09bd418dfe54be4841c619b6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 20:01:54 +0200
Subject: [PATCH 245/256] Update client api schema

---
 .../packages/api-client/src/schema/schema.ts  | 309 ++++++++++--------
 .../src/components/Tool/ToolSourceSchema.json |   2 +-
 .../webapp/frontend/src/schema/schema.ts      |  68 ++--
 3 files changed, 225 insertions(+), 154 deletions(-)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index 795f8d4b084..8dc7ff1755b 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -12940,30 +12940,42 @@ export interface components {
         };
         /** FilePatternDatasetCollectionDescription */
         FilePatternDatasetCollectionDescription: {
-            /** Assign Primary Output */
+            /**
+             * Assign Primary Output
+             * @default false
+             */
             assign_primary_output: boolean;
             /** Directory */
-            directory: string | null;
+            directory?: string | null;
             /**
              * Discover Via
+             * @default pattern
              * @constant
              */
             discover_via: "pattern";
             /** Format */
-            format: string | null;
-            /** Match Relative Path */
+            format?: string | null;
+            /**
+             * Match Relative Path
+             * @default false
+             */
             match_relative_path: boolean;
             /** Pattern */
             pattern: string;
-            /** Recurse */
+            /**
+             * Recurse
+             * @default false
+             */
             recurse: boolean;
             /**
              * Sort Comp
+             * @default lexical
              * @enum {string}
              */
             sort_comp: "lexical" | "numeric";
             /**
              * Sort Key
+             * @default filename
              * @enum {string}
              */
             sort_key: "filename" | "name" | "designation" | "dbkey";
@@ -12972,7 +12984,10 @@ export interface components {
              * @default false
              */
             sort_reverse: boolean;
-            /** Visible */
+            /**
+             * Visible
+             * @default false
+             */
             visible: boolean;
         };
         /** FileRequestUri */
@@ -16040,6 +16055,29 @@ export interface components {
              */
             type: "in_range";
         };
+        /** IncomingToolOutputBoolean */
+        IncomingToolOutputBoolean: {
+            /**
+             * Hidden
+             * @description If true, the output will not be shown in the history.
+             */
+            hidden?: boolean | null;
+            /**
+             * Label
+             * @description Output label. Will be used as dataset name in history.
+             */
+            label?: string | null;
+            /**
+             * Name
+             * @description Parameter name. Used when referencing parameter in workflows.
+             */
+            name: string;
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "boolean";
+        };
         /** IncomingToolOutputCollection */
         IncomingToolOutputCollection: {
             /** Collection Type */
@@ -16133,6 +16171,75 @@ export interface components {
              */
             type: "data";
         };
+        /** IncomingToolOutputFloat */
+        IncomingToolOutputFloat: {
+            /**
+             * Hidden
+             * @description If true, the output will not be shown in the history.
+             */
+            hidden?: boolean | null;
+            /**
+             * Label
+             * @description Output label. Will be used as dataset name in history.
+             */
+            label?: string | null;
+            /**
+             * Name
+             * @description Parameter name. Used when referencing parameter in workflows.
+             */
+            name: string;
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "float";
+        };
+        /** IncomingToolOutputInteger */
+        IncomingToolOutputInteger: {
+            /**
+             * Hidden
+             * @description If true, the output will not be shown in the history.
+             */
+            hidden?: boolean | null;
+            /**
+             * Label
+             * @description Output label. Will be used as dataset name in history.
+             */
+            label?: string | null;
+            /**
+             * Name
+             * @description Parameter name. Used when referencing parameter in workflows.
+             */
+            name: string;
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "integer";
+        };
+        /** IncomingToolOutputText */
+        IncomingToolOutputText: {
+            /**
+             * Hidden
+             * @description If true, the output will not be shown in the history.
+             */
+            hidden?: boolean | null;
+            /**
+             * Label
+             * @description Output label. Will be used as dataset name in history.
+             */
+            label?: string | null;
+            /**
+             * Name
+             * @description Parameter name. Used when referencing parameter in workflows.
+             */
+            name: string;
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "text";
+        };
         /** InferredCollectionTypeLogEntry */
         InferredCollectionTypeLogEntry: {
             /** From Columns */
@@ -24182,116 +24289,37 @@ export interface components {
              */
             uuid: string;
         };
-        /** ToolOutputBoolean */
-        ToolOutputBoolean: {
-            /**
-             * Hidden
-             * @description If true, the output will not be shown in the history.
-             */
-            hidden: unknown;
-            /**
-             * Label
-             * @description Output label. Will be used as dataset name in history.
-             */
-            label?: string | null;
-            /**
-             * Name
-             * @description Parameter name. Used when referencing parameter in workflows.
-             */
-            name: unknown;
-            /**
-             * @description discriminator enum property added by openapi-typescript
-             * @enum {string}
-             */
-            type: "boolean";
-        };
-        /** ToolOutputFloat */
-        ToolOutputFloat: {
-            /**
-             * Hidden
-             * @description If true, the output will not be shown in the history.
-             */
-            hidden: unknown;
-            /**
-             * Label
-             * @description Output label. Will be used as dataset name in history.
-             */
-            label?: string | null;
-            /**
-             * Name
-             * @description Parameter name. Used when referencing parameter in workflows.
-             */
-            name: unknown;
-            /**
-             * @description discriminator enum property added by openapi-typescript
-             * @enum {string}
-             */
-            type: "float";
-        };
-        /** ToolOutputInteger */
-        ToolOutputInteger: {
-            /**
-             * Hidden
-             * @description If true, the output will not be shown in the history.
-             */
-            hidden: unknown;
-            /**
-             * Label
-             * @description Output label. Will be used as dataset name in history.
-             */
-            label?: string | null;
-            /**
-             * Name
-             * @description Parameter name. Used when referencing parameter in workflows.
-             */
-            name: unknown;
-            /**
-             * @description discriminator enum property added by openapi-typescript
-             * @enum {string}
-             */
-            type: "integer";
-        };
-        /** ToolOutputText */
-        ToolOutputText: {
-            /**
-             * Hidden
-             * @description If true, the output will not be shown in the history.
-             */
-            hidden: unknown;
-            /**
-             * Label
-             * @description Output label. Will be used as dataset name in history.
-             */
-            label?: string | null;
-            /**
-             * Name
-             * @description Parameter name. Used when referencing parameter in workflows.
-             */
-            name: unknown;
-            /**
-             * @description discriminator enum property added by openapi-typescript
-             * @enum {string}
-             */
-            type: "text";
-        };
         /** ToolProvidedMetadataDatasetCollection */
         ToolProvidedMetadataDatasetCollection: {
-            /** Assign Primary Output */
+            /**
+             * Assign Primary Output
+             * @default false
+             */
             assign_primary_output: boolean;
             /** Directory */
-            directory: string | null;
+            directory?: string | null;
             /**
              * Discover Via
+             * @default tool_provided_metadata
              * @constant
              */
             discover_via: "tool_provided_metadata";
             /** Format */
-            format: string | null;
-            /** Match Relative Path */
+            format?: string | null;
+            /**
+             * Match Relative Path
+             * @default false
+             */
             match_relative_path: boolean;
-            /** Recurse */
+            /**
+             * Recurse
+             * @default false
+             */
             recurse: boolean;
-            /** Visible */
+            /**
+             * Visible
+             * @default false
+             */
             visible: boolean;
         };
         /** ToolReportForDataset */
@@ -25696,7 +25724,15 @@ export interface components {
              */
             version: string;
         };
-        /** UserToolSource */
+        /**
+         * UserToolSource
+         * @description Full unprivileged tool source, including the optional ``tests`` block.
+         *
+         *     This is the model persisted and validated on the API surface
+         *     (``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring
+         *     uses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added
+         *     back here so direct authors and stored rows can still carry tests.
+         */
         "UserToolSource-Input": {
             /** citations */
             citations?: components["schemas"]["Citation"][] | null;
@@ -25759,10 +25795,10 @@ export interface components {
             outputs: (
                 | components["schemas"]["IncomingToolOutputDataset"]
                 | components["schemas"]["IncomingToolOutputCollection"]
-                | components["schemas"]["ToolOutputText"]
-                | components["schemas"]["ToolOutputInteger"]
-                | components["schemas"]["ToolOutputFloat"]
-                | components["schemas"]["ToolOutputBoolean"]
+                | components["schemas"]["IncomingToolOutputText"]
+                | components["schemas"]["IncomingToolOutputInteger"]
+                | components["schemas"]["IncomingToolOutputFloat"]
+                | components["schemas"]["IncomingToolOutputBoolean"]
             )[];
             /** profile */
             profile?: number | null;
@@ -25781,21 +25817,25 @@ export interface components {
             /**
              * shell_command
              * @description A string that contains the command to be executed. Parameters can be referenced inside $().
-             * @example head -n '$(inputs.n_lines)' '$(inputs.data_input.path)'
+             * @example head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt
              */
             shell_command: string;
             /** tests */
             tests?: components["schemas"]["YamlToolTest-Input"][] | null;
-            /**
-             * version
-             * @description Version for the tool.
-             * @example 0.1.0
-             */
+            /** version */
             version?: string | null;
             /** xrefs */
             xrefs?: components["schemas"]["XrefDict"][] | null;
         };
-        /** UserToolSource */
+        /**
+         * UserToolSource
+         * @description Full unprivileged tool source, including the optional ``tests`` block.
+         *
+         *     This is the model persisted and validated on the API surface
+         *     (``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring
+         *     uses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added
+         *     back here so direct authors and stored rows can still carry tests.
+         */
         "UserToolSource-Output": {
             /** citations */
             citations?: components["schemas"]["Citation"][] | null;
@@ -25858,10 +25898,10 @@ export interface components {
             outputs: (
                 | components["schemas"]["IncomingToolOutputDataset"]
                 | components["schemas"]["IncomingToolOutputCollection"]
-                | components["schemas"]["ToolOutputText"]
-                | components["schemas"]["ToolOutputInteger"]
-                | components["schemas"]["ToolOutputFloat"]
-                | components["schemas"]["ToolOutputBoolean"]
+                | components["schemas"]["IncomingToolOutputText"]
+                | components["schemas"]["IncomingToolOutputInteger"]
+                | components["schemas"]["IncomingToolOutputFloat"]
+                | components["schemas"]["IncomingToolOutputBoolean"]
             )[];
             /** profile */
             profile?: number | null;
@@ -25880,16 +25920,12 @@ export interface components {
             /**
              * shell_command
              * @description A string that contains the command to be executed. Parameters can be referenced inside $().
-             * @example head -n '$(inputs.n_lines)' '$(inputs.data_input.path)'
+             * @example head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt
              */
             shell_command: string;
             /** tests */
             tests?: components["schemas"]["YamlToolTest-Output"][] | null;
-            /**
-             * version
-             * @description Version for the tool.
-             * @example 0.1.0
-             */
+            /** version */
             version?: string | null;
             /** xrefs */
             xrefs?: components["schemas"]["XrefDict"][] | null;
@@ -27230,12 +27266,19 @@ export interface components {
             help?: string | null;
             /** Label */
             label?: string | null;
-            /** Max */
+            /**
+             * Max
+             * @description Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; leave unset for a single-dataset input.
+             */
             max?: number | null;
-            /** Min */
+            /**
+             * Min
+             * @description Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. Do NOT set this for a single-dataset input -- a data input is already required by default, so leave 'min' unset unless the input accepts multiple datasets.
+             */
             min?: number | null;
             /**
              * Multiple
+             * @description Set true to accept several datasets (a list) for this input instead of one.
              * @default false
              */
             multiple: boolean;
@@ -27639,10 +27682,10 @@ export interface components {
             outputs: (
                 | components["schemas"]["IncomingToolOutputDataset"]
                 | components["schemas"]["IncomingToolOutputCollection"]
-                | components["schemas"]["ToolOutputText"]
-                | components["schemas"]["ToolOutputInteger"]
-                | components["schemas"]["ToolOutputFloat"]
-                | components["schemas"]["ToolOutputBoolean"]
+                | components["schemas"]["IncomingToolOutputText"]
+                | components["schemas"]["IncomingToolOutputInteger"]
+                | components["schemas"]["IncomingToolOutputFloat"]
+                | components["schemas"]["IncomingToolOutputBoolean"]
             )[];
             /** profile */
             profile?: number | null;
@@ -27661,7 +27704,7 @@ export interface components {
             /**
              * shell_command
              * @description A string that contains the command to be executed. Parameters can be referenced inside $().
-             * @example head -n '$(inputs.n_lines)' '$(inputs.data_input.path)'
+             * @example head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt
              */
             shell_command: string;
             /** tests */
diff --git a/client/src/components/Tool/ToolSourceSchema.json b/client/src/components/Tool/ToolSourceSchema.json
index f37d024117f..98d4218c564 100644
--- a/client/src/components/Tool/ToolSourceSchema.json
+++ b/client/src/components/Tool/ToolSourceSchema.json
@@ -1 +1 @@
-{"$defs": {"Citation": {"properties": {"type": {"title": "Type", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["type", "content"], "title": "Citation", "type": "object"}, "CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "Container": {"properties": {"type": {"enum": ["docker", "singularity"], "title": "Type", "type": "string"}, "container_id": {"title": "Container Id", "type": "string"}}, "required": ["type", "container_id"], "title": "Container", "type": "object"}, "ContainerRequirement": {"properties": {"type": {"const": "container", "title": "Type", "type": "string"}, "container": {"$ref": "#/$defs/Container"}}, "required": ["type", "container"], "title": "ContainerRequirement", "type": "object"}, "EmptyFieldParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "empty_field", "default": "empty_field", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "EmptyFieldParameterValidatorModel", "type": "object"}, "FilePatternDatasetCollectionDescription": {"properties": {"discover_via": {"const": "pattern", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Format"}, "visible": {"title": "Visible", "type": "boolean"}, "assign_primary_output": {"title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Directory"}, "recurse": {"title": "Recurse", "type": "boolean"}, "match_relative_path": {"title": "Match Relative Path", "type": "boolean"}, "sort_key": {"enum": ["filename", "name", "designation", "dbkey"], "title": "Sort Key", "type": "string"}, "sort_comp": {"enum": ["lexical", "numeric"], "title": "Sort Comp", "type": "string"}, "sort_reverse": {"default": false, "title": "Sort Reverse", "type": "boolean"}, "pattern": {"title": "Pattern", "type": "string"}}, "required": ["discover_via", "format", "visible", "assign_primary_output", "directory", "recurse", "match_relative_path", "sort_key", "sort_comp", "pattern"], "title": "FilePatternDatasetCollectionDescription", "type": "object"}, "HelpContent": {"properties": {"format": {"enum": ["restructuredtext", "plain_text", "markdown"], "title": "Format", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["format", "content"], "title": "HelpContent", "type": "object"}, "InRangeParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "in_range", "default": "in_range", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "exclude_min": {"default": false, "title": "Exclude Min", "type": "boolean"}, "exclude_max": {"default": false, "title": "Exclude Max", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "InRangeParameterValidatorModel", "type": "object"}, "IncomingToolOutputCollection": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "collection_type_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type Source"}, "collection_type_from_rules": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type From Rules"}, "structured_like": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Structured Like"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}}, "required": ["type"], "title": "IncomingToolOutputCollection", "type": "object"}, "IncomingToolOutputDataset": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The short name for the output datatype.", "title": "Format"}, "format_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.", "title": "Format Source"}, "metadata_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This copies the metadata information from the tool\u2019s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.", "title": "Metadata Source"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}, "from_work_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Relative path to a file produced by the tool in its working directory. Output\u2019s contents are set to this file\u2019s contents.", "title": "from_work_dir"}, "precreate_directory": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Precreate Directory"}}, "required": ["type"], "title": "IncomingToolOutputDataset", "type": "object"}, "JavascriptRequirement": {"properties": {"type": {"const": "javascript", "title": "Type", "type": "string"}, "expression_lib": {"anyOf": [{"items": {"description": "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.", "examples": ["function pickValue() {\n    if (inputs.conditional_parameter.test_parameter == \"a\") {\n        return inputs.conditional_parameter.integer_parameter\n    } else {\n        return inputs.conditional_parameter.boolean_parameter\n    }\n}"], "title": "expression_lib", "type": "string"}, "type": "array"}, {"type": "null"}], "title": "Expression Lib"}}, "required": ["type", "expression_lib"], "title": "JavascriptRequirement", "type": "object"}, "LengthParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "length", "default": "length", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "LengthParameterValidatorModel", "type": "object"}, "NoOptionsParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "no_options", "default": "no_options", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "NoOptionsParameterValidatorModel", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RegexParameterValidatorModel": {"additionalProperties": false, "description": "Check if a regular expression **matches** the value, i.e. appears\nat the beginning of the value. To enforce a match of the complete value use\n``$`` at the end of the expression. The expression is given is the content\nof the validator tag. Note that for ``selects`` each option is checked\nseparately.", "properties": {"type": {"const": "regex", "default": "regex", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}, "expression": {"title": "Expression", "type": "string"}}, "required": ["expression"], "title": "RegexParameterValidatorModel", "type": "object"}, "ResourceRequirement": {"properties": {"type": {"const": "resource", "title": "Type", "type": "string"}, "cores_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 1, "description": "Minimum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Min"}, "cores_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Max"}, "ram_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 256, "description": "Minimum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Min"}, "ram_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Max"}, "tmpdir_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Min"}, "tmpdir_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Max"}, "cuda_version_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Version Min"}, "cuda_compute_capability": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Compute Capability"}, "gpu_memory_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Gpu Memory Min"}, "cuda_device_count_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Min"}, "cuda_device_count_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Max"}, "shm_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Shm Size"}, "timelimit": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum time in seconds the tool is allowed to run. Job will be terminated if exceeded.", "title": "Timelimit"}}, "required": ["type"], "title": "ResourceRequirement", "type": "object"}, "TestCollectionCollectionElementAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}}, "title": "TestCollectionCollectionElementAssertions", "type": "object"}, "TestCollectionDatasetElementAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestCollectionDatasetElementAssertions", "type": "object"}, "TestCollectionOutputAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}, "element_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Element Count"}, "attributes": {"anyOf": [{"$ref": "#/$defs/CollectionAttributes"}, {"type": "null"}], "default": null, "title": "Attributes"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "TestCollectionOutputAssertions", "type": "object"}, "TestDataOutputAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestDataOutputAssertions", "type": "object"}, "ToolOutputBoolean": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "boolean", "title": "Type", "type": "string"}}, "required": ["name", "hidden", "type"], "title": "ToolOutputBoolean", "type": "object"}, "ToolOutputFloat": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "float", "title": "Type", "type": "string"}}, "required": ["name", "hidden", "type"], "title": "ToolOutputFloat", "type": "object"}, "ToolOutputInteger": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "integer", "title": "Type", "type": "string"}}, "required": ["name", "hidden", "type"], "title": "ToolOutputInteger", "type": "object"}, "ToolOutputText": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "text", "title": "Type", "type": "string"}}, "required": ["name", "hidden", "type"], "title": "ToolOutputText", "type": "object"}, "ToolProvidedMetadataDatasetCollection": {"properties": {"discover_via": {"const": "tool_provided_metadata", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Format"}, "visible": {"title": "Visible", "type": "boolean"}, "assign_primary_output": {"title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "title": "Directory"}, "recurse": {"title": "Recurse", "type": "boolean"}, "match_relative_path": {"title": "Match Relative Path", "type": "boolean"}}, "required": ["discover_via", "format", "visible", "assign_primary_output", "directory", "recurse", "match_relative_path"], "title": "ToolProvidedMetadataDatasetCollection", "type": "object"}, "XrefDict": {"additionalProperties": false, "properties": {"value": {"title": "value", "type": "string"}, "type": {"title": "type", "type": "string"}}, "required": ["value", "type"], "title": "XrefDict", "type": "object"}, "YamlBooleanParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "boolean", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Value"}}, "required": ["name", "type"], "title": "YamlBooleanParameter", "type": "object"}, "YamlColorParameter": {"additionalProperties": false, 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{"$ref": "#/$defs/has_image_channels_model"}, {"$ref": "#/$defs/has_image_depth_model"}, {"$ref": "#/$defs/has_image_frames_model"}, {"$ref": "#/$defs/has_image_height_model"}, {"$ref": "#/$defs/has_image_mean_intensity_model"}, {"$ref": "#/$defs/has_image_mean_object_size_model"}, {"$ref": "#/$defs/has_image_n_labels_model"}, {"$ref": "#/$defs/has_image_width_model"}]}, {"$ref": "#/$defs/has_line_model_nested"}, {"$ref": "#/$defs/has_line_matching_model_nested"}, {"$ref": "#/$defs/has_n_lines_model_nested"}, {"$ref": "#/$defs/has_text_model_nested"}, {"$ref": "#/$defs/has_text_matching_model_nested"}, {"$ref": "#/$defs/not_has_text_model_nested"}, {"$ref": "#/$defs/has_n_columns_model_nested"}, {"$ref": "#/$defs/attribute_is_model_nested"}, {"$ref": "#/$defs/attribute_matches_model_nested"}, {"$ref": "#/$defs/element_text_model_nested"}, {"$ref": "#/$defs/element_text_is_model_nested"}, {"$ref": "#/$defs/element_text_matches_model_nested"}, {"$ref": "#/$defs/has_element_with_path_model_nested"}, {"$ref": "#/$defs/has_n_elements_with_path_model_nested"}, {"$ref": "#/$defs/is_valid_xml_model_nested"}, {"$ref": "#/$defs/xml_element_model_nested"}, {"$ref": "#/$defs/has_json_property_with_text_model_nested"}, {"$ref": "#/$defs/has_json_property_with_value_model_nested"}, {"$ref": "#/$defs/has_h5_attribute_model_nested"}, {"$ref": "#/$defs/has_h5_keys_model_nested"}, {"$ref": "#/$defs/has_archive_member_model_nested"}, {"$ref": "#/$defs/has_size_model_nested"}, {"$ref": "#/$defs/has_image_center_of_mass_model_nested"}, {"$ref": "#/$defs/has_image_channels_model_nested"}, {"$ref": "#/$defs/has_image_depth_model_nested"}, {"$ref": "#/$defs/has_image_frames_model_nested"}, {"$ref": "#/$defs/has_image_height_model_nested"}, {"$ref": "#/$defs/has_image_mean_intensity_model_nested"}, {"$ref": "#/$defs/has_image_mean_object_size_model_nested"}, {"$ref": "#/$defs/has_image_n_labels_model_nested"}, {"$ref": "#/$defs/has_image_width_model_nested"}]}, "title": "assertion_list", "type": "array"}, "attribute_is_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` is the specified ``text``.\n\nFor example:\n\n```xml\n<attribute_is path=\"outerElement/innerElement1\" attribute=\"foo\" text=\"bar\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_is", "default": "attribute_is", "title": "That", "type": "string"}}, "required": ["path", "attribute", "text"], "title": "Assert Attribute Is", "type": "object"}, "attribute_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_is": {"$ref": "#/$defs/base_attribute_is_model", "title": "Assert Attribute Is"}}, "required": ["attribute_is"], "title": "Assert Attribute Is (Nested)", "type": "object"}, "attribute_matches_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` matches the regular expression specified by ``expression``.\n\nFor example:\n\n```xml\n<attribute_matches path=\"outerElement/innerElement2\" attribute=\"foo2\" expression=\"bar\\d+\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_matches", "default": "attribute_matches", "title": "That", "type": "string"}}, "required": ["path", "attribute", "expression"], "title": "Assert Attribute Matches", "type": "object"}, "attribute_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_matches": {"$ref": "#/$defs/base_attribute_matches_model", "title": "Assert Attribute Matches"}}, "required": ["attribute_matches"], "title": "Assert Attribute Matches (Nested)", "type": "object"}, "base_attribute_is_model": {"additionalProperties": false, "description": "base model for attribute_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "text"], "title": "base_attribute_is_model", "type": "object"}, "base_attribute_matches_model": {"additionalProperties": false, "description": "base model for attribute_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "expression"], "title": "base_attribute_matches_model", "type": "object"}, "base_element_text_is_model": {"additionalProperties": false, "description": "base model for element_text_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "text"], "title": "base_element_text_is_model", "type": "object"}, "base_element_text_matches_model": {"additionalProperties": false, "description": "base model for element_text_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "expression"], "title": "base_element_text_matches_model", "type": "object"}, "base_element_text_model": {"additionalProperties": false, "description": "base model for element_text describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_element_text_model", "type": "object"}, "base_has_archive_member_model": {"additionalProperties": false, "description": "base model for has_archive_member describing attributes.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_has_archive_member_model", "type": "object"}, "base_has_element_with_path_model": {"additionalProperties": false, "description": "base model for has_element_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_element_with_path_model", "type": "object"}, "base_has_h5_attribute_model": {"additionalProperties": false, "description": "base model for has_h5_attribute describing attributes.", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}}, "required": ["key", "value"], "title": "base_has_h5_attribute_model", "type": "object"}, "base_has_h5_keys_model": {"additionalProperties": false, "description": "base model for has_h5_keys describing attributes.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}}, "required": ["keys"], "title": "base_has_h5_keys_model", "type": "object"}, "base_has_image_center_of_mass_model": {"additionalProperties": false, "description": "base model for has_image_center_of_mass describing attributes.", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}}, "required": ["center_of_mass"], "title": "base_has_image_center_of_mass_model", "type": "object"}, "base_has_image_channels_model": {"additionalProperties": false, "description": "base model for has_image_channels describing attributes.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_channels_model", "type": "object"}, "base_has_image_depth_model": {"additionalProperties": false, "description": "base model for has_image_depth describing attributes.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_depth_model", "type": "object"}, "base_has_image_frames_model": {"additionalProperties": false, "description": "base model for has_image_frames describing attributes.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_frames_model", "type": "object"}, "base_has_image_height_model": {"additionalProperties": false, "description": "base model for has_image_height describing attributes.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_height_model", "type": "object"}, "base_has_image_mean_intensity_model": {"additionalProperties": false, "description": "base model for has_image_mean_intensity describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}}, "title": "base_has_image_mean_intensity_model", "type": "object"}, "base_has_image_mean_object_size_model": {"additionalProperties": false, "description": "base model for has_image_mean_object_size describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}}, "title": "base_has_image_mean_object_size_model", "type": "object"}, "base_has_image_n_labels_model": {"additionalProperties": false, "description": "base model for has_image_n_labels describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_n_labels_model", "type": "object"}, "base_has_image_width_model": {"additionalProperties": false, "description": "base model for has_image_width describing attributes.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_width_model", "type": "object"}, "base_has_json_property_with_text_model": {"additionalProperties": false, "description": "base model for has_json_property_with_text describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}}, "required": ["property", "text"], "title": "base_has_json_property_with_text_model", "type": "object"}, "base_has_json_property_with_value_model": {"additionalProperties": false, "description": "base model for has_json_property_with_value describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}}, "required": ["property", "value"], "title": "base_has_json_property_with_value_model", "type": "object"}, "base_has_line_matching_model": {"additionalProperties": false, "description": "base model for has_line_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_line_matching_model", "type": "object"}, "base_has_line_model": {"additionalProperties": false, "description": "base model for has_line describing attributes.", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["line"], "title": "base_has_line_model", "type": "object"}, "base_has_n_columns_model": {"additionalProperties": false, "description": "base model for has_n_columns describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_columns_model", "type": "object"}, "base_has_n_elements_with_path_model": {"additionalProperties": false, "description": "base model for has_n_elements_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_n_elements_with_path_model", "type": "object"}, "base_has_n_lines_model": {"additionalProperties": false, "description": "base model for has_n_lines describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_lines_model", "type": "object"}, "base_has_size_model": {"additionalProperties": false, "description": "base model for has_size describing attributes.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_size_model", "type": "object"}, "base_has_text_matching_model": {"additionalProperties": false, "description": "base model for has_text_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_text_matching_model", "type": "object"}, "base_has_text_model": {"additionalProperties": false, "description": "base model for has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["text"], "title": "base_has_text_model", "type": "object"}, "base_is_valid_xml_model": {"additionalProperties": false, "description": "base model for is_valid_xml describing attributes.", "properties": {}, "title": "base_is_valid_xml_model", "type": "object"}, "base_not_has_text_model": {"additionalProperties": false, "description": "base model for not_has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}}, "required": ["text"], "title": "base_not_has_text_model", "type": "object"}, "base_xml_element_model": {"additionalProperties": false, "description": "base model for xml_element describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_xml_element_model", "type": "object"}, "element_text_is_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path`` is\nthe specified ``text``.\n\nFor example:\n\n```xml\n<element_text_is path=\"BlastOutput_program\" text=\"blastp\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_is", "default": "element_text_is", "title": "That", "type": "string"}}, "required": ["path", "text"], "title": "Assert Element Text Is", "type": "object"}, "element_text_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_is": {"$ref": "#/$defs/base_element_text_is_model", "title": "Assert Element Text Is"}}, "required": ["element_text_is"], "title": "Assert Element Text Is (Nested)", "type": "object"}, "element_text_matches_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path``\nmatches the regular expression defined by ``expression``.\n\nFor example:\n\n```xml\n<element_text_matches path=\"BlastOutput_version\" expression=\"BLASTP\\s+2\\.2.*\"/>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_matches", "default": "element_text_matches", "title": "That", "type": "string"}}, "required": ["path", "expression"], "title": "Assert Element Text Matches", "type": "object"}, "element_text_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_matches": {"$ref": "#/$defs/base_element_text_matches_model", "title": "Assert Element Text Matches"}}, "required": ["element_text_matches"], "title": "Assert Element Text Matches (Nested)", "type": "object"}, "element_text_model": {"additionalProperties": false, "description": "This tag allows the developer to recurisively specify additional assertions as\nchild elements about just the text contained in the element specified by the\nXPath-like ``path``, e.g.\n\n```xml\n<element_text path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def\">\n  <not_has_text text=\"EDK72998.1\" />\n</element_text>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the implicit assertions can be inverted.\nThe sub-assertions, which have their own ``negate`` attribute, are not affected\nby ``negate``.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "element_text", "default": "element_text", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Element Text", "type": "object"}, "element_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text": {"$ref": "#/$defs/base_element_text_model", "title": "Assert Element Text"}}, "required": ["element_text"], "title": "Assert Element Text (Nested)", "type": "object"}, "has_archive_member_model": {"additionalProperties": false, "description": "This tag allows to check if ``path`` is contained in a compressed file.\n\nThe path is a regular expression that is matched against the full paths of the objects in\nthe compressed file (remember that \"matching\" means it is checked if a prefix of\nthe full path of an archive member is described by the regular expression).\nValid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that\ndepending on the archive creation method:\n\n- full paths of the members may be prefixed with ``./``\n- directories may be treated as empty files\n\n```xml\n<has_archive_member path=\"./path/to/my-file.txt\"/>\n```\n\nWith ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of\narchive members matching ``path`` can be expressed. The following could be used,\ne.g., to assert an archive containing n&plusmn;1 elements out of which at least\n4 need to have a ``txt`` extension.\n\n```xml\n<has_archive_member path=\".*\" n=\"10\" delta=\"1\"/>\n<has_archive_member path=\".*\\.txt\" min=\"4\"/>\n```\n\nIn addition the tag can contain additional assertions as child elements about\nthe first member in the archive matching the regular expression ``path``. For\ninstance\n\n```xml\n<has_archive_member path=\".*/my-file.txt\">\n  <not_has_text text=\"EDK72998.1\"/>\n</has_archive_member>\n```\n\nIf the ``all`` attribute is set to ``true`` then all archive members are subject\nto the assertions. Note that, archive members matching the ``path`` are sorted\nalphabetically.\n\nThe ``negate`` attribute of the ``has_archive_member`` assertion only affects\nthe asserts on the presence and number of matching archive members, but not any\nsub-assertions (which can offer the ``negate`` attribute on their own).  The\ncheck if the file is an archive at all, which is also done by the function, is\nnot affected.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "has_archive_member", "default": "has_archive_member", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Archive Member", "type": "object"}, "has_archive_member_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_archive_member": {"$ref": "#/$defs/base_has_archive_member_model", "title": "Assert Has Archive Member"}}, "required": ["has_archive_member"], "title": "Assert Has Archive Member (Nested)", "type": "object"}, "has_element_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains at least one element (or tag) with the specified\nXPath-like ``path``, e.g.\n\n```xml\n<has_element_with_path path=\"BlastOutput_param/Parameters/Parameters_matrix\" />\n```\n\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_element_with_path", "default": "has_element_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Element With Path", "type": "object"}, "has_element_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_element_with_path": {"$ref": "#/$defs/base_has_element_with_path_model", "title": "Assert Has Element With Path"}}, "required": ["has_element_with_path"], "title": "Assert Has Element With Path (Nested)", "type": "object"}, "has_h5_attribute_model": {"additionalProperties": false, "description": "Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.\n\n```xml\n<has_h5_attribute key=\"nchroms\" value=\"15\" />\n```", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}, "that": {"const": "has_h5_attribute", "default": "has_h5_attribute", "title": "That", "type": "string"}}, "required": ["key", "value"], "title": "Assert Has H5 Attribute", "type": "object"}, "has_h5_attribute_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_attribute": {"$ref": "#/$defs/base_has_h5_attribute_model", "title": "Assert Has H5 Attribute"}}, "required": ["has_h5_attribute"], "title": "Assert Has H5 Attribute (Nested)", "type": "object"}, "has_h5_keys_model": {"additionalProperties": false, "description": "Asserts the specified HDF5 output has the given keys.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}, "that": {"const": "has_h5_keys", "default": "has_h5_keys", "title": "That", "type": "string"}}, "required": ["keys"], "title": "Assert Has H5 Keys", "type": "object"}, "has_h5_keys_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_keys": {"$ref": "#/$defs/base_has_h5_keys_model", "title": "Assert Has H5 Keys"}}, "required": ["has_h5_keys"], "title": "Assert Has H5 Keys (Nested)", "type": "object"}, "has_image_center_of_mass_model": {"additionalProperties": false, "description": "Asserts the specified output is an image and has the specified center of mass.\n\nAsserts the output is an image and has a specific center of mass,\nor has an Euclidean distance of ``eps`` or less to that point (e.g.,\n``<has_image_center_of_mass center_of_mass=\"511.07, 223.34\" />``).", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}, "that": {"const": "has_image_center_of_mass", "default": "has_image_center_of_mass", "title": "That", "type": "string"}}, "required": ["center_of_mass"], "title": "Assert Has Image Center Of Mass", "type": "object"}, "has_image_center_of_mass_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_center_of_mass": {"$ref": "#/$defs/base_has_image_center_of_mass_model", "title": "Assert Has Image Center Of Mass"}}, "required": ["has_image_center_of_mass"], "title": "Assert Has Image Center Of Mass (Nested)", "type": "object"}, "has_image_channels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of channels.\n\nThe number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels=\"3\" />``).\n\nAlternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_channels", "default": "has_image_channels", "title": "That", "type": "string"}}, "title": "Assert Has Image Channels", "type": "object"}, "has_image_channels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_channels": {"$ref": "#/$defs/base_has_image_channels_model", "title": "Assert Has Image Channels"}}, "required": ["has_image_channels"], "title": "Assert Has Image Channels (Nested)", "type": "object"}, "has_image_depth_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific depth (number of slices).\n\nThe depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected depth can be specified by ``min`` and/or ``max``.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_depth", "default": "has_image_depth", "title": "That", "type": "string"}}, "title": "Assert Has Image Depth", "type": "object"}, "has_image_depth_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_depth": {"$ref": "#/$defs/base_has_image_depth_model", "title": "Assert Has Image Depth"}}, "required": ["has_image_depth"], "title": "Assert Has Image Depth (Nested)", "type": "object"}, "has_image_frames_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of frames (number of time steps).\n\nThe number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_frames", "default": "has_image_frames", "title": "That", "type": "string"}}, "title": "Assert Has Image Frames", "type": "object"}, "has_image_frames_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_frames": {"$ref": "#/$defs/base_has_image_frames_model", "title": "Assert Has Image Frames"}}, "required": ["has_image_frames"], "title": "Assert Has Image Frames (Nested)", "type": "object"}, "has_image_height_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific height (in pixels).\n\nThe height is plus/minus ``delta`` (e.g., ``<has_image_height height=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected height can be specified by ``min`` and/or ``max``.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_height", "default": "has_image_height", "title": "That", "type": "string"}}, "title": "Assert Has Image Height", "type": "object"}, "has_image_height_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_height": {"$ref": "#/$defs/base_has_image_height_model", "title": "Assert Has Image Height"}}, "required": ["has_image_height"], "title": "Assert Has Image Height (Nested)", "type": "object"}, "has_image_mean_intensity_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific mean intensity value.\n\nThe mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity=\"0.83\" />``).\nAlternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}, "that": {"const": "has_image_mean_intensity", "default": "has_image_mean_intensity", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Intensity", "type": "object"}, "has_image_mean_intensity_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_intensity": {"$ref": "#/$defs/base_has_image_mean_intensity_model", "title": "Assert Has Image Mean Intensity"}}, "required": ["has_image_mean_intensity"], "title": "Assert Has Image Mean Intensity (Nested)", "type": "object"}, "has_image_mean_object_size_model": {"additionalProperties": false, "description": "Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),\n\nThe mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size=\"111.87\" exclude_labels=\"0\" />``).\n\nThe labels must be unique.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}, "that": {"const": "has_image_mean_object_size", "default": "has_image_mean_object_size", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Object Size", "type": "object"}, "has_image_mean_object_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_object_size": {"$ref": "#/$defs/base_has_image_mean_object_size_model", "title": "Assert Has Image Mean Object Size"}}, "required": ["has_image_mean_object_size"], "title": "Assert Has Image Mean Object Size (Nested)", "type": "object"}, "has_image_n_labels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has the specified labels.\n\nLabels can be a number of labels or unique values (e.g.,\n``<has_image_n_labels n=\"187\" exclude_labels=\"0\" />``).\n\nThe primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_n_labels", "default": "has_image_n_labels", "title": "That", "type": "string"}}, "title": "Assert Has Image N Labels", "type": "object"}, "has_image_n_labels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_n_labels": {"$ref": "#/$defs/base_has_image_n_labels_model", "title": "Assert Has Image N Labels"}}, "required": ["has_image_n_labels"], "title": "Assert Has Image N Labels (Nested)", "type": "object"}, "has_image_width_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific width (in pixels).\n\nThe width is plus/minus ``delta`` (e.g., ``<has_image_width width=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected width can be specified by ``min`` and/or ``max``.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_width", "default": "has_image_width", "title": "That", "type": "string"}}, "title": "Assert Has Image Width", "type": "object"}, "has_image_width_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_width": {"$ref": "#/$defs/base_has_image_width_model", "title": "Assert Has Image Width"}}, "required": ["has_image_width"], "title": "Assert Has Image Width (Nested)", "type": "object"}, "has_json_property_with_text_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified text (i.e. string) value.\n\n```xml\n<has_json_property_with_text property=\"color\" text=\"red\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}, "that": {"const": "has_json_property_with_text", "default": "has_json_property_with_text", "title": "That", "type": "string"}}, "required": ["property", "text"], "title": "Assert Has Json Property With Text", "type": "object"}, "has_json_property_with_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_text": {"$ref": "#/$defs/base_has_json_property_with_text_model", "title": "Assert Has Json Property With Text"}}, "required": ["has_json_property_with_text"], "title": "Assert Has Json Property With Text (Nested)", "type": "object"}, "has_json_property_with_value_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified JSON value.\n\n```xml\n<has_json_property_with_value property=\"skipped_columns\" value=\"[1, 3, 5]\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}, "that": {"const": "has_json_property_with_value", "default": "has_json_property_with_value", "title": "That", "type": "string"}}, "required": ["property", "value"], "title": "Assert Has Json Property With Value", "type": "object"}, "has_json_property_with_value_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_value": {"$ref": "#/$defs/base_has_json_property_with_value_model", "title": "Assert Has Json Property With Value"}}, "required": ["has_json_property_with_value"], "title": "Assert Has Json Property With Value (Nested)", "type": "object"}, "has_line_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains a line matching the\nregular expression specified by the argument expression. If n is given\nthe assertion checks for exactly n occurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line_matching", "default": "has_line_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Line Matching", "type": "object"}, "has_line_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line_matching": {"$ref": "#/$defs/base_has_line_matching_model", "title": "Assert Has Line Matching"}}, "required": ["has_line_matching"], "title": "Assert Has Line Matching (Nested)", "type": "object"}, "has_line_model": {"additionalProperties": false, "description": "Asserts the specified output contains the line specified by the\nargument line. The exact number of occurrences can be optionally\nspecified by the argument n", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line", "default": "has_line", "title": "That", "type": "string"}}, "required": ["line"], "title": "Assert Has Line", "type": "object"}, "has_line_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line": {"$ref": "#/$defs/base_has_line_model", "title": "Assert Has Line"}}, "required": ["has_line"], "title": "Assert Has Line (Nested)", "type": "object"}, "has_n_columns_model": {"additionalProperties": false, "description": "Asserts tabular output  contains the specified\nnumber (``n``) of columns.\n\nFor instance, ``<has_n_columns n=\"3\"/>``. The assertion tests only the first line.\nNumber of columns can optionally also be specified with ``delta``. Alternatively the\nrange of expected occurrences can be specified by ``min`` and/or ``max``.\n\nOptionally a column separator (``sep``, default is ``       ``) `and comment character(s)\ncan be specified (``comment``, default is empty string). The first non-comment\nline is used for determining the number of columns.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_columns", "default": "has_n_columns", "title": "That", "type": "string"}}, "title": "Assert Has N Columns", "type": "object"}, "has_n_columns_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_columns": {"$ref": "#/$defs/base_has_n_columns_model", "title": "Assert Has N Columns"}}, "required": ["has_n_columns"], "title": "Assert Has N Columns (Nested)", "type": "object"}, "has_n_elements_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or\ntags) with the specified XPath-like ``path``.\n\nFor example:\n\n```xml\n<has_n_elements_with_path n=\"9\" path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num\" />\n```\n\nAlternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes\ncan be used to specify the range of the expected number of occurrences.\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_elements_with_path", "default": "has_n_elements_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has N Elements With Path", "type": "object"}, "has_n_elements_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_elements_with_path": {"$ref": "#/$defs/base_has_n_elements_with_path_model", "title": "Assert Has N Elements With Path"}}, "required": ["has_n_elements_with_path"], "title": "Assert Has N Elements With Path (Nested)", "type": "object"}, "has_n_lines_model": {"additionalProperties": false, "description": "Asserts the specified output contains ``n`` lines allowing\nfor a difference in the number of lines (delta)\nor relative differebce in the number of lines", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_lines", "default": "has_n_lines", "title": "That", "type": "string"}}, "title": "Assert Has N Lines", "type": "object"}, "has_n_lines_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_lines": {"$ref": "#/$defs/base_has_n_lines_model", "title": "Assert Has N Lines"}}, "required": ["has_n_lines"], "title": "Assert Has N Lines (Nested)", "type": "object"}, "has_size_model": {"additionalProperties": false, "description": "Asserts the specified output has a size of the specified value\n\nAttributes size and value or synonyms though value is considered deprecated.\nThe size optionally allows for absolute (``delta``) difference.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_size", "default": "has_size", "title": "That", "type": "string"}}, "title": "Assert Has Size", "type": "object"}, "has_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_size": {"$ref": "#/$defs/base_has_size_model", "title": "Assert Has Size"}}, "required": ["has_size"], "title": "Assert Has Size (Nested)", "type": "object"}, "has_text_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains text matching the\nregular expression specified by the argument expression.\nIf n is given the assertion checks for exactly n (nonoverlapping)\noccurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text_matching", "default": "has_text_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Text Matching", "type": "object"}, "has_text_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text_matching": {"$ref": "#/$defs/base_has_text_matching_model", "title": "Assert Has Text Matching"}}, "required": ["has_text_matching"], "title": "Assert Has Text Matching (Nested)", "type": "object"}, "has_text_model": {"additionalProperties": false, "description": "Asserts specified output contains the substring specified by\nthe argument text. The exact number of occurrences can be\noptionally specified by the argument n", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text", "default": "has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Has Text", "type": "object"}, "has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text": {"$ref": "#/$defs/base_has_text_model", "title": "Assert Has Text"}}, "required": ["has_text"], "title": "Assert Has Text (Nested)", "type": "object"}, "is_valid_xml_model": {"additionalProperties": false, "description": "Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).", "properties": {"that": {"const": "is_valid_xml", "default": "is_valid_xml", "title": "That", "type": "string"}}, "title": "Assert Is Valid Xml", "type": "object"}, "is_valid_xml_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"is_valid_xml": {"$ref": "#/$defs/base_is_valid_xml_model", "title": "Assert Is Valid Xml"}}, "required": ["is_valid_xml"], "title": "Assert Is Valid Xml (Nested)", "type": "object"}, "not_has_text_model": {"additionalProperties": false, "description": "Asserts specified output does not contain the substring\nspecified by the argument text", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "that": {"const": "not_has_text", "default": "not_has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Not Has Text", "type": "object"}, "not_has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"not_has_text": {"$ref": "#/$defs/base_not_has_text_model", "title": "Assert Not Has Text"}}, "required": ["not_has_text"], "title": "Assert Not Has Text (Nested)", "type": "object"}, "xml_element_model": {"additionalProperties": false, "description": "Assert if the XML file contains element(s) or tag(s) with the specified\n[XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``\nor ``min`` and ``max`` are given also the number of occurrences is checked.\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem\"/>\n  <xml_element path=\"./elem/more[2]\"/>\n  <xml_element path=\".//more\" n=\"3\" delta=\"1\"/>\n</assert_contents>\n```\n\nWith ``negate=\"true\"`` the outcome of the assertions wrt the presence and number\nof ``path`` can be negated. If there are any sub assertions then check them against\n\n- the content of the attribute ``attribute``\n- the element's text if no attribute is given\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem/more[2]\" attribute=\"name\">\n    <has_text_matching expression=\"foo$\"/>\n  </xml_element>\n</assert_contents>\n```\n\nSub-assertions are not subject to the ``negate`` attribute of ``xml_element``.\nIf ``all`` is ``true`` then the sub assertions are checked for all occurrences.\n\nNote that all other XML assertions can be expressed by this assertion (Galaxy\nalso implements the other assertions by calling this one).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "xml_element", "default": "xml_element", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Xml Element", "type": "object"}, "xml_element_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"xml_element": {"$ref": "#/$defs/base_xml_element_model", "title": "Assert Xml Element"}}, "required": ["xml_element"], "title": "Assert Xml Element (Nested)", "type": "object"}}, "additionalProperties": false, "properties": {"id": {"anyOf": [{"maxLength": 255, "minLength": 3, "pattern": "^[a-z][a-z0-9_-]*$", "type": "string"}, {"type": "null"}], "default": null, "description": "Unique identifier for the tool. Lowercase, must start with a letter, may contain letters, digits, '_' and '-'.", "examples": ["my-cool-tool"], "title": "id"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Version for the tool.", "examples": ["0.1.0"], "title": "version"}, "name": {"description": "The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.", "minLength": 5, "title": "name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The description is displayed in the tool menu immediately following the hyperlink for the tool.", "title": "description"}, "configfiles": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTemplateConfigFile"}, "type": "array"}, {"type": "null"}], "default": null, "description": "A list of config files for this tool.", "title": "configfiles"}, "requirements": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/JavascriptRequirement"}, {"$ref": "#/$defs/ResourceRequirement"}, {"$ref": "#/$defs/ContainerRequirement"}]}, "type": "array"}, {"type": "null"}], "default": [], "description": "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.", "title": "requirements"}, "shell_command": {"description": "A string that contains the command to be executed. Parameters can be referenced inside $().", "examples": ["head -n '$(inputs.n_lines)' '$(inputs.data_input.path)'"], "title": "shell_command", "type": "string"}, "inputs": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "inputs", "type": "array"}, "outputs": {"default": [], "items": {"discriminator": {"mapping": {"boolean": "#/$defs/ToolOutputBoolean", "collection": "#/$defs/IncomingToolOutputCollection", "data": "#/$defs/IncomingToolOutputDataset", "float": "#/$defs/ToolOutputFloat", "integer": "#/$defs/ToolOutputInteger", "text": "#/$defs/ToolOutputText"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/IncomingToolOutputDataset"}, {"$ref": "#/$defs/IncomingToolOutputCollection"}, {"$ref": "#/$defs/ToolOutputText"}, {"$ref": "#/$defs/ToolOutputInteger"}, {"$ref": "#/$defs/ToolOutputFloat"}, {"$ref": "#/$defs/ToolOutputBoolean"}]}, "title": "outputs", "type": "array"}, "citations": {"anyOf": [{"items": {"$ref": "#/$defs/Citation"}, "type": "array"}, {"type": "null"}], "default": null, "title": "citations"}, "license": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.", "examples": ["MIT"], "title": "license"}, "edam_operations": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_operations"}, "edam_topics": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_topics"}, "xrefs": {"anyOf": [{"items": {"$ref": "#/$defs/XrefDict"}, "type": "array"}, {"type": "null"}], "default": null, "title": "xrefs"}, "profile": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "profile"}, "help": {"anyOf": [{"$ref": "#/$defs/HelpContent"}, {"type": "null"}], "default": null, "description": "Help text shown below the tool interface.", "title": "help"}, "tests": {"anyOf": [{"items": {"$ref": "#/$defs/YamlToolTest"}, "type": "array"}, {"type": "null"}], "default": null, "title": "tests"}, "class": {"const": "GalaxyUserTool", "title": "class_", "type": "string"}, "container": {"description": "Container image to use for this tool.", "examples": ["quay.io/biocontainers/python:3.13"], "title": "container", "type": "string"}}, "required": ["name", "shell_command", "class", "container"], "title": "UserToolSource", "type": "object"}
+{"$defs": {"Citation": {"properties": {"type": {"title": "Type", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["type", "content"], "title": "Citation", "type": "object"}, "CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "Container": {"properties": {"type": {"enum": ["docker", "singularity"], "title": "Type", "type": "string"}, "container_id": {"title": "Container Id", "type": "string"}}, "required": ["type", "container_id"], "title": "Container", "type": "object"}, "ContainerRequirement": {"properties": {"type": {"const": "container", "title": "Type", "type": "string"}, "container": {"$ref": "#/$defs/Container"}}, "required": ["type", "container"], "title": "ContainerRequirement", "type": "object"}, "EmptyFieldParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "empty_field", "default": "empty_field", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "EmptyFieldParameterValidatorModel", "type": "object"}, "FilePatternDatasetCollectionDescription": {"properties": {"discover_via": {"const": "pattern", "default": "pattern", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}, "sort_key": {"default": "filename", "enum": ["filename", "name", "designation", "dbkey"], "title": "Sort Key", "type": "string"}, "sort_comp": {"default": "lexical", "enum": ["lexical", "numeric"], "title": "Sort Comp", "type": "string"}, "sort_reverse": {"default": false, "title": "Sort Reverse", "type": "boolean"}, "pattern": {"title": "Pattern", "type": "string"}}, "required": ["pattern"], "title": "FilePatternDatasetCollectionDescription", "type": "object"}, "HelpContent": {"properties": {"format": {"enum": ["restructuredtext", "plain_text", "markdown"], "title": "Format", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["format", "content"], "title": "HelpContent", "type": "object"}, "InRangeParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "in_range", "default": "in_range", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "exclude_min": {"default": false, "title": "Exclude Min", "type": "boolean"}, "exclude_max": {"default": false, "title": "Exclude Max", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "InRangeParameterValidatorModel", "type": "object"}, "IncomingToolOutputBoolean": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "boolean", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputBoolean", "type": "object"}, "IncomingToolOutputCollection": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "collection_type_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type Source"}, "collection_type_from_rules": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type From Rules"}, "structured_like": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Structured Like"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}}, "required": ["type"], "title": "IncomingToolOutputCollection", "type": "object"}, "IncomingToolOutputDataset": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The short name for the output datatype.", "title": "Format"}, "format_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.", "title": "Format Source"}, "metadata_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This copies the metadata information from the tool\u2019s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.", "title": "Metadata Source"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}, "from_work_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Relative path to a file produced by the tool in its working directory. Output\u2019s contents are set to this file\u2019s contents.", "title": "from_work_dir"}, "precreate_directory": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Precreate Directory"}}, "required": ["type"], "title": "IncomingToolOutputDataset", "type": "object"}, "IncomingToolOutputFloat": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "float", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputFloat", "type": "object"}, "IncomingToolOutputInteger": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "integer", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputInteger", "type": "object"}, "IncomingToolOutputText": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "text", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputText", "type": "object"}, "JavascriptRequirement": {"properties": {"type": {"const": "javascript", "title": "Type", "type": "string"}, "expression_lib": {"anyOf": [{"items": {"description": "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.", "examples": ["function pickValue() {\n    if (inputs.conditional_parameter.test_parameter == \"a\") {\n        return inputs.conditional_parameter.integer_parameter\n    } else {\n        return inputs.conditional_parameter.boolean_parameter\n    }\n}"], "title": "expression_lib", "type": "string"}, "type": "array"}, {"type": "null"}], "title": "Expression Lib"}}, "required": ["type", "expression_lib"], "title": "JavascriptRequirement", "type": "object"}, "LengthParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "length", "default": "length", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "LengthParameterValidatorModel", "type": "object"}, "NoOptionsParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "no_options", "default": "no_options", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "NoOptionsParameterValidatorModel", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RegexParameterValidatorModel": {"additionalProperties": false, "description": "Check if a regular expression **matches** the value, i.e. appears\nat the beginning of the value. To enforce a match of the complete value use\n``$`` at the end of the expression. The expression is given is the content\nof the validator tag. Note that for ``selects`` each option is checked\nseparately.", "properties": {"type": {"const": "regex", "default": "regex", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}, "expression": {"title": "Expression", "type": "string"}}, "required": ["expression"], "title": "RegexParameterValidatorModel", "type": "object"}, "ResourceRequirement": {"properties": {"type": {"const": "resource", "title": "Type", "type": "string"}, "cores_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 1, "description": "Minimum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Min"}, "cores_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Max"}, "ram_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 256, "description": "Minimum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Min"}, "ram_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Max"}, "tmpdir_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Min"}, "tmpdir_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Max"}, "cuda_version_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Version Min"}, "cuda_compute_capability": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Compute Capability"}, "gpu_memory_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Gpu Memory Min"}, "cuda_device_count_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Min"}, "cuda_device_count_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Max"}, "shm_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Shm Size"}, "timelimit": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum time in seconds the tool is allowed to run. Job will be terminated if exceeded.", "title": "Timelimit"}}, "required": ["type"], "title": "ResourceRequirement", "type": "object"}, "TestCollectionCollectionElementAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}}, "title": "TestCollectionCollectionElementAssertions", "type": "object"}, "TestCollectionDatasetElementAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestCollectionDatasetElementAssertions", "type": "object"}, "TestCollectionOutputAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}, "element_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Element Count"}, "attributes": {"anyOf": [{"$ref": "#/$defs/CollectionAttributes"}, {"type": "null"}], "default": null, "title": "Attributes"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "TestCollectionOutputAssertions", "type": "object"}, "TestDataOutputAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestDataOutputAssertions", "type": "object"}, "ToolProvidedMetadataDatasetCollection": {"properties": {"discover_via": {"const": "tool_provided_metadata", "default": "tool_provided_metadata", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}}, "title": "ToolProvidedMetadataDatasetCollection", "type": "object"}, "XrefDict": {"additionalProperties": false, "properties": {"value": {"title": "value", "type": "string"}, "type": {"title": "type", "type": "string"}}, "required": ["value", "type"], "title": "XrefDict", "type": "object"}, "YamlBooleanParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "boolean", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Value"}}, "required": ["name", "type"], "title": "YamlBooleanParameter", "type": "object"}, "YamlColorParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "color", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}}, "required": ["name", "type"], "title": "YamlColorParameter", "type": "object"}, "YamlConditionalParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "conditional", "title": "Type", "type": "string"}, "test_parameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "select": "#/$defs/YamlSelectParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}], "title": "Test Parameter"}, "whens": {"items": {"$ref": "#/$defs/YamlConditionalWhen"}, "minItems": 1, "title": "Whens", "type": "array"}}, "required": ["name", "type", "test_parameter", "whens"], "title": "YamlConditionalParameter", "type": "object"}, "YamlConditionalWhen": {"additionalProperties": false, "properties": {"discriminator": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "title": "Discriminator"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["discriminator"], "title": "YamlConditionalWhen", "type": "object"}, "YamlDataCollectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data_collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}}, "required": ["name", "type"], "title": "YamlDataCollectionParameter", "type": "object"}, "YamlDataParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}, "multiple": {"default": false, "description": "Set true to accept several datasets (a list) for this input instead of one.", "title": "Multiple", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. Do NOT set this for a single-dataset input -- a data input is already required by default, so leave 'min' unset unless the input accepts multiple datasets.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; leave unset for a single-dataset input.", "title": "Max"}}, "required": ["name", "type"], "title": "YamlDataParameter", "type": "object"}, "YamlFloatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "float", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlFloatParameter", "type": "object"}, "YamlGalaxyToolParameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "color": "#/$defs/YamlColorParameter", "conditional": "#/$defs/YamlConditionalParameter", "data": "#/$defs/YamlDataParameter", "data_collection": "#/$defs/YamlDataCollectionParameter", "float": "#/$defs/YamlFloatParameter", "integer": "#/$defs/YamlIntegerParameter", "repeat": "#/$defs/YamlRepeatParameter", "section": "#/$defs/YamlSectionParameter", "select": "#/$defs/YamlSelectParameter", "text": "#/$defs/YamlTextParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlIntegerParameter"}, {"$ref": "#/$defs/YamlFloatParameter"}, {"$ref": "#/$defs/YamlTextParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}, {"$ref": "#/$defs/YamlColorParameter"}, {"$ref": "#/$defs/YamlDataParameter"}, {"$ref": "#/$defs/YamlDataCollectionParameter"}, {"$ref": "#/$defs/YamlConditionalParameter"}, {"$ref": "#/$defs/YamlRepeatParameter"}, {"$ref": "#/$defs/YamlSectionParameter"}], "title": "YamlGalaxyToolParameter"}, "YamlIntegerParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "integer", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlIntegerParameter", "type": "object"}, "YamlLabelValue": {"description": "YAML-friendly option model \u2014 ``selected`` defaults to ``False``.", "properties": {"label": {"title": "Label", "type": "string"}, "value": {"title": "Value", "type": "string"}, "selected": {"default": false, "title": "Selected", "type": "boolean"}}, "required": ["label", "value"], "title": "YamlLabelValue", "type": "object"}, "YamlRepeatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "repeat", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}}, "required": ["name", "type"], "title": "YamlRepeatParameter", "type": "object"}, "YamlSectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "section", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["name", "type"], "title": "YamlSectionParameter", "type": "object"}, "YamlSelectParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "select", "title": "Type", "type": "string"}, "options": {"items": {"$ref": "#/$defs/YamlLabelValue"}, "minItems": 1, "title": "Options", "type": "array"}, "multiple": {"default": false, "title": "Multiple", "type": "boolean"}, "validators": {"default": [], "items": {"$ref": "#/$defs/NoOptionsParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type", "options"], "title": "YamlSelectParameter", "type": "object"}, "YamlTemplateConfigFile": {"properties": {"content": {"title": "Content", "type": "string"}, "name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Name"}, "filename": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Filename"}, "eval_engine": {"const": "ecmascript", "default": "ecmascript", "title": "Eval Engine", "type": "string"}}, "required": ["content"], "title": "YamlTemplateConfigFile", "type": "object"}, "YamlTestCredential": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credentials group.", "title": "Name", "type": "string"}, "variables": {"default": [], "description": "Variables exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Variables", "type": "array"}, "secrets": {"default": [], "description": "Secrets exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Secrets", "type": "array"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Version of the credential definition.", "title": "Version"}}, "required": ["name"], "title": "YamlTestCredential", "type": "object"}, "YamlTestCredentialValue": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credential variable or secret.", "title": "Name", "type": "string"}, "value": {"description": "Value of the credential variable or secret.", "title": "Value", "type": "string"}}, "required": ["name", "value"], "title": "YamlTestCredentialValue", "type": "object"}, "YamlTextParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "text", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}, "area": {"default": false, "title": "Area", "type": "boolean"}, "validators": {"default": [], "items": {"anyOf": [{"$ref": "#/$defs/LengthParameterValidatorModel"}, {"$ref": "#/$defs/RegexParameterValidatorModel"}, {"$ref": "#/$defs/EmptyFieldParameterValidatorModel"}]}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlTextParameter", "type": "object"}, "YamlToolTest": {"additionalProperties": false, "description": "In-tool test case as authored in YAML tool fixtures.", "properties": {"doc": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Human-readable description of this test case.", "title": "Doc"}, "inputs": {"anyOf": [{"additionalProperties": {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}, {"items": {}, "type": "array"}, {"additionalProperties": true, "type": "object"}]}, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of input parameter names to test values.", "title": "Inputs"}, "outputs": {"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionOutputAssertions"}, {"$ref": "#/$defs/TestDataOutputAssertions"}, {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}]}]}, "default": {}, "description": "Mapping of output names to expected values or assertions.", "title": "Outputs", "type": "object"}, "assert_stdout": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard output.", "title": "Assert Stdout"}, "assert_stderr": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard error.", "title": "Assert Stderr"}, "command": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the executed command line.", "title": "Command"}, "expect_exit_code": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected process exit code.", "title": "Expect Exit Code"}, "expect_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the tool is expected to produce an error.", "title": "Expect Failure"}, "expect_test_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the test itself is expected to fail.", "title": "Expect Test Failure"}, "credentials": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTestCredential"}, "type": "array"}, {"type": "null"}], "default": null, "description": "Credentials to inject for this test case.", "title": "Credentials"}}, "title": "YamlToolTest", "type": "object"}, "assertion_dict": {"additionalProperties": false, "properties": {"has_line": {"anyOf": [{"$ref": "#/$defs/base_has_line_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line"}, "has_line_matching": {"anyOf": [{"$ref": "#/$defs/base_has_line_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line Matching"}, "has_n_lines": {"anyOf": [{"$ref": "#/$defs/base_has_n_lines_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Lines"}, "has_text": {"anyOf": [{"$ref": "#/$defs/base_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text"}, "has_text_matching": {"anyOf": [{"$ref": "#/$defs/base_has_text_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text Matching"}, "not_has_text": {"anyOf": [{"$ref": "#/$defs/base_not_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Not Has Text"}, "has_n_columns": {"anyOf": [{"$ref": "#/$defs/base_has_n_columns_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Columns"}, "attribute_is": {"anyOf": [{"$ref": "#/$defs/base_attribute_is_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Is"}, "attribute_matches": {"anyOf": [{"$ref": "#/$defs/base_attribute_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Matches"}, "element_text": {"anyOf": [{"$ref": "#/$defs/base_element_text_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text"}, "element_text_is": {"anyOf": [{"$ref": "#/$defs/base_element_text_is_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Is"}, "element_text_matches": {"anyOf": [{"$ref": "#/$defs/base_element_text_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Matches"}, "has_element_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_element_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has Element With Path"}, "has_n_elements_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_n_elements_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Elements With Path"}, "is_valid_xml": {"anyOf": [{"$ref": "#/$defs/base_is_valid_xml_model"}, {"type": "null"}], "default": null, "title": "Assert Is Valid Xml"}, "xml_element": {"anyOf": [{"$ref": "#/$defs/base_xml_element_model"}, {"type": "null"}], "default": null, "title": "Assert Xml Element"}, "has_json_property_with_text": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Text"}, "has_json_property_with_value": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_value_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Value"}, "has_h5_attribute": {"anyOf": [{"$ref": "#/$defs/base_has_h5_attribute_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Attribute"}, "has_h5_keys": {"anyOf": [{"$ref": "#/$defs/base_has_h5_keys_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Keys"}, "has_archive_member": {"anyOf": [{"$ref": "#/$defs/base_has_archive_member_model"}, {"type": "null"}], "default": null, "title": "Assert Has Archive Member"}, "has_size": {"anyOf": [{"$ref": "#/$defs/base_has_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Size"}, "has_image_center_of_mass": {"anyOf": [{"$ref": "#/$defs/base_has_image_center_of_mass_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Center Of Mass"}, "has_image_channels": {"anyOf": [{"$ref": "#/$defs/base_has_image_channels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Channels"}, "has_image_depth": {"anyOf": [{"$ref": "#/$defs/base_has_image_depth_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Depth"}, "has_image_frames": {"anyOf": [{"$ref": "#/$defs/base_has_image_frames_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Frames"}, "has_image_height": {"anyOf": [{"$ref": "#/$defs/base_has_image_height_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Height"}, "has_image_mean_intensity": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_intensity_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Intensity"}, "has_image_mean_object_size": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_object_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Object Size"}, "has_image_n_labels": {"anyOf": [{"$ref": "#/$defs/base_has_image_n_labels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image N Labels"}, "has_image_width": {"anyOf": [{"$ref": "#/$defs/base_has_image_width_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Width"}}, "title": "assertion_dict", "type": "object"}, "assertion_list": {"items": {"anyOf": [{"discriminator": {"mapping": {"attribute_is": "#/$defs/attribute_is_model", "attribute_matches": "#/$defs/attribute_matches_model", "element_text": "#/$defs/element_text_model", "element_text_is": "#/$defs/element_text_is_model", "element_text_matches": "#/$defs/element_text_matches_model", "has_archive_member": "#/$defs/has_archive_member_model", "has_element_with_path": "#/$defs/has_element_with_path_model", "has_h5_attribute": "#/$defs/has_h5_attribute_model", "has_h5_keys": "#/$defs/has_h5_keys_model", "has_image_center_of_mass": "#/$defs/has_image_center_of_mass_model", "has_image_channels": "#/$defs/has_image_channels_model", "has_image_depth": "#/$defs/has_image_depth_model", "has_image_frames": "#/$defs/has_image_frames_model", "has_image_height": "#/$defs/has_image_height_model", "has_image_mean_intensity": "#/$defs/has_image_mean_intensity_model", "has_image_mean_object_size": "#/$defs/has_image_mean_object_size_model", "has_image_n_labels": "#/$defs/has_image_n_labels_model", "has_image_width": "#/$defs/has_image_width_model", "has_json_property_with_text": "#/$defs/has_json_property_with_text_model", "has_json_property_with_value": "#/$defs/has_json_property_with_value_model", "has_line": "#/$defs/has_line_model", "has_line_matching": "#/$defs/has_line_matching_model", "has_n_columns": "#/$defs/has_n_columns_model", "has_n_elements_with_path": "#/$defs/has_n_elements_with_path_model", "has_n_lines": "#/$defs/has_n_lines_model", "has_size": "#/$defs/has_size_model", "has_text": "#/$defs/has_text_model", "has_text_matching": "#/$defs/has_text_matching_model", "is_valid_xml": "#/$defs/is_valid_xml_model", "not_has_text": "#/$defs/not_has_text_model", "xml_element": "#/$defs/xml_element_model"}, "propertyName": "that"}, "oneOf": [{"$ref": "#/$defs/has_line_model"}, {"$ref": "#/$defs/has_line_matching_model"}, {"$ref": "#/$defs/has_n_lines_model"}, {"$ref": "#/$defs/has_text_model"}, {"$ref": "#/$defs/has_text_matching_model"}, {"$ref": "#/$defs/not_has_text_model"}, {"$ref": "#/$defs/has_n_columns_model"}, {"$ref": "#/$defs/attribute_is_model"}, {"$ref": "#/$defs/attribute_matches_model"}, {"$ref": "#/$defs/element_text_model"}, {"$ref": "#/$defs/element_text_is_model"}, {"$ref": "#/$defs/element_text_matches_model"}, {"$ref": "#/$defs/has_element_with_path_model"}, {"$ref": "#/$defs/has_n_elements_with_path_model"}, {"$ref": "#/$defs/is_valid_xml_model"}, {"$ref": "#/$defs/xml_element_model"}, {"$ref": "#/$defs/has_json_property_with_text_model"}, {"$ref": "#/$defs/has_json_property_with_value_model"}, {"$ref": "#/$defs/has_h5_attribute_model"}, {"$ref": "#/$defs/has_h5_keys_model"}, {"$ref": "#/$defs/has_archive_member_model"}, {"$ref": "#/$defs/has_size_model"}, {"$ref": "#/$defs/has_image_center_of_mass_model"}, {"$ref": "#/$defs/has_image_channels_model"}, {"$ref": "#/$defs/has_image_depth_model"}, {"$ref": "#/$defs/has_image_frames_model"}, {"$ref": "#/$defs/has_image_height_model"}, {"$ref": "#/$defs/has_image_mean_intensity_model"}, {"$ref": "#/$defs/has_image_mean_object_size_model"}, {"$ref": "#/$defs/has_image_n_labels_model"}, {"$ref": "#/$defs/has_image_width_model"}]}, {"$ref": "#/$defs/has_line_model_nested"}, {"$ref": "#/$defs/has_line_matching_model_nested"}, {"$ref": "#/$defs/has_n_lines_model_nested"}, {"$ref": "#/$defs/has_text_model_nested"}, {"$ref": "#/$defs/has_text_matching_model_nested"}, {"$ref": "#/$defs/not_has_text_model_nested"}, {"$ref": "#/$defs/has_n_columns_model_nested"}, {"$ref": "#/$defs/attribute_is_model_nested"}, {"$ref": "#/$defs/attribute_matches_model_nested"}, {"$ref": "#/$defs/element_text_model_nested"}, {"$ref": "#/$defs/element_text_is_model_nested"}, {"$ref": "#/$defs/element_text_matches_model_nested"}, {"$ref": "#/$defs/has_element_with_path_model_nested"}, {"$ref": "#/$defs/has_n_elements_with_path_model_nested"}, {"$ref": "#/$defs/is_valid_xml_model_nested"}, {"$ref": "#/$defs/xml_element_model_nested"}, {"$ref": "#/$defs/has_json_property_with_text_model_nested"}, {"$ref": "#/$defs/has_json_property_with_value_model_nested"}, {"$ref": "#/$defs/has_h5_attribute_model_nested"}, {"$ref": "#/$defs/has_h5_keys_model_nested"}, {"$ref": "#/$defs/has_archive_member_model_nested"}, {"$ref": "#/$defs/has_size_model_nested"}, {"$ref": "#/$defs/has_image_center_of_mass_model_nested"}, {"$ref": "#/$defs/has_image_channels_model_nested"}, {"$ref": "#/$defs/has_image_depth_model_nested"}, {"$ref": "#/$defs/has_image_frames_model_nested"}, {"$ref": "#/$defs/has_image_height_model_nested"}, {"$ref": "#/$defs/has_image_mean_intensity_model_nested"}, {"$ref": "#/$defs/has_image_mean_object_size_model_nested"}, {"$ref": "#/$defs/has_image_n_labels_model_nested"}, {"$ref": "#/$defs/has_image_width_model_nested"}]}, "title": "assertion_list", "type": "array"}, "attribute_is_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` is the specified ``text``.\n\nFor example:\n\n```xml\n<attribute_is path=\"outerElement/innerElement1\" attribute=\"foo\" text=\"bar\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_is", "default": "attribute_is", "title": "That", "type": "string"}}, "required": ["path", "attribute", "text"], "title": "Assert Attribute Is", "type": "object"}, "attribute_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_is": {"$ref": "#/$defs/base_attribute_is_model", "title": "Assert Attribute Is"}}, "required": ["attribute_is"], "title": "Assert Attribute Is (Nested)", "type": "object"}, "attribute_matches_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` matches the regular expression specified by ``expression``.\n\nFor example:\n\n```xml\n<attribute_matches path=\"outerElement/innerElement2\" attribute=\"foo2\" expression=\"bar\\d+\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_matches", "default": "attribute_matches", "title": "That", "type": "string"}}, "required": ["path", "attribute", "expression"], "title": "Assert Attribute Matches", "type": "object"}, "attribute_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_matches": {"$ref": "#/$defs/base_attribute_matches_model", "title": "Assert Attribute Matches"}}, "required": ["attribute_matches"], "title": "Assert Attribute Matches (Nested)", "type": "object"}, "base_attribute_is_model": {"additionalProperties": false, "description": "base model for attribute_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "text"], "title": "base_attribute_is_model", "type": "object"}, "base_attribute_matches_model": {"additionalProperties": false, "description": "base model for attribute_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "expression"], "title": "base_attribute_matches_model", "type": "object"}, "base_element_text_is_model": {"additionalProperties": false, "description": "base model for element_text_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "text"], "title": "base_element_text_is_model", "type": "object"}, "base_element_text_matches_model": {"additionalProperties": false, "description": "base model for element_text_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "expression"], "title": "base_element_text_matches_model", "type": "object"}, "base_element_text_model": {"additionalProperties": false, "description": "base model for element_text describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_element_text_model", "type": "object"}, "base_has_archive_member_model": {"additionalProperties": false, "description": "base model for has_archive_member describing attributes.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_has_archive_member_model", "type": "object"}, "base_has_element_with_path_model": {"additionalProperties": false, "description": "base model for has_element_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_element_with_path_model", "type": "object"}, "base_has_h5_attribute_model": {"additionalProperties": false, "description": "base model for has_h5_attribute describing attributes.", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}}, "required": ["key", "value"], "title": "base_has_h5_attribute_model", "type": "object"}, "base_has_h5_keys_model": {"additionalProperties": false, "description": "base model for has_h5_keys describing attributes.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}}, "required": ["keys"], "title": "base_has_h5_keys_model", "type": "object"}, "base_has_image_center_of_mass_model": {"additionalProperties": false, "description": "base model for has_image_center_of_mass describing attributes.", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}}, "required": ["center_of_mass"], "title": "base_has_image_center_of_mass_model", "type": "object"}, "base_has_image_channels_model": {"additionalProperties": false, "description": "base model for has_image_channels describing attributes.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_channels_model", "type": "object"}, "base_has_image_depth_model": {"additionalProperties": false, "description": "base model for has_image_depth describing attributes.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_depth_model", "type": "object"}, "base_has_image_frames_model": {"additionalProperties": false, "description": "base model for has_image_frames describing attributes.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_frames_model", "type": "object"}, "base_has_image_height_model": {"additionalProperties": false, "description": "base model for has_image_height describing attributes.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_height_model", "type": "object"}, "base_has_image_mean_intensity_model": {"additionalProperties": false, "description": "base model for has_image_mean_intensity describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}}, "title": "base_has_image_mean_intensity_model", "type": "object"}, "base_has_image_mean_object_size_model": {"additionalProperties": false, "description": "base model for has_image_mean_object_size describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}}, "title": "base_has_image_mean_object_size_model", "type": "object"}, "base_has_image_n_labels_model": {"additionalProperties": false, "description": "base model for has_image_n_labels describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_n_labels_model", "type": "object"}, "base_has_image_width_model": {"additionalProperties": false, "description": "base model for has_image_width describing attributes.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_width_model", "type": "object"}, "base_has_json_property_with_text_model": {"additionalProperties": false, "description": "base model for has_json_property_with_text describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}}, "required": ["property", "text"], "title": "base_has_json_property_with_text_model", "type": "object"}, "base_has_json_property_with_value_model": {"additionalProperties": false, "description": "base model for has_json_property_with_value describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}}, "required": ["property", "value"], "title": "base_has_json_property_with_value_model", "type": "object"}, "base_has_line_matching_model": {"additionalProperties": false, "description": "base model for has_line_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_line_matching_model", "type": "object"}, "base_has_line_model": {"additionalProperties": false, "description": "base model for has_line describing attributes.", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["line"], "title": "base_has_line_model", "type": "object"}, "base_has_n_columns_model": {"additionalProperties": false, "description": "base model for has_n_columns describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_columns_model", "type": "object"}, "base_has_n_elements_with_path_model": {"additionalProperties": false, "description": "base model for has_n_elements_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_n_elements_with_path_model", "type": "object"}, "base_has_n_lines_model": {"additionalProperties": false, "description": "base model for has_n_lines describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_lines_model", "type": "object"}, "base_has_size_model": {"additionalProperties": false, "description": "base model for has_size describing attributes.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_size_model", "type": "object"}, "base_has_text_matching_model": {"additionalProperties": false, "description": "base model for has_text_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_text_matching_model", "type": "object"}, "base_has_text_model": {"additionalProperties": false, "description": "base model for has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["text"], "title": "base_has_text_model", "type": "object"}, "base_is_valid_xml_model": {"additionalProperties": false, "description": "base model for is_valid_xml describing attributes.", "properties": {}, "title": "base_is_valid_xml_model", "type": "object"}, "base_not_has_text_model": {"additionalProperties": false, "description": "base model for not_has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}}, "required": ["text"], "title": "base_not_has_text_model", "type": "object"}, "base_xml_element_model": {"additionalProperties": false, "description": "base model for xml_element describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_xml_element_model", "type": "object"}, "element_text_is_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path`` is\nthe specified ``text``.\n\nFor example:\n\n```xml\n<element_text_is path=\"BlastOutput_program\" text=\"blastp\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_is", "default": "element_text_is", "title": "That", "type": "string"}}, "required": ["path", "text"], "title": "Assert Element Text Is", "type": "object"}, "element_text_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_is": {"$ref": "#/$defs/base_element_text_is_model", "title": "Assert Element Text Is"}}, "required": ["element_text_is"], "title": "Assert Element Text Is (Nested)", "type": "object"}, "element_text_matches_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path``\nmatches the regular expression defined by ``expression``.\n\nFor example:\n\n```xml\n<element_text_matches path=\"BlastOutput_version\" expression=\"BLASTP\\s+2\\.2.*\"/>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_matches", "default": "element_text_matches", "title": "That", "type": "string"}}, "required": ["path", "expression"], "title": "Assert Element Text Matches", "type": "object"}, "element_text_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_matches": {"$ref": "#/$defs/base_element_text_matches_model", "title": "Assert Element Text Matches"}}, "required": ["element_text_matches"], "title": "Assert Element Text Matches (Nested)", "type": "object"}, "element_text_model": {"additionalProperties": false, "description": "This tag allows the developer to recurisively specify additional assertions as\nchild elements about just the text contained in the element specified by the\nXPath-like ``path``, e.g.\n\n```xml\n<element_text path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def\">\n  <not_has_text text=\"EDK72998.1\" />\n</element_text>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the implicit assertions can be inverted.\nThe sub-assertions, which have their own ``negate`` attribute, are not affected\nby ``negate``.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "element_text", "default": "element_text", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Element Text", "type": "object"}, "element_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text": {"$ref": "#/$defs/base_element_text_model", "title": "Assert Element Text"}}, "required": ["element_text"], "title": "Assert Element Text (Nested)", "type": "object"}, "has_archive_member_model": {"additionalProperties": false, "description": "This tag allows to check if ``path`` is contained in a compressed file.\n\nThe path is a regular expression that is matched against the full paths of the objects in\nthe compressed file (remember that \"matching\" means it is checked if a prefix of\nthe full path of an archive member is described by the regular expression).\nValid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that\ndepending on the archive creation method:\n\n- full paths of the members may be prefixed with ``./``\n- directories may be treated as empty files\n\n```xml\n<has_archive_member path=\"./path/to/my-file.txt\"/>\n```\n\nWith ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of\narchive members matching ``path`` can be expressed. The following could be used,\ne.g., to assert an archive containing n&plusmn;1 elements out of which at least\n4 need to have a ``txt`` extension.\n\n```xml\n<has_archive_member path=\".*\" n=\"10\" delta=\"1\"/>\n<has_archive_member path=\".*\\.txt\" min=\"4\"/>\n```\n\nIn addition the tag can contain additional assertions as child elements about\nthe first member in the archive matching the regular expression ``path``. For\ninstance\n\n```xml\n<has_archive_member path=\".*/my-file.txt\">\n  <not_has_text text=\"EDK72998.1\"/>\n</has_archive_member>\n```\n\nIf the ``all`` attribute is set to ``true`` then all archive members are subject\nto the assertions. Note that, archive members matching the ``path`` are sorted\nalphabetically.\n\nThe ``negate`` attribute of the ``has_archive_member`` assertion only affects\nthe asserts on the presence and number of matching archive members, but not any\nsub-assertions (which can offer the ``negate`` attribute on their own).  The\ncheck if the file is an archive at all, which is also done by the function, is\nnot affected.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "has_archive_member", "default": "has_archive_member", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Archive Member", "type": "object"}, "has_archive_member_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_archive_member": {"$ref": "#/$defs/base_has_archive_member_model", "title": "Assert Has Archive Member"}}, "required": ["has_archive_member"], "title": "Assert Has Archive Member (Nested)", "type": "object"}, "has_element_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains at least one element (or tag) with the specified\nXPath-like ``path``, e.g.\n\n```xml\n<has_element_with_path path=\"BlastOutput_param/Parameters/Parameters_matrix\" />\n```\n\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_element_with_path", "default": "has_element_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Element With Path", "type": "object"}, "has_element_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_element_with_path": {"$ref": "#/$defs/base_has_element_with_path_model", "title": "Assert Has Element With Path"}}, "required": ["has_element_with_path"], "title": "Assert Has Element With Path (Nested)", "type": "object"}, "has_h5_attribute_model": {"additionalProperties": false, "description": "Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.\n\n```xml\n<has_h5_attribute key=\"nchroms\" value=\"15\" />\n```", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}, "that": {"const": "has_h5_attribute", "default": "has_h5_attribute", "title": "That", "type": "string"}}, "required": ["key", "value"], "title": "Assert Has H5 Attribute", "type": "object"}, "has_h5_attribute_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_attribute": {"$ref": "#/$defs/base_has_h5_attribute_model", "title": "Assert Has H5 Attribute"}}, "required": ["has_h5_attribute"], "title": "Assert Has H5 Attribute (Nested)", "type": "object"}, "has_h5_keys_model": {"additionalProperties": false, "description": "Asserts the specified HDF5 output has the given keys.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}, "that": {"const": "has_h5_keys", "default": "has_h5_keys", "title": "That", "type": "string"}}, "required": ["keys"], "title": "Assert Has H5 Keys", "type": "object"}, "has_h5_keys_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_keys": {"$ref": "#/$defs/base_has_h5_keys_model", "title": "Assert Has H5 Keys"}}, "required": ["has_h5_keys"], "title": "Assert Has H5 Keys (Nested)", "type": "object"}, "has_image_center_of_mass_model": {"additionalProperties": false, "description": "Asserts the specified output is an image and has the specified center of mass.\n\nAsserts the output is an image and has a specific center of mass,\nor has an Euclidean distance of ``eps`` or less to that point (e.g.,\n``<has_image_center_of_mass center_of_mass=\"511.07, 223.34\" />``).", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}, "that": {"const": "has_image_center_of_mass", "default": "has_image_center_of_mass", "title": "That", "type": "string"}}, "required": ["center_of_mass"], "title": "Assert Has Image Center Of Mass", "type": "object"}, "has_image_center_of_mass_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_center_of_mass": {"$ref": "#/$defs/base_has_image_center_of_mass_model", "title": "Assert Has Image Center Of Mass"}}, "required": ["has_image_center_of_mass"], "title": "Assert Has Image Center Of Mass (Nested)", "type": "object"}, "has_image_channels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of channels.\n\nThe number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels=\"3\" />``).\n\nAlternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_channels", "default": "has_image_channels", "title": "That", "type": "string"}}, "title": "Assert Has Image Channels", "type": "object"}, "has_image_channels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_channels": {"$ref": "#/$defs/base_has_image_channels_model", "title": "Assert Has Image Channels"}}, "required": ["has_image_channels"], "title": "Assert Has Image Channels (Nested)", "type": "object"}, "has_image_depth_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific depth (number of slices).\n\nThe depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected depth can be specified by ``min`` and/or ``max``.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_depth", "default": "has_image_depth", "title": "That", "type": "string"}}, "title": "Assert Has Image Depth", "type": "object"}, "has_image_depth_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_depth": {"$ref": "#/$defs/base_has_image_depth_model", "title": "Assert Has Image Depth"}}, "required": ["has_image_depth"], "title": "Assert Has Image Depth (Nested)", "type": "object"}, "has_image_frames_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of frames (number of time steps).\n\nThe number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_frames", "default": "has_image_frames", "title": "That", "type": "string"}}, "title": "Assert Has Image Frames", "type": "object"}, "has_image_frames_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_frames": {"$ref": "#/$defs/base_has_image_frames_model", "title": "Assert Has Image Frames"}}, "required": ["has_image_frames"], "title": "Assert Has Image Frames (Nested)", "type": "object"}, "has_image_height_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific height (in pixels).\n\nThe height is plus/minus ``delta`` (e.g., ``<has_image_height height=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected height can be specified by ``min`` and/or ``max``.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_height", "default": "has_image_height", "title": "That", "type": "string"}}, "title": "Assert Has Image Height", "type": "object"}, "has_image_height_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_height": {"$ref": "#/$defs/base_has_image_height_model", "title": "Assert Has Image Height"}}, "required": ["has_image_height"], "title": "Assert Has Image Height (Nested)", "type": "object"}, "has_image_mean_intensity_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific mean intensity value.\n\nThe mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity=\"0.83\" />``).\nAlternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}, "that": {"const": "has_image_mean_intensity", "default": "has_image_mean_intensity", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Intensity", "type": "object"}, "has_image_mean_intensity_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_intensity": {"$ref": "#/$defs/base_has_image_mean_intensity_model", "title": "Assert Has Image Mean Intensity"}}, "required": ["has_image_mean_intensity"], "title": "Assert Has Image Mean Intensity (Nested)", "type": "object"}, "has_image_mean_object_size_model": {"additionalProperties": false, "description": "Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),\n\nThe mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size=\"111.87\" exclude_labels=\"0\" />``).\n\nThe labels must be unique.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}, "that": {"const": "has_image_mean_object_size", "default": "has_image_mean_object_size", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Object Size", "type": "object"}, "has_image_mean_object_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_object_size": {"$ref": "#/$defs/base_has_image_mean_object_size_model", "title": "Assert Has Image Mean Object Size"}}, "required": ["has_image_mean_object_size"], "title": "Assert Has Image Mean Object Size (Nested)", "type": "object"}, "has_image_n_labels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has the specified labels.\n\nLabels can be a number of labels or unique values (e.g.,\n``<has_image_n_labels n=\"187\" exclude_labels=\"0\" />``).\n\nThe primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_n_labels", "default": "has_image_n_labels", "title": "That", "type": "string"}}, "title": "Assert Has Image N Labels", "type": "object"}, "has_image_n_labels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_n_labels": {"$ref": "#/$defs/base_has_image_n_labels_model", "title": "Assert Has Image N Labels"}}, "required": ["has_image_n_labels"], "title": "Assert Has Image N Labels (Nested)", "type": "object"}, "has_image_width_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific width (in pixels).\n\nThe width is plus/minus ``delta`` (e.g., ``<has_image_width width=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected width can be specified by ``min`` and/or ``max``.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_width", "default": "has_image_width", "title": "That", "type": "string"}}, "title": "Assert Has Image Width", "type": "object"}, "has_image_width_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_width": {"$ref": "#/$defs/base_has_image_width_model", "title": "Assert Has Image Width"}}, "required": ["has_image_width"], "title": "Assert Has Image Width (Nested)", "type": "object"}, "has_json_property_with_text_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified text (i.e. string) value.\n\n```xml\n<has_json_property_with_text property=\"color\" text=\"red\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}, "that": {"const": "has_json_property_with_text", "default": "has_json_property_with_text", "title": "That", "type": "string"}}, "required": ["property", "text"], "title": "Assert Has Json Property With Text", "type": "object"}, "has_json_property_with_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_text": {"$ref": "#/$defs/base_has_json_property_with_text_model", "title": "Assert Has Json Property With Text"}}, "required": ["has_json_property_with_text"], "title": "Assert Has Json Property With Text (Nested)", "type": "object"}, "has_json_property_with_value_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified JSON value.\n\n```xml\n<has_json_property_with_value property=\"skipped_columns\" value=\"[1, 3, 5]\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}, "that": {"const": "has_json_property_with_value", "default": "has_json_property_with_value", "title": "That", "type": "string"}}, "required": ["property", "value"], "title": "Assert Has Json Property With Value", "type": "object"}, "has_json_property_with_value_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_value": {"$ref": "#/$defs/base_has_json_property_with_value_model", "title": "Assert Has Json Property With Value"}}, "required": ["has_json_property_with_value"], "title": "Assert Has Json Property With Value (Nested)", "type": "object"}, "has_line_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains a line matching the\nregular expression specified by the argument expression. If n is given\nthe assertion checks for exactly n occurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line_matching", "default": "has_line_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Line Matching", "type": "object"}, "has_line_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line_matching": {"$ref": "#/$defs/base_has_line_matching_model", "title": "Assert Has Line Matching"}}, "required": ["has_line_matching"], "title": "Assert Has Line Matching (Nested)", "type": "object"}, "has_line_model": {"additionalProperties": false, "description": "Asserts the specified output contains the line specified by the\nargument line. The exact number of occurrences can be optionally\nspecified by the argument n", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line", "default": "has_line", "title": "That", "type": "string"}}, "required": ["line"], "title": "Assert Has Line", "type": "object"}, "has_line_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line": {"$ref": "#/$defs/base_has_line_model", "title": "Assert Has Line"}}, "required": ["has_line"], "title": "Assert Has Line (Nested)", "type": "object"}, "has_n_columns_model": {"additionalProperties": false, "description": "Asserts tabular output  contains the specified\nnumber (``n``) of columns.\n\nFor instance, ``<has_n_columns n=\"3\"/>``. The assertion tests only the first line.\nNumber of columns can optionally also be specified with ``delta``. Alternatively the\nrange of expected occurrences can be specified by ``min`` and/or ``max``.\n\nOptionally a column separator (``sep``, default is ``       ``) `and comment character(s)\ncan be specified (``comment``, default is empty string). The first non-comment\nline is used for determining the number of columns.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_columns", "default": "has_n_columns", "title": "That", "type": "string"}}, "title": "Assert Has N Columns", "type": "object"}, "has_n_columns_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_columns": {"$ref": "#/$defs/base_has_n_columns_model", "title": "Assert Has N Columns"}}, "required": ["has_n_columns"], "title": "Assert Has N Columns (Nested)", "type": "object"}, "has_n_elements_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or\ntags) with the specified XPath-like ``path``.\n\nFor example:\n\n```xml\n<has_n_elements_with_path n=\"9\" path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num\" />\n```\n\nAlternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes\ncan be used to specify the range of the expected number of occurrences.\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_elements_with_path", "default": "has_n_elements_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has N Elements With Path", "type": "object"}, "has_n_elements_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_elements_with_path": {"$ref": "#/$defs/base_has_n_elements_with_path_model", "title": "Assert Has N Elements With Path"}}, "required": ["has_n_elements_with_path"], "title": "Assert Has N Elements With Path (Nested)", "type": "object"}, "has_n_lines_model": {"additionalProperties": false, "description": "Asserts the specified output contains ``n`` lines allowing\nfor a difference in the number of lines (delta)\nor relative differebce in the number of lines", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_lines", "default": "has_n_lines", "title": "That", "type": "string"}}, "title": "Assert Has N Lines", "type": "object"}, "has_n_lines_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_lines": {"$ref": "#/$defs/base_has_n_lines_model", "title": "Assert Has N Lines"}}, "required": ["has_n_lines"], "title": "Assert Has N Lines (Nested)", "type": "object"}, "has_size_model": {"additionalProperties": false, "description": "Asserts the specified output has a size of the specified value\n\nAttributes size and value or synonyms though value is considered deprecated.\nThe size optionally allows for absolute (``delta``) difference.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_size", "default": "has_size", "title": "That", "type": "string"}}, "title": "Assert Has Size", "type": "object"}, "has_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_size": {"$ref": "#/$defs/base_has_size_model", "title": "Assert Has Size"}}, "required": ["has_size"], "title": "Assert Has Size (Nested)", "type": "object"}, "has_text_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains text matching the\nregular expression specified by the argument expression.\nIf n is given the assertion checks for exactly n (nonoverlapping)\noccurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text_matching", "default": "has_text_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Text Matching", "type": "object"}, "has_text_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text_matching": {"$ref": "#/$defs/base_has_text_matching_model", "title": "Assert Has Text Matching"}}, "required": ["has_text_matching"], "title": "Assert Has Text Matching (Nested)", "type": "object"}, "has_text_model": {"additionalProperties": false, "description": "Asserts specified output contains the substring specified by\nthe argument text. The exact number of occurrences can be\noptionally specified by the argument n", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text", "default": "has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Has Text", "type": "object"}, "has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text": {"$ref": "#/$defs/base_has_text_model", "title": "Assert Has Text"}}, "required": ["has_text"], "title": "Assert Has Text (Nested)", "type": "object"}, "is_valid_xml_model": {"additionalProperties": false, "description": "Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).", "properties": {"that": {"const": "is_valid_xml", "default": "is_valid_xml", "title": "That", "type": "string"}}, "title": "Assert Is Valid Xml", "type": "object"}, "is_valid_xml_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"is_valid_xml": {"$ref": "#/$defs/base_is_valid_xml_model", "title": "Assert Is Valid Xml"}}, "required": ["is_valid_xml"], "title": "Assert Is Valid Xml (Nested)", "type": "object"}, "not_has_text_model": {"additionalProperties": false, "description": "Asserts specified output does not contain the substring\nspecified by the argument text", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "that": {"const": "not_has_text", "default": "not_has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Not Has Text", "type": "object"}, "not_has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"not_has_text": {"$ref": "#/$defs/base_not_has_text_model", "title": "Assert Not Has Text"}}, "required": ["not_has_text"], "title": "Assert Not Has Text (Nested)", "type": "object"}, "xml_element_model": {"additionalProperties": false, "description": "Assert if the XML file contains element(s) or tag(s) with the specified\n[XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``\nor ``min`` and ``max`` are given also the number of occurrences is checked.\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem\"/>\n  <xml_element path=\"./elem/more[2]\"/>\n  <xml_element path=\".//more\" n=\"3\" delta=\"1\"/>\n</assert_contents>\n```\n\nWith ``negate=\"true\"`` the outcome of the assertions wrt the presence and number\nof ``path`` can be negated. If there are any sub assertions then check them against\n\n- the content of the attribute ``attribute``\n- the element's text if no attribute is given\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem/more[2]\" attribute=\"name\">\n    <has_text_matching expression=\"foo$\"/>\n  </xml_element>\n</assert_contents>\n```\n\nSub-assertions are not subject to the ``negate`` attribute of ``xml_element``.\nIf ``all`` is ``true`` then the sub assertions are checked for all occurrences.\n\nNote that all other XML assertions can be expressed by this assertion (Galaxy\nalso implements the other assertions by calling this one).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "xml_element", "default": "xml_element", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Xml Element", "type": "object"}, "xml_element_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"xml_element": {"$ref": "#/$defs/base_xml_element_model", "title": "Assert Xml Element"}}, "required": ["xml_element"], "title": "Assert Xml Element (Nested)", "type": "object"}}, "additionalProperties": false, "description": "Full unprivileged tool source, including the optional ``tests`` block.\n\nThis is the model persisted and validated on the API surface\n(``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring\nuses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added\nback here so direct authors and stored rows can still carry tests.", "properties": {"id": {"anyOf": [{"maxLength": 255, "minLength": 3, "pattern": "^[a-z][a-z0-9_-]*$", "type": "string"}, {"type": "null"}], "default": null, "description": "Unique identifier for the tool. Lowercase, must start with a letter, may contain letters, digits, '_' and '-'.", "examples": ["my-cool-tool"], "title": "id"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "version"}, "name": {"description": "The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.", "minLength": 5, "title": "name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The description is displayed in the tool menu immediately following the hyperlink for the tool.", "title": "description"}, "configfiles": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTemplateConfigFile"}, "type": "array"}, {"type": "null"}], "default": null, "description": "A list of config files for this tool.", "title": "configfiles"}, "requirements": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/JavascriptRequirement"}, {"$ref": "#/$defs/ResourceRequirement"}, {"$ref": "#/$defs/ContainerRequirement"}]}, "type": "array"}, {"type": "null"}], "default": [], "description": "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.", "title": "requirements"}, "shell_command": {"description": "A string that contains the command to be executed. Parameters can be referenced inside $().", "examples": ["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"], "title": "shell_command", "type": "string"}, "inputs": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "inputs", "type": "array"}, "outputs": {"default": [], "items": {"discriminator": {"mapping": {"boolean": "#/$defs/IncomingToolOutputBoolean", "collection": "#/$defs/IncomingToolOutputCollection", "data": "#/$defs/IncomingToolOutputDataset", "float": "#/$defs/IncomingToolOutputFloat", "integer": "#/$defs/IncomingToolOutputInteger", "text": "#/$defs/IncomingToolOutputText"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/IncomingToolOutputDataset"}, {"$ref": "#/$defs/IncomingToolOutputCollection"}, {"$ref": "#/$defs/IncomingToolOutputText"}, {"$ref": "#/$defs/IncomingToolOutputInteger"}, {"$ref": "#/$defs/IncomingToolOutputFloat"}, {"$ref": "#/$defs/IncomingToolOutputBoolean"}]}, "title": "outputs", "type": "array"}, "citations": {"anyOf": [{"items": {"$ref": "#/$defs/Citation"}, "type": "array"}, {"type": "null"}], "default": null, "title": "citations"}, "license": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.", "examples": ["MIT"], "title": "license"}, "edam_operations": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_operations"}, "edam_topics": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_topics"}, "xrefs": {"anyOf": [{"items": {"$ref": "#/$defs/XrefDict"}, "type": "array"}, {"type": "null"}], "default": null, "title": "xrefs"}, "profile": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "profile"}, "help": {"anyOf": [{"$ref": "#/$defs/HelpContent"}, {"type": "null"}], "default": null, "description": "Help text shown below the tool interface.", "title": "help"}, "class": {"const": "GalaxyUserTool", "title": "class_", "type": "string"}, "container": {"description": "Container image to use for this tool.", "examples": ["quay.io/biocontainers/python:3.13"], "title": "container", "type": "string"}, "tests": {"anyOf": [{"items": {"$ref": "#/$defs/YamlToolTest"}, "type": "array"}, {"type": "null"}], "default": null, "title": "tests"}}, "required": ["name", "shell_command", "class", "container"], "title": "UserToolSource", "type": "object"}
\ No newline at end of file
diff --git a/lib/tool_shed/webapp/frontend/src/schema/schema.ts b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
index f3ed67a6bd5..743d57f8967 100644
--- a/lib/tool_shed/webapp/frontend/src/schema/schema.ts
+++ b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
@@ -2046,30 +2046,42 @@ export interface components {
         }
         /** FilePatternDatasetCollectionDescription */
         FilePatternDatasetCollectionDescription: {
-            /** Assign Primary Output */
+            /**
+             * Assign Primary Output
+             * @default false
+             */
             assign_primary_output: boolean
             /** Directory */
-            directory: string | null
+            directory?: string | null
             /**
              * Discover Via
+             * @default pattern
              * @constant
              */
             discover_via: "pattern"
             /** Format */
-            format: string | null
-            /** Match Relative Path */
+            format?: string | null
+            /**
+             * Match Relative Path
+             * @default false
+             */
             match_relative_path: boolean
             /** Pattern */
             pattern: string
-            /** Recurse */
+            /**
+             * Recurse
+             * @default false
+             */
             recurse: boolean
             /**
              * Sort Comp
+             * @default lexical
              * @enum {string}
              */
             sort_comp: "lexical" | "numeric"
             /**
              * Sort Key
+             * @default filename
              * @enum {string}
              */
             sort_key: "filename" | "name" | "designation" | "dbkey"
@@ -2078,7 +2090,10 @@ export interface components {
              * @default false
              */
             sort_reverse: boolean
-            /** Visible */
+            /**
+             * Visible
+             * @default false
+             */
             visible: boolean
         }
         /** FloatParameterModel */
@@ -3627,7 +3642,7 @@ export interface components {
              * Hidden
              * @description If true, the output will not be shown in the history.
              */
-            hidden: unknown
+            hidden: boolean
             /**
              * Label
              * @description Output label. Will be used as dataset name in history.
@@ -3637,7 +3652,7 @@ export interface components {
              * Name
              * @description Parameter name. Used when referencing parameter in workflows.
              */
-            name: unknown
+            name: string
             /**
              * @description discriminator enum property added by openapi-typescript
              * @enum {string}
@@ -3743,7 +3758,7 @@ export interface components {
              * Hidden
              * @description If true, the output will not be shown in the history.
              */
-            hidden: unknown
+            hidden: boolean
             /**
              * Label
              * @description Output label. Will be used as dataset name in history.
@@ -3753,7 +3768,7 @@ export interface components {
              * Name
              * @description Parameter name. Used when referencing parameter in workflows.
              */
-            name: unknown
+            name: string
             /**
              * @description discriminator enum property added by openapi-typescript
              * @enum {string}
@@ -3766,7 +3781,7 @@ export interface components {
              * Hidden
              * @description If true, the output will not be shown in the history.
              */
-            hidden: unknown
+            hidden: boolean
             /**
              * Label
              * @description Output label. Will be used as dataset name in history.
@@ -3776,7 +3791,7 @@ export interface components {
              * Name
              * @description Parameter name. Used when referencing parameter in workflows.
              */
-            name: unknown
+            name: string
             /**
              * @description discriminator enum property added by openapi-typescript
              * @enum {string}
@@ -3789,7 +3804,7 @@ export interface components {
              * Hidden
              * @description If true, the output will not be shown in the history.
              */
-            hidden: unknown
+            hidden: boolean
             /**
              * Label
              * @description Output label. Will be used as dataset name in history.
@@ -3799,7 +3814,7 @@ export interface components {
              * Name
              * @description Parameter name. Used when referencing parameter in workflows.
              */
-            name: unknown
+            name: string
             /**
              * @description discriminator enum property added by openapi-typescript
              * @enum {string}
@@ -3808,22 +3823,35 @@ export interface components {
         }
         /** ToolProvidedMetadataDatasetCollection */
         ToolProvidedMetadataDatasetCollection: {
-            /** Assign Primary Output */
+            /**
+             * Assign Primary Output
+             * @default false
+             */
             assign_primary_output: boolean
             /** Directory */
-            directory: string | null
+            directory?: string | null
             /**
              * Discover Via
+             * @default tool_provided_metadata
              * @constant
              */
             discover_via: "tool_provided_metadata"
             /** Format */
-            format: string | null
-            /** Match Relative Path */
+            format?: string | null
+            /**
+             * Match Relative Path
+             * @default false
+             */
             match_relative_path: boolean
-            /** Recurse */
+            /**
+             * Recurse
+             * @default false
+             */
             recurse: boolean
-            /** Visible */
+            /**
+             * Visible
+             * @default false
+             */
             visible: boolean
         }
         /** ToolVersion */

From 0f3d87cff251bf7f29a9cbf6484726d20564b7b7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 20:26:13 +0200
Subject: [PATCH 246/256] Fix mypy errors

- UserToolSource.version relaxes the authoring view's required str to
  Optional[str] (intentional; pydantic allows the override) -- silence the
  attribute-override check.
- Narrow Optional / discriminated-union types in the new tests before
  attribute access (help, discover_datasets descriptors).
---
 lib/galaxy/tool_util_models/__init__.py     |  4 +++-
 test/unit/tool_util/test_yaml_parameters.py | 17 ++++++++++++++---
 2 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_util_models/__init__.py b/lib/galaxy/tool_util_models/__init__.py
index 6048873ba1c..6cb7fee91ee 100644
--- a/lib/galaxy/tool_util_models/__init__.py
+++ b/lib/galaxy/tool_util_models/__init__.py
@@ -372,7 +372,9 @@ class UserToolSource(UserToolSourceAuthoringView):
     # Relax ``version`` back to optional for the persisted/full model: stored rows
     # and API submissions from older Galaxy versions may lack it, and the lift path
     # must still validate them. Only the LLM-authoring view (parent) requires it.
-    version: Optional[str] = None
+    # mypy flags the parent's required ``str`` being widened to ``Optional[str]``;
+    # pydantic supports the override and the relaxation is intentional here.
+    version: Optional[str] = None  # type: ignore[assignment]
     tests: Optional[List["YamlToolTest"]] = None
 
 
diff --git a/test/unit/tool_util/test_yaml_parameters.py b/test/unit/tool_util/test_yaml_parameters.py
index 3742eb5378b..f036a5ab7d6 100644
--- a/test/unit/tool_util/test_yaml_parameters.py
+++ b/test/unit/tool_util/test_yaml_parameters.py
@@ -381,6 +381,7 @@ def test_help_string_lenient_coerces_strict_rejects():
         "help": "### plain string help",
     }
     t = UserToolSourceAuthoringView.model_validate(doc, context=AGENT_LENIENT_CONTEXT)
+    assert t.help is not None
     assert t.help.format == "markdown" and t.help.content == "### plain string help"
 
     with pytest.raises(ValidationError):
@@ -431,7 +432,10 @@ def test_select_top_level_value_lenient_coerces_strict_rejects():
 def test_collection_output_wraps_single_discover_datasets_lenient_only():
     """Agent-ingest (lenient): a single discovery descriptor object is wrapped into a
     one-element list. Strict: reject ('Input should be a valid array')."""
-    from galaxy.tool_util_models.tool_outputs import IncomingToolOutputCollection
+    from galaxy.tool_util_models.tool_outputs import (
+        FilePatternDatasetCollectionDescription,
+        IncomingToolOutputCollection,
+    )
 
     doc = {
         "type": "collection",
@@ -442,7 +446,9 @@ def test_collection_output_wraps_single_discover_datasets_lenient_only():
     out = IncomingToolOutputCollection.model_validate(doc, context=AGENT_LENIENT_CONTEXT)
     assert isinstance(out.discover_datasets, list)
     assert len(out.discover_datasets) == 1
-    assert out.discover_datasets[0].pattern == "split_.*\\.fasta"
+    first = out.discover_datasets[0]
+    assert isinstance(first, FilePatternDatasetCollectionDescription)
+    assert first.pattern == "split_.*\\.fasta"
 
     with pytest.raises(ValidationError):
         IncomingToolOutputCollection.model_validate(doc)
@@ -453,7 +459,10 @@ def test_collection_discovery_only_requires_pattern():
     attributes default to the XML parser's values (visible=False, recurse=False,
     sort_key=filename, sort_comp=lexical, discover_via=pattern). Requiring all of
     them made `discover_datasets` nearly impossible to author by hand."""
-    from galaxy.tool_util_models.tool_outputs import IncomingToolOutputCollection
+    from galaxy.tool_util_models.tool_outputs import (
+        FilePatternDatasetCollectionDescription,
+        IncomingToolOutputCollection,
+    )
 
     out = IncomingToolOutputCollection.model_validate(
         {
@@ -463,7 +472,9 @@ def test_collection_discovery_only_requires_pattern():
             "discover_datasets": [{"pattern": "split_.*\\.fasta", "format": "fasta"}],
         }
     )
+    assert out.discover_datasets is not None
     d = out.discover_datasets[0]
+    assert isinstance(d, FilePatternDatasetCollectionDescription)
     assert d.discover_via == "pattern"
     assert (d.visible, d.assign_primary_output, d.recurse, d.match_relative_path) == (False, False, False, False)
     assert (d.sort_key, d.sort_comp) == ("filename", "lexical")

From a575822b172dc77cc662715e5b6249dd4d801b08 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 21:30:43 +0200
Subject: [PATCH 247/256] Revert "Scope liberal-input coercions to agent ingest
 via validation context"

This reverts commit f59798a6847169d42b9d58358f67b6420e3bdd3b.
---
 lib/galaxy/agents/custom_tool.py              |  5 -
 lib/galaxy/tool_util_models/__init__.py       | 12 ---
 lib/galaxy/tool_util_models/_base.py          | 16 ----
 lib/galaxy/tool_util_models/tool_outputs.py   | 20 +---
 .../tool_util_models/yaml_parameters.py       | 79 +---------------
 test/unit/tool_util/test_yaml_parameters.py   | 92 +------------------
 .../user_tool_source_validation_cases.yml     | 40 --------
 7 files changed, 6 insertions(+), 258 deletions(-)

diff --git a/lib/galaxy/agents/custom_tool.py b/lib/galaxy/agents/custom_tool.py
index b7a5150368f..ec5b2295cfc 100644
--- a/lib/galaxy/agents/custom_tool.py
+++ b/lib/galaxy/agents/custom_tool.py
@@ -32,7 +32,6 @@ from galaxy.tool_util_models import (
     UserToolSource,
     UserToolSourceAuthoringView,
 )
-from galaxy.tool_util_models._base import AGENT_LENIENT_CONTEXT
 from .base import (
     ActionSuggestion,
     ActionType,
@@ -190,10 +189,6 @@ class CustomToolAgent(BaseGalaxyAgent):
             output_type=UserToolSourceAuthoringView,
             system_prompt=self.get_system_prompt(),
             retries=self._get_retries(default=0),
-            # Opt this (agent-ingest) path into the liberal-input coercions. The
-            # canonical API/storage validation runs without this context and stays
-            # strict, so coercion is scoped to model output only.
-            validation_context=AGENT_LENIENT_CONTEXT,
         )
 
     def get_system_prompt(self) -> str:
diff --git a/lib/galaxy/tool_util_models/__init__.py b/lib/galaxy/tool_util_models/__init__.py
index 6cb7fee91ee..1e67c01f1e8 100644
--- a/lib/galaxy/tool_util_models/__init__.py
+++ b/lib/galaxy/tool_util_models/__init__.py
@@ -40,7 +40,6 @@ from typing_extensions import (
 
 from ._base import (
     CollectionType,
-    lenient_coercion_enabled,
     StrictModel,
     ToolSourceBaseModel,
 )
@@ -201,17 +200,6 @@ class _DynamicToolSourceBase(ToolSourceBaseModel):
             normalize_dict(values, ["inputs", "outputs"])
         return values
 
-    @field_validator("help", mode="before")
-    @classmethod
-    def _coerce_help_string(cls, v, info):
-        # LLMs (and authors used to the XML <help> element) naturally provide help as
-        # a plain string, but the model stores it as {format, content}. In agent-ingest
-        # mode, accept a bare string and treat it as markdown; strict validation
-        # requires the explicit {format, content} object.
-        if lenient_coercion_enabled(info) and isinstance(v, str):
-            return {"format": "markdown", "content": v}
-        return v
-
     @field_validator("name", "version", mode="after")
     @classmethod
     def _reject_blank_strings(cls, v: Optional[str]) -> Optional[str]:
diff --git a/lib/galaxy/tool_util_models/_base.py b/lib/galaxy/tool_util_models/_base.py
index f92de2064e9..cf53028b625 100644
--- a/lib/galaxy/tool_util_models/_base.py
+++ b/lib/galaxy/tool_util_models/_base.py
@@ -18,22 +18,6 @@ class StrictModel(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
 
-# Liberal-input coercions (accepting the loose shapes LLMs emit -- a string ``help``,
-# a ``value`` on a select, a single ``discover_datasets`` object, a meaningless
-# ``min`` on a single data input) are gated on this validation-context flag so they
-# apply ONLY when ingesting agent output. The canonical API / storage / lift path
-# validates without it and stays strict, surfacing those shapes as errors instead of
-# silently rewriting them. The agent opts in via ``Agent(validation_context=AGENT_LENIENT_CONTEXT)``.
-LENIENT_CONTEXT_KEY = "lenient"
-AGENT_LENIENT_CONTEXT = {LENIENT_CONTEXT_KEY: True}
-
-
-def lenient_coercion_enabled(info) -> bool:
-    """True when validation is running in agent-ingest mode (see above)."""
-    context = getattr(info, "context", None)
-    return bool(isinstance(context, dict) and context.get(LENIENT_CONTEXT_KEY))
-
-
 def _check_collection_type(v: str) -> str:
     if len(v) == 0:
         raise ValueError("Invalid empty collection_type specified.")
diff --git a/lib/galaxy/tool_util_models/tool_outputs.py b/lib/galaxy/tool_util_models/tool_outputs.py
index 38262b91d51..868761ebf43 100644
--- a/lib/galaxy/tool_util_models/tool_outputs.py
+++ b/lib/galaxy/tool_util_models/tool_outputs.py
@@ -16,7 +16,6 @@ from typing import (
 
 from pydantic import (
     Field,
-    field_validator,
     model_validator,
 )
 from typing_extensions import (
@@ -25,10 +24,7 @@ from typing_extensions import (
     TypeVar,
 )
 
-from ._base import (
-    lenient_coercion_enabled,
-    ToolSourceBaseModel,
-)
+from ._base import ToolSourceBaseModel
 
 AnyT = TypeVar("AnyT")
 NotRequired = Optional[AnyT]
@@ -38,16 +34,6 @@ IncomingNotRequiredStringT = TypeVar("IncomingNotRequiredStringT")
 # Use IncomingNotRequired when concrete key: Optional[str] = None would be incorrect
 
 
-def _single_to_list(v: Any, info: Any) -> Any:
-    # LLMs often provide a single ``discover_datasets`` descriptor object where the
-    # model expects a list of them. In agent-ingest mode, wrap a bare dict so it
-    # validates; strict validation requires the list form ("Input should be a valid
-    # array"), keeping the canonical schema to one shape.
-    if lenient_coercion_enabled(info) and isinstance(v, dict):
-        return [v]
-    return v
-
-
 class GenericToolOutputBaseModel(ToolSourceBaseModel, Generic[IncomingNotRequiredBoolT, IncomingNotRequiredStringT]):
     name: Annotated[
         IncomingNotRequiredStringT, Field(description="Parameter name. Used when referencing parameter in workflows.")
@@ -120,8 +106,6 @@ class GenericToolOutputDataset(
     ] = None
     precreate_directory: Optional[bool] = False
 
-    _wrap_discover_datasets = field_validator("discover_datasets", mode="before")(_single_to_list)
-
 
 class ToolOutputDataset(GenericToolOutputDataset[bool, str]): ...
 
@@ -167,8 +151,6 @@ class GenericToolOutputCollection(
     structured_like: Optional[str] = None
     discover_datasets: Optional[List[DatasetCollectionDescriptionT]] = None
 
-    _wrap_discover_datasets = field_validator("discover_datasets", mode="before")(_single_to_list)
-
     @model_validator(mode="before")
     @classmethod
     def _lift_legacy_structure(cls, values):
diff --git a/lib/galaxy/tool_util_models/yaml_parameters.py b/lib/galaxy/tool_util_models/yaml_parameters.py
index 2276fbddaba..6b94ee5f0ea 100644
--- a/lib/galaxy/tool_util_models/yaml_parameters.py
+++ b/lib/galaxy/tool_util_models/yaml_parameters.py
@@ -24,16 +24,13 @@ from pydantic import (
     ConfigDict,
     Field,
     field_validator,
-    model_validator,
     RootModel,
 )
-from pydantic_core import PydanticCustomError
 from typing_extensions import (
     Annotated,
     Literal,
 )
 
-from ._base import lenient_coercion_enabled
 from .parameter_validators import (
     EmptyFieldParameterValidatorModel,
     InRangeParameterValidatorModel,
@@ -165,29 +162,6 @@ class YamlSelectParameter(_YamlParamBase):
     multiple: bool = False
     validators: List[YamlSelectValidators] = []
 
-    @model_validator(mode="before")
-    @classmethod
-    def _coerce_default_value(cls, data, info):
-        # LLMs naturally express a select's default as a top-level ``value`` (as
-        # other param types do), but selects mark the default via ``selected: true``
-        # on an option. In agent-ingest mode, accept ``value`` and fold it into the
-        # matching option; strict validation leaves it for ``extra="forbid"`` to
-        # reject, so the canonical schema keeps one way to express a default.
-        if lenient_coercion_enabled(info) and isinstance(data, dict) and "value" in data:
-            data = dict(data)  # don't mutate the caller's dict
-            default = data.pop("value")
-            options = data.get("options")
-            if isinstance(options, list):
-                data["options"] = [
-                    (
-                        {**option, "selected": True}
-                        if isinstance(option, dict) and option.get("value") == default
-                        else option
-                    )
-                    for option in options
-                ]
-        return data
-
     def to_internal(self) -> SelectParameterModel:
         return SelectParameterModel(
             type="select",
@@ -217,62 +191,15 @@ def _split_format(v):
 class YamlDataParameter(_YamlParamBase):
     type: Literal["data"]
     format: List[str] = ["data"]
-    multiple: Annotated[
-        bool,
-        Field(description="Set true to accept several datasets (a list) for this input instead of one."),
-    ] = False
-    min: Annotated[
-        Optional[int],
-        Field(
-            description=(
-                "Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. "
-                "Do NOT set this for a single-dataset input -- a data input is already required by default, "
-                "so leave 'min' unset unless the input accepts multiple datasets."
-            )
-        ),
-    ] = None
-    max: Annotated[
-        Optional[int],
-        Field(
-            description=(
-                "Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; "
-                "leave unset for a single-dataset input."
-            )
-        ),
-    ] = None
+    multiple: bool = False
+    min: Optional[int] = None
+    max: Optional[int] = None
 
     @field_validator("format", mode="before")
     @classmethod
     def _coerce_format(cls, v):
         return _split_format(v)
 
-    @model_validator(mode="after")
-    def _check_min_max_without_multiple(self, info) -> "YamlDataParameter":
-        # min/max are the min/max number of *datasets*, which only has meaning for a
-        # multiple-dataset input -- the runtime (galaxy.tools.parameters.basic
-        # .DataToolParameter) rejects them outright on a single one.
-        #
-        # Agent-ingest (lenient): LLMs routinely add `min: 1` to a single data input
-        # to mean "required" (already the default), so drop the meaningless bound
-        # rather than fail the otherwise-fine tool.
-        # Strict (API / storage): raise -- a human/programmatic author should see the
-        # mistake, not have their value silently discarded.
-        if self.multiple or (self.min is None and self.max is None):
-            return self
-        if lenient_coercion_enabled(info):
-            self.min = None
-            self.max = None
-            return self
-        for bound in ("min", "max"):
-            if getattr(self, bound) is not None:
-                raise PydanticCustomError(
-                    "dynamic_tool.data_min_max_requires_multiple",
-                    "cannot specify '{bound}' on a single data parameter; "
-                    "set 'multiple: true' if the parameter should accept multiple datasets",
-                    {"bound": bound},
-                )
-        return self
-
     def to_internal(self) -> DataParameterModel:
         return DataParameterModel(
             type="data",
diff --git a/test/unit/tool_util/test_yaml_parameters.py b/test/unit/tool_util/test_yaml_parameters.py
index f036a5ab7d6..52d45148943 100644
--- a/test/unit/tool_util/test_yaml_parameters.py
+++ b/test/unit/tool_util/test_yaml_parameters.py
@@ -15,7 +15,6 @@ from galaxy.tool_util_models import (
     UserToolSource,
     UserToolSourceAuthoringView,
 )
-from galaxy.tool_util_models._base import AGENT_LENIENT_CONTEXT
 from galaxy.tool_util_models.parameters import (
     BooleanParameterModel,
     ConditionalParameterModel,
@@ -31,9 +30,8 @@ from galaxy.tool_util_models.parameters import (
 from galaxy.tool_util_models.yaml_parameters import YamlGalaxyToolParameter
 
 
-def _validate(input_dict, lenient=False):
-    context = AGENT_LENIENT_CONTEXT if lenient else None
-    return YamlGalaxyToolParameter.model_validate(input_dict, context=context)
+def _validate(input_dict):
+    return YamlGalaxyToolParameter.model_validate(input_dict)
 
 
 # ---------------------------------------------------------------------------
@@ -368,92 +366,6 @@ def test_authoring_view_drops_tests_and_shrinks_schema():
     assert slim < full * 0.5, f"authoring view not slim enough: {slim} vs {full}"
 
 
-def test_help_string_lenient_coerces_strict_rejects():
-    """Agent-ingest (lenient): a bare string `help` becomes {format: markdown, content}.
-    Strict: the object form is required."""
-    doc = {
-        "class": "GalaxyUserTool",
-        "name": "Help tool",
-        "version": "0.1.0",
-        "container": "busybox",
-        "shell_command": "echo hi > out.txt",
-        "outputs": [{"type": "data", "name": "out", "from_work_dir": "out.txt"}],
-        "help": "### plain string help",
-    }
-    t = UserToolSourceAuthoringView.model_validate(doc, context=AGENT_LENIENT_CONTEXT)
-    assert t.help is not None
-    assert t.help.format == "markdown" and t.help.content == "### plain string help"
-
-    with pytest.raises(ValidationError):
-        UserToolSourceAuthoringView.model_validate(doc)
-
-
-def test_single_data_param_drops_meaningless_min_max_lenient_only():
-    """Agent-ingest (lenient): `min`/`max` on a single data input are meaningless
-    (a model adds `min: 1` to mean "required", already the default), so drop them.
-    Strict: reject -- a human/programmatic author shouldn't have a value silently
-    discarded."""
-    p = _validate({"type": "data", "name": "x", "min": 1, "max": 3}, lenient=True)
-    assert p.root.min is None and p.root.max is None
-    assert p.root.multiple is False
-
-    with pytest.raises(ValidationError):
-        _validate({"type": "data", "name": "x", "min": 1})
-
-
-def test_multiple_data_param_keeps_min_max():
-    """When the input genuinely accepts a list (`multiple: true`), the bounds are
-    valid and preserved in both modes."""
-    for lenient in (True, False):
-        p = _validate({"type": "data", "name": "x", "multiple": True, "min": 2, "max": 5}, lenient=lenient)
-        assert (p.root.min, p.root.max) == (2, 5)
-
-
-def test_select_top_level_value_lenient_coerces_strict_rejects():
-    """Agent-ingest (lenient): a select's top-level `value` is folded into
-    `selected: true` on the matching option. Strict: `extra="forbid"` rejects it, so
-    the canonical schema keeps one way to express a default."""
-    doc = {
-        "type": "select",
-        "name": "mode",
-        "value": "invert",
-        "options": [
-            {"label": "Keep matching", "value": "match"},
-            {"label": "Invert", "value": "invert"},
-        ],
-    }
-    p = _validate(doc, lenient=True)
-    assert {o.value: o.selected for o in p.root.options} == {"match": False, "invert": True}
-
-    with pytest.raises(ValidationError):
-        _validate(doc)
-
-
-def test_collection_output_wraps_single_discover_datasets_lenient_only():
-    """Agent-ingest (lenient): a single discovery descriptor object is wrapped into a
-    one-element list. Strict: reject ('Input should be a valid array')."""
-    from galaxy.tool_util_models.tool_outputs import (
-        FilePatternDatasetCollectionDescription,
-        IncomingToolOutputCollection,
-    )
-
-    doc = {
-        "type": "collection",
-        "name": "seqs",
-        "collection_type": "list",
-        "discover_datasets": {"discover_via": "pattern", "pattern": "split_.*\\.fasta"},
-    }
-    out = IncomingToolOutputCollection.model_validate(doc, context=AGENT_LENIENT_CONTEXT)
-    assert isinstance(out.discover_datasets, list)
-    assert len(out.discover_datasets) == 1
-    first = out.discover_datasets[0]
-    assert isinstance(first, FilePatternDatasetCollectionDescription)
-    assert first.pattern == "split_.*\\.fasta"
-
-    with pytest.raises(ValidationError):
-        IncomingToolOutputCollection.model_validate(doc)
-
-
 def test_collection_discovery_only_requires_pattern():
     """A discovery descriptor should validate from just a `pattern`; the boilerplate
     attributes default to the XML parser's values (visible=False, recurse=False,
diff --git a/test/unit/tool_util/user_tool_source_validation_cases.yml b/test/unit/tool_util/user_tool_source_validation_cases.yml
index d941f885ddd..d3ad5936fb1 100644
--- a/test/unit/tool_util/user_tool_source_validation_cases.yml
+++ b/test/unit/tool_util/user_tool_source_validation_cases.yml
@@ -195,46 +195,6 @@ cases:
       citations: null
     valid: true
 
-  # NOTE: these cases validate the STRICT, canonical UserToolSource (no lenient
-  # context). The liberal-input coercions (string help, `min` on single data, a
-  # select `value`, a single discover_datasets object) are scoped to agent ingest
-  # and are exercised in test_yaml_parameters with the lenient validation context.
-
-  - name: help_as_plain_string_rejected_strict
-    # Strict path requires the {format, content} object; the string form is only
-    # accepted in agent-ingest (lenient) mode.
-    doc:
-      help: "### Overview\nThis tool does a thing."
-    expected_errors:
-      - loc: help
-        code: model_type
-
-  - name: data_min_without_multiple_rejected_strict
-    # `min`/`max` on a single data parameter blow up at tool-build time
-    # (galaxy.tools.parameters.basic.DataToolParameter); the strict path rejects
-    # them. (Agent ingest drops the meaningless bound instead.)
-    doc:
-      inputs:
-        - {type: data, name: data_input, min: 1}
-    expected_errors:
-      - loc: inputs.0.data
-        code: dynamic_tool.data_min_max_requires_multiple
-
-  - name: data_max_without_multiple_rejected_strict
-    doc:
-      inputs:
-        - {type: data, name: data_input, max: 5}
-    expected_errors:
-      - loc: inputs.0.data
-        code: dynamic_tool.data_min_max_requires_multiple
-
-  - name: data_min_max_with_multiple_accepted
-    doc:
-      shell_command: "cat '$(inputs.data_input.path)' > out.txt"
-      inputs:
-        - {type: data, name: data_input, multiple: true, min: 1, max: 5}
-    valid: true
-
   - name: format_validation_errors_distillation
     # Exact distilled bullet text used by ``format_validation_errors`` so
     # downstream UIs (the agent's bullet list, API 4xx bodies) have a

From 6e82d7a41dad1eb752053076f676d5fc9451ab58 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 21:47:04 +0200
Subject: [PATCH 248/256] Require `version` on all user tool sources

Drop the Optional override (and its type: ignore) on UserToolSource so version
is required throughout, matching the authoring view, the lint check, and the
build path -- one rule instead of two. A stored row that predates the
requirement no longer lifts to "ok"; lift_user_tool_source returns it as the
raw dict with status "invalid", so its author still sees and can fix what they
defined (the endpoint never 500s).
---
 lib/galaxy/tool_util_models/__init__.py             | 13 ++++++-------
 .../test_user_tool_source_response.py               | 13 +++++++++++++
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/tool_util_models/__init__.py b/lib/galaxy/tool_util_models/__init__.py
index 1e67c01f1e8..bde1138d6ac 100644
--- a/lib/galaxy/tool_util_models/__init__.py
+++ b/lib/galaxy/tool_util_models/__init__.py
@@ -357,12 +357,9 @@ class UserToolSource(UserToolSourceAuthoringView):
     back here so direct authors and stored rows can still carry tests.
     """
 
-    # Relax ``version`` back to optional for the persisted/full model: stored rows
-    # and API submissions from older Galaxy versions may lack it, and the lift path
-    # must still validate them. Only the LLM-authoring view (parent) requires it.
-    # mypy flags the parent's required ``str`` being widened to ``Optional[str]``;
-    # pydantic supports the override and the relaxation is intentional here.
-    version: Optional[str] = None  # type: ignore[assignment]
+    # ``version`` is required (inherited from UserToolSourceAuthoringView). A stored
+    # row that predates the requirement won't validate; ``lift_user_tool_source``
+    # returns it as the raw dict with status "invalid" so its author still sees it.
     tests: Optional[List["YamlToolTest"]] = None
 
 
@@ -394,7 +391,9 @@ DynamicToolSources = Annotated[Union[UserToolSource, YamlToolSource], Field(disc
 #   - on `extra_forbidden`-only failure: strips the offending paths and
 #     re-validates. Returns ("lifted", parsed_model, dropped_paths).
 #   - on any other failure: returns ("invalid", original_dict, error_summary).
-#     The endpoint exposes this so legacy/broken rows don't crash the API.
+#     The endpoint exposes this so legacy/broken rows don't crash the API -- e.g.
+#     a stored row that predates the required `version` comes back as the raw dict
+#     with status "invalid", so its author can still see and fix what they defined.
 # ---------------------------------------------------------------------------
 
 LiftStatus = Literal["ok", "lifted", "invalid"]
diff --git a/test/unit/tool_util_models/test_user_tool_source_response.py b/test/unit/tool_util_models/test_user_tool_source_response.py
index 99f4ff17d21..290f409a5ff 100644
--- a/test/unit/tool_util_models/test_user_tool_source_response.py
+++ b/test/unit/tool_util_models/test_user_tool_source_response.py
@@ -47,6 +47,7 @@ BASE_TOOL: Dict[str, Any] = {
     "class": "GalaxyUserTool",
     "id": "legacy-tool",
     "name": "Legacy",
+    "version": "1.0.0",
     "container": "busybox",
     "shell_command": "echo $(inputs.msg)",
     "outputs": [],
@@ -87,6 +88,18 @@ def test_lift_status_lifted_for_drift_only():
         assert "argument" not in inp
 
 
+def test_lift_status_invalid_for_missing_version_still_returns_tool():
+    """`version` is required, so a stored row that predates the requirement can't be
+    auto-lifted. It is still returned to its author -- as the raw dict with an
+    'invalid' status -- so they can see and fix what they defined, rather than the
+    endpoint 500-ing or hiding the tool."""
+    versionless = {k: v for k, v in BASE_TOOL.items() if k != "version"}
+    status, parsed, errors = lift_user_tool_source(versionless)
+    assert status == "invalid"
+    assert parsed == versionless  # returned verbatim
+    assert any("version" in e for e in errors)
+
+
 def test_lift_handles_nested_conditional_drift():
     value = {
         **BASE_TOOL,

From c7d881268e30d66cdecc825dcf7e33396ccd5a55 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 21:54:55 +0200
Subject: [PATCH 249/256] Restore min/max/multiple field descriptions on data
 inputs

These schema descriptions (only valid with multiple=true; leave unset on a
single data input) were lost during an earlier rebase. They steer the model
away from putting a meaningless 'min' on a single data parameter.
---
 .../src/components/Tool/ToolSourceSchema.json |  2 +-
 .../tool_util_models/yaml_parameters.py       | 26 ++++++++++++++++---
 2 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Tool/ToolSourceSchema.json b/client/src/components/Tool/ToolSourceSchema.json
index 98d4218c564..85e7a7ddfcb 100644
--- a/client/src/components/Tool/ToolSourceSchema.json
+++ b/client/src/components/Tool/ToolSourceSchema.json
@@ -1 +1 @@
-{"$defs": {"Citation": {"properties": {"type": {"title": "Type", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["type", "content"], "title": "Citation", "type": "object"}, "CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "Container": {"properties": {"type": {"enum": ["docker", "singularity"], "title": "Type", "type": "string"}, "container_id": {"title": "Container Id", "type": "string"}}, "required": ["type", "container_id"], "title": "Container", "type": "object"}, "ContainerRequirement": {"properties": {"type": {"const": "container", "title": "Type", "type": "string"}, "container": {"$ref": "#/$defs/Container"}}, "required": ["type", "container"], "title": "ContainerRequirement", "type": "object"}, "EmptyFieldParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "empty_field", "default": "empty_field", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "EmptyFieldParameterValidatorModel", "type": "object"}, "FilePatternDatasetCollectionDescription": {"properties": {"discover_via": {"const": "pattern", "default": "pattern", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}, "sort_key": {"default": "filename", "enum": ["filename", "name", "designation", "dbkey"], "title": "Sort Key", "type": "string"}, "sort_comp": {"default": "lexical", "enum": ["lexical", "numeric"], "title": "Sort Comp", "type": "string"}, "sort_reverse": {"default": false, "title": "Sort Reverse", "type": "boolean"}, "pattern": {"title": "Pattern", "type": "string"}}, "required": ["pattern"], "title": "FilePatternDatasetCollectionDescription", "type": "object"}, "HelpContent": {"properties": {"format": {"enum": ["restructuredtext", "plain_text", "markdown"], "title": "Format", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["format", "content"], "title": "HelpContent", "type": "object"}, "InRangeParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "in_range", "default": "in_range", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "exclude_min": {"default": false, "title": "Exclude Min", "type": "boolean"}, "exclude_max": {"default": false, "title": "Exclude Max", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "InRangeParameterValidatorModel", "type": "object"}, "IncomingToolOutputBoolean": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "boolean", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputBoolean", "type": "object"}, "IncomingToolOutputCollection": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "collection_type_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type Source"}, "collection_type_from_rules": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type From Rules"}, "structured_like": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Structured Like"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}}, "required": ["type"], "title": "IncomingToolOutputCollection", "type": "object"}, "IncomingToolOutputDataset": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The short name for the output datatype.", "title": "Format"}, "format_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.", "title": "Format Source"}, "metadata_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This copies the metadata information from the tool\u2019s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.", "title": "Metadata Source"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}, "from_work_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Relative path to a file produced by the tool in its working directory. Output\u2019s contents are set to this file\u2019s contents.", "title": "from_work_dir"}, "precreate_directory": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Precreate Directory"}}, "required": ["type"], "title": "IncomingToolOutputDataset", "type": "object"}, "IncomingToolOutputFloat": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "float", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputFloat", "type": "object"}, "IncomingToolOutputInteger": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "integer", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputInteger", "type": "object"}, "IncomingToolOutputText": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "text", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputText", "type": "object"}, "JavascriptRequirement": {"properties": {"type": {"const": "javascript", "title": "Type", "type": "string"}, "expression_lib": {"anyOf": [{"items": {"description": "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.", "examples": ["function pickValue() {\n    if (inputs.conditional_parameter.test_parameter == \"a\") {\n        return inputs.conditional_parameter.integer_parameter\n    } else {\n        return inputs.conditional_parameter.boolean_parameter\n    }\n}"], "title": "expression_lib", "type": "string"}, "type": "array"}, {"type": "null"}], "title": "Expression Lib"}}, "required": ["type", "expression_lib"], "title": "JavascriptRequirement", "type": "object"}, "LengthParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "length", "default": "length", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "LengthParameterValidatorModel", "type": "object"}, "NoOptionsParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "no_options", "default": "no_options", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "NoOptionsParameterValidatorModel", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RegexParameterValidatorModel": {"additionalProperties": false, "description": "Check if a regular expression **matches** the value, i.e. appears\nat the beginning of the value. To enforce a match of the complete value use\n``$`` at the end of the expression. The expression is given is the content\nof the validator tag. Note that for ``selects`` each option is checked\nseparately.", "properties": {"type": {"const": "regex", "default": "regex", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}, "expression": {"title": "Expression", "type": "string"}}, "required": ["expression"], "title": "RegexParameterValidatorModel", "type": "object"}, "ResourceRequirement": {"properties": {"type": {"const": "resource", "title": "Type", "type": "string"}, "cores_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 1, "description": "Minimum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Min"}, "cores_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Max"}, "ram_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 256, "description": "Minimum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Min"}, "ram_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Max"}, "tmpdir_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Min"}, "tmpdir_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Max"}, "cuda_version_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Version Min"}, "cuda_compute_capability": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Compute Capability"}, "gpu_memory_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Gpu Memory Min"}, "cuda_device_count_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Min"}, "cuda_device_count_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Max"}, "shm_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Shm Size"}, "timelimit": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum time in seconds the tool is allowed to run. Job will be terminated if exceeded.", "title": "Timelimit"}}, "required": ["type"], "title": "ResourceRequirement", "type": "object"}, "TestCollectionCollectionElementAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}}, "title": "TestCollectionCollectionElementAssertions", "type": "object"}, "TestCollectionDatasetElementAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestCollectionDatasetElementAssertions", "type": "object"}, "TestCollectionOutputAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}, "element_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Element Count"}, "attributes": {"anyOf": [{"$ref": "#/$defs/CollectionAttributes"}, {"type": "null"}], "default": null, "title": "Attributes"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "TestCollectionOutputAssertions", "type": "object"}, "TestDataOutputAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestDataOutputAssertions", "type": "object"}, "ToolProvidedMetadataDatasetCollection": {"properties": {"discover_via": {"const": "tool_provided_metadata", "default": "tool_provided_metadata", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}}, "title": "ToolProvidedMetadataDatasetCollection", "type": "object"}, "XrefDict": {"additionalProperties": false, "properties": {"value": {"title": "value", "type": "string"}, "type": {"title": "type", "type": "string"}}, "required": ["value", "type"], "title": "XrefDict", "type": "object"}, "YamlBooleanParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "boolean", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Value"}}, "required": ["name", "type"], "title": "YamlBooleanParameter", "type": "object"}, "YamlColorParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "color", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}}, "required": ["name", "type"], "title": "YamlColorParameter", "type": "object"}, "YamlConditionalParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "conditional", "title": "Type", "type": "string"}, "test_parameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "select": "#/$defs/YamlSelectParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}], "title": "Test Parameter"}, "whens": {"items": {"$ref": "#/$defs/YamlConditionalWhen"}, "minItems": 1, "title": "Whens", "type": "array"}}, "required": ["name", "type", "test_parameter", "whens"], "title": "YamlConditionalParameter", "type": "object"}, "YamlConditionalWhen": {"additionalProperties": false, "properties": {"discriminator": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "title": "Discriminator"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["discriminator"], "title": "YamlConditionalWhen", "type": "object"}, "YamlDataCollectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data_collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}}, "required": ["name", "type"], "title": "YamlDataCollectionParameter", "type": "object"}, "YamlDataParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}, "multiple": {"default": false, "description": "Set true to accept several datasets (a list) for this input instead of one.", "title": "Multiple", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. Do NOT set this for a single-dataset input -- a data input is already required by default, so leave 'min' unset unless the input accepts multiple datasets.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; leave unset for a single-dataset input.", "title": "Max"}}, "required": ["name", "type"], "title": "YamlDataParameter", "type": "object"}, "YamlFloatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "float", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlFloatParameter", "type": "object"}, "YamlGalaxyToolParameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "color": "#/$defs/YamlColorParameter", "conditional": "#/$defs/YamlConditionalParameter", "data": "#/$defs/YamlDataParameter", "data_collection": "#/$defs/YamlDataCollectionParameter", "float": "#/$defs/YamlFloatParameter", "integer": "#/$defs/YamlIntegerParameter", "repeat": "#/$defs/YamlRepeatParameter", "section": "#/$defs/YamlSectionParameter", "select": "#/$defs/YamlSelectParameter", "text": "#/$defs/YamlTextParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlIntegerParameter"}, {"$ref": "#/$defs/YamlFloatParameter"}, {"$ref": "#/$defs/YamlTextParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}, {"$ref": "#/$defs/YamlColorParameter"}, {"$ref": "#/$defs/YamlDataParameter"}, {"$ref": "#/$defs/YamlDataCollectionParameter"}, {"$ref": "#/$defs/YamlConditionalParameter"}, {"$ref": "#/$defs/YamlRepeatParameter"}, {"$ref": "#/$defs/YamlSectionParameter"}], "title": "YamlGalaxyToolParameter"}, "YamlIntegerParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "integer", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlIntegerParameter", "type": "object"}, "YamlLabelValue": {"description": "YAML-friendly option model \u2014 ``selected`` defaults to ``False``.", "properties": {"label": {"title": "Label", "type": "string"}, "value": {"title": "Value", "type": "string"}, "selected": {"default": false, "title": "Selected", "type": "boolean"}}, "required": ["label", "value"], "title": "YamlLabelValue", "type": "object"}, "YamlRepeatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "repeat", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}}, "required": ["name", "type"], "title": "YamlRepeatParameter", "type": "object"}, "YamlSectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "section", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["name", "type"], "title": "YamlSectionParameter", "type": "object"}, "YamlSelectParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "select", "title": "Type", "type": "string"}, "options": {"items": {"$ref": "#/$defs/YamlLabelValue"}, "minItems": 1, "title": "Options", "type": "array"}, "multiple": {"default": false, "title": "Multiple", "type": "boolean"}, "validators": {"default": [], "items": {"$ref": "#/$defs/NoOptionsParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type", "options"], "title": "YamlSelectParameter", "type": "object"}, "YamlTemplateConfigFile": {"properties": {"content": {"title": "Content", "type": "string"}, "name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Name"}, "filename": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Filename"}, "eval_engine": {"const": "ecmascript", "default": "ecmascript", "title": "Eval Engine", "type": "string"}}, "required": ["content"], "title": "YamlTemplateConfigFile", "type": "object"}, "YamlTestCredential": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credentials group.", "title": "Name", "type": "string"}, "variables": {"default": [], "description": "Variables exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Variables", "type": "array"}, "secrets": {"default": [], "description": "Secrets exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Secrets", "type": "array"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Version of the credential definition.", "title": "Version"}}, "required": ["name"], "title": "YamlTestCredential", "type": "object"}, "YamlTestCredentialValue": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credential variable or secret.", "title": "Name", "type": "string"}, "value": {"description": "Value of the credential variable or secret.", "title": "Value", "type": "string"}}, "required": ["name", "value"], "title": "YamlTestCredentialValue", "type": "object"}, "YamlTextParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "text", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}, "area": {"default": false, "title": "Area", "type": "boolean"}, "validators": {"default": [], "items": {"anyOf": [{"$ref": "#/$defs/LengthParameterValidatorModel"}, {"$ref": "#/$defs/RegexParameterValidatorModel"}, {"$ref": "#/$defs/EmptyFieldParameterValidatorModel"}]}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlTextParameter", "type": "object"}, "YamlToolTest": {"additionalProperties": false, "description": "In-tool test case as authored in YAML tool fixtures.", "properties": {"doc": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Human-readable description of this test case.", "title": "Doc"}, "inputs": {"anyOf": [{"additionalProperties": {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}, {"items": {}, "type": "array"}, {"additionalProperties": true, "type": "object"}]}, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of input parameter names to test values.", "title": "Inputs"}, "outputs": {"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionOutputAssertions"}, {"$ref": "#/$defs/TestDataOutputAssertions"}, {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}]}]}, "default": {}, "description": "Mapping of output names to expected values or assertions.", "title": "Outputs", "type": "object"}, "assert_stdout": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard output.", "title": "Assert Stdout"}, "assert_stderr": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard error.", "title": "Assert Stderr"}, "command": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the executed command line.", "title": "Command"}, "expect_exit_code": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected process exit code.", "title": "Expect Exit Code"}, "expect_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the tool is expected to produce an error.", "title": "Expect Failure"}, "expect_test_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the test itself is expected to fail.", "title": "Expect Test Failure"}, "credentials": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTestCredential"}, "type": "array"}, {"type": "null"}], "default": null, "description": "Credentials to inject for this test case.", "title": "Credentials"}}, "title": "YamlToolTest", "type": "object"}, "assertion_dict": {"additionalProperties": false, "properties": {"has_line": {"anyOf": [{"$ref": "#/$defs/base_has_line_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line"}, "has_line_matching": {"anyOf": [{"$ref": "#/$defs/base_has_line_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line Matching"}, "has_n_lines": {"anyOf": [{"$ref": "#/$defs/base_has_n_lines_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Lines"}, "has_text": {"anyOf": [{"$ref": "#/$defs/base_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text"}, "has_text_matching": {"anyOf": [{"$ref": "#/$defs/base_has_text_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text Matching"}, "not_has_text": {"anyOf": [{"$ref": "#/$defs/base_not_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Not Has Text"}, "has_n_columns": {"anyOf": [{"$ref": "#/$defs/base_has_n_columns_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Columns"}, "attribute_is": {"anyOf": [{"$ref": "#/$defs/base_attribute_is_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Is"}, "attribute_matches": {"anyOf": [{"$ref": "#/$defs/base_attribute_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Matches"}, "element_text": {"anyOf": [{"$ref": "#/$defs/base_element_text_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text"}, "element_text_is": {"anyOf": [{"$ref": "#/$defs/base_element_text_is_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Is"}, "element_text_matches": {"anyOf": [{"$ref": "#/$defs/base_element_text_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Matches"}, "has_element_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_element_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has Element With Path"}, "has_n_elements_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_n_elements_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Elements With Path"}, "is_valid_xml": {"anyOf": [{"$ref": "#/$defs/base_is_valid_xml_model"}, {"type": "null"}], "default": null, "title": "Assert Is Valid Xml"}, "xml_element": {"anyOf": [{"$ref": "#/$defs/base_xml_element_model"}, {"type": "null"}], "default": null, "title": "Assert Xml Element"}, "has_json_property_with_text": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Text"}, "has_json_property_with_value": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_value_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Value"}, "has_h5_attribute": {"anyOf": [{"$ref": "#/$defs/base_has_h5_attribute_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Attribute"}, "has_h5_keys": {"anyOf": [{"$ref": "#/$defs/base_has_h5_keys_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Keys"}, "has_archive_member": {"anyOf": [{"$ref": "#/$defs/base_has_archive_member_model"}, {"type": "null"}], "default": null, "title": "Assert Has Archive Member"}, "has_size": {"anyOf": [{"$ref": "#/$defs/base_has_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Size"}, "has_image_center_of_mass": {"anyOf": [{"$ref": "#/$defs/base_has_image_center_of_mass_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Center Of Mass"}, "has_image_channels": {"anyOf": [{"$ref": "#/$defs/base_has_image_channels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Channels"}, "has_image_depth": {"anyOf": [{"$ref": "#/$defs/base_has_image_depth_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Depth"}, "has_image_frames": {"anyOf": [{"$ref": "#/$defs/base_has_image_frames_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Frames"}, "has_image_height": {"anyOf": [{"$ref": "#/$defs/base_has_image_height_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Height"}, "has_image_mean_intensity": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_intensity_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Intensity"}, "has_image_mean_object_size": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_object_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Object Size"}, "has_image_n_labels": {"anyOf": [{"$ref": "#/$defs/base_has_image_n_labels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image N Labels"}, "has_image_width": {"anyOf": [{"$ref": "#/$defs/base_has_image_width_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Width"}}, "title": "assertion_dict", "type": "object"}, "assertion_list": {"items": {"anyOf": [{"discriminator": {"mapping": {"attribute_is": "#/$defs/attribute_is_model", "attribute_matches": "#/$defs/attribute_matches_model", "element_text": "#/$defs/element_text_model", "element_text_is": "#/$defs/element_text_is_model", "element_text_matches": "#/$defs/element_text_matches_model", "has_archive_member": "#/$defs/has_archive_member_model", "has_element_with_path": "#/$defs/has_element_with_path_model", "has_h5_attribute": "#/$defs/has_h5_attribute_model", "has_h5_keys": "#/$defs/has_h5_keys_model", "has_image_center_of_mass": "#/$defs/has_image_center_of_mass_model", "has_image_channels": "#/$defs/has_image_channels_model", "has_image_depth": "#/$defs/has_image_depth_model", "has_image_frames": "#/$defs/has_image_frames_model", "has_image_height": "#/$defs/has_image_height_model", "has_image_mean_intensity": "#/$defs/has_image_mean_intensity_model", "has_image_mean_object_size": "#/$defs/has_image_mean_object_size_model", "has_image_n_labels": "#/$defs/has_image_n_labels_model", "has_image_width": "#/$defs/has_image_width_model", "has_json_property_with_text": "#/$defs/has_json_property_with_text_model", "has_json_property_with_value": "#/$defs/has_json_property_with_value_model", "has_line": "#/$defs/has_line_model", "has_line_matching": "#/$defs/has_line_matching_model", "has_n_columns": "#/$defs/has_n_columns_model", "has_n_elements_with_path": "#/$defs/has_n_elements_with_path_model", "has_n_lines": "#/$defs/has_n_lines_model", "has_size": "#/$defs/has_size_model", "has_text": "#/$defs/has_text_model", "has_text_matching": "#/$defs/has_text_matching_model", "is_valid_xml": "#/$defs/is_valid_xml_model", "not_has_text": "#/$defs/not_has_text_model", "xml_element": "#/$defs/xml_element_model"}, "propertyName": "that"}, "oneOf": [{"$ref": "#/$defs/has_line_model"}, {"$ref": "#/$defs/has_line_matching_model"}, {"$ref": "#/$defs/has_n_lines_model"}, {"$ref": "#/$defs/has_text_model"}, {"$ref": "#/$defs/has_text_matching_model"}, {"$ref": "#/$defs/not_has_text_model"}, {"$ref": "#/$defs/has_n_columns_model"}, {"$ref": "#/$defs/attribute_is_model"}, {"$ref": "#/$defs/attribute_matches_model"}, {"$ref": "#/$defs/element_text_model"}, {"$ref": "#/$defs/element_text_is_model"}, {"$ref": "#/$defs/element_text_matches_model"}, {"$ref": "#/$defs/has_element_with_path_model"}, {"$ref": "#/$defs/has_n_elements_with_path_model"}, {"$ref": "#/$defs/is_valid_xml_model"}, {"$ref": "#/$defs/xml_element_model"}, {"$ref": "#/$defs/has_json_property_with_text_model"}, {"$ref": "#/$defs/has_json_property_with_value_model"}, {"$ref": "#/$defs/has_h5_attribute_model"}, {"$ref": "#/$defs/has_h5_keys_model"}, {"$ref": "#/$defs/has_archive_member_model"}, {"$ref": "#/$defs/has_size_model"}, {"$ref": "#/$defs/has_image_center_of_mass_model"}, {"$ref": "#/$defs/has_image_channels_model"}, {"$ref": "#/$defs/has_image_depth_model"}, {"$ref": "#/$defs/has_image_frames_model"}, {"$ref": "#/$defs/has_image_height_model"}, {"$ref": "#/$defs/has_image_mean_intensity_model"}, {"$ref": "#/$defs/has_image_mean_object_size_model"}, {"$ref": "#/$defs/has_image_n_labels_model"}, {"$ref": "#/$defs/has_image_width_model"}]}, {"$ref": "#/$defs/has_line_model_nested"}, {"$ref": "#/$defs/has_line_matching_model_nested"}, {"$ref": "#/$defs/has_n_lines_model_nested"}, {"$ref": "#/$defs/has_text_model_nested"}, {"$ref": "#/$defs/has_text_matching_model_nested"}, {"$ref": "#/$defs/not_has_text_model_nested"}, {"$ref": "#/$defs/has_n_columns_model_nested"}, {"$ref": "#/$defs/attribute_is_model_nested"}, {"$ref": "#/$defs/attribute_matches_model_nested"}, {"$ref": "#/$defs/element_text_model_nested"}, {"$ref": "#/$defs/element_text_is_model_nested"}, {"$ref": "#/$defs/element_text_matches_model_nested"}, {"$ref": "#/$defs/has_element_with_path_model_nested"}, {"$ref": "#/$defs/has_n_elements_with_path_model_nested"}, {"$ref": "#/$defs/is_valid_xml_model_nested"}, {"$ref": "#/$defs/xml_element_model_nested"}, {"$ref": "#/$defs/has_json_property_with_text_model_nested"}, {"$ref": "#/$defs/has_json_property_with_value_model_nested"}, {"$ref": "#/$defs/has_h5_attribute_model_nested"}, {"$ref": "#/$defs/has_h5_keys_model_nested"}, {"$ref": "#/$defs/has_archive_member_model_nested"}, {"$ref": "#/$defs/has_size_model_nested"}, {"$ref": "#/$defs/has_image_center_of_mass_model_nested"}, {"$ref": "#/$defs/has_image_channels_model_nested"}, {"$ref": "#/$defs/has_image_depth_model_nested"}, {"$ref": "#/$defs/has_image_frames_model_nested"}, {"$ref": "#/$defs/has_image_height_model_nested"}, {"$ref": "#/$defs/has_image_mean_intensity_model_nested"}, {"$ref": "#/$defs/has_image_mean_object_size_model_nested"}, {"$ref": "#/$defs/has_image_n_labels_model_nested"}, {"$ref": "#/$defs/has_image_width_model_nested"}]}, "title": "assertion_list", "type": "array"}, "attribute_is_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` is the specified ``text``.\n\nFor example:\n\n```xml\n<attribute_is path=\"outerElement/innerElement1\" attribute=\"foo\" text=\"bar\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_is", "default": "attribute_is", "title": "That", "type": "string"}}, "required": ["path", "attribute", "text"], "title": "Assert Attribute Is", "type": "object"}, "attribute_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_is": {"$ref": "#/$defs/base_attribute_is_model", "title": "Assert Attribute Is"}}, "required": ["attribute_is"], "title": "Assert Attribute Is (Nested)", "type": "object"}, "attribute_matches_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` matches the regular expression specified by ``expression``.\n\nFor example:\n\n```xml\n<attribute_matches path=\"outerElement/innerElement2\" attribute=\"foo2\" expression=\"bar\\d+\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_matches", "default": "attribute_matches", "title": "That", "type": "string"}}, "required": ["path", "attribute", "expression"], "title": "Assert Attribute Matches", "type": "object"}, "attribute_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_matches": {"$ref": "#/$defs/base_attribute_matches_model", "title": "Assert Attribute Matches"}}, "required": ["attribute_matches"], "title": "Assert Attribute Matches (Nested)", "type": "object"}, "base_attribute_is_model": {"additionalProperties": false, "description": "base model for attribute_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "text"], "title": "base_attribute_is_model", "type": "object"}, "base_attribute_matches_model": {"additionalProperties": false, "description": "base model for attribute_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "expression"], "title": "base_attribute_matches_model", "type": "object"}, "base_element_text_is_model": {"additionalProperties": false, "description": "base model for element_text_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "text"], "title": "base_element_text_is_model", "type": "object"}, "base_element_text_matches_model": {"additionalProperties": false, "description": "base model for element_text_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "expression"], "title": "base_element_text_matches_model", "type": "object"}, "base_element_text_model": {"additionalProperties": false, "description": "base model for element_text describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_element_text_model", "type": "object"}, "base_has_archive_member_model": {"additionalProperties": false, "description": "base model for has_archive_member describing attributes.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_has_archive_member_model", "type": "object"}, "base_has_element_with_path_model": {"additionalProperties": false, "description": "base model for has_element_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_element_with_path_model", "type": "object"}, "base_has_h5_attribute_model": {"additionalProperties": false, "description": "base model for has_h5_attribute describing attributes.", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}}, "required": ["key", "value"], "title": "base_has_h5_attribute_model", "type": "object"}, "base_has_h5_keys_model": {"additionalProperties": false, "description": "base model for has_h5_keys describing attributes.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}}, "required": ["keys"], "title": "base_has_h5_keys_model", "type": "object"}, "base_has_image_center_of_mass_model": {"additionalProperties": false, "description": "base model for has_image_center_of_mass describing attributes.", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}}, "required": ["center_of_mass"], "title": "base_has_image_center_of_mass_model", "type": "object"}, "base_has_image_channels_model": {"additionalProperties": false, "description": "base model for has_image_channels describing attributes.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_channels_model", "type": "object"}, "base_has_image_depth_model": {"additionalProperties": false, "description": "base model for has_image_depth describing attributes.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_depth_model", "type": "object"}, "base_has_image_frames_model": {"additionalProperties": false, "description": "base model for has_image_frames describing attributes.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_frames_model", "type": "object"}, "base_has_image_height_model": {"additionalProperties": false, "description": "base model for has_image_height describing attributes.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_height_model", "type": "object"}, "base_has_image_mean_intensity_model": {"additionalProperties": false, "description": "base model for has_image_mean_intensity describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}}, "title": "base_has_image_mean_intensity_model", "type": "object"}, "base_has_image_mean_object_size_model": {"additionalProperties": false, "description": "base model for has_image_mean_object_size describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}}, "title": "base_has_image_mean_object_size_model", "type": "object"}, "base_has_image_n_labels_model": {"additionalProperties": false, "description": "base model for has_image_n_labels describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_n_labels_model", "type": "object"}, "base_has_image_width_model": {"additionalProperties": false, "description": "base model for has_image_width describing attributes.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_width_model", "type": "object"}, "base_has_json_property_with_text_model": {"additionalProperties": false, "description": "base model for has_json_property_with_text describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}}, "required": ["property", "text"], "title": "base_has_json_property_with_text_model", "type": "object"}, "base_has_json_property_with_value_model": {"additionalProperties": false, "description": "base model for has_json_property_with_value describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}}, "required": ["property", "value"], "title": "base_has_json_property_with_value_model", "type": "object"}, "base_has_line_matching_model": {"additionalProperties": false, "description": "base model for has_line_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_line_matching_model", "type": "object"}, "base_has_line_model": {"additionalProperties": false, "description": "base model for has_line describing attributes.", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["line"], "title": "base_has_line_model", "type": "object"}, "base_has_n_columns_model": {"additionalProperties": false, "description": "base model for has_n_columns describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_columns_model", "type": "object"}, "base_has_n_elements_with_path_model": {"additionalProperties": false, "description": "base model for has_n_elements_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_n_elements_with_path_model", "type": "object"}, "base_has_n_lines_model": {"additionalProperties": false, "description": "base model for has_n_lines describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_lines_model", "type": "object"}, "base_has_size_model": {"additionalProperties": false, "description": "base model for has_size describing attributes.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_size_model", "type": "object"}, "base_has_text_matching_model": {"additionalProperties": false, "description": "base model for has_text_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_text_matching_model", "type": "object"}, "base_has_text_model": {"additionalProperties": false, "description": "base model for has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["text"], "title": "base_has_text_model", "type": "object"}, "base_is_valid_xml_model": {"additionalProperties": false, "description": "base model for is_valid_xml describing attributes.", "properties": {}, "title": "base_is_valid_xml_model", "type": "object"}, "base_not_has_text_model": {"additionalProperties": false, "description": "base model for not_has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}}, "required": ["text"], "title": "base_not_has_text_model", "type": "object"}, "base_xml_element_model": {"additionalProperties": false, "description": "base model for xml_element describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_xml_element_model", "type": "object"}, "element_text_is_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path`` is\nthe specified ``text``.\n\nFor example:\n\n```xml\n<element_text_is path=\"BlastOutput_program\" text=\"blastp\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_is", "default": "element_text_is", "title": "That", "type": "string"}}, "required": ["path", "text"], "title": "Assert Element Text Is", "type": "object"}, "element_text_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_is": {"$ref": "#/$defs/base_element_text_is_model", "title": "Assert Element Text Is"}}, "required": ["element_text_is"], "title": "Assert Element Text Is (Nested)", "type": "object"}, "element_text_matches_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path``\nmatches the regular expression defined by ``expression``.\n\nFor example:\n\n```xml\n<element_text_matches path=\"BlastOutput_version\" expression=\"BLASTP\\s+2\\.2.*\"/>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_matches", "default": "element_text_matches", "title": "That", "type": "string"}}, "required": ["path", "expression"], "title": "Assert Element Text Matches", "type": "object"}, "element_text_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_matches": {"$ref": "#/$defs/base_element_text_matches_model", "title": "Assert Element Text Matches"}}, "required": ["element_text_matches"], "title": "Assert Element Text Matches (Nested)", "type": "object"}, "element_text_model": {"additionalProperties": false, "description": "This tag allows the developer to recurisively specify additional assertions as\nchild elements about just the text contained in the element specified by the\nXPath-like ``path``, e.g.\n\n```xml\n<element_text path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def\">\n  <not_has_text text=\"EDK72998.1\" />\n</element_text>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the implicit assertions can be inverted.\nThe sub-assertions, which have their own ``negate`` attribute, are not affected\nby ``negate``.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "element_text", "default": "element_text", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Element Text", "type": "object"}, "element_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text": {"$ref": "#/$defs/base_element_text_model", "title": "Assert Element Text"}}, "required": ["element_text"], "title": "Assert Element Text (Nested)", "type": "object"}, "has_archive_member_model": {"additionalProperties": false, "description": "This tag allows to check if ``path`` is contained in a compressed file.\n\nThe path is a regular expression that is matched against the full paths of the objects in\nthe compressed file (remember that \"matching\" means it is checked if a prefix of\nthe full path of an archive member is described by the regular expression).\nValid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that\ndepending on the archive creation method:\n\n- full paths of the members may be prefixed with ``./``\n- directories may be treated as empty files\n\n```xml\n<has_archive_member path=\"./path/to/my-file.txt\"/>\n```\n\nWith ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of\narchive members matching ``path`` can be expressed. The following could be used,\ne.g., to assert an archive containing n&plusmn;1 elements out of which at least\n4 need to have a ``txt`` extension.\n\n```xml\n<has_archive_member path=\".*\" n=\"10\" delta=\"1\"/>\n<has_archive_member path=\".*\\.txt\" min=\"4\"/>\n```\n\nIn addition the tag can contain additional assertions as child elements about\nthe first member in the archive matching the regular expression ``path``. For\ninstance\n\n```xml\n<has_archive_member path=\".*/my-file.txt\">\n  <not_has_text text=\"EDK72998.1\"/>\n</has_archive_member>\n```\n\nIf the ``all`` attribute is set to ``true`` then all archive members are subject\nto the assertions. Note that, archive members matching the ``path`` are sorted\nalphabetically.\n\nThe ``negate`` attribute of the ``has_archive_member`` assertion only affects\nthe asserts on the presence and number of matching archive members, but not any\nsub-assertions (which can offer the ``negate`` attribute on their own).  The\ncheck if the file is an archive at all, which is also done by the function, is\nnot affected.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "has_archive_member", "default": "has_archive_member", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Archive Member", "type": "object"}, "has_archive_member_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_archive_member": {"$ref": "#/$defs/base_has_archive_member_model", "title": "Assert Has Archive Member"}}, "required": ["has_archive_member"], "title": "Assert Has Archive Member (Nested)", "type": "object"}, "has_element_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains at least one element (or tag) with the specified\nXPath-like ``path``, e.g.\n\n```xml\n<has_element_with_path path=\"BlastOutput_param/Parameters/Parameters_matrix\" />\n```\n\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_element_with_path", "default": "has_element_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Element With Path", "type": "object"}, "has_element_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_element_with_path": {"$ref": "#/$defs/base_has_element_with_path_model", "title": "Assert Has Element With Path"}}, "required": ["has_element_with_path"], "title": "Assert Has Element With Path (Nested)", "type": "object"}, "has_h5_attribute_model": {"additionalProperties": false, "description": "Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.\n\n```xml\n<has_h5_attribute key=\"nchroms\" value=\"15\" />\n```", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}, "that": {"const": "has_h5_attribute", "default": "has_h5_attribute", "title": "That", "type": "string"}}, "required": ["key", "value"], "title": "Assert Has H5 Attribute", "type": "object"}, "has_h5_attribute_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_attribute": {"$ref": "#/$defs/base_has_h5_attribute_model", "title": "Assert Has H5 Attribute"}}, "required": ["has_h5_attribute"], "title": "Assert Has H5 Attribute (Nested)", "type": "object"}, "has_h5_keys_model": {"additionalProperties": false, "description": "Asserts the specified HDF5 output has the given keys.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}, "that": {"const": "has_h5_keys", "default": "has_h5_keys", "title": "That", "type": "string"}}, "required": ["keys"], "title": "Assert Has H5 Keys", "type": "object"}, "has_h5_keys_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_keys": {"$ref": "#/$defs/base_has_h5_keys_model", "title": "Assert Has H5 Keys"}}, "required": ["has_h5_keys"], "title": "Assert Has H5 Keys (Nested)", "type": "object"}, "has_image_center_of_mass_model": {"additionalProperties": false, "description": "Asserts the specified output is an image and has the specified center of mass.\n\nAsserts the output is an image and has a specific center of mass,\nor has an Euclidean distance of ``eps`` or less to that point (e.g.,\n``<has_image_center_of_mass center_of_mass=\"511.07, 223.34\" />``).", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}, "that": {"const": "has_image_center_of_mass", "default": "has_image_center_of_mass", "title": "That", "type": "string"}}, "required": ["center_of_mass"], "title": "Assert Has Image Center Of Mass", "type": "object"}, "has_image_center_of_mass_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_center_of_mass": {"$ref": "#/$defs/base_has_image_center_of_mass_model", "title": "Assert Has Image Center Of Mass"}}, "required": ["has_image_center_of_mass"], "title": "Assert Has Image Center Of Mass (Nested)", "type": "object"}, "has_image_channels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of channels.\n\nThe number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels=\"3\" />``).\n\nAlternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_channels", "default": "has_image_channels", "title": "That", "type": "string"}}, "title": "Assert Has Image Channels", "type": "object"}, "has_image_channels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_channels": {"$ref": "#/$defs/base_has_image_channels_model", "title": "Assert Has Image Channels"}}, "required": ["has_image_channels"], "title": "Assert Has Image Channels (Nested)", "type": "object"}, "has_image_depth_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific depth (number of slices).\n\nThe depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected depth can be specified by ``min`` and/or ``max``.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_depth", "default": "has_image_depth", "title": "That", "type": "string"}}, "title": "Assert Has Image Depth", "type": "object"}, "has_image_depth_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_depth": {"$ref": "#/$defs/base_has_image_depth_model", "title": "Assert Has Image Depth"}}, "required": ["has_image_depth"], "title": "Assert Has Image Depth (Nested)", "type": "object"}, "has_image_frames_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of frames (number of time steps).\n\nThe number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_frames", "default": "has_image_frames", "title": "That", "type": "string"}}, "title": "Assert Has Image Frames", "type": "object"}, "has_image_frames_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_frames": {"$ref": "#/$defs/base_has_image_frames_model", "title": "Assert Has Image Frames"}}, "required": ["has_image_frames"], "title": "Assert Has Image Frames (Nested)", "type": "object"}, "has_image_height_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific height (in pixels).\n\nThe height is plus/minus ``delta`` (e.g., ``<has_image_height height=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected height can be specified by ``min`` and/or ``max``.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_height", "default": "has_image_height", "title": "That", "type": "string"}}, "title": "Assert Has Image Height", "type": "object"}, "has_image_height_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_height": {"$ref": "#/$defs/base_has_image_height_model", "title": "Assert Has Image Height"}}, "required": ["has_image_height"], "title": "Assert Has Image Height (Nested)", "type": "object"}, "has_image_mean_intensity_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific mean intensity value.\n\nThe mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity=\"0.83\" />``).\nAlternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}, "that": {"const": "has_image_mean_intensity", "default": "has_image_mean_intensity", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Intensity", "type": "object"}, "has_image_mean_intensity_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_intensity": {"$ref": "#/$defs/base_has_image_mean_intensity_model", "title": "Assert Has Image Mean Intensity"}}, "required": ["has_image_mean_intensity"], "title": "Assert Has Image Mean Intensity (Nested)", "type": "object"}, "has_image_mean_object_size_model": {"additionalProperties": false, "description": "Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),\n\nThe mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size=\"111.87\" exclude_labels=\"0\" />``).\n\nThe labels must be unique.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}, "that": {"const": "has_image_mean_object_size", "default": "has_image_mean_object_size", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Object Size", "type": "object"}, "has_image_mean_object_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_object_size": {"$ref": "#/$defs/base_has_image_mean_object_size_model", "title": "Assert Has Image Mean Object Size"}}, "required": ["has_image_mean_object_size"], "title": "Assert Has Image Mean Object Size (Nested)", "type": "object"}, "has_image_n_labels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has the specified labels.\n\nLabels can be a number of labels or unique values (e.g.,\n``<has_image_n_labels n=\"187\" exclude_labels=\"0\" />``).\n\nThe primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_n_labels", "default": "has_image_n_labels", "title": "That", "type": "string"}}, "title": "Assert Has Image N Labels", "type": "object"}, "has_image_n_labels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_n_labels": {"$ref": "#/$defs/base_has_image_n_labels_model", "title": "Assert Has Image N Labels"}}, "required": ["has_image_n_labels"], "title": "Assert Has Image N Labels (Nested)", "type": "object"}, "has_image_width_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific width (in pixels).\n\nThe width is plus/minus ``delta`` (e.g., ``<has_image_width width=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected width can be specified by ``min`` and/or ``max``.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_width", "default": "has_image_width", "title": "That", "type": "string"}}, "title": "Assert Has Image Width", "type": "object"}, "has_image_width_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_width": {"$ref": "#/$defs/base_has_image_width_model", "title": "Assert Has Image Width"}}, "required": ["has_image_width"], "title": "Assert Has Image Width (Nested)", "type": "object"}, "has_json_property_with_text_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified text (i.e. string) value.\n\n```xml\n<has_json_property_with_text property=\"color\" text=\"red\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}, "that": {"const": "has_json_property_with_text", "default": "has_json_property_with_text", "title": "That", "type": "string"}}, "required": ["property", "text"], "title": "Assert Has Json Property With Text", "type": "object"}, "has_json_property_with_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_text": {"$ref": "#/$defs/base_has_json_property_with_text_model", "title": "Assert Has Json Property With Text"}}, "required": ["has_json_property_with_text"], "title": "Assert Has Json Property With Text (Nested)", "type": "object"}, "has_json_property_with_value_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified JSON value.\n\n```xml\n<has_json_property_with_value property=\"skipped_columns\" value=\"[1, 3, 5]\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}, "that": {"const": "has_json_property_with_value", "default": "has_json_property_with_value", "title": "That", "type": "string"}}, "required": ["property", "value"], "title": "Assert Has Json Property With Value", "type": "object"}, "has_json_property_with_value_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_value": {"$ref": "#/$defs/base_has_json_property_with_value_model", "title": "Assert Has Json Property With Value"}}, "required": ["has_json_property_with_value"], "title": "Assert Has Json Property With Value (Nested)", "type": "object"}, "has_line_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains a line matching the\nregular expression specified by the argument expression. If n is given\nthe assertion checks for exactly n occurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line_matching", "default": "has_line_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Line Matching", "type": "object"}, "has_line_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line_matching": {"$ref": "#/$defs/base_has_line_matching_model", "title": "Assert Has Line Matching"}}, "required": ["has_line_matching"], "title": "Assert Has Line Matching (Nested)", "type": "object"}, "has_line_model": {"additionalProperties": false, "description": "Asserts the specified output contains the line specified by the\nargument line. The exact number of occurrences can be optionally\nspecified by the argument n", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line", "default": "has_line", "title": "That", "type": "string"}}, "required": ["line"], "title": "Assert Has Line", "type": "object"}, "has_line_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line": {"$ref": "#/$defs/base_has_line_model", "title": "Assert Has Line"}}, "required": ["has_line"], "title": "Assert Has Line (Nested)", "type": "object"}, "has_n_columns_model": {"additionalProperties": false, "description": "Asserts tabular output  contains the specified\nnumber (``n``) of columns.\n\nFor instance, ``<has_n_columns n=\"3\"/>``. The assertion tests only the first line.\nNumber of columns can optionally also be specified with ``delta``. Alternatively the\nrange of expected occurrences can be specified by ``min`` and/or ``max``.\n\nOptionally a column separator (``sep``, default is ``       ``) `and comment character(s)\ncan be specified (``comment``, default is empty string). The first non-comment\nline is used for determining the number of columns.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_columns", "default": "has_n_columns", "title": "That", "type": "string"}}, "title": "Assert Has N Columns", "type": "object"}, "has_n_columns_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_columns": {"$ref": "#/$defs/base_has_n_columns_model", "title": "Assert Has N Columns"}}, "required": ["has_n_columns"], "title": "Assert Has N Columns (Nested)", "type": "object"}, "has_n_elements_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or\ntags) with the specified XPath-like ``path``.\n\nFor example:\n\n```xml\n<has_n_elements_with_path n=\"9\" path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num\" />\n```\n\nAlternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes\ncan be used to specify the range of the expected number of occurrences.\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_elements_with_path", "default": "has_n_elements_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has N Elements With Path", "type": "object"}, "has_n_elements_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_elements_with_path": {"$ref": "#/$defs/base_has_n_elements_with_path_model", "title": "Assert Has N Elements With Path"}}, "required": ["has_n_elements_with_path"], "title": "Assert Has N Elements With Path (Nested)", "type": "object"}, "has_n_lines_model": {"additionalProperties": false, "description": "Asserts the specified output contains ``n`` lines allowing\nfor a difference in the number of lines (delta)\nor relative differebce in the number of lines", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_lines", "default": "has_n_lines", "title": "That", "type": "string"}}, "title": "Assert Has N Lines", "type": "object"}, "has_n_lines_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_lines": {"$ref": "#/$defs/base_has_n_lines_model", "title": "Assert Has N Lines"}}, "required": ["has_n_lines"], "title": "Assert Has N Lines (Nested)", "type": "object"}, "has_size_model": {"additionalProperties": false, "description": "Asserts the specified output has a size of the specified value\n\nAttributes size and value or synonyms though value is considered deprecated.\nThe size optionally allows for absolute (``delta``) difference.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_size", "default": "has_size", "title": "That", "type": "string"}}, "title": "Assert Has Size", "type": "object"}, "has_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_size": {"$ref": "#/$defs/base_has_size_model", "title": "Assert Has Size"}}, "required": ["has_size"], "title": "Assert Has Size (Nested)", "type": "object"}, "has_text_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains text matching the\nregular expression specified by the argument expression.\nIf n is given the assertion checks for exactly n (nonoverlapping)\noccurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text_matching", "default": "has_text_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Text Matching", "type": "object"}, "has_text_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text_matching": {"$ref": "#/$defs/base_has_text_matching_model", "title": "Assert Has Text Matching"}}, "required": ["has_text_matching"], "title": "Assert Has Text Matching (Nested)", "type": "object"}, "has_text_model": {"additionalProperties": false, "description": "Asserts specified output contains the substring specified by\nthe argument text. The exact number of occurrences can be\noptionally specified by the argument n", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text", "default": "has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Has Text", "type": "object"}, "has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text": {"$ref": "#/$defs/base_has_text_model", "title": "Assert Has Text"}}, "required": ["has_text"], "title": "Assert Has Text (Nested)", "type": "object"}, "is_valid_xml_model": {"additionalProperties": false, "description": "Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).", "properties": {"that": {"const": "is_valid_xml", "default": "is_valid_xml", "title": "That", "type": "string"}}, "title": "Assert Is Valid Xml", "type": "object"}, "is_valid_xml_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"is_valid_xml": {"$ref": "#/$defs/base_is_valid_xml_model", "title": "Assert Is Valid Xml"}}, "required": ["is_valid_xml"], "title": "Assert Is Valid Xml (Nested)", "type": "object"}, "not_has_text_model": {"additionalProperties": false, "description": "Asserts specified output does not contain the substring\nspecified by the argument text", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "that": {"const": "not_has_text", "default": "not_has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Not Has Text", "type": "object"}, "not_has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"not_has_text": {"$ref": "#/$defs/base_not_has_text_model", "title": "Assert Not Has Text"}}, "required": ["not_has_text"], "title": "Assert Not Has Text (Nested)", "type": "object"}, "xml_element_model": {"additionalProperties": false, "description": "Assert if the XML file contains element(s) or tag(s) with the specified\n[XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``\nor ``min`` and ``max`` are given also the number of occurrences is checked.\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem\"/>\n  <xml_element path=\"./elem/more[2]\"/>\n  <xml_element path=\".//more\" n=\"3\" delta=\"1\"/>\n</assert_contents>\n```\n\nWith ``negate=\"true\"`` the outcome of the assertions wrt the presence and number\nof ``path`` can be negated. If there are any sub assertions then check them against\n\n- the content of the attribute ``attribute``\n- the element's text if no attribute is given\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem/more[2]\" attribute=\"name\">\n    <has_text_matching expression=\"foo$\"/>\n  </xml_element>\n</assert_contents>\n```\n\nSub-assertions are not subject to the ``negate`` attribute of ``xml_element``.\nIf ``all`` is ``true`` then the sub assertions are checked for all occurrences.\n\nNote that all other XML assertions can be expressed by this assertion (Galaxy\nalso implements the other assertions by calling this one).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "xml_element", "default": "xml_element", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Xml Element", "type": "object"}, "xml_element_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"xml_element": {"$ref": "#/$defs/base_xml_element_model", "title": "Assert Xml Element"}}, "required": ["xml_element"], "title": "Assert Xml Element (Nested)", "type": "object"}}, "additionalProperties": false, "description": "Full unprivileged tool source, including the optional ``tests`` block.\n\nThis is the model persisted and validated on the API surface\n(``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring\nuses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added\nback here so direct authors and stored rows can still carry tests.", "properties": {"id": {"anyOf": [{"maxLength": 255, "minLength": 3, "pattern": "^[a-z][a-z0-9_-]*$", "type": "string"}, {"type": "null"}], "default": null, "description": "Unique identifier for the tool. Lowercase, must start with a letter, may contain letters, digits, '_' and '-'.", "examples": ["my-cool-tool"], "title": "id"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "version"}, "name": {"description": "The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.", "minLength": 5, "title": "name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The description is displayed in the tool menu immediately following the hyperlink for the tool.", "title": "description"}, "configfiles": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTemplateConfigFile"}, "type": "array"}, {"type": "null"}], "default": null, "description": "A list of config files for this tool.", "title": "configfiles"}, "requirements": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/JavascriptRequirement"}, {"$ref": "#/$defs/ResourceRequirement"}, {"$ref": "#/$defs/ContainerRequirement"}]}, "type": "array"}, {"type": "null"}], "default": [], "description": "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.", "title": "requirements"}, "shell_command": {"description": "A string that contains the command to be executed. Parameters can be referenced inside $().", "examples": ["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"], "title": "shell_command", "type": "string"}, "inputs": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "inputs", "type": "array"}, "outputs": {"default": [], "items": {"discriminator": {"mapping": {"boolean": "#/$defs/IncomingToolOutputBoolean", "collection": "#/$defs/IncomingToolOutputCollection", "data": "#/$defs/IncomingToolOutputDataset", "float": "#/$defs/IncomingToolOutputFloat", "integer": "#/$defs/IncomingToolOutputInteger", "text": "#/$defs/IncomingToolOutputText"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/IncomingToolOutputDataset"}, {"$ref": "#/$defs/IncomingToolOutputCollection"}, {"$ref": "#/$defs/IncomingToolOutputText"}, {"$ref": "#/$defs/IncomingToolOutputInteger"}, {"$ref": "#/$defs/IncomingToolOutputFloat"}, {"$ref": "#/$defs/IncomingToolOutputBoolean"}]}, "title": "outputs", "type": "array"}, "citations": {"anyOf": [{"items": {"$ref": "#/$defs/Citation"}, "type": "array"}, {"type": "null"}], "default": null, "title": "citations"}, "license": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.", "examples": ["MIT"], "title": "license"}, "edam_operations": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_operations"}, "edam_topics": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_topics"}, "xrefs": {"anyOf": [{"items": {"$ref": "#/$defs/XrefDict"}, "type": "array"}, {"type": "null"}], "default": null, "title": "xrefs"}, "profile": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "profile"}, "help": {"anyOf": [{"$ref": "#/$defs/HelpContent"}, {"type": "null"}], "default": null, "description": "Help text shown below the tool interface.", "title": "help"}, "class": {"const": "GalaxyUserTool", "title": "class_", "type": "string"}, "container": {"description": "Container image to use for this tool.", "examples": ["quay.io/biocontainers/python:3.13"], "title": "container", "type": "string"}, "tests": {"anyOf": [{"items": {"$ref": "#/$defs/YamlToolTest"}, "type": "array"}, {"type": "null"}], "default": null, "title": "tests"}}, "required": ["name", "shell_command", "class", "container"], "title": "UserToolSource", "type": "object"}
\ No newline at end of file
+{"$defs": {"Citation": {"properties": {"type": {"title": "Type", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["type", "content"], "title": "Citation", "type": "object"}, "CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "Container": {"properties": {"type": {"enum": ["docker", "singularity"], "title": "Type", "type": "string"}, "container_id": {"title": "Container Id", "type": "string"}}, "required": ["type", "container_id"], "title": "Container", "type": "object"}, "ContainerRequirement": {"properties": {"type": {"const": "container", "title": "Type", "type": "string"}, "container": {"$ref": "#/$defs/Container"}}, "required": ["type", "container"], "title": "ContainerRequirement", "type": "object"}, "EmptyFieldParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "empty_field", "default": "empty_field", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "EmptyFieldParameterValidatorModel", "type": "object"}, "FilePatternDatasetCollectionDescription": {"properties": {"discover_via": {"const": "pattern", "default": "pattern", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}, "sort_key": {"default": "filename", "enum": ["filename", "name", "designation", "dbkey"], "title": "Sort Key", "type": "string"}, "sort_comp": {"default": "lexical", "enum": ["lexical", "numeric"], "title": "Sort Comp", "type": "string"}, "sort_reverse": {"default": false, "title": "Sort Reverse", "type": "boolean"}, "pattern": {"title": "Pattern", "type": "string"}}, "required": ["pattern"], "title": "FilePatternDatasetCollectionDescription", "type": "object"}, "HelpContent": {"properties": {"format": {"enum": ["restructuredtext", "plain_text", "markdown"], "title": "Format", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["format", "content"], "title": "HelpContent", "type": "object"}, "InRangeParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "in_range", "default": "in_range", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "exclude_min": {"default": false, "title": "Exclude Min", "type": "boolean"}, "exclude_max": {"default": false, "title": "Exclude Max", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "InRangeParameterValidatorModel", "type": "object"}, "IncomingToolOutputBoolean": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "boolean", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputBoolean", "type": "object"}, "IncomingToolOutputCollection": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "collection_type_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type Source"}, "collection_type_from_rules": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type From Rules"}, "structured_like": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Structured Like"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}}, "required": ["type"], "title": "IncomingToolOutputCollection", "type": "object"}, "IncomingToolOutputDataset": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The short name for the output datatype.", "title": "Format"}, "format_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.", "title": "Format Source"}, "metadata_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This copies the metadata information from the tool\u2019s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.", "title": "Metadata Source"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}, "from_work_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Relative path to a file produced by the tool in its working directory. Output\u2019s contents are set to this file\u2019s contents.", "title": "from_work_dir"}, "precreate_directory": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Precreate Directory"}}, "required": ["type"], "title": "IncomingToolOutputDataset", "type": "object"}, "IncomingToolOutputFloat": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "float", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputFloat", "type": "object"}, "IncomingToolOutputInteger": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "integer", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputInteger", "type": "object"}, "IncomingToolOutputText": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "text", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputText", "type": "object"}, "JavascriptRequirement": {"properties": {"type": {"const": "javascript", "title": "Type", "type": "string"}, "expression_lib": {"anyOf": [{"items": {"description": "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.", "examples": ["function pickValue() {\n    if (inputs.conditional_parameter.test_parameter == \"a\") {\n        return inputs.conditional_parameter.integer_parameter\n    } else {\n        return inputs.conditional_parameter.boolean_parameter\n    }\n}"], "title": "expression_lib", "type": "string"}, "type": "array"}, {"type": "null"}], "title": "Expression Lib"}}, "required": ["type", "expression_lib"], "title": "JavascriptRequirement", "type": "object"}, "LengthParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "length", "default": "length", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "LengthParameterValidatorModel", "type": "object"}, "NoOptionsParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "no_options", "default": "no_options", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "NoOptionsParameterValidatorModel", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RegexParameterValidatorModel": {"additionalProperties": false, "description": "Check if a regular expression **matches** the value, i.e. appears\nat the beginning of the value. To enforce a match of the complete value use\n``$`` at the end of the expression. The expression is given is the content\nof the validator tag. Note that for ``selects`` each option is checked\nseparately.", "properties": {"type": {"const": "regex", "default": "regex", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}, "expression": {"title": "Expression", "type": "string"}}, "required": ["expression"], "title": "RegexParameterValidatorModel", "type": "object"}, "ResourceRequirement": {"properties": {"type": {"const": "resource", "title": "Type", "type": "string"}, "cores_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 1, "description": "Minimum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Min"}, "cores_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Max"}, "ram_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 256, "description": "Minimum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Min"}, "ram_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Max"}, "tmpdir_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Min"}, "tmpdir_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Max"}, "cuda_version_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Version Min"}, "cuda_compute_capability": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Compute Capability"}, "gpu_memory_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Gpu Memory Min"}, "cuda_device_count_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Min"}, "cuda_device_count_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Max"}, "shm_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Shm Size"}, "timelimit": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum time in seconds the tool is allowed to run. Job will be terminated if exceeded.", "title": "Timelimit"}}, "required": ["type"], "title": "ResourceRequirement", "type": "object"}, "TestCollectionCollectionElementAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}}, "title": "TestCollectionCollectionElementAssertions", "type": "object"}, "TestCollectionDatasetElementAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestCollectionDatasetElementAssertions", "type": "object"}, "TestCollectionOutputAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}, "element_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Element Count"}, "attributes": {"anyOf": [{"$ref": "#/$defs/CollectionAttributes"}, {"type": "null"}], "default": null, "title": "Attributes"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "TestCollectionOutputAssertions", "type": "object"}, "TestDataOutputAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestDataOutputAssertions", "type": "object"}, "ToolProvidedMetadataDatasetCollection": {"properties": {"discover_via": {"const": "tool_provided_metadata", "default": "tool_provided_metadata", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}}, "title": "ToolProvidedMetadataDatasetCollection", "type": "object"}, "XrefDict": {"additionalProperties": false, "properties": {"value": {"title": "value", "type": "string"}, "type": {"title": "type", "type": "string"}}, "required": ["value", "type"], "title": "XrefDict", "type": "object"}, "YamlBooleanParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "boolean", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Value"}}, "required": ["name", "type"], "title": "YamlBooleanParameter", "type": "object"}, "YamlColorParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "color", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}}, "required": ["name", "type"], "title": "YamlColorParameter", "type": "object"}, "YamlConditionalParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "conditional", "title": "Type", "type": "string"}, "test_parameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "select": "#/$defs/YamlSelectParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}], "title": "Test Parameter"}, "whens": {"items": {"$ref": "#/$defs/YamlConditionalWhen"}, "minItems": 1, "title": "Whens", "type": "array"}}, "required": ["name", "type", "test_parameter", "whens"], "title": "YamlConditionalParameter", "type": "object"}, "YamlConditionalWhen": {"additionalProperties": false, "properties": {"discriminator": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "title": "Discriminator"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["discriminator"], "title": "YamlConditionalWhen", "type": "object"}, "YamlDataCollectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data_collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}}, "required": ["name", "type"], "title": "YamlDataCollectionParameter", "type": "object"}, "YamlDataParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}, "multiple": {"default": false, "title": "Multiple", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}}, "required": ["name", "type"], "title": "YamlDataParameter", "type": "object"}, "YamlFloatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "float", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlFloatParameter", "type": "object"}, "YamlGalaxyToolParameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "color": "#/$defs/YamlColorParameter", "conditional": "#/$defs/YamlConditionalParameter", "data": "#/$defs/YamlDataParameter", "data_collection": "#/$defs/YamlDataCollectionParameter", "float": "#/$defs/YamlFloatParameter", "integer": "#/$defs/YamlIntegerParameter", "repeat": "#/$defs/YamlRepeatParameter", "section": "#/$defs/YamlSectionParameter", "select": "#/$defs/YamlSelectParameter", "text": "#/$defs/YamlTextParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlIntegerParameter"}, {"$ref": "#/$defs/YamlFloatParameter"}, {"$ref": "#/$defs/YamlTextParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}, {"$ref": "#/$defs/YamlColorParameter"}, {"$ref": "#/$defs/YamlDataParameter"}, {"$ref": "#/$defs/YamlDataCollectionParameter"}, {"$ref": "#/$defs/YamlConditionalParameter"}, {"$ref": "#/$defs/YamlRepeatParameter"}, {"$ref": "#/$defs/YamlSectionParameter"}], "title": "YamlGalaxyToolParameter"}, "YamlIntegerParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "integer", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlIntegerParameter", "type": "object"}, "YamlLabelValue": {"description": "YAML-friendly option model \u2014 ``selected`` defaults to ``False``.", "properties": {"label": {"title": "Label", "type": "string"}, "value": {"title": "Value", "type": "string"}, "selected": {"default": false, "title": "Selected", "type": "boolean"}}, "required": ["label", "value"], "title": "YamlLabelValue", "type": "object"}, "YamlRepeatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "repeat", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}}, "required": ["name", "type"], "title": "YamlRepeatParameter", "type": "object"}, "YamlSectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "section", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["name", "type"], "title": "YamlSectionParameter", "type": "object"}, "YamlSelectParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "select", "title": "Type", "type": "string"}, "options": {"items": {"$ref": "#/$defs/YamlLabelValue"}, "minItems": 1, "title": "Options", "type": "array"}, "multiple": {"default": false, "title": "Multiple", "type": "boolean"}, "validators": {"default": [], "items": {"$ref": "#/$defs/NoOptionsParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type", "options"], "title": "YamlSelectParameter", "type": "object"}, "YamlTemplateConfigFile": {"properties": {"content": {"title": "Content", "type": "string"}, "name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Name"}, "filename": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Filename"}, "eval_engine": {"const": "ecmascript", "default": "ecmascript", "title": "Eval Engine", "type": "string"}}, "required": ["content"], "title": "YamlTemplateConfigFile", "type": "object"}, "YamlTestCredential": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credentials group.", "title": "Name", "type": "string"}, "variables": {"default": [], "description": "Variables exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Variables", "type": "array"}, "secrets": {"default": [], "description": "Secrets exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Secrets", "type": "array"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Version of the credential definition.", "title": "Version"}}, "required": ["name"], "title": "YamlTestCredential", "type": "object"}, "YamlTestCredentialValue": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credential variable or secret.", "title": "Name", "type": "string"}, "value": {"description": "Value of the credential variable or secret.", "title": "Value", "type": "string"}}, "required": ["name", "value"], "title": "YamlTestCredentialValue", "type": "object"}, "YamlTextParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "text", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}, "area": {"default": false, "title": "Area", "type": "boolean"}, "validators": {"default": [], "items": {"anyOf": [{"$ref": "#/$defs/LengthParameterValidatorModel"}, {"$ref": "#/$defs/RegexParameterValidatorModel"}, {"$ref": "#/$defs/EmptyFieldParameterValidatorModel"}]}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlTextParameter", "type": "object"}, "YamlToolTest": {"additionalProperties": false, "description": "In-tool test case as authored in YAML tool fixtures.", "properties": {"doc": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Human-readable description of this test case.", "title": "Doc"}, "inputs": {"anyOf": [{"additionalProperties": {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}, {"items": {}, "type": "array"}, {"additionalProperties": true, "type": "object"}]}, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of input parameter names to test values.", "title": "Inputs"}, "outputs": {"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionOutputAssertions"}, {"$ref": "#/$defs/TestDataOutputAssertions"}, {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}]}]}, "default": {}, "description": "Mapping of output names to expected values or assertions.", "title": "Outputs", "type": "object"}, "assert_stdout": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard output.", "title": "Assert Stdout"}, "assert_stderr": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard error.", "title": "Assert Stderr"}, "command": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the executed command line.", "title": "Command"}, "expect_exit_code": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected process exit code.", "title": "Expect Exit Code"}, "expect_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the tool is expected to produce an error.", "title": "Expect Failure"}, "expect_test_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the test itself is expected to fail.", "title": "Expect Test Failure"}, "credentials": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTestCredential"}, "type": "array"}, {"type": "null"}], "default": null, "description": "Credentials to inject for this test case.", "title": "Credentials"}}, "title": "YamlToolTest", "type": "object"}, "assertion_dict": {"additionalProperties": false, "properties": {"has_line": {"anyOf": [{"$ref": "#/$defs/base_has_line_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line"}, "has_line_matching": {"anyOf": [{"$ref": "#/$defs/base_has_line_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line Matching"}, "has_n_lines": {"anyOf": [{"$ref": "#/$defs/base_has_n_lines_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Lines"}, "has_text": {"anyOf": [{"$ref": "#/$defs/base_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text"}, "has_text_matching": {"anyOf": [{"$ref": "#/$defs/base_has_text_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text Matching"}, "not_has_text": {"anyOf": [{"$ref": "#/$defs/base_not_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Not Has Text"}, "has_n_columns": {"anyOf": [{"$ref": "#/$defs/base_has_n_columns_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Columns"}, "attribute_is": {"anyOf": [{"$ref": "#/$defs/base_attribute_is_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Is"}, "attribute_matches": {"anyOf": [{"$ref": "#/$defs/base_attribute_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Matches"}, "element_text": {"anyOf": [{"$ref": "#/$defs/base_element_text_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text"}, "element_text_is": {"anyOf": [{"$ref": "#/$defs/base_element_text_is_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Is"}, "element_text_matches": {"anyOf": [{"$ref": "#/$defs/base_element_text_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Matches"}, "has_element_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_element_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has Element With Path"}, "has_n_elements_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_n_elements_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Elements With Path"}, "is_valid_xml": {"anyOf": [{"$ref": "#/$defs/base_is_valid_xml_model"}, {"type": "null"}], "default": null, "title": "Assert Is Valid Xml"}, "xml_element": {"anyOf": [{"$ref": "#/$defs/base_xml_element_model"}, {"type": "null"}], "default": null, "title": "Assert Xml Element"}, "has_json_property_with_text": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Text"}, "has_json_property_with_value": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_value_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Value"}, "has_h5_attribute": {"anyOf": [{"$ref": "#/$defs/base_has_h5_attribute_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Attribute"}, "has_h5_keys": {"anyOf": [{"$ref": "#/$defs/base_has_h5_keys_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Keys"}, "has_archive_member": {"anyOf": [{"$ref": "#/$defs/base_has_archive_member_model"}, {"type": "null"}], "default": null, "title": "Assert Has Archive Member"}, "has_size": {"anyOf": [{"$ref": "#/$defs/base_has_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Size"}, "has_image_center_of_mass": {"anyOf": [{"$ref": "#/$defs/base_has_image_center_of_mass_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Center Of Mass"}, "has_image_channels": {"anyOf": [{"$ref": "#/$defs/base_has_image_channels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Channels"}, "has_image_depth": {"anyOf": [{"$ref": "#/$defs/base_has_image_depth_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Depth"}, "has_image_frames": {"anyOf": [{"$ref": "#/$defs/base_has_image_frames_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Frames"}, "has_image_height": {"anyOf": [{"$ref": "#/$defs/base_has_image_height_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Height"}, "has_image_mean_intensity": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_intensity_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Intensity"}, "has_image_mean_object_size": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_object_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Object Size"}, "has_image_n_labels": {"anyOf": [{"$ref": "#/$defs/base_has_image_n_labels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image N Labels"}, "has_image_width": {"anyOf": [{"$ref": "#/$defs/base_has_image_width_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Width"}}, "title": "assertion_dict", "type": "object"}, "assertion_list": {"items": {"anyOf": [{"discriminator": {"mapping": {"attribute_is": "#/$defs/attribute_is_model", "attribute_matches": "#/$defs/attribute_matches_model", "element_text": "#/$defs/element_text_model", "element_text_is": "#/$defs/element_text_is_model", "element_text_matches": "#/$defs/element_text_matches_model", "has_archive_member": "#/$defs/has_archive_member_model", "has_element_with_path": "#/$defs/has_element_with_path_model", "has_h5_attribute": "#/$defs/has_h5_attribute_model", "has_h5_keys": "#/$defs/has_h5_keys_model", "has_image_center_of_mass": "#/$defs/has_image_center_of_mass_model", "has_image_channels": "#/$defs/has_image_channels_model", "has_image_depth": "#/$defs/has_image_depth_model", "has_image_frames": "#/$defs/has_image_frames_model", "has_image_height": "#/$defs/has_image_height_model", "has_image_mean_intensity": "#/$defs/has_image_mean_intensity_model", "has_image_mean_object_size": "#/$defs/has_image_mean_object_size_model", "has_image_n_labels": "#/$defs/has_image_n_labels_model", "has_image_width": "#/$defs/has_image_width_model", "has_json_property_with_text": "#/$defs/has_json_property_with_text_model", "has_json_property_with_value": "#/$defs/has_json_property_with_value_model", "has_line": "#/$defs/has_line_model", "has_line_matching": "#/$defs/has_line_matching_model", "has_n_columns": "#/$defs/has_n_columns_model", "has_n_elements_with_path": "#/$defs/has_n_elements_with_path_model", "has_n_lines": "#/$defs/has_n_lines_model", "has_size": "#/$defs/has_size_model", "has_text": "#/$defs/has_text_model", "has_text_matching": "#/$defs/has_text_matching_model", "is_valid_xml": "#/$defs/is_valid_xml_model", "not_has_text": "#/$defs/not_has_text_model", "xml_element": "#/$defs/xml_element_model"}, "propertyName": "that"}, "oneOf": [{"$ref": "#/$defs/has_line_model"}, {"$ref": "#/$defs/has_line_matching_model"}, {"$ref": "#/$defs/has_n_lines_model"}, {"$ref": "#/$defs/has_text_model"}, {"$ref": "#/$defs/has_text_matching_model"}, {"$ref": "#/$defs/not_has_text_model"}, {"$ref": "#/$defs/has_n_columns_model"}, {"$ref": "#/$defs/attribute_is_model"}, {"$ref": "#/$defs/attribute_matches_model"}, {"$ref": "#/$defs/element_text_model"}, {"$ref": "#/$defs/element_text_is_model"}, {"$ref": "#/$defs/element_text_matches_model"}, {"$ref": "#/$defs/has_element_with_path_model"}, {"$ref": "#/$defs/has_n_elements_with_path_model"}, {"$ref": "#/$defs/is_valid_xml_model"}, {"$ref": "#/$defs/xml_element_model"}, {"$ref": "#/$defs/has_json_property_with_text_model"}, {"$ref": "#/$defs/has_json_property_with_value_model"}, {"$ref": "#/$defs/has_h5_attribute_model"}, {"$ref": "#/$defs/has_h5_keys_model"}, {"$ref": "#/$defs/has_archive_member_model"}, {"$ref": "#/$defs/has_size_model"}, {"$ref": "#/$defs/has_image_center_of_mass_model"}, {"$ref": "#/$defs/has_image_channels_model"}, {"$ref": "#/$defs/has_image_depth_model"}, {"$ref": "#/$defs/has_image_frames_model"}, {"$ref": "#/$defs/has_image_height_model"}, {"$ref": "#/$defs/has_image_mean_intensity_model"}, {"$ref": "#/$defs/has_image_mean_object_size_model"}, {"$ref": "#/$defs/has_image_n_labels_model"}, {"$ref": "#/$defs/has_image_width_model"}]}, {"$ref": "#/$defs/has_line_model_nested"}, {"$ref": "#/$defs/has_line_matching_model_nested"}, {"$ref": "#/$defs/has_n_lines_model_nested"}, {"$ref": "#/$defs/has_text_model_nested"}, {"$ref": "#/$defs/has_text_matching_model_nested"}, {"$ref": "#/$defs/not_has_text_model_nested"}, {"$ref": "#/$defs/has_n_columns_model_nested"}, {"$ref": "#/$defs/attribute_is_model_nested"}, {"$ref": "#/$defs/attribute_matches_model_nested"}, {"$ref": "#/$defs/element_text_model_nested"}, {"$ref": "#/$defs/element_text_is_model_nested"}, {"$ref": "#/$defs/element_text_matches_model_nested"}, {"$ref": "#/$defs/has_element_with_path_model_nested"}, {"$ref": "#/$defs/has_n_elements_with_path_model_nested"}, {"$ref": "#/$defs/is_valid_xml_model_nested"}, {"$ref": "#/$defs/xml_element_model_nested"}, {"$ref": "#/$defs/has_json_property_with_text_model_nested"}, {"$ref": "#/$defs/has_json_property_with_value_model_nested"}, {"$ref": "#/$defs/has_h5_attribute_model_nested"}, {"$ref": "#/$defs/has_h5_keys_model_nested"}, {"$ref": "#/$defs/has_archive_member_model_nested"}, {"$ref": "#/$defs/has_size_model_nested"}, {"$ref": "#/$defs/has_image_center_of_mass_model_nested"}, {"$ref": "#/$defs/has_image_channels_model_nested"}, {"$ref": "#/$defs/has_image_depth_model_nested"}, {"$ref": "#/$defs/has_image_frames_model_nested"}, {"$ref": "#/$defs/has_image_height_model_nested"}, {"$ref": "#/$defs/has_image_mean_intensity_model_nested"}, {"$ref": "#/$defs/has_image_mean_object_size_model_nested"}, {"$ref": "#/$defs/has_image_n_labels_model_nested"}, {"$ref": "#/$defs/has_image_width_model_nested"}]}, "title": "assertion_list", "type": "array"}, "attribute_is_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` is the specified ``text``.\n\nFor example:\n\n```xml\n<attribute_is path=\"outerElement/innerElement1\" attribute=\"foo\" text=\"bar\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_is", "default": "attribute_is", "title": "That", "type": "string"}}, "required": ["path", "attribute", "text"], "title": "Assert Attribute Is", "type": "object"}, "attribute_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_is": {"$ref": "#/$defs/base_attribute_is_model", "title": "Assert Attribute Is"}}, "required": ["attribute_is"], "title": "Assert Attribute Is (Nested)", "type": "object"}, "attribute_matches_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` matches the regular expression specified by ``expression``.\n\nFor example:\n\n```xml\n<attribute_matches path=\"outerElement/innerElement2\" attribute=\"foo2\" expression=\"bar\\d+\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_matches", "default": "attribute_matches", "title": "That", "type": "string"}}, "required": ["path", "attribute", "expression"], "title": "Assert Attribute Matches", "type": "object"}, "attribute_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_matches": {"$ref": "#/$defs/base_attribute_matches_model", "title": "Assert Attribute Matches"}}, "required": ["attribute_matches"], "title": "Assert Attribute Matches (Nested)", "type": "object"}, "base_attribute_is_model": {"additionalProperties": false, "description": "base model for attribute_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "text"], "title": "base_attribute_is_model", "type": "object"}, "base_attribute_matches_model": {"additionalProperties": false, "description": "base model for attribute_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "expression"], "title": "base_attribute_matches_model", "type": "object"}, "base_element_text_is_model": {"additionalProperties": false, "description": "base model for element_text_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "text"], "title": "base_element_text_is_model", "type": "object"}, "base_element_text_matches_model": {"additionalProperties": false, "description": "base model for element_text_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "expression"], "title": "base_element_text_matches_model", "type": "object"}, "base_element_text_model": {"additionalProperties": false, "description": "base model for element_text describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_element_text_model", "type": "object"}, "base_has_archive_member_model": {"additionalProperties": false, "description": "base model for has_archive_member describing attributes.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_has_archive_member_model", "type": "object"}, "base_has_element_with_path_model": {"additionalProperties": false, "description": "base model for has_element_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_element_with_path_model", "type": "object"}, "base_has_h5_attribute_model": {"additionalProperties": false, "description": "base model for has_h5_attribute describing attributes.", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}}, "required": ["key", "value"], "title": "base_has_h5_attribute_model", "type": "object"}, "base_has_h5_keys_model": {"additionalProperties": false, "description": "base model for has_h5_keys describing attributes.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}}, "required": ["keys"], "title": "base_has_h5_keys_model", "type": "object"}, "base_has_image_center_of_mass_model": {"additionalProperties": false, "description": "base model for has_image_center_of_mass describing attributes.", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}}, "required": ["center_of_mass"], "title": "base_has_image_center_of_mass_model", "type": "object"}, "base_has_image_channels_model": {"additionalProperties": false, "description": "base model for has_image_channels describing attributes.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_channels_model", "type": "object"}, "base_has_image_depth_model": {"additionalProperties": false, "description": "base model for has_image_depth describing attributes.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_depth_model", "type": "object"}, "base_has_image_frames_model": {"additionalProperties": false, "description": "base model for has_image_frames describing attributes.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_frames_model", "type": "object"}, "base_has_image_height_model": {"additionalProperties": false, "description": "base model for has_image_height describing attributes.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_height_model", "type": "object"}, "base_has_image_mean_intensity_model": {"additionalProperties": false, "description": "base model for has_image_mean_intensity describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}}, "title": "base_has_image_mean_intensity_model", "type": "object"}, "base_has_image_mean_object_size_model": {"additionalProperties": false, "description": "base model for has_image_mean_object_size describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}}, "title": "base_has_image_mean_object_size_model", "type": "object"}, "base_has_image_n_labels_model": {"additionalProperties": false, "description": "base model for has_image_n_labels describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_n_labels_model", "type": "object"}, "base_has_image_width_model": {"additionalProperties": false, "description": "base model for has_image_width describing attributes.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_width_model", "type": "object"}, "base_has_json_property_with_text_model": {"additionalProperties": false, "description": "base model for has_json_property_with_text describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}}, "required": ["property", "text"], "title": "base_has_json_property_with_text_model", "type": "object"}, "base_has_json_property_with_value_model": {"additionalProperties": false, "description": "base model for has_json_property_with_value describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}}, "required": ["property", "value"], "title": "base_has_json_property_with_value_model", "type": "object"}, "base_has_line_matching_model": {"additionalProperties": false, "description": "base model for has_line_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_line_matching_model", "type": "object"}, "base_has_line_model": {"additionalProperties": false, "description": "base model for has_line describing attributes.", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["line"], "title": "base_has_line_model", "type": "object"}, "base_has_n_columns_model": {"additionalProperties": false, "description": "base model for has_n_columns describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_columns_model", "type": "object"}, "base_has_n_elements_with_path_model": {"additionalProperties": false, "description": "base model for has_n_elements_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_n_elements_with_path_model", "type": "object"}, "base_has_n_lines_model": {"additionalProperties": false, "description": "base model for has_n_lines describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_lines_model", "type": "object"}, "base_has_size_model": {"additionalProperties": false, "description": "base model for has_size describing attributes.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_size_model", "type": "object"}, "base_has_text_matching_model": {"additionalProperties": false, "description": "base model for has_text_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_text_matching_model", "type": "object"}, "base_has_text_model": {"additionalProperties": false, "description": "base model for has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["text"], "title": "base_has_text_model", "type": "object"}, "base_is_valid_xml_model": {"additionalProperties": false, "description": "base model for is_valid_xml describing attributes.", "properties": {}, "title": "base_is_valid_xml_model", "type": "object"}, "base_not_has_text_model": {"additionalProperties": false, "description": "base model for not_has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}}, "required": ["text"], "title": "base_not_has_text_model", "type": "object"}, "base_xml_element_model": {"additionalProperties": false, "description": "base model for xml_element describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_xml_element_model", "type": "object"}, "element_text_is_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path`` is\nthe specified ``text``.\n\nFor example:\n\n```xml\n<element_text_is path=\"BlastOutput_program\" text=\"blastp\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_is", "default": "element_text_is", "title": "That", "type": "string"}}, "required": ["path", "text"], "title": "Assert Element Text Is", "type": "object"}, "element_text_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_is": {"$ref": "#/$defs/base_element_text_is_model", "title": "Assert Element Text Is"}}, "required": ["element_text_is"], "title": "Assert Element Text Is (Nested)", "type": "object"}, "element_text_matches_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path``\nmatches the regular expression defined by ``expression``.\n\nFor example:\n\n```xml\n<element_text_matches path=\"BlastOutput_version\" expression=\"BLASTP\\s+2\\.2.*\"/>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_matches", "default": "element_text_matches", "title": "That", "type": "string"}}, "required": ["path", "expression"], "title": "Assert Element Text Matches", "type": "object"}, "element_text_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_matches": {"$ref": "#/$defs/base_element_text_matches_model", "title": "Assert Element Text Matches"}}, "required": ["element_text_matches"], "title": "Assert Element Text Matches (Nested)", "type": "object"}, "element_text_model": {"additionalProperties": false, "description": "This tag allows the developer to recurisively specify additional assertions as\nchild elements about just the text contained in the element specified by the\nXPath-like ``path``, e.g.\n\n```xml\n<element_text path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def\">\n  <not_has_text text=\"EDK72998.1\" />\n</element_text>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the implicit assertions can be inverted.\nThe sub-assertions, which have their own ``negate`` attribute, are not affected\nby ``negate``.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "element_text", "default": "element_text", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Element Text", "type": "object"}, "element_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text": {"$ref": "#/$defs/base_element_text_model", "title": "Assert Element Text"}}, "required": ["element_text"], "title": "Assert Element Text (Nested)", "type": "object"}, "has_archive_member_model": {"additionalProperties": false, "description": "This tag allows to check if ``path`` is contained in a compressed file.\n\nThe path is a regular expression that is matched against the full paths of the objects in\nthe compressed file (remember that \"matching\" means it is checked if a prefix of\nthe full path of an archive member is described by the regular expression).\nValid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that\ndepending on the archive creation method:\n\n- full paths of the members may be prefixed with ``./``\n- directories may be treated as empty files\n\n```xml\n<has_archive_member path=\"./path/to/my-file.txt\"/>\n```\n\nWith ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of\narchive members matching ``path`` can be expressed. The following could be used,\ne.g., to assert an archive containing n&plusmn;1 elements out of which at least\n4 need to have a ``txt`` extension.\n\n```xml\n<has_archive_member path=\".*\" n=\"10\" delta=\"1\"/>\n<has_archive_member path=\".*\\.txt\" min=\"4\"/>\n```\n\nIn addition the tag can contain additional assertions as child elements about\nthe first member in the archive matching the regular expression ``path``. For\ninstance\n\n```xml\n<has_archive_member path=\".*/my-file.txt\">\n  <not_has_text text=\"EDK72998.1\"/>\n</has_archive_member>\n```\n\nIf the ``all`` attribute is set to ``true`` then all archive members are subject\nto the assertions. Note that, archive members matching the ``path`` are sorted\nalphabetically.\n\nThe ``negate`` attribute of the ``has_archive_member`` assertion only affects\nthe asserts on the presence and number of matching archive members, but not any\nsub-assertions (which can offer the ``negate`` attribute on their own).  The\ncheck if the file is an archive at all, which is also done by the function, is\nnot affected.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "has_archive_member", "default": "has_archive_member", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Archive Member", "type": "object"}, "has_archive_member_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_archive_member": {"$ref": "#/$defs/base_has_archive_member_model", "title": "Assert Has Archive Member"}}, "required": ["has_archive_member"], "title": "Assert Has Archive Member (Nested)", "type": "object"}, "has_element_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains at least one element (or tag) with the specified\nXPath-like ``path``, e.g.\n\n```xml\n<has_element_with_path path=\"BlastOutput_param/Parameters/Parameters_matrix\" />\n```\n\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_element_with_path", "default": "has_element_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Element With Path", "type": "object"}, "has_element_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_element_with_path": {"$ref": "#/$defs/base_has_element_with_path_model", "title": "Assert Has Element With Path"}}, "required": ["has_element_with_path"], "title": "Assert Has Element With Path (Nested)", "type": "object"}, "has_h5_attribute_model": {"additionalProperties": false, "description": "Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.\n\n```xml\n<has_h5_attribute key=\"nchroms\" value=\"15\" />\n```", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}, "that": {"const": "has_h5_attribute", "default": "has_h5_attribute", "title": "That", "type": "string"}}, "required": ["key", "value"], "title": "Assert Has H5 Attribute", "type": "object"}, "has_h5_attribute_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_attribute": {"$ref": "#/$defs/base_has_h5_attribute_model", "title": "Assert Has H5 Attribute"}}, "required": ["has_h5_attribute"], "title": "Assert Has H5 Attribute (Nested)", "type": "object"}, "has_h5_keys_model": {"additionalProperties": false, "description": "Asserts the specified HDF5 output has the given keys.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}, "that": {"const": "has_h5_keys", "default": "has_h5_keys", "title": "That", "type": "string"}}, "required": ["keys"], "title": "Assert Has H5 Keys", "type": "object"}, "has_h5_keys_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_keys": {"$ref": "#/$defs/base_has_h5_keys_model", "title": "Assert Has H5 Keys"}}, "required": ["has_h5_keys"], "title": "Assert Has H5 Keys (Nested)", "type": "object"}, "has_image_center_of_mass_model": {"additionalProperties": false, "description": "Asserts the specified output is an image and has the specified center of mass.\n\nAsserts the output is an image and has a specific center of mass,\nor has an Euclidean distance of ``eps`` or less to that point (e.g.,\n``<has_image_center_of_mass center_of_mass=\"511.07, 223.34\" />``).", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}, "that": {"const": "has_image_center_of_mass", "default": "has_image_center_of_mass", "title": "That", "type": "string"}}, "required": ["center_of_mass"], "title": "Assert Has Image Center Of Mass", "type": "object"}, "has_image_center_of_mass_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_center_of_mass": {"$ref": "#/$defs/base_has_image_center_of_mass_model", "title": "Assert Has Image Center Of Mass"}}, "required": ["has_image_center_of_mass"], "title": "Assert Has Image Center Of Mass (Nested)", "type": "object"}, "has_image_channels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of channels.\n\nThe number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels=\"3\" />``).\n\nAlternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_channels", "default": "has_image_channels", "title": "That", "type": "string"}}, "title": "Assert Has Image Channels", "type": "object"}, "has_image_channels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_channels": {"$ref": "#/$defs/base_has_image_channels_model", "title": "Assert Has Image Channels"}}, "required": ["has_image_channels"], "title": "Assert Has Image Channels (Nested)", "type": "object"}, "has_image_depth_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific depth (number of slices).\n\nThe depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected depth can be specified by ``min`` and/or ``max``.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_depth", "default": "has_image_depth", "title": "That", "type": "string"}}, "title": "Assert Has Image Depth", "type": "object"}, "has_image_depth_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_depth": {"$ref": "#/$defs/base_has_image_depth_model", "title": "Assert Has Image Depth"}}, "required": ["has_image_depth"], "title": "Assert Has Image Depth (Nested)", "type": "object"}, "has_image_frames_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of frames (number of time steps).\n\nThe number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_frames", "default": "has_image_frames", "title": "That", "type": "string"}}, "title": "Assert Has Image Frames", "type": "object"}, "has_image_frames_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_frames": {"$ref": "#/$defs/base_has_image_frames_model", "title": "Assert Has Image Frames"}}, "required": ["has_image_frames"], "title": "Assert Has Image Frames (Nested)", "type": "object"}, "has_image_height_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific height (in pixels).\n\nThe height is plus/minus ``delta`` (e.g., ``<has_image_height height=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected height can be specified by ``min`` and/or ``max``.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_height", "default": "has_image_height", "title": "That", "type": "string"}}, "title": "Assert Has Image Height", "type": "object"}, "has_image_height_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_height": {"$ref": "#/$defs/base_has_image_height_model", "title": "Assert Has Image Height"}}, "required": ["has_image_height"], "title": "Assert Has Image Height (Nested)", "type": "object"}, "has_image_mean_intensity_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific mean intensity value.\n\nThe mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity=\"0.83\" />``).\nAlternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}, "that": {"const": "has_image_mean_intensity", "default": "has_image_mean_intensity", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Intensity", "type": "object"}, "has_image_mean_intensity_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_intensity": {"$ref": "#/$defs/base_has_image_mean_intensity_model", "title": "Assert Has Image Mean Intensity"}}, "required": ["has_image_mean_intensity"], "title": "Assert Has Image Mean Intensity (Nested)", "type": "object"}, "has_image_mean_object_size_model": {"additionalProperties": false, "description": "Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),\n\nThe mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size=\"111.87\" exclude_labels=\"0\" />``).\n\nThe labels must be unique.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}, "that": {"const": "has_image_mean_object_size", "default": "has_image_mean_object_size", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Object Size", "type": "object"}, "has_image_mean_object_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_object_size": {"$ref": "#/$defs/base_has_image_mean_object_size_model", "title": "Assert Has Image Mean Object Size"}}, "required": ["has_image_mean_object_size"], "title": "Assert Has Image Mean Object Size (Nested)", "type": "object"}, "has_image_n_labels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has the specified labels.\n\nLabels can be a number of labels or unique values (e.g.,\n``<has_image_n_labels n=\"187\" exclude_labels=\"0\" />``).\n\nThe primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_n_labels", "default": "has_image_n_labels", "title": "That", "type": "string"}}, "title": "Assert Has Image N Labels", "type": "object"}, "has_image_n_labels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_n_labels": {"$ref": "#/$defs/base_has_image_n_labels_model", "title": "Assert Has Image N Labels"}}, "required": ["has_image_n_labels"], "title": "Assert Has Image N Labels (Nested)", "type": "object"}, "has_image_width_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific width (in pixels).\n\nThe width is plus/minus ``delta`` (e.g., ``<has_image_width width=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected width can be specified by ``min`` and/or ``max``.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_width", "default": "has_image_width", "title": "That", "type": "string"}}, "title": "Assert Has Image Width", "type": "object"}, "has_image_width_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_width": {"$ref": "#/$defs/base_has_image_width_model", "title": "Assert Has Image Width"}}, "required": ["has_image_width"], "title": "Assert Has Image Width (Nested)", "type": "object"}, "has_json_property_with_text_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified text (i.e. string) value.\n\n```xml\n<has_json_property_with_text property=\"color\" text=\"red\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}, "that": {"const": "has_json_property_with_text", "default": "has_json_property_with_text", "title": "That", "type": "string"}}, "required": ["property", "text"], "title": "Assert Has Json Property With Text", "type": "object"}, "has_json_property_with_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_text": {"$ref": "#/$defs/base_has_json_property_with_text_model", "title": "Assert Has Json Property With Text"}}, "required": ["has_json_property_with_text"], "title": "Assert Has Json Property With Text (Nested)", "type": "object"}, "has_json_property_with_value_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified JSON value.\n\n```xml\n<has_json_property_with_value property=\"skipped_columns\" value=\"[1, 3, 5]\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}, "that": {"const": "has_json_property_with_value", "default": "has_json_property_with_value", "title": "That", "type": "string"}}, "required": ["property", "value"], "title": "Assert Has Json Property With Value", "type": "object"}, "has_json_property_with_value_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_value": {"$ref": "#/$defs/base_has_json_property_with_value_model", "title": "Assert Has Json Property With Value"}}, "required": ["has_json_property_with_value"], "title": "Assert Has Json Property With Value (Nested)", "type": "object"}, "has_line_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains a line matching the\nregular expression specified by the argument expression. If n is given\nthe assertion checks for exactly n occurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line_matching", "default": "has_line_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Line Matching", "type": "object"}, "has_line_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line_matching": {"$ref": "#/$defs/base_has_line_matching_model", "title": "Assert Has Line Matching"}}, "required": ["has_line_matching"], "title": "Assert Has Line Matching (Nested)", "type": "object"}, "has_line_model": {"additionalProperties": false, "description": "Asserts the specified output contains the line specified by the\nargument line. The exact number of occurrences can be optionally\nspecified by the argument n", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line", "default": "has_line", "title": "That", "type": "string"}}, "required": ["line"], "title": "Assert Has Line", "type": "object"}, "has_line_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line": {"$ref": "#/$defs/base_has_line_model", "title": "Assert Has Line"}}, "required": ["has_line"], "title": "Assert Has Line (Nested)", "type": "object"}, "has_n_columns_model": {"additionalProperties": false, "description": "Asserts tabular output  contains the specified\nnumber (``n``) of columns.\n\nFor instance, ``<has_n_columns n=\"3\"/>``. The assertion tests only the first line.\nNumber of columns can optionally also be specified with ``delta``. Alternatively the\nrange of expected occurrences can be specified by ``min`` and/or ``max``.\n\nOptionally a column separator (``sep``, default is ``       ``) `and comment character(s)\ncan be specified (``comment``, default is empty string). The first non-comment\nline is used for determining the number of columns.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_columns", "default": "has_n_columns", "title": "That", "type": "string"}}, "title": "Assert Has N Columns", "type": "object"}, "has_n_columns_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_columns": {"$ref": "#/$defs/base_has_n_columns_model", "title": "Assert Has N Columns"}}, "required": ["has_n_columns"], "title": "Assert Has N Columns (Nested)", "type": "object"}, "has_n_elements_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or\ntags) with the specified XPath-like ``path``.\n\nFor example:\n\n```xml\n<has_n_elements_with_path n=\"9\" path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num\" />\n```\n\nAlternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes\ncan be used to specify the range of the expected number of occurrences.\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_elements_with_path", "default": "has_n_elements_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has N Elements With Path", "type": "object"}, "has_n_elements_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_elements_with_path": {"$ref": "#/$defs/base_has_n_elements_with_path_model", "title": "Assert Has N Elements With Path"}}, "required": ["has_n_elements_with_path"], "title": "Assert Has N Elements With Path (Nested)", "type": "object"}, "has_n_lines_model": {"additionalProperties": false, "description": "Asserts the specified output contains ``n`` lines allowing\nfor a difference in the number of lines (delta)\nor relative differebce in the number of lines", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_lines", "default": "has_n_lines", "title": "That", "type": "string"}}, "title": "Assert Has N Lines", "type": "object"}, "has_n_lines_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_lines": {"$ref": "#/$defs/base_has_n_lines_model", "title": "Assert Has N Lines"}}, "required": ["has_n_lines"], "title": "Assert Has N Lines (Nested)", "type": "object"}, "has_size_model": {"additionalProperties": false, "description": "Asserts the specified output has a size of the specified value\n\nAttributes size and value or synonyms though value is considered deprecated.\nThe size optionally allows for absolute (``delta``) difference.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_size", "default": "has_size", "title": "That", "type": "string"}}, "title": "Assert Has Size", "type": "object"}, "has_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_size": {"$ref": "#/$defs/base_has_size_model", "title": "Assert Has Size"}}, "required": ["has_size"], "title": "Assert Has Size (Nested)", "type": "object"}, "has_text_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains text matching the\nregular expression specified by the argument expression.\nIf n is given the assertion checks for exactly n (nonoverlapping)\noccurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text_matching", "default": "has_text_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Text Matching", "type": "object"}, "has_text_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text_matching": {"$ref": "#/$defs/base_has_text_matching_model", "title": "Assert Has Text Matching"}}, "required": ["has_text_matching"], "title": "Assert Has Text Matching (Nested)", "type": "object"}, "has_text_model": {"additionalProperties": false, "description": "Asserts specified output contains the substring specified by\nthe argument text. The exact number of occurrences can be\noptionally specified by the argument n", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text", "default": "has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Has Text", "type": "object"}, "has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text": {"$ref": "#/$defs/base_has_text_model", "title": "Assert Has Text"}}, "required": ["has_text"], "title": "Assert Has Text (Nested)", "type": "object"}, "is_valid_xml_model": {"additionalProperties": false, "description": "Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).", "properties": {"that": {"const": "is_valid_xml", "default": "is_valid_xml", "title": "That", "type": "string"}}, "title": "Assert Is Valid Xml", "type": "object"}, "is_valid_xml_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"is_valid_xml": {"$ref": "#/$defs/base_is_valid_xml_model", "title": "Assert Is Valid Xml"}}, "required": ["is_valid_xml"], "title": "Assert Is Valid Xml (Nested)", "type": "object"}, "not_has_text_model": {"additionalProperties": false, "description": "Asserts specified output does not contain the substring\nspecified by the argument text", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "that": {"const": "not_has_text", "default": "not_has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Not Has Text", "type": "object"}, "not_has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"not_has_text": {"$ref": "#/$defs/base_not_has_text_model", "title": "Assert Not Has Text"}}, "required": ["not_has_text"], "title": "Assert Not Has Text (Nested)", "type": "object"}, "xml_element_model": {"additionalProperties": false, "description": "Assert if the XML file contains element(s) or tag(s) with the specified\n[XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``\nor ``min`` and ``max`` are given also the number of occurrences is checked.\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem\"/>\n  <xml_element path=\"./elem/more[2]\"/>\n  <xml_element path=\".//more\" n=\"3\" delta=\"1\"/>\n</assert_contents>\n```\n\nWith ``negate=\"true\"`` the outcome of the assertions wrt the presence and number\nof ``path`` can be negated. If there are any sub assertions then check them against\n\n- the content of the attribute ``attribute``\n- the element's text if no attribute is given\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem/more[2]\" attribute=\"name\">\n    <has_text_matching expression=\"foo$\"/>\n  </xml_element>\n</assert_contents>\n```\n\nSub-assertions are not subject to the ``negate`` attribute of ``xml_element``.\nIf ``all`` is ``true`` then the sub assertions are checked for all occurrences.\n\nNote that all other XML assertions can be expressed by this assertion (Galaxy\nalso implements the other assertions by calling this one).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "xml_element", "default": "xml_element", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Xml Element", "type": "object"}, "xml_element_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"xml_element": {"$ref": "#/$defs/base_xml_element_model", "title": "Assert Xml Element"}}, "required": ["xml_element"], "title": "Assert Xml Element (Nested)", "type": "object"}}, "additionalProperties": false, "description": "Full unprivileged tool source, including the optional ``tests`` block.\n\nThis is the model persisted and validated on the API surface\n(``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring\nuses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added\nback here so direct authors and stored rows can still carry tests.", "properties": {"id": {"anyOf": [{"maxLength": 255, "minLength": 3, "pattern": "^[a-z][a-z0-9_-]*$", "type": "string"}, {"type": "null"}], "default": null, "description": "Unique identifier for the tool. Lowercase, must start with a letter, may contain letters, digits, '_' and '-'.", "examples": ["my-cool-tool"], "title": "id"}, "version": {"description": "Version for the tool.", "examples": ["0.1.0"], "title": "version", "type": "string"}, "name": {"description": "The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.", "minLength": 5, "title": "name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The description is displayed in the tool menu immediately following the hyperlink for the tool.", "title": "description"}, "configfiles": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTemplateConfigFile"}, "type": "array"}, {"type": "null"}], "default": null, "description": "A list of config files for this tool.", "title": "configfiles"}, "requirements": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/JavascriptRequirement"}, {"$ref": "#/$defs/ResourceRequirement"}, {"$ref": "#/$defs/ContainerRequirement"}]}, "type": "array"}, {"type": "null"}], "default": [], "description": "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.", "title": "requirements"}, "shell_command": {"description": "A string that contains the command to be executed. Parameters can be referenced inside $().", "examples": ["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"], "title": "shell_command", "type": "string"}, "inputs": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "inputs", "type": "array"}, "outputs": {"default": [], "items": {"discriminator": {"mapping": {"boolean": "#/$defs/IncomingToolOutputBoolean", "collection": "#/$defs/IncomingToolOutputCollection", "data": "#/$defs/IncomingToolOutputDataset", "float": "#/$defs/IncomingToolOutputFloat", "integer": "#/$defs/IncomingToolOutputInteger", "text": "#/$defs/IncomingToolOutputText"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/IncomingToolOutputDataset"}, {"$ref": "#/$defs/IncomingToolOutputCollection"}, {"$ref": "#/$defs/IncomingToolOutputText"}, {"$ref": "#/$defs/IncomingToolOutputInteger"}, {"$ref": "#/$defs/IncomingToolOutputFloat"}, {"$ref": "#/$defs/IncomingToolOutputBoolean"}]}, "title": "outputs", "type": "array"}, "citations": {"anyOf": [{"items": {"$ref": "#/$defs/Citation"}, "type": "array"}, {"type": "null"}], "default": null, "title": "citations"}, "license": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.", "examples": ["MIT"], "title": "license"}, "edam_operations": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_operations"}, "edam_topics": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_topics"}, "xrefs": {"anyOf": [{"items": {"$ref": "#/$defs/XrefDict"}, "type": "array"}, {"type": "null"}], "default": null, "title": "xrefs"}, "profile": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "profile"}, "help": {"anyOf": [{"$ref": "#/$defs/HelpContent"}, {"type": "null"}], "default": null, "description": "Help text shown below the tool interface.", "title": "help"}, "class": {"const": "GalaxyUserTool", "title": "class_", "type": "string"}, "container": {"description": "Container image to use for this tool.", "examples": ["quay.io/biocontainers/python:3.13"], "title": "container", "type": "string"}, "tests": {"anyOf": [{"items": {"$ref": "#/$defs/YamlToolTest"}, "type": "array"}, {"type": "null"}], "default": null, "title": "tests"}}, "required": ["version", "name", "shell_command", "class", "container"], "title": "UserToolSource", "type": "object"}
\ No newline at end of file
diff --git a/lib/galaxy/tool_util_models/yaml_parameters.py b/lib/galaxy/tool_util_models/yaml_parameters.py
index 6b94ee5f0ea..9feff67e411 100644
--- a/lib/galaxy/tool_util_models/yaml_parameters.py
+++ b/lib/galaxy/tool_util_models/yaml_parameters.py
@@ -191,9 +191,29 @@ def _split_format(v):
 class YamlDataParameter(_YamlParamBase):
     type: Literal["data"]
     format: List[str] = ["data"]
-    multiple: bool = False
-    min: Optional[int] = None
-    max: Optional[int] = None
+    multiple: Annotated[
+        bool,
+        Field(description="Set true to accept several datasets (a list) for this input instead of one."),
+    ] = False
+    min: Annotated[
+        Optional[int],
+        Field(
+            description=(
+                "Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. "
+                "Do NOT set this for a single-dataset input -- a data input is already required by default, "
+                "so leave 'min' unset unless the input accepts multiple datasets."
+            )
+        ),
+    ] = None
+    max: Annotated[
+        Optional[int],
+        Field(
+            description=(
+                "Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; "
+                "leave unset for a single-dataset input."
+            )
+        ),
+    ] = None
 
     @field_validator("format", mode="before")
     @classmethod

From f102564ad7252fbfc28108359d4b8abf12bb014f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 18 Jun 2026 21:59:04 +0200
Subject: [PATCH 250/256] Rebuild schemas

---
 client/packages/api-client/src/schema/schema.ts  | 16 ++++++++++++----
 client/src/components/Tool/ToolSourceSchema.json |  2 +-
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index 8dc7ff1755b..a15dd3f7bb9 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -25822,8 +25822,12 @@ export interface components {
             shell_command: string;
             /** tests */
             tests?: components["schemas"]["YamlToolTest-Input"][] | null;
-            /** version */
-            version?: string | null;
+            /**
+             * version
+             * @description Version for the tool.
+             * @example 0.1.0
+             */
+            version: string;
             /** xrefs */
             xrefs?: components["schemas"]["XrefDict"][] | null;
         };
@@ -25925,8 +25929,12 @@ export interface components {
             shell_command: string;
             /** tests */
             tests?: components["schemas"]["YamlToolTest-Output"][] | null;
-            /** version */
-            version?: string | null;
+            /**
+             * version
+             * @description Version for the tool.
+             * @example 0.1.0
+             */
+            version: string;
             /** xrefs */
             xrefs?: components["schemas"]["XrefDict"][] | null;
         };
diff --git a/client/src/components/Tool/ToolSourceSchema.json b/client/src/components/Tool/ToolSourceSchema.json
index 85e7a7ddfcb..02eee957129 100644
--- a/client/src/components/Tool/ToolSourceSchema.json
+++ b/client/src/components/Tool/ToolSourceSchema.json
@@ -1 +1 @@
-{"$defs": {"Citation": {"properties": {"type": {"title": "Type", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["type", "content"], "title": "Citation", "type": "object"}, "CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "Container": {"properties": {"type": {"enum": ["docker", "singularity"], "title": "Type", "type": "string"}, "container_id": {"title": "Container Id", "type": "string"}}, "required": ["type", "container_id"], "title": "Container", "type": "object"}, "ContainerRequirement": {"properties": {"type": {"const": "container", "title": "Type", "type": "string"}, "container": {"$ref": "#/$defs/Container"}}, "required": ["type", "container"], "title": "ContainerRequirement", "type": "object"}, "EmptyFieldParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "empty_field", "default": "empty_field", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "EmptyFieldParameterValidatorModel", "type": "object"}, "FilePatternDatasetCollectionDescription": {"properties": {"discover_via": {"const": "pattern", "default": "pattern", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}, "sort_key": {"default": "filename", "enum": ["filename", "name", "designation", "dbkey"], "title": "Sort Key", "type": "string"}, "sort_comp": {"default": "lexical", "enum": ["lexical", "numeric"], "title": "Sort Comp", "type": "string"}, "sort_reverse": {"default": false, "title": "Sort Reverse", "type": "boolean"}, "pattern": {"title": "Pattern", "type": "string"}}, "required": ["pattern"], "title": "FilePatternDatasetCollectionDescription", "type": "object"}, "HelpContent": {"properties": {"format": {"enum": ["restructuredtext", "plain_text", "markdown"], "title": "Format", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["format", "content"], "title": "HelpContent", "type": "object"}, "InRangeParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "in_range", "default": "in_range", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "exclude_min": {"default": false, "title": "Exclude Min", "type": "boolean"}, "exclude_max": {"default": false, "title": "Exclude Max", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "InRangeParameterValidatorModel", "type": "object"}, "IncomingToolOutputBoolean": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "boolean", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputBoolean", "type": "object"}, "IncomingToolOutputCollection": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "collection_type_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type Source"}, "collection_type_from_rules": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type From Rules"}, "structured_like": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Structured Like"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}}, "required": ["type"], "title": "IncomingToolOutputCollection", "type": "object"}, "IncomingToolOutputDataset": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The short name for the output datatype.", "title": "Format"}, "format_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.", "title": "Format Source"}, "metadata_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This copies the metadata information from the tool\u2019s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.", "title": "Metadata Source"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}, "from_work_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Relative path to a file produced by the tool in its working directory. Output\u2019s contents are set to this file\u2019s contents.", "title": "from_work_dir"}, "precreate_directory": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Precreate Directory"}}, "required": ["type"], "title": "IncomingToolOutputDataset", "type": "object"}, "IncomingToolOutputFloat": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "float", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputFloat", "type": "object"}, "IncomingToolOutputInteger": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "integer", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputInteger", "type": "object"}, "IncomingToolOutputText": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "text", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputText", "type": "object"}, "JavascriptRequirement": {"properties": {"type": {"const": "javascript", "title": "Type", "type": "string"}, "expression_lib": {"anyOf": [{"items": {"description": "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.", "examples": ["function pickValue() {\n    if (inputs.conditional_parameter.test_parameter == \"a\") {\n        return inputs.conditional_parameter.integer_parameter\n    } else {\n        return inputs.conditional_parameter.boolean_parameter\n    }\n}"], "title": "expression_lib", "type": "string"}, "type": "array"}, {"type": "null"}], "title": "Expression Lib"}}, "required": ["type", "expression_lib"], "title": "JavascriptRequirement", "type": "object"}, "LengthParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "length", "default": "length", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "LengthParameterValidatorModel", "type": "object"}, "NoOptionsParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "no_options", "default": "no_options", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "NoOptionsParameterValidatorModel", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RegexParameterValidatorModel": {"additionalProperties": false, "description": "Check if a regular expression **matches** the value, i.e. appears\nat the beginning of the value. To enforce a match of the complete value use\n``$`` at the end of the expression. The expression is given is the content\nof the validator tag. Note that for ``selects`` each option is checked\nseparately.", "properties": {"type": {"const": "regex", "default": "regex", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}, "expression": {"title": "Expression", "type": "string"}}, "required": ["expression"], "title": "RegexParameterValidatorModel", "type": "object"}, "ResourceRequirement": {"properties": {"type": {"const": "resource", "title": "Type", "type": "string"}, "cores_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 1, "description": "Minimum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Min"}, "cores_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Max"}, "ram_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 256, "description": "Minimum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Min"}, "ram_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Max"}, "tmpdir_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Min"}, "tmpdir_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Max"}, "cuda_version_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Version Min"}, "cuda_compute_capability": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Compute Capability"}, "gpu_memory_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Gpu Memory Min"}, "cuda_device_count_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Min"}, "cuda_device_count_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Max"}, "shm_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Shm Size"}, "timelimit": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum time in seconds the tool is allowed to run. Job will be terminated if exceeded.", "title": "Timelimit"}}, "required": ["type"], "title": "ResourceRequirement", "type": "object"}, "TestCollectionCollectionElementAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}}, "title": "TestCollectionCollectionElementAssertions", "type": "object"}, "TestCollectionDatasetElementAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestCollectionDatasetElementAssertions", "type": "object"}, "TestCollectionOutputAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}, "element_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Element Count"}, "attributes": {"anyOf": [{"$ref": "#/$defs/CollectionAttributes"}, {"type": "null"}], "default": null, "title": "Attributes"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "TestCollectionOutputAssertions", "type": "object"}, "TestDataOutputAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestDataOutputAssertions", "type": "object"}, "ToolProvidedMetadataDatasetCollection": {"properties": {"discover_via": {"const": "tool_provided_metadata", "default": "tool_provided_metadata", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}}, "title": "ToolProvidedMetadataDatasetCollection", "type": "object"}, "XrefDict": {"additionalProperties": false, "properties": {"value": {"title": "value", "type": "string"}, "type": {"title": "type", "type": "string"}}, "required": ["value", "type"], "title": "XrefDict", "type": "object"}, "YamlBooleanParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "boolean", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Value"}}, "required": ["name", "type"], "title": "YamlBooleanParameter", "type": "object"}, "YamlColorParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "color", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}}, "required": ["name", "type"], "title": "YamlColorParameter", "type": "object"}, "YamlConditionalParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "conditional", "title": "Type", "type": "string"}, "test_parameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "select": "#/$defs/YamlSelectParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}], "title": "Test Parameter"}, "whens": {"items": {"$ref": "#/$defs/YamlConditionalWhen"}, "minItems": 1, "title": "Whens", "type": "array"}}, "required": ["name", "type", "test_parameter", "whens"], "title": "YamlConditionalParameter", "type": "object"}, "YamlConditionalWhen": {"additionalProperties": false, "properties": {"discriminator": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "title": "Discriminator"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["discriminator"], "title": "YamlConditionalWhen", "type": "object"}, "YamlDataCollectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data_collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}}, "required": ["name", "type"], "title": "YamlDataCollectionParameter", "type": "object"}, "YamlDataParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}, "multiple": {"default": false, "title": "Multiple", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}}, "required": ["name", "type"], "title": "YamlDataParameter", "type": "object"}, "YamlFloatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "float", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlFloatParameter", "type": "object"}, "YamlGalaxyToolParameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "color": "#/$defs/YamlColorParameter", "conditional": "#/$defs/YamlConditionalParameter", "data": "#/$defs/YamlDataParameter", "data_collection": "#/$defs/YamlDataCollectionParameter", "float": "#/$defs/YamlFloatParameter", "integer": "#/$defs/YamlIntegerParameter", "repeat": "#/$defs/YamlRepeatParameter", "section": "#/$defs/YamlSectionParameter", "select": "#/$defs/YamlSelectParameter", "text": "#/$defs/YamlTextParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlIntegerParameter"}, {"$ref": "#/$defs/YamlFloatParameter"}, {"$ref": "#/$defs/YamlTextParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}, {"$ref": "#/$defs/YamlColorParameter"}, {"$ref": "#/$defs/YamlDataParameter"}, {"$ref": "#/$defs/YamlDataCollectionParameter"}, {"$ref": "#/$defs/YamlConditionalParameter"}, {"$ref": "#/$defs/YamlRepeatParameter"}, {"$ref": "#/$defs/YamlSectionParameter"}], "title": "YamlGalaxyToolParameter"}, "YamlIntegerParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "integer", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlIntegerParameter", "type": "object"}, "YamlLabelValue": {"description": "YAML-friendly option model \u2014 ``selected`` defaults to ``False``.", "properties": {"label": {"title": "Label", "type": "string"}, "value": {"title": "Value", "type": "string"}, "selected": {"default": false, "title": "Selected", "type": "boolean"}}, "required": ["label", "value"], "title": "YamlLabelValue", "type": "object"}, "YamlRepeatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "repeat", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}}, "required": ["name", "type"], "title": "YamlRepeatParameter", "type": "object"}, "YamlSectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "section", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["name", "type"], "title": "YamlSectionParameter", "type": "object"}, "YamlSelectParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "select", "title": "Type", "type": "string"}, "options": {"items": {"$ref": "#/$defs/YamlLabelValue"}, "minItems": 1, "title": "Options", "type": "array"}, "multiple": {"default": false, "title": "Multiple", "type": "boolean"}, "validators": {"default": [], "items": {"$ref": "#/$defs/NoOptionsParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type", "options"], "title": "YamlSelectParameter", "type": "object"}, "YamlTemplateConfigFile": {"properties": {"content": {"title": "Content", "type": "string"}, "name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Name"}, "filename": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Filename"}, "eval_engine": {"const": "ecmascript", "default": "ecmascript", "title": "Eval Engine", "type": "string"}}, "required": ["content"], "title": "YamlTemplateConfigFile", "type": "object"}, "YamlTestCredential": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credentials group.", "title": "Name", "type": "string"}, "variables": {"default": [], "description": "Variables exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Variables", "type": "array"}, "secrets": {"default": [], "description": "Secrets exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Secrets", "type": "array"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Version of the credential definition.", "title": "Version"}}, "required": ["name"], "title": "YamlTestCredential", "type": "object"}, "YamlTestCredentialValue": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credential variable or secret.", "title": "Name", "type": "string"}, "value": {"description": "Value of the credential variable or secret.", "title": "Value", "type": "string"}}, "required": ["name", "value"], "title": "YamlTestCredentialValue", "type": "object"}, "YamlTextParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "text", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}, "area": {"default": false, "title": "Area", "type": "boolean"}, "validators": {"default": [], "items": {"anyOf": [{"$ref": "#/$defs/LengthParameterValidatorModel"}, {"$ref": "#/$defs/RegexParameterValidatorModel"}, {"$ref": "#/$defs/EmptyFieldParameterValidatorModel"}]}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlTextParameter", "type": "object"}, "YamlToolTest": {"additionalProperties": false, "description": "In-tool test case as authored in YAML tool fixtures.", "properties": {"doc": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Human-readable description of this test case.", "title": "Doc"}, "inputs": {"anyOf": [{"additionalProperties": {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}, {"items": {}, "type": "array"}, {"additionalProperties": true, "type": "object"}]}, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of input parameter names to test values.", "title": "Inputs"}, "outputs": {"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionOutputAssertions"}, {"$ref": "#/$defs/TestDataOutputAssertions"}, {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}]}]}, "default": {}, "description": "Mapping of output names to expected values or assertions.", "title": "Outputs", "type": "object"}, "assert_stdout": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard output.", "title": "Assert Stdout"}, "assert_stderr": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard error.", "title": "Assert Stderr"}, "command": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the executed command line.", "title": "Command"}, "expect_exit_code": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected process exit code.", "title": "Expect Exit Code"}, "expect_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the tool is expected to produce an error.", "title": "Expect Failure"}, "expect_test_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the test itself is expected to fail.", "title": "Expect Test Failure"}, "credentials": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTestCredential"}, "type": "array"}, {"type": "null"}], "default": null, "description": "Credentials to inject for this test case.", "title": "Credentials"}}, "title": "YamlToolTest", "type": "object"}, "assertion_dict": {"additionalProperties": false, "properties": {"has_line": {"anyOf": [{"$ref": "#/$defs/base_has_line_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line"}, "has_line_matching": {"anyOf": [{"$ref": "#/$defs/base_has_line_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line Matching"}, "has_n_lines": {"anyOf": [{"$ref": "#/$defs/base_has_n_lines_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Lines"}, "has_text": {"anyOf": [{"$ref": "#/$defs/base_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text"}, "has_text_matching": {"anyOf": [{"$ref": "#/$defs/base_has_text_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text Matching"}, "not_has_text": {"anyOf": [{"$ref": "#/$defs/base_not_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Not Has Text"}, "has_n_columns": {"anyOf": [{"$ref": "#/$defs/base_has_n_columns_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Columns"}, "attribute_is": {"anyOf": [{"$ref": "#/$defs/base_attribute_is_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Is"}, "attribute_matches": {"anyOf": [{"$ref": "#/$defs/base_attribute_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Matches"}, "element_text": {"anyOf": [{"$ref": "#/$defs/base_element_text_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text"}, "element_text_is": {"anyOf": [{"$ref": "#/$defs/base_element_text_is_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Is"}, "element_text_matches": {"anyOf": [{"$ref": "#/$defs/base_element_text_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Matches"}, "has_element_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_element_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has Element With Path"}, "has_n_elements_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_n_elements_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Elements With Path"}, "is_valid_xml": {"anyOf": [{"$ref": "#/$defs/base_is_valid_xml_model"}, {"type": "null"}], "default": null, "title": "Assert Is Valid Xml"}, "xml_element": {"anyOf": [{"$ref": "#/$defs/base_xml_element_model"}, {"type": "null"}], "default": null, "title": "Assert Xml Element"}, "has_json_property_with_text": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Text"}, "has_json_property_with_value": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_value_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Value"}, "has_h5_attribute": {"anyOf": [{"$ref": "#/$defs/base_has_h5_attribute_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Attribute"}, "has_h5_keys": {"anyOf": [{"$ref": "#/$defs/base_has_h5_keys_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Keys"}, "has_archive_member": {"anyOf": [{"$ref": "#/$defs/base_has_archive_member_model"}, {"type": "null"}], "default": null, "title": "Assert Has Archive Member"}, "has_size": {"anyOf": [{"$ref": "#/$defs/base_has_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Size"}, "has_image_center_of_mass": {"anyOf": [{"$ref": "#/$defs/base_has_image_center_of_mass_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Center Of Mass"}, "has_image_channels": {"anyOf": [{"$ref": "#/$defs/base_has_image_channels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Channels"}, "has_image_depth": {"anyOf": [{"$ref": "#/$defs/base_has_image_depth_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Depth"}, "has_image_frames": {"anyOf": [{"$ref": "#/$defs/base_has_image_frames_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Frames"}, "has_image_height": {"anyOf": [{"$ref": "#/$defs/base_has_image_height_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Height"}, "has_image_mean_intensity": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_intensity_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Intensity"}, "has_image_mean_object_size": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_object_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Object Size"}, "has_image_n_labels": {"anyOf": [{"$ref": "#/$defs/base_has_image_n_labels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image N Labels"}, "has_image_width": {"anyOf": [{"$ref": "#/$defs/base_has_image_width_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Width"}}, "title": "assertion_dict", "type": "object"}, "assertion_list": {"items": {"anyOf": [{"discriminator": {"mapping": {"attribute_is": "#/$defs/attribute_is_model", "attribute_matches": "#/$defs/attribute_matches_model", "element_text": "#/$defs/element_text_model", "element_text_is": "#/$defs/element_text_is_model", "element_text_matches": "#/$defs/element_text_matches_model", "has_archive_member": "#/$defs/has_archive_member_model", "has_element_with_path": "#/$defs/has_element_with_path_model", "has_h5_attribute": "#/$defs/has_h5_attribute_model", "has_h5_keys": "#/$defs/has_h5_keys_model", "has_image_center_of_mass": "#/$defs/has_image_center_of_mass_model", "has_image_channels": "#/$defs/has_image_channels_model", "has_image_depth": "#/$defs/has_image_depth_model", "has_image_frames": "#/$defs/has_image_frames_model", "has_image_height": "#/$defs/has_image_height_model", "has_image_mean_intensity": "#/$defs/has_image_mean_intensity_model", "has_image_mean_object_size": "#/$defs/has_image_mean_object_size_model", "has_image_n_labels": "#/$defs/has_image_n_labels_model", "has_image_width": "#/$defs/has_image_width_model", "has_json_property_with_text": "#/$defs/has_json_property_with_text_model", "has_json_property_with_value": "#/$defs/has_json_property_with_value_model", "has_line": "#/$defs/has_line_model", "has_line_matching": "#/$defs/has_line_matching_model", "has_n_columns": "#/$defs/has_n_columns_model", "has_n_elements_with_path": "#/$defs/has_n_elements_with_path_model", "has_n_lines": "#/$defs/has_n_lines_model", "has_size": "#/$defs/has_size_model", "has_text": "#/$defs/has_text_model", "has_text_matching": "#/$defs/has_text_matching_model", "is_valid_xml": "#/$defs/is_valid_xml_model", "not_has_text": "#/$defs/not_has_text_model", "xml_element": "#/$defs/xml_element_model"}, "propertyName": "that"}, "oneOf": [{"$ref": "#/$defs/has_line_model"}, {"$ref": "#/$defs/has_line_matching_model"}, {"$ref": "#/$defs/has_n_lines_model"}, {"$ref": "#/$defs/has_text_model"}, {"$ref": "#/$defs/has_text_matching_model"}, {"$ref": "#/$defs/not_has_text_model"}, {"$ref": "#/$defs/has_n_columns_model"}, {"$ref": "#/$defs/attribute_is_model"}, {"$ref": "#/$defs/attribute_matches_model"}, {"$ref": "#/$defs/element_text_model"}, {"$ref": "#/$defs/element_text_is_model"}, {"$ref": "#/$defs/element_text_matches_model"}, {"$ref": "#/$defs/has_element_with_path_model"}, {"$ref": "#/$defs/has_n_elements_with_path_model"}, {"$ref": "#/$defs/is_valid_xml_model"}, {"$ref": "#/$defs/xml_element_model"}, {"$ref": "#/$defs/has_json_property_with_text_model"}, {"$ref": "#/$defs/has_json_property_with_value_model"}, {"$ref": "#/$defs/has_h5_attribute_model"}, {"$ref": "#/$defs/has_h5_keys_model"}, {"$ref": "#/$defs/has_archive_member_model"}, {"$ref": "#/$defs/has_size_model"}, {"$ref": "#/$defs/has_image_center_of_mass_model"}, {"$ref": "#/$defs/has_image_channels_model"}, {"$ref": "#/$defs/has_image_depth_model"}, {"$ref": "#/$defs/has_image_frames_model"}, {"$ref": "#/$defs/has_image_height_model"}, {"$ref": "#/$defs/has_image_mean_intensity_model"}, {"$ref": "#/$defs/has_image_mean_object_size_model"}, {"$ref": "#/$defs/has_image_n_labels_model"}, {"$ref": "#/$defs/has_image_width_model"}]}, {"$ref": "#/$defs/has_line_model_nested"}, {"$ref": "#/$defs/has_line_matching_model_nested"}, {"$ref": "#/$defs/has_n_lines_model_nested"}, {"$ref": "#/$defs/has_text_model_nested"}, {"$ref": "#/$defs/has_text_matching_model_nested"}, {"$ref": "#/$defs/not_has_text_model_nested"}, {"$ref": "#/$defs/has_n_columns_model_nested"}, {"$ref": "#/$defs/attribute_is_model_nested"}, {"$ref": "#/$defs/attribute_matches_model_nested"}, {"$ref": "#/$defs/element_text_model_nested"}, {"$ref": "#/$defs/element_text_is_model_nested"}, {"$ref": "#/$defs/element_text_matches_model_nested"}, {"$ref": "#/$defs/has_element_with_path_model_nested"}, {"$ref": "#/$defs/has_n_elements_with_path_model_nested"}, {"$ref": "#/$defs/is_valid_xml_model_nested"}, {"$ref": "#/$defs/xml_element_model_nested"}, {"$ref": "#/$defs/has_json_property_with_text_model_nested"}, {"$ref": "#/$defs/has_json_property_with_value_model_nested"}, {"$ref": "#/$defs/has_h5_attribute_model_nested"}, {"$ref": "#/$defs/has_h5_keys_model_nested"}, {"$ref": "#/$defs/has_archive_member_model_nested"}, {"$ref": "#/$defs/has_size_model_nested"}, {"$ref": "#/$defs/has_image_center_of_mass_model_nested"}, {"$ref": "#/$defs/has_image_channels_model_nested"}, {"$ref": "#/$defs/has_image_depth_model_nested"}, {"$ref": "#/$defs/has_image_frames_model_nested"}, {"$ref": "#/$defs/has_image_height_model_nested"}, {"$ref": "#/$defs/has_image_mean_intensity_model_nested"}, {"$ref": "#/$defs/has_image_mean_object_size_model_nested"}, {"$ref": "#/$defs/has_image_n_labels_model_nested"}, {"$ref": "#/$defs/has_image_width_model_nested"}]}, "title": "assertion_list", "type": "array"}, "attribute_is_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` is the specified ``text``.\n\nFor example:\n\n```xml\n<attribute_is path=\"outerElement/innerElement1\" attribute=\"foo\" text=\"bar\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_is", "default": "attribute_is", "title": "That", "type": "string"}}, "required": ["path", "attribute", "text"], "title": "Assert Attribute Is", "type": "object"}, "attribute_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_is": {"$ref": "#/$defs/base_attribute_is_model", "title": "Assert Attribute Is"}}, "required": ["attribute_is"], "title": "Assert Attribute Is (Nested)", "type": "object"}, "attribute_matches_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` matches the regular expression specified by ``expression``.\n\nFor example:\n\n```xml\n<attribute_matches path=\"outerElement/innerElement2\" attribute=\"foo2\" expression=\"bar\\d+\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_matches", "default": "attribute_matches", "title": "That", "type": "string"}}, "required": ["path", "attribute", "expression"], "title": "Assert Attribute Matches", "type": "object"}, "attribute_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_matches": {"$ref": "#/$defs/base_attribute_matches_model", "title": "Assert Attribute Matches"}}, "required": ["attribute_matches"], "title": "Assert Attribute Matches (Nested)", "type": "object"}, "base_attribute_is_model": {"additionalProperties": false, "description": "base model for attribute_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "text"], "title": "base_attribute_is_model", "type": "object"}, "base_attribute_matches_model": {"additionalProperties": false, "description": "base model for attribute_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "expression"], "title": "base_attribute_matches_model", "type": "object"}, "base_element_text_is_model": {"additionalProperties": false, "description": "base model for element_text_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "text"], "title": "base_element_text_is_model", "type": "object"}, "base_element_text_matches_model": {"additionalProperties": false, "description": "base model for element_text_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "expression"], "title": "base_element_text_matches_model", "type": "object"}, "base_element_text_model": {"additionalProperties": false, "description": "base model for element_text describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_element_text_model", "type": "object"}, "base_has_archive_member_model": {"additionalProperties": false, "description": "base model for has_archive_member describing attributes.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_has_archive_member_model", "type": "object"}, "base_has_element_with_path_model": {"additionalProperties": false, "description": "base model for has_element_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_element_with_path_model", "type": "object"}, "base_has_h5_attribute_model": {"additionalProperties": false, "description": "base model for has_h5_attribute describing attributes.", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}}, "required": ["key", "value"], "title": "base_has_h5_attribute_model", "type": "object"}, "base_has_h5_keys_model": {"additionalProperties": false, "description": "base model for has_h5_keys describing attributes.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}}, "required": ["keys"], "title": "base_has_h5_keys_model", "type": "object"}, "base_has_image_center_of_mass_model": {"additionalProperties": false, "description": "base model for has_image_center_of_mass describing attributes.", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}}, "required": ["center_of_mass"], "title": "base_has_image_center_of_mass_model", "type": "object"}, "base_has_image_channels_model": {"additionalProperties": false, "description": "base model for has_image_channels describing attributes.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_channels_model", "type": "object"}, "base_has_image_depth_model": {"additionalProperties": false, "description": "base model for has_image_depth describing attributes.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_depth_model", "type": "object"}, "base_has_image_frames_model": {"additionalProperties": false, "description": "base model for has_image_frames describing attributes.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_frames_model", "type": "object"}, "base_has_image_height_model": {"additionalProperties": false, "description": "base model for has_image_height describing attributes.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_height_model", "type": "object"}, "base_has_image_mean_intensity_model": {"additionalProperties": false, "description": "base model for has_image_mean_intensity describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}}, "title": "base_has_image_mean_intensity_model", "type": "object"}, "base_has_image_mean_object_size_model": {"additionalProperties": false, "description": "base model for has_image_mean_object_size describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}}, "title": "base_has_image_mean_object_size_model", "type": "object"}, "base_has_image_n_labels_model": {"additionalProperties": false, "description": "base model for has_image_n_labels describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_n_labels_model", "type": "object"}, "base_has_image_width_model": {"additionalProperties": false, "description": "base model for has_image_width describing attributes.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_width_model", "type": "object"}, "base_has_json_property_with_text_model": {"additionalProperties": false, "description": "base model for has_json_property_with_text describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}}, "required": ["property", "text"], "title": "base_has_json_property_with_text_model", "type": "object"}, "base_has_json_property_with_value_model": {"additionalProperties": false, "description": "base model for has_json_property_with_value describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}}, "required": ["property", "value"], "title": "base_has_json_property_with_value_model", "type": "object"}, "base_has_line_matching_model": {"additionalProperties": false, "description": "base model for has_line_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_line_matching_model", "type": "object"}, "base_has_line_model": {"additionalProperties": false, "description": "base model for has_line describing attributes.", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["line"], "title": "base_has_line_model", "type": "object"}, "base_has_n_columns_model": {"additionalProperties": false, "description": "base model for has_n_columns describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_columns_model", "type": "object"}, "base_has_n_elements_with_path_model": {"additionalProperties": false, "description": "base model for has_n_elements_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_n_elements_with_path_model", "type": "object"}, "base_has_n_lines_model": {"additionalProperties": false, "description": "base model for has_n_lines describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_lines_model", "type": "object"}, "base_has_size_model": {"additionalProperties": false, "description": "base model for has_size describing attributes.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_size_model", "type": "object"}, "base_has_text_matching_model": {"additionalProperties": false, "description": "base model for has_text_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_text_matching_model", "type": "object"}, "base_has_text_model": {"additionalProperties": false, "description": "base model for has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["text"], "title": "base_has_text_model", "type": "object"}, "base_is_valid_xml_model": {"additionalProperties": false, "description": "base model for is_valid_xml describing attributes.", "properties": {}, "title": "base_is_valid_xml_model", "type": "object"}, "base_not_has_text_model": {"additionalProperties": false, "description": "base model for not_has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}}, "required": ["text"], "title": "base_not_has_text_model", "type": "object"}, "base_xml_element_model": {"additionalProperties": false, "description": "base model for xml_element describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_xml_element_model", "type": "object"}, "element_text_is_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path`` is\nthe specified ``text``.\n\nFor example:\n\n```xml\n<element_text_is path=\"BlastOutput_program\" text=\"blastp\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_is", "default": "element_text_is", "title": "That", "type": "string"}}, "required": ["path", "text"], "title": "Assert Element Text Is", "type": "object"}, "element_text_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_is": {"$ref": "#/$defs/base_element_text_is_model", "title": "Assert Element Text Is"}}, "required": ["element_text_is"], "title": "Assert Element Text Is (Nested)", "type": "object"}, "element_text_matches_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path``\nmatches the regular expression defined by ``expression``.\n\nFor example:\n\n```xml\n<element_text_matches path=\"BlastOutput_version\" expression=\"BLASTP\\s+2\\.2.*\"/>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_matches", "default": "element_text_matches", "title": "That", "type": "string"}}, "required": ["path", "expression"], "title": "Assert Element Text Matches", "type": "object"}, "element_text_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_matches": {"$ref": "#/$defs/base_element_text_matches_model", "title": "Assert Element Text Matches"}}, "required": ["element_text_matches"], "title": "Assert Element Text Matches (Nested)", "type": "object"}, "element_text_model": {"additionalProperties": false, "description": "This tag allows the developer to recurisively specify additional assertions as\nchild elements about just the text contained in the element specified by the\nXPath-like ``path``, e.g.\n\n```xml\n<element_text path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def\">\n  <not_has_text text=\"EDK72998.1\" />\n</element_text>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the implicit assertions can be inverted.\nThe sub-assertions, which have their own ``negate`` attribute, are not affected\nby ``negate``.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "element_text", "default": "element_text", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Element Text", "type": "object"}, "element_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text": {"$ref": "#/$defs/base_element_text_model", "title": "Assert Element Text"}}, "required": ["element_text"], "title": "Assert Element Text (Nested)", "type": "object"}, "has_archive_member_model": {"additionalProperties": false, "description": "This tag allows to check if ``path`` is contained in a compressed file.\n\nThe path is a regular expression that is matched against the full paths of the objects in\nthe compressed file (remember that \"matching\" means it is checked if a prefix of\nthe full path of an archive member is described by the regular expression).\nValid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that\ndepending on the archive creation method:\n\n- full paths of the members may be prefixed with ``./``\n- directories may be treated as empty files\n\n```xml\n<has_archive_member path=\"./path/to/my-file.txt\"/>\n```\n\nWith ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of\narchive members matching ``path`` can be expressed. The following could be used,\ne.g., to assert an archive containing n&plusmn;1 elements out of which at least\n4 need to have a ``txt`` extension.\n\n```xml\n<has_archive_member path=\".*\" n=\"10\" delta=\"1\"/>\n<has_archive_member path=\".*\\.txt\" min=\"4\"/>\n```\n\nIn addition the tag can contain additional assertions as child elements about\nthe first member in the archive matching the regular expression ``path``. For\ninstance\n\n```xml\n<has_archive_member path=\".*/my-file.txt\">\n  <not_has_text text=\"EDK72998.1\"/>\n</has_archive_member>\n```\n\nIf the ``all`` attribute is set to ``true`` then all archive members are subject\nto the assertions. Note that, archive members matching the ``path`` are sorted\nalphabetically.\n\nThe ``negate`` attribute of the ``has_archive_member`` assertion only affects\nthe asserts on the presence and number of matching archive members, but not any\nsub-assertions (which can offer the ``negate`` attribute on their own).  The\ncheck if the file is an archive at all, which is also done by the function, is\nnot affected.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "has_archive_member", "default": "has_archive_member", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Archive Member", "type": "object"}, "has_archive_member_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_archive_member": {"$ref": "#/$defs/base_has_archive_member_model", "title": "Assert Has Archive Member"}}, "required": ["has_archive_member"], "title": "Assert Has Archive Member (Nested)", "type": "object"}, "has_element_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains at least one element (or tag) with the specified\nXPath-like ``path``, e.g.\n\n```xml\n<has_element_with_path path=\"BlastOutput_param/Parameters/Parameters_matrix\" />\n```\n\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_element_with_path", "default": "has_element_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Element With Path", "type": "object"}, "has_element_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_element_with_path": {"$ref": "#/$defs/base_has_element_with_path_model", "title": "Assert Has Element With Path"}}, "required": ["has_element_with_path"], "title": "Assert Has Element With Path (Nested)", "type": "object"}, "has_h5_attribute_model": {"additionalProperties": false, "description": "Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.\n\n```xml\n<has_h5_attribute key=\"nchroms\" value=\"15\" />\n```", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}, "that": {"const": "has_h5_attribute", "default": "has_h5_attribute", "title": "That", "type": "string"}}, "required": ["key", "value"], "title": "Assert Has H5 Attribute", "type": "object"}, "has_h5_attribute_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_attribute": {"$ref": "#/$defs/base_has_h5_attribute_model", "title": "Assert Has H5 Attribute"}}, "required": ["has_h5_attribute"], "title": "Assert Has H5 Attribute (Nested)", "type": "object"}, "has_h5_keys_model": {"additionalProperties": false, "description": "Asserts the specified HDF5 output has the given keys.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}, "that": {"const": "has_h5_keys", "default": "has_h5_keys", "title": "That", "type": "string"}}, "required": ["keys"], "title": "Assert Has H5 Keys", "type": "object"}, "has_h5_keys_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_keys": {"$ref": "#/$defs/base_has_h5_keys_model", "title": "Assert Has H5 Keys"}}, "required": ["has_h5_keys"], "title": "Assert Has H5 Keys (Nested)", "type": "object"}, "has_image_center_of_mass_model": {"additionalProperties": false, "description": "Asserts the specified output is an image and has the specified center of mass.\n\nAsserts the output is an image and has a specific center of mass,\nor has an Euclidean distance of ``eps`` or less to that point (e.g.,\n``<has_image_center_of_mass center_of_mass=\"511.07, 223.34\" />``).", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}, "that": {"const": "has_image_center_of_mass", "default": "has_image_center_of_mass", "title": "That", "type": "string"}}, "required": ["center_of_mass"], "title": "Assert Has Image Center Of Mass", "type": "object"}, "has_image_center_of_mass_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_center_of_mass": {"$ref": "#/$defs/base_has_image_center_of_mass_model", "title": "Assert Has Image Center Of Mass"}}, "required": ["has_image_center_of_mass"], "title": "Assert Has Image Center Of Mass (Nested)", "type": "object"}, "has_image_channels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of channels.\n\nThe number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels=\"3\" />``).\n\nAlternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_channels", "default": "has_image_channels", "title": "That", "type": "string"}}, "title": "Assert Has Image Channels", "type": "object"}, "has_image_channels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_channels": {"$ref": "#/$defs/base_has_image_channels_model", "title": "Assert Has Image Channels"}}, "required": ["has_image_channels"], "title": "Assert Has Image Channels (Nested)", "type": "object"}, "has_image_depth_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific depth (number of slices).\n\nThe depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected depth can be specified by ``min`` and/or ``max``.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_depth", "default": "has_image_depth", "title": "That", "type": "string"}}, "title": "Assert Has Image Depth", "type": "object"}, "has_image_depth_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_depth": {"$ref": "#/$defs/base_has_image_depth_model", "title": "Assert Has Image Depth"}}, "required": ["has_image_depth"], "title": "Assert Has Image Depth (Nested)", "type": "object"}, "has_image_frames_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of frames (number of time steps).\n\nThe number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_frames", "default": "has_image_frames", "title": "That", "type": "string"}}, "title": "Assert Has Image Frames", "type": "object"}, "has_image_frames_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_frames": {"$ref": "#/$defs/base_has_image_frames_model", "title": "Assert Has Image Frames"}}, "required": ["has_image_frames"], "title": "Assert Has Image Frames (Nested)", "type": "object"}, "has_image_height_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific height (in pixels).\n\nThe height is plus/minus ``delta`` (e.g., ``<has_image_height height=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected height can be specified by ``min`` and/or ``max``.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_height", "default": "has_image_height", "title": "That", "type": "string"}}, "title": "Assert Has Image Height", "type": "object"}, "has_image_height_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_height": {"$ref": "#/$defs/base_has_image_height_model", "title": "Assert Has Image Height"}}, "required": ["has_image_height"], "title": "Assert Has Image Height (Nested)", "type": "object"}, "has_image_mean_intensity_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific mean intensity value.\n\nThe mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity=\"0.83\" />``).\nAlternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}, "that": {"const": "has_image_mean_intensity", "default": "has_image_mean_intensity", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Intensity", "type": "object"}, "has_image_mean_intensity_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_intensity": {"$ref": "#/$defs/base_has_image_mean_intensity_model", "title": "Assert Has Image Mean Intensity"}}, "required": ["has_image_mean_intensity"], "title": "Assert Has Image Mean Intensity (Nested)", "type": "object"}, "has_image_mean_object_size_model": {"additionalProperties": false, "description": "Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),\n\nThe mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size=\"111.87\" exclude_labels=\"0\" />``).\n\nThe labels must be unique.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}, "that": {"const": "has_image_mean_object_size", "default": "has_image_mean_object_size", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Object Size", "type": "object"}, "has_image_mean_object_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_object_size": {"$ref": "#/$defs/base_has_image_mean_object_size_model", "title": "Assert Has Image Mean Object Size"}}, "required": ["has_image_mean_object_size"], "title": "Assert Has Image Mean Object Size (Nested)", "type": "object"}, "has_image_n_labels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has the specified labels.\n\nLabels can be a number of labels or unique values (e.g.,\n``<has_image_n_labels n=\"187\" exclude_labels=\"0\" />``).\n\nThe primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_n_labels", "default": "has_image_n_labels", "title": "That", "type": "string"}}, "title": "Assert Has Image N Labels", "type": "object"}, "has_image_n_labels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_n_labels": {"$ref": "#/$defs/base_has_image_n_labels_model", "title": "Assert Has Image N Labels"}}, "required": ["has_image_n_labels"], "title": "Assert Has Image N Labels (Nested)", "type": "object"}, "has_image_width_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific width (in pixels).\n\nThe width is plus/minus ``delta`` (e.g., ``<has_image_width width=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected width can be specified by ``min`` and/or ``max``.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_width", "default": "has_image_width", "title": "That", "type": "string"}}, "title": "Assert Has Image Width", "type": "object"}, "has_image_width_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_width": {"$ref": "#/$defs/base_has_image_width_model", "title": "Assert Has Image Width"}}, "required": ["has_image_width"], "title": "Assert Has Image Width (Nested)", "type": "object"}, "has_json_property_with_text_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified text (i.e. string) value.\n\n```xml\n<has_json_property_with_text property=\"color\" text=\"red\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}, "that": {"const": "has_json_property_with_text", "default": "has_json_property_with_text", "title": "That", "type": "string"}}, "required": ["property", "text"], "title": "Assert Has Json Property With Text", "type": "object"}, "has_json_property_with_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_text": {"$ref": "#/$defs/base_has_json_property_with_text_model", "title": "Assert Has Json Property With Text"}}, "required": ["has_json_property_with_text"], "title": "Assert Has Json Property With Text (Nested)", "type": "object"}, "has_json_property_with_value_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified JSON value.\n\n```xml\n<has_json_property_with_value property=\"skipped_columns\" value=\"[1, 3, 5]\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}, "that": {"const": "has_json_property_with_value", "default": "has_json_property_with_value", "title": "That", "type": "string"}}, "required": ["property", "value"], "title": "Assert Has Json Property With Value", "type": "object"}, "has_json_property_with_value_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_value": {"$ref": "#/$defs/base_has_json_property_with_value_model", "title": "Assert Has Json Property With Value"}}, "required": ["has_json_property_with_value"], "title": "Assert Has Json Property With Value (Nested)", "type": "object"}, "has_line_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains a line matching the\nregular expression specified by the argument expression. If n is given\nthe assertion checks for exactly n occurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line_matching", "default": "has_line_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Line Matching", "type": "object"}, "has_line_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line_matching": {"$ref": "#/$defs/base_has_line_matching_model", "title": "Assert Has Line Matching"}}, "required": ["has_line_matching"], "title": "Assert Has Line Matching (Nested)", "type": "object"}, "has_line_model": {"additionalProperties": false, "description": "Asserts the specified output contains the line specified by the\nargument line. The exact number of occurrences can be optionally\nspecified by the argument n", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line", "default": "has_line", "title": "That", "type": "string"}}, "required": ["line"], "title": "Assert Has Line", "type": "object"}, "has_line_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line": {"$ref": "#/$defs/base_has_line_model", "title": "Assert Has Line"}}, "required": ["has_line"], "title": "Assert Has Line (Nested)", "type": "object"}, "has_n_columns_model": {"additionalProperties": false, "description": "Asserts tabular output  contains the specified\nnumber (``n``) of columns.\n\nFor instance, ``<has_n_columns n=\"3\"/>``. The assertion tests only the first line.\nNumber of columns can optionally also be specified with ``delta``. Alternatively the\nrange of expected occurrences can be specified by ``min`` and/or ``max``.\n\nOptionally a column separator (``sep``, default is ``       ``) `and comment character(s)\ncan be specified (``comment``, default is empty string). The first non-comment\nline is used for determining the number of columns.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_columns", "default": "has_n_columns", "title": "That", "type": "string"}}, "title": "Assert Has N Columns", "type": "object"}, "has_n_columns_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_columns": {"$ref": "#/$defs/base_has_n_columns_model", "title": "Assert Has N Columns"}}, "required": ["has_n_columns"], "title": "Assert Has N Columns (Nested)", "type": "object"}, "has_n_elements_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or\ntags) with the specified XPath-like ``path``.\n\nFor example:\n\n```xml\n<has_n_elements_with_path n=\"9\" path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num\" />\n```\n\nAlternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes\ncan be used to specify the range of the expected number of occurrences.\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_elements_with_path", "default": "has_n_elements_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has N Elements With Path", "type": "object"}, "has_n_elements_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_elements_with_path": {"$ref": "#/$defs/base_has_n_elements_with_path_model", "title": "Assert Has N Elements With Path"}}, "required": ["has_n_elements_with_path"], "title": "Assert Has N Elements With Path (Nested)", "type": "object"}, "has_n_lines_model": {"additionalProperties": false, "description": "Asserts the specified output contains ``n`` lines allowing\nfor a difference in the number of lines (delta)\nor relative differebce in the number of lines", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_lines", "default": "has_n_lines", "title": "That", "type": "string"}}, "title": "Assert Has N Lines", "type": "object"}, "has_n_lines_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_lines": {"$ref": "#/$defs/base_has_n_lines_model", "title": "Assert Has N Lines"}}, "required": ["has_n_lines"], "title": "Assert Has N Lines (Nested)", "type": "object"}, "has_size_model": {"additionalProperties": false, "description": "Asserts the specified output has a size of the specified value\n\nAttributes size and value or synonyms though value is considered deprecated.\nThe size optionally allows for absolute (``delta``) difference.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_size", "default": "has_size", "title": "That", "type": "string"}}, "title": "Assert Has Size", "type": "object"}, "has_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_size": {"$ref": "#/$defs/base_has_size_model", "title": "Assert Has Size"}}, "required": ["has_size"], "title": "Assert Has Size (Nested)", "type": "object"}, "has_text_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains text matching the\nregular expression specified by the argument expression.\nIf n is given the assertion checks for exactly n (nonoverlapping)\noccurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text_matching", "default": "has_text_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Text Matching", "type": "object"}, "has_text_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text_matching": {"$ref": "#/$defs/base_has_text_matching_model", "title": "Assert Has Text Matching"}}, "required": ["has_text_matching"], "title": "Assert Has Text Matching (Nested)", "type": "object"}, "has_text_model": {"additionalProperties": false, "description": "Asserts specified output contains the substring specified by\nthe argument text. The exact number of occurrences can be\noptionally specified by the argument n", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text", "default": "has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Has Text", "type": "object"}, "has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text": {"$ref": "#/$defs/base_has_text_model", "title": "Assert Has Text"}}, "required": ["has_text"], "title": "Assert Has Text (Nested)", "type": "object"}, "is_valid_xml_model": {"additionalProperties": false, "description": "Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).", "properties": {"that": {"const": "is_valid_xml", "default": "is_valid_xml", "title": "That", "type": "string"}}, "title": "Assert Is Valid Xml", "type": "object"}, "is_valid_xml_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"is_valid_xml": {"$ref": "#/$defs/base_is_valid_xml_model", "title": "Assert Is Valid Xml"}}, "required": ["is_valid_xml"], "title": "Assert Is Valid Xml (Nested)", "type": "object"}, "not_has_text_model": {"additionalProperties": false, "description": "Asserts specified output does not contain the substring\nspecified by the argument text", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "that": {"const": "not_has_text", "default": "not_has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Not Has Text", "type": "object"}, "not_has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"not_has_text": {"$ref": "#/$defs/base_not_has_text_model", "title": "Assert Not Has Text"}}, "required": ["not_has_text"], "title": "Assert Not Has Text (Nested)", "type": "object"}, "xml_element_model": {"additionalProperties": false, "description": "Assert if the XML file contains element(s) or tag(s) with the specified\n[XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``\nor ``min`` and ``max`` are given also the number of occurrences is checked.\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem\"/>\n  <xml_element path=\"./elem/more[2]\"/>\n  <xml_element path=\".//more\" n=\"3\" delta=\"1\"/>\n</assert_contents>\n```\n\nWith ``negate=\"true\"`` the outcome of the assertions wrt the presence and number\nof ``path`` can be negated. If there are any sub assertions then check them against\n\n- the content of the attribute ``attribute``\n- the element's text if no attribute is given\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem/more[2]\" attribute=\"name\">\n    <has_text_matching expression=\"foo$\"/>\n  </xml_element>\n</assert_contents>\n```\n\nSub-assertions are not subject to the ``negate`` attribute of ``xml_element``.\nIf ``all`` is ``true`` then the sub assertions are checked for all occurrences.\n\nNote that all other XML assertions can be expressed by this assertion (Galaxy\nalso implements the other assertions by calling this one).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "xml_element", "default": "xml_element", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Xml Element", "type": "object"}, "xml_element_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"xml_element": {"$ref": "#/$defs/base_xml_element_model", "title": "Assert Xml Element"}}, "required": ["xml_element"], "title": "Assert Xml Element (Nested)", "type": "object"}}, "additionalProperties": false, "description": "Full unprivileged tool source, including the optional ``tests`` block.\n\nThis is the model persisted and validated on the API surface\n(``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring\nuses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added\nback here so direct authors and stored rows can still carry tests.", "properties": {"id": {"anyOf": [{"maxLength": 255, "minLength": 3, "pattern": "^[a-z][a-z0-9_-]*$", "type": "string"}, {"type": "null"}], "default": null, "description": "Unique identifier for the tool. Lowercase, must start with a letter, may contain letters, digits, '_' and '-'.", "examples": ["my-cool-tool"], "title": "id"}, "version": {"description": "Version for the tool.", "examples": ["0.1.0"], "title": "version", "type": "string"}, "name": {"description": "The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.", "minLength": 5, "title": "name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The description is displayed in the tool menu immediately following the hyperlink for the tool.", "title": "description"}, "configfiles": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTemplateConfigFile"}, "type": "array"}, {"type": "null"}], "default": null, "description": "A list of config files for this tool.", "title": "configfiles"}, "requirements": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/JavascriptRequirement"}, {"$ref": "#/$defs/ResourceRequirement"}, {"$ref": "#/$defs/ContainerRequirement"}]}, "type": "array"}, {"type": "null"}], "default": [], "description": "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.", "title": "requirements"}, "shell_command": {"description": "A string that contains the command to be executed. Parameters can be referenced inside $().", "examples": ["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"], "title": "shell_command", "type": "string"}, "inputs": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "inputs", "type": "array"}, "outputs": {"default": [], "items": {"discriminator": {"mapping": {"boolean": "#/$defs/IncomingToolOutputBoolean", "collection": "#/$defs/IncomingToolOutputCollection", "data": "#/$defs/IncomingToolOutputDataset", "float": "#/$defs/IncomingToolOutputFloat", "integer": "#/$defs/IncomingToolOutputInteger", "text": "#/$defs/IncomingToolOutputText"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/IncomingToolOutputDataset"}, {"$ref": "#/$defs/IncomingToolOutputCollection"}, {"$ref": "#/$defs/IncomingToolOutputText"}, {"$ref": "#/$defs/IncomingToolOutputInteger"}, {"$ref": "#/$defs/IncomingToolOutputFloat"}, {"$ref": "#/$defs/IncomingToolOutputBoolean"}]}, "title": "outputs", "type": "array"}, "citations": {"anyOf": [{"items": {"$ref": "#/$defs/Citation"}, "type": "array"}, {"type": "null"}], "default": null, "title": "citations"}, "license": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.", "examples": ["MIT"], "title": "license"}, "edam_operations": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_operations"}, "edam_topics": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_topics"}, "xrefs": {"anyOf": [{"items": {"$ref": "#/$defs/XrefDict"}, "type": "array"}, {"type": "null"}], "default": null, "title": "xrefs"}, "profile": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "profile"}, "help": {"anyOf": [{"$ref": "#/$defs/HelpContent"}, {"type": "null"}], "default": null, "description": "Help text shown below the tool interface.", "title": "help"}, "class": {"const": "GalaxyUserTool", "title": "class_", "type": "string"}, "container": {"description": "Container image to use for this tool.", "examples": ["quay.io/biocontainers/python:3.13"], "title": "container", "type": "string"}, "tests": {"anyOf": [{"items": {"$ref": "#/$defs/YamlToolTest"}, "type": "array"}, {"type": "null"}], "default": null, "title": "tests"}}, "required": ["version", "name", "shell_command", "class", "container"], "title": "UserToolSource", "type": "object"}
\ No newline at end of file
+{"$defs": {"Citation": {"properties": {"type": {"title": "Type", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["type", "content"], "title": "Citation", "type": "object"}, "CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "Container": {"properties": {"type": {"enum": ["docker", "singularity"], "title": "Type", "type": "string"}, "container_id": {"title": "Container Id", "type": "string"}}, "required": ["type", "container_id"], "title": "Container", "type": "object"}, "ContainerRequirement": {"properties": {"type": {"const": "container", "title": "Type", "type": "string"}, "container": {"$ref": "#/$defs/Container"}}, "required": ["type", "container"], "title": "ContainerRequirement", "type": "object"}, "EmptyFieldParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "empty_field", "default": "empty_field", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "EmptyFieldParameterValidatorModel", "type": "object"}, "FilePatternDatasetCollectionDescription": {"properties": {"discover_via": {"const": "pattern", "default": "pattern", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}, "sort_key": {"default": "filename", "enum": ["filename", "name", "designation", "dbkey"], "title": "Sort Key", "type": "string"}, "sort_comp": {"default": "lexical", "enum": ["lexical", "numeric"], "title": "Sort Comp", "type": "string"}, "sort_reverse": {"default": false, "title": "Sort Reverse", "type": "boolean"}, "pattern": {"title": "Pattern", "type": "string"}}, "required": ["pattern"], "title": "FilePatternDatasetCollectionDescription", "type": "object"}, "HelpContent": {"properties": {"format": {"enum": ["restructuredtext", "plain_text", "markdown"], "title": "Format", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["format", "content"], "title": "HelpContent", "type": "object"}, "InRangeParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "in_range", "default": "in_range", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "exclude_min": {"default": false, "title": "Exclude Min", "type": "boolean"}, "exclude_max": {"default": false, "title": "Exclude Max", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "InRangeParameterValidatorModel", "type": "object"}, "IncomingToolOutputBoolean": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "boolean", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputBoolean", "type": "object"}, "IncomingToolOutputCollection": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "collection_type_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type Source"}, "collection_type_from_rules": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type From Rules"}, "structured_like": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Structured Like"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}}, "required": ["type"], "title": "IncomingToolOutputCollection", "type": "object"}, "IncomingToolOutputDataset": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The short name for the output datatype.", "title": "Format"}, "format_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.", "title": "Format Source"}, "metadata_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This copies the metadata information from the tool\u2019s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.", "title": "Metadata Source"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}, "from_work_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Relative path to a file produced by the tool in its working directory. Output\u2019s contents are set to this file\u2019s contents.", "title": "from_work_dir"}, "precreate_directory": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Precreate Directory"}}, "required": ["type"], "title": "IncomingToolOutputDataset", "type": "object"}, "IncomingToolOutputFloat": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "float", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputFloat", "type": "object"}, "IncomingToolOutputInteger": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "integer", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputInteger", "type": "object"}, "IncomingToolOutputText": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "text", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputText", "type": "object"}, "JavascriptRequirement": {"properties": {"type": {"const": "javascript", "title": "Type", "type": "string"}, "expression_lib": {"anyOf": [{"items": {"description": "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.", "examples": ["function pickValue() {\n    if (inputs.conditional_parameter.test_parameter == \"a\") {\n        return inputs.conditional_parameter.integer_parameter\n    } else {\n        return inputs.conditional_parameter.boolean_parameter\n    }\n}"], "title": "expression_lib", "type": "string"}, "type": "array"}, {"type": "null"}], "title": "Expression Lib"}}, "required": ["type", "expression_lib"], "title": "JavascriptRequirement", "type": "object"}, "LengthParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "length", "default": "length", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "LengthParameterValidatorModel", "type": "object"}, "NoOptionsParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "no_options", "default": "no_options", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "NoOptionsParameterValidatorModel", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RegexParameterValidatorModel": {"additionalProperties": false, "description": "Check if a regular expression **matches** the value, i.e. appears\nat the beginning of the value. To enforce a match of the complete value use\n``$`` at the end of the expression. The expression is given is the content\nof the validator tag. Note that for ``selects`` each option is checked\nseparately.", "properties": {"type": {"const": "regex", "default": "regex", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}, "expression": {"title": "Expression", "type": "string"}}, "required": ["expression"], "title": "RegexParameterValidatorModel", "type": "object"}, "ResourceRequirement": {"properties": {"type": {"const": "resource", "title": "Type", "type": "string"}, "cores_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 1, "description": "Minimum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Min"}, "cores_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Max"}, "ram_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 256, "description": "Minimum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Min"}, "ram_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Max"}, "tmpdir_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Min"}, "tmpdir_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Max"}, "cuda_version_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Version Min"}, "cuda_compute_capability": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Compute Capability"}, "gpu_memory_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Gpu Memory Min"}, "cuda_device_count_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Min"}, "cuda_device_count_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Max"}, "shm_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Shm Size"}, "timelimit": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum time in seconds the tool is allowed to run. Job will be terminated if exceeded.", "title": "Timelimit"}}, "required": ["type"], "title": "ResourceRequirement", "type": "object"}, "TestCollectionCollectionElementAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}}, "title": "TestCollectionCollectionElementAssertions", "type": "object"}, "TestCollectionDatasetElementAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestCollectionDatasetElementAssertions", "type": "object"}, "TestCollectionOutputAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}, "element_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Element Count"}, "attributes": {"anyOf": [{"$ref": "#/$defs/CollectionAttributes"}, {"type": "null"}], "default": null, "title": "Attributes"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "TestCollectionOutputAssertions", "type": "object"}, "TestDataOutputAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestDataOutputAssertions", "type": "object"}, "ToolProvidedMetadataDatasetCollection": {"properties": {"discover_via": {"const": "tool_provided_metadata", "default": "tool_provided_metadata", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}}, "title": "ToolProvidedMetadataDatasetCollection", "type": "object"}, "XrefDict": {"additionalProperties": false, "properties": {"value": {"title": "value", "type": "string"}, "type": {"title": "type", "type": "string"}}, "required": ["value", "type"], "title": "XrefDict", "type": "object"}, "YamlBooleanParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "boolean", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Value"}}, "required": ["name", "type"], "title": "YamlBooleanParameter", "type": "object"}, "YamlColorParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "color", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}}, "required": ["name", "type"], "title": "YamlColorParameter", "type": "object"}, "YamlConditionalParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "conditional", "title": "Type", "type": "string"}, "test_parameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "select": "#/$defs/YamlSelectParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}], "title": "Test Parameter"}, "whens": {"items": {"$ref": "#/$defs/YamlConditionalWhen"}, "minItems": 1, "title": "Whens", "type": "array"}}, "required": ["name", "type", "test_parameter", "whens"], "title": "YamlConditionalParameter", "type": "object"}, "YamlConditionalWhen": {"additionalProperties": false, "properties": {"discriminator": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "title": "Discriminator"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["discriminator"], "title": "YamlConditionalWhen", "type": "object"}, "YamlDataCollectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data_collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}}, "required": ["name", "type"], "title": "YamlDataCollectionParameter", "type": "object"}, "YamlDataParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}, "multiple": {"default": false, "description": "Set true to accept several datasets (a list) for this input instead of one.", "title": "Multiple", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. Do NOT set this for a single-dataset input -- a data input is already required by default, so leave 'min' unset unless the input accepts multiple datasets.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; leave unset for a single-dataset input.", "title": "Max"}}, "required": ["name", "type"], "title": "YamlDataParameter", "type": "object"}, "YamlFloatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "float", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlFloatParameter", "type": "object"}, "YamlGalaxyToolParameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "color": "#/$defs/YamlColorParameter", "conditional": "#/$defs/YamlConditionalParameter", "data": "#/$defs/YamlDataParameter", "data_collection": "#/$defs/YamlDataCollectionParameter", "float": "#/$defs/YamlFloatParameter", "integer": "#/$defs/YamlIntegerParameter", "repeat": "#/$defs/YamlRepeatParameter", "section": "#/$defs/YamlSectionParameter", "select": "#/$defs/YamlSelectParameter", "text": "#/$defs/YamlTextParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlIntegerParameter"}, {"$ref": "#/$defs/YamlFloatParameter"}, {"$ref": "#/$defs/YamlTextParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}, {"$ref": "#/$defs/YamlColorParameter"}, {"$ref": "#/$defs/YamlDataParameter"}, {"$ref": "#/$defs/YamlDataCollectionParameter"}, {"$ref": "#/$defs/YamlConditionalParameter"}, {"$ref": "#/$defs/YamlRepeatParameter"}, {"$ref": "#/$defs/YamlSectionParameter"}], "title": "YamlGalaxyToolParameter"}, "YamlIntegerParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "integer", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlIntegerParameter", "type": "object"}, "YamlLabelValue": {"description": "YAML-friendly option model \u2014 ``selected`` defaults to ``False``.", "properties": {"label": {"title": "Label", "type": "string"}, "value": {"title": "Value", "type": "string"}, "selected": {"default": false, "title": "Selected", "type": "boolean"}}, "required": ["label", "value"], "title": "YamlLabelValue", "type": "object"}, "YamlRepeatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "repeat", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}}, "required": ["name", "type"], "title": "YamlRepeatParameter", "type": "object"}, "YamlSectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "section", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["name", "type"], "title": "YamlSectionParameter", "type": "object"}, "YamlSelectParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "select", "title": "Type", "type": "string"}, "options": {"items": {"$ref": "#/$defs/YamlLabelValue"}, "minItems": 1, "title": "Options", "type": "array"}, "multiple": {"default": false, "title": "Multiple", "type": "boolean"}, "validators": {"default": [], "items": {"$ref": "#/$defs/NoOptionsParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type", "options"], "title": "YamlSelectParameter", "type": "object"}, "YamlTemplateConfigFile": {"properties": {"content": {"title": "Content", "type": "string"}, "name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Name"}, "filename": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Filename"}, "eval_engine": {"const": "ecmascript", "default": "ecmascript", "title": "Eval Engine", "type": "string"}}, "required": ["content"], "title": "YamlTemplateConfigFile", "type": "object"}, "YamlTestCredential": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credentials group.", "title": "Name", "type": "string"}, "variables": {"default": [], "description": "Variables exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Variables", "type": "array"}, "secrets": {"default": [], "description": "Secrets exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Secrets", "type": "array"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Version of the credential definition.", "title": "Version"}}, "required": ["name"], "title": "YamlTestCredential", "type": "object"}, "YamlTestCredentialValue": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credential variable or secret.", "title": "Name", "type": "string"}, "value": {"description": "Value of the credential variable or secret.", "title": "Value", "type": "string"}}, "required": ["name", "value"], "title": "YamlTestCredentialValue", "type": "object"}, "YamlTextParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "text", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}, "area": {"default": false, "title": "Area", "type": "boolean"}, "validators": {"default": [], "items": {"anyOf": [{"$ref": "#/$defs/LengthParameterValidatorModel"}, {"$ref": "#/$defs/RegexParameterValidatorModel"}, {"$ref": "#/$defs/EmptyFieldParameterValidatorModel"}]}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlTextParameter", "type": "object"}, "YamlToolTest": {"additionalProperties": false, "description": "In-tool test case as authored in YAML tool fixtures.", "properties": {"doc": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Human-readable description of this test case.", "title": "Doc"}, "inputs": {"anyOf": [{"additionalProperties": {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}, {"items": {}, "type": "array"}, {"additionalProperties": true, "type": "object"}]}, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of input parameter names to test values.", "title": "Inputs"}, "outputs": {"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionOutputAssertions"}, {"$ref": "#/$defs/TestDataOutputAssertions"}, {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}]}]}, "default": {}, "description": "Mapping of output names to expected values or assertions.", "title": "Outputs", "type": "object"}, "assert_stdout": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard output.", "title": "Assert Stdout"}, "assert_stderr": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard error.", "title": "Assert Stderr"}, "command": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the executed command line.", "title": "Command"}, "expect_exit_code": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected process exit code.", "title": "Expect Exit Code"}, "expect_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the tool is expected to produce an error.", "title": "Expect Failure"}, "expect_test_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the test itself is expected to fail.", "title": "Expect Test Failure"}, "credentials": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTestCredential"}, "type": "array"}, {"type": "null"}], "default": null, "description": "Credentials to inject for this test case.", "title": "Credentials"}}, "title": "YamlToolTest", "type": "object"}, "assertion_dict": {"additionalProperties": false, "properties": {"has_line": {"anyOf": [{"$ref": "#/$defs/base_has_line_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line"}, "has_line_matching": {"anyOf": [{"$ref": "#/$defs/base_has_line_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line Matching"}, "has_n_lines": {"anyOf": [{"$ref": "#/$defs/base_has_n_lines_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Lines"}, "has_text": {"anyOf": [{"$ref": "#/$defs/base_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text"}, "has_text_matching": {"anyOf": [{"$ref": "#/$defs/base_has_text_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text Matching"}, "not_has_text": {"anyOf": [{"$ref": "#/$defs/base_not_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Not Has Text"}, "has_n_columns": {"anyOf": [{"$ref": "#/$defs/base_has_n_columns_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Columns"}, "attribute_is": {"anyOf": [{"$ref": "#/$defs/base_attribute_is_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Is"}, "attribute_matches": {"anyOf": [{"$ref": "#/$defs/base_attribute_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Matches"}, "element_text": {"anyOf": [{"$ref": "#/$defs/base_element_text_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text"}, "element_text_is": {"anyOf": [{"$ref": "#/$defs/base_element_text_is_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Is"}, "element_text_matches": {"anyOf": [{"$ref": "#/$defs/base_element_text_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Matches"}, "has_element_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_element_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has Element With Path"}, "has_n_elements_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_n_elements_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Elements With Path"}, "is_valid_xml": {"anyOf": [{"$ref": "#/$defs/base_is_valid_xml_model"}, {"type": "null"}], "default": null, "title": "Assert Is Valid Xml"}, "xml_element": {"anyOf": [{"$ref": "#/$defs/base_xml_element_model"}, {"type": "null"}], "default": null, "title": "Assert Xml Element"}, "has_json_property_with_text": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Text"}, "has_json_property_with_value": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_value_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Value"}, "has_h5_attribute": {"anyOf": [{"$ref": "#/$defs/base_has_h5_attribute_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Attribute"}, "has_h5_keys": {"anyOf": [{"$ref": "#/$defs/base_has_h5_keys_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Keys"}, "has_archive_member": {"anyOf": [{"$ref": "#/$defs/base_has_archive_member_model"}, {"type": "null"}], "default": null, "title": "Assert Has Archive Member"}, "has_size": {"anyOf": [{"$ref": "#/$defs/base_has_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Size"}, "has_image_center_of_mass": {"anyOf": [{"$ref": "#/$defs/base_has_image_center_of_mass_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Center Of Mass"}, "has_image_channels": {"anyOf": [{"$ref": "#/$defs/base_has_image_channels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Channels"}, "has_image_depth": {"anyOf": [{"$ref": "#/$defs/base_has_image_depth_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Depth"}, "has_image_frames": {"anyOf": [{"$ref": "#/$defs/base_has_image_frames_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Frames"}, "has_image_height": {"anyOf": [{"$ref": "#/$defs/base_has_image_height_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Height"}, "has_image_mean_intensity": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_intensity_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Intensity"}, "has_image_mean_object_size": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_object_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Object Size"}, "has_image_n_labels": {"anyOf": [{"$ref": "#/$defs/base_has_image_n_labels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image N Labels"}, "has_image_width": {"anyOf": [{"$ref": "#/$defs/base_has_image_width_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Width"}}, "title": "assertion_dict", "type": "object"}, "assertion_list": {"items": {"anyOf": [{"discriminator": {"mapping": {"attribute_is": "#/$defs/attribute_is_model", "attribute_matches": "#/$defs/attribute_matches_model", "element_text": "#/$defs/element_text_model", "element_text_is": "#/$defs/element_text_is_model", "element_text_matches": "#/$defs/element_text_matches_model", "has_archive_member": "#/$defs/has_archive_member_model", "has_element_with_path": "#/$defs/has_element_with_path_model", "has_h5_attribute": "#/$defs/has_h5_attribute_model", "has_h5_keys": "#/$defs/has_h5_keys_model", "has_image_center_of_mass": "#/$defs/has_image_center_of_mass_model", "has_image_channels": "#/$defs/has_image_channels_model", "has_image_depth": "#/$defs/has_image_depth_model", "has_image_frames": "#/$defs/has_image_frames_model", "has_image_height": "#/$defs/has_image_height_model", "has_image_mean_intensity": "#/$defs/has_image_mean_intensity_model", "has_image_mean_object_size": "#/$defs/has_image_mean_object_size_model", "has_image_n_labels": "#/$defs/has_image_n_labels_model", "has_image_width": "#/$defs/has_image_width_model", "has_json_property_with_text": "#/$defs/has_json_property_with_text_model", "has_json_property_with_value": "#/$defs/has_json_property_with_value_model", "has_line": "#/$defs/has_line_model", "has_line_matching": "#/$defs/has_line_matching_model", "has_n_columns": "#/$defs/has_n_columns_model", "has_n_elements_with_path": "#/$defs/has_n_elements_with_path_model", "has_n_lines": "#/$defs/has_n_lines_model", "has_size": "#/$defs/has_size_model", "has_text": "#/$defs/has_text_model", "has_text_matching": "#/$defs/has_text_matching_model", "is_valid_xml": "#/$defs/is_valid_xml_model", "not_has_text": "#/$defs/not_has_text_model", "xml_element": "#/$defs/xml_element_model"}, "propertyName": "that"}, "oneOf": [{"$ref": "#/$defs/has_line_model"}, {"$ref": "#/$defs/has_line_matching_model"}, {"$ref": "#/$defs/has_n_lines_model"}, {"$ref": "#/$defs/has_text_model"}, {"$ref": "#/$defs/has_text_matching_model"}, {"$ref": "#/$defs/not_has_text_model"}, {"$ref": "#/$defs/has_n_columns_model"}, {"$ref": "#/$defs/attribute_is_model"}, {"$ref": "#/$defs/attribute_matches_model"}, {"$ref": "#/$defs/element_text_model"}, {"$ref": "#/$defs/element_text_is_model"}, {"$ref": "#/$defs/element_text_matches_model"}, {"$ref": "#/$defs/has_element_with_path_model"}, {"$ref": "#/$defs/has_n_elements_with_path_model"}, {"$ref": "#/$defs/is_valid_xml_model"}, {"$ref": "#/$defs/xml_element_model"}, {"$ref": "#/$defs/has_json_property_with_text_model"}, {"$ref": "#/$defs/has_json_property_with_value_model"}, {"$ref": "#/$defs/has_h5_attribute_model"}, {"$ref": "#/$defs/has_h5_keys_model"}, {"$ref": "#/$defs/has_archive_member_model"}, {"$ref": "#/$defs/has_size_model"}, {"$ref": "#/$defs/has_image_center_of_mass_model"}, {"$ref": "#/$defs/has_image_channels_model"}, {"$ref": "#/$defs/has_image_depth_model"}, {"$ref": "#/$defs/has_image_frames_model"}, {"$ref": "#/$defs/has_image_height_model"}, {"$ref": "#/$defs/has_image_mean_intensity_model"}, {"$ref": "#/$defs/has_image_mean_object_size_model"}, {"$ref": "#/$defs/has_image_n_labels_model"}, {"$ref": "#/$defs/has_image_width_model"}]}, {"$ref": "#/$defs/has_line_model_nested"}, {"$ref": "#/$defs/has_line_matching_model_nested"}, {"$ref": "#/$defs/has_n_lines_model_nested"}, {"$ref": "#/$defs/has_text_model_nested"}, {"$ref": "#/$defs/has_text_matching_model_nested"}, {"$ref": "#/$defs/not_has_text_model_nested"}, {"$ref": "#/$defs/has_n_columns_model_nested"}, {"$ref": "#/$defs/attribute_is_model_nested"}, {"$ref": "#/$defs/attribute_matches_model_nested"}, {"$ref": "#/$defs/element_text_model_nested"}, {"$ref": "#/$defs/element_text_is_model_nested"}, {"$ref": "#/$defs/element_text_matches_model_nested"}, {"$ref": "#/$defs/has_element_with_path_model_nested"}, {"$ref": "#/$defs/has_n_elements_with_path_model_nested"}, {"$ref": "#/$defs/is_valid_xml_model_nested"}, {"$ref": "#/$defs/xml_element_model_nested"}, {"$ref": "#/$defs/has_json_property_with_text_model_nested"}, {"$ref": "#/$defs/has_json_property_with_value_model_nested"}, {"$ref": "#/$defs/has_h5_attribute_model_nested"}, {"$ref": "#/$defs/has_h5_keys_model_nested"}, {"$ref": "#/$defs/has_archive_member_model_nested"}, {"$ref": "#/$defs/has_size_model_nested"}, {"$ref": "#/$defs/has_image_center_of_mass_model_nested"}, {"$ref": "#/$defs/has_image_channels_model_nested"}, {"$ref": "#/$defs/has_image_depth_model_nested"}, {"$ref": "#/$defs/has_image_frames_model_nested"}, {"$ref": "#/$defs/has_image_height_model_nested"}, {"$ref": "#/$defs/has_image_mean_intensity_model_nested"}, {"$ref": "#/$defs/has_image_mean_object_size_model_nested"}, {"$ref": "#/$defs/has_image_n_labels_model_nested"}, {"$ref": "#/$defs/has_image_width_model_nested"}]}, "title": "assertion_list", "type": "array"}, "attribute_is_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` is the specified ``text``.\n\nFor example:\n\n```xml\n<attribute_is path=\"outerElement/innerElement1\" attribute=\"foo\" text=\"bar\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_is", "default": "attribute_is", "title": "That", "type": "string"}}, "required": ["path", "attribute", "text"], "title": "Assert Attribute Is", "type": "object"}, "attribute_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_is": {"$ref": "#/$defs/base_attribute_is_model", "title": "Assert Attribute Is"}}, "required": ["attribute_is"], "title": "Assert Attribute Is (Nested)", "type": "object"}, "attribute_matches_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` matches the regular expression specified by ``expression``.\n\nFor example:\n\n```xml\n<attribute_matches path=\"outerElement/innerElement2\" attribute=\"foo2\" expression=\"bar\\d+\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_matches", "default": "attribute_matches", "title": "That", "type": "string"}}, "required": ["path", "attribute", "expression"], "title": "Assert Attribute Matches", "type": "object"}, "attribute_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_matches": {"$ref": "#/$defs/base_attribute_matches_model", "title": "Assert Attribute Matches"}}, "required": ["attribute_matches"], "title": "Assert Attribute Matches (Nested)", "type": "object"}, "base_attribute_is_model": {"additionalProperties": false, "description": "base model for attribute_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "text"], "title": "base_attribute_is_model", "type": "object"}, "base_attribute_matches_model": {"additionalProperties": false, "description": "base model for attribute_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "expression"], "title": "base_attribute_matches_model", "type": "object"}, "base_element_text_is_model": {"additionalProperties": false, "description": "base model for element_text_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "text"], "title": "base_element_text_is_model", "type": "object"}, "base_element_text_matches_model": {"additionalProperties": false, "description": "base model for element_text_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "expression"], "title": "base_element_text_matches_model", "type": "object"}, "base_element_text_model": {"additionalProperties": false, "description": "base model for element_text describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_element_text_model", "type": "object"}, "base_has_archive_member_model": {"additionalProperties": false, "description": "base model for has_archive_member describing attributes.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_has_archive_member_model", "type": "object"}, "base_has_element_with_path_model": {"additionalProperties": false, "description": "base model for has_element_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_element_with_path_model", "type": "object"}, "base_has_h5_attribute_model": {"additionalProperties": false, "description": "base model for has_h5_attribute describing attributes.", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}}, "required": ["key", "value"], "title": "base_has_h5_attribute_model", "type": "object"}, "base_has_h5_keys_model": {"additionalProperties": false, "description": "base model for has_h5_keys describing attributes.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}}, "required": ["keys"], "title": "base_has_h5_keys_model", "type": "object"}, "base_has_image_center_of_mass_model": {"additionalProperties": false, "description": "base model for has_image_center_of_mass describing attributes.", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}}, "required": ["center_of_mass"], "title": "base_has_image_center_of_mass_model", "type": "object"}, "base_has_image_channels_model": {"additionalProperties": false, "description": "base model for has_image_channels describing attributes.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_channels_model", "type": "object"}, "base_has_image_depth_model": {"additionalProperties": false, "description": "base model for has_image_depth describing attributes.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_depth_model", "type": "object"}, "base_has_image_frames_model": {"additionalProperties": false, "description": "base model for has_image_frames describing attributes.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_frames_model", "type": "object"}, "base_has_image_height_model": {"additionalProperties": false, "description": "base model for has_image_height describing attributes.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_height_model", "type": "object"}, "base_has_image_mean_intensity_model": {"additionalProperties": false, "description": "base model for has_image_mean_intensity describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}}, "title": "base_has_image_mean_intensity_model", "type": "object"}, "base_has_image_mean_object_size_model": {"additionalProperties": false, "description": "base model for has_image_mean_object_size describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}}, "title": "base_has_image_mean_object_size_model", "type": "object"}, "base_has_image_n_labels_model": {"additionalProperties": false, "description": "base model for has_image_n_labels describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_n_labels_model", "type": "object"}, "base_has_image_width_model": {"additionalProperties": false, "description": "base model for has_image_width describing attributes.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_width_model", "type": "object"}, "base_has_json_property_with_text_model": {"additionalProperties": false, "description": "base model for has_json_property_with_text describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}}, "required": ["property", "text"], "title": "base_has_json_property_with_text_model", "type": "object"}, "base_has_json_property_with_value_model": {"additionalProperties": false, "description": "base model for has_json_property_with_value describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}}, "required": ["property", "value"], "title": "base_has_json_property_with_value_model", "type": "object"}, "base_has_line_matching_model": {"additionalProperties": false, "description": "base model for has_line_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_line_matching_model", "type": "object"}, "base_has_line_model": {"additionalProperties": false, "description": "base model for has_line describing attributes.", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["line"], "title": "base_has_line_model", "type": "object"}, "base_has_n_columns_model": {"additionalProperties": false, "description": "base model for has_n_columns describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_columns_model", "type": "object"}, "base_has_n_elements_with_path_model": {"additionalProperties": false, "description": "base model for has_n_elements_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_n_elements_with_path_model", "type": "object"}, "base_has_n_lines_model": {"additionalProperties": false, "description": "base model for has_n_lines describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_lines_model", "type": "object"}, "base_has_size_model": {"additionalProperties": false, "description": "base model for has_size describing attributes.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_size_model", "type": "object"}, "base_has_text_matching_model": {"additionalProperties": false, "description": "base model for has_text_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_text_matching_model", "type": "object"}, "base_has_text_model": {"additionalProperties": false, "description": "base model for has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["text"], "title": "base_has_text_model", "type": "object"}, "base_is_valid_xml_model": {"additionalProperties": false, "description": "base model for is_valid_xml describing attributes.", "properties": {}, "title": "base_is_valid_xml_model", "type": "object"}, "base_not_has_text_model": {"additionalProperties": false, "description": "base model for not_has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}}, "required": ["text"], "title": "base_not_has_text_model", "type": "object"}, "base_xml_element_model": {"additionalProperties": false, "description": "base model for xml_element describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_xml_element_model", "type": "object"}, "element_text_is_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path`` is\nthe specified ``text``.\n\nFor example:\n\n```xml\n<element_text_is path=\"BlastOutput_program\" text=\"blastp\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_is", "default": "element_text_is", "title": "That", "type": "string"}}, "required": ["path", "text"], "title": "Assert Element Text Is", "type": "object"}, "element_text_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_is": {"$ref": "#/$defs/base_element_text_is_model", "title": "Assert Element Text Is"}}, "required": ["element_text_is"], "title": "Assert Element Text Is (Nested)", "type": "object"}, "element_text_matches_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path``\nmatches the regular expression defined by ``expression``.\n\nFor example:\n\n```xml\n<element_text_matches path=\"BlastOutput_version\" expression=\"BLASTP\\s+2\\.2.*\"/>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_matches", "default": "element_text_matches", "title": "That", "type": "string"}}, "required": ["path", "expression"], "title": "Assert Element Text Matches", "type": "object"}, "element_text_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_matches": {"$ref": "#/$defs/base_element_text_matches_model", "title": "Assert Element Text Matches"}}, "required": ["element_text_matches"], "title": "Assert Element Text Matches (Nested)", "type": "object"}, "element_text_model": {"additionalProperties": false, "description": "This tag allows the developer to recurisively specify additional assertions as\nchild elements about just the text contained in the element specified by the\nXPath-like ``path``, e.g.\n\n```xml\n<element_text path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def\">\n  <not_has_text text=\"EDK72998.1\" />\n</element_text>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the implicit assertions can be inverted.\nThe sub-assertions, which have their own ``negate`` attribute, are not affected\nby ``negate``.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "element_text", "default": "element_text", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Element Text", "type": "object"}, "element_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text": {"$ref": "#/$defs/base_element_text_model", "title": "Assert Element Text"}}, "required": ["element_text"], "title": "Assert Element Text (Nested)", "type": "object"}, "has_archive_member_model": {"additionalProperties": false, "description": "This tag allows to check if ``path`` is contained in a compressed file.\n\nThe path is a regular expression that is matched against the full paths of the objects in\nthe compressed file (remember that \"matching\" means it is checked if a prefix of\nthe full path of an archive member is described by the regular expression).\nValid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that\ndepending on the archive creation method:\n\n- full paths of the members may be prefixed with ``./``\n- directories may be treated as empty files\n\n```xml\n<has_archive_member path=\"./path/to/my-file.txt\"/>\n```\n\nWith ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of\narchive members matching ``path`` can be expressed. The following could be used,\ne.g., to assert an archive containing n&plusmn;1 elements out of which at least\n4 need to have a ``txt`` extension.\n\n```xml\n<has_archive_member path=\".*\" n=\"10\" delta=\"1\"/>\n<has_archive_member path=\".*\\.txt\" min=\"4\"/>\n```\n\nIn addition the tag can contain additional assertions as child elements about\nthe first member in the archive matching the regular expression ``path``. For\ninstance\n\n```xml\n<has_archive_member path=\".*/my-file.txt\">\n  <not_has_text text=\"EDK72998.1\"/>\n</has_archive_member>\n```\n\nIf the ``all`` attribute is set to ``true`` then all archive members are subject\nto the assertions. Note that, archive members matching the ``path`` are sorted\nalphabetically.\n\nThe ``negate`` attribute of the ``has_archive_member`` assertion only affects\nthe asserts on the presence and number of matching archive members, but not any\nsub-assertions (which can offer the ``negate`` attribute on their own).  The\ncheck if the file is an archive at all, which is also done by the function, is\nnot affected.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "has_archive_member", "default": "has_archive_member", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Archive Member", "type": "object"}, "has_archive_member_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_archive_member": {"$ref": "#/$defs/base_has_archive_member_model", "title": "Assert Has Archive Member"}}, "required": ["has_archive_member"], "title": "Assert Has Archive Member (Nested)", "type": "object"}, "has_element_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains at least one element (or tag) with the specified\nXPath-like ``path``, e.g.\n\n```xml\n<has_element_with_path path=\"BlastOutput_param/Parameters/Parameters_matrix\" />\n```\n\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_element_with_path", "default": "has_element_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Element With Path", "type": "object"}, "has_element_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_element_with_path": {"$ref": "#/$defs/base_has_element_with_path_model", "title": "Assert Has Element With Path"}}, "required": ["has_element_with_path"], "title": "Assert Has Element With Path (Nested)", "type": "object"}, "has_h5_attribute_model": {"additionalProperties": false, "description": "Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.\n\n```xml\n<has_h5_attribute key=\"nchroms\" value=\"15\" />\n```", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}, "that": {"const": "has_h5_attribute", "default": "has_h5_attribute", "title": "That", "type": "string"}}, "required": ["key", "value"], "title": "Assert Has H5 Attribute", "type": "object"}, "has_h5_attribute_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_attribute": {"$ref": "#/$defs/base_has_h5_attribute_model", "title": "Assert Has H5 Attribute"}}, "required": ["has_h5_attribute"], "title": "Assert Has H5 Attribute (Nested)", "type": "object"}, "has_h5_keys_model": {"additionalProperties": false, "description": "Asserts the specified HDF5 output has the given keys.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}, "that": {"const": "has_h5_keys", "default": "has_h5_keys", "title": "That", "type": "string"}}, "required": ["keys"], "title": "Assert Has H5 Keys", "type": "object"}, "has_h5_keys_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_keys": {"$ref": "#/$defs/base_has_h5_keys_model", "title": "Assert Has H5 Keys"}}, "required": ["has_h5_keys"], "title": "Assert Has H5 Keys (Nested)", "type": "object"}, "has_image_center_of_mass_model": {"additionalProperties": false, "description": "Asserts the specified output is an image and has the specified center of mass.\n\nAsserts the output is an image and has a specific center of mass,\nor has an Euclidean distance of ``eps`` or less to that point (e.g.,\n``<has_image_center_of_mass center_of_mass=\"511.07, 223.34\" />``).", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}, "that": {"const": "has_image_center_of_mass", "default": "has_image_center_of_mass", "title": "That", "type": "string"}}, "required": ["center_of_mass"], "title": "Assert Has Image Center Of Mass", "type": "object"}, "has_image_center_of_mass_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_center_of_mass": {"$ref": "#/$defs/base_has_image_center_of_mass_model", "title": "Assert Has Image Center Of Mass"}}, "required": ["has_image_center_of_mass"], "title": "Assert Has Image Center Of Mass (Nested)", "type": "object"}, "has_image_channels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of channels.\n\nThe number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels=\"3\" />``).\n\nAlternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_channels", "default": "has_image_channels", "title": "That", "type": "string"}}, "title": "Assert Has Image Channels", "type": "object"}, "has_image_channels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_channels": {"$ref": "#/$defs/base_has_image_channels_model", "title": "Assert Has Image Channels"}}, "required": ["has_image_channels"], "title": "Assert Has Image Channels (Nested)", "type": "object"}, "has_image_depth_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific depth (number of slices).\n\nThe depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected depth can be specified by ``min`` and/or ``max``.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_depth", "default": "has_image_depth", "title": "That", "type": "string"}}, "title": "Assert Has Image Depth", "type": "object"}, "has_image_depth_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_depth": {"$ref": "#/$defs/base_has_image_depth_model", "title": "Assert Has Image Depth"}}, "required": ["has_image_depth"], "title": "Assert Has Image Depth (Nested)", "type": "object"}, "has_image_frames_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of frames (number of time steps).\n\nThe number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_frames", "default": "has_image_frames", "title": "That", "type": "string"}}, "title": "Assert Has Image Frames", "type": "object"}, "has_image_frames_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_frames": {"$ref": "#/$defs/base_has_image_frames_model", "title": "Assert Has Image Frames"}}, "required": ["has_image_frames"], "title": "Assert Has Image Frames (Nested)", "type": "object"}, "has_image_height_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific height (in pixels).\n\nThe height is plus/minus ``delta`` (e.g., ``<has_image_height height=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected height can be specified by ``min`` and/or ``max``.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_height", "default": "has_image_height", "title": "That", "type": "string"}}, "title": "Assert Has Image Height", "type": "object"}, "has_image_height_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_height": {"$ref": "#/$defs/base_has_image_height_model", "title": "Assert Has Image Height"}}, "required": ["has_image_height"], "title": "Assert Has Image Height (Nested)", "type": "object"}, "has_image_mean_intensity_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific mean intensity value.\n\nThe mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity=\"0.83\" />``).\nAlternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}, "that": {"const": "has_image_mean_intensity", "default": "has_image_mean_intensity", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Intensity", "type": "object"}, "has_image_mean_intensity_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_intensity": {"$ref": "#/$defs/base_has_image_mean_intensity_model", "title": "Assert Has Image Mean Intensity"}}, "required": ["has_image_mean_intensity"], "title": "Assert Has Image Mean Intensity (Nested)", "type": "object"}, "has_image_mean_object_size_model": {"additionalProperties": false, "description": "Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),\n\nThe mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size=\"111.87\" exclude_labels=\"0\" />``).\n\nThe labels must be unique.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}, "that": {"const": "has_image_mean_object_size", "default": "has_image_mean_object_size", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Object Size", "type": "object"}, "has_image_mean_object_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_object_size": {"$ref": "#/$defs/base_has_image_mean_object_size_model", "title": "Assert Has Image Mean Object Size"}}, "required": ["has_image_mean_object_size"], "title": "Assert Has Image Mean Object Size (Nested)", "type": "object"}, "has_image_n_labels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has the specified labels.\n\nLabels can be a number of labels or unique values (e.g.,\n``<has_image_n_labels n=\"187\" exclude_labels=\"0\" />``).\n\nThe primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_n_labels", "default": "has_image_n_labels", "title": "That", "type": "string"}}, "title": "Assert Has Image N Labels", "type": "object"}, "has_image_n_labels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_n_labels": {"$ref": "#/$defs/base_has_image_n_labels_model", "title": "Assert Has Image N Labels"}}, "required": ["has_image_n_labels"], "title": "Assert Has Image N Labels (Nested)", "type": "object"}, "has_image_width_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific width (in pixels).\n\nThe width is plus/minus ``delta`` (e.g., ``<has_image_width width=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected width can be specified by ``min`` and/or ``max``.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_width", "default": "has_image_width", "title": "That", "type": "string"}}, "title": "Assert Has Image Width", "type": "object"}, "has_image_width_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_width": {"$ref": "#/$defs/base_has_image_width_model", "title": "Assert Has Image Width"}}, "required": ["has_image_width"], "title": "Assert Has Image Width (Nested)", "type": "object"}, "has_json_property_with_text_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified text (i.e. string) value.\n\n```xml\n<has_json_property_with_text property=\"color\" text=\"red\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}, "that": {"const": "has_json_property_with_text", "default": "has_json_property_with_text", "title": "That", "type": "string"}}, "required": ["property", "text"], "title": "Assert Has Json Property With Text", "type": "object"}, "has_json_property_with_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_text": {"$ref": "#/$defs/base_has_json_property_with_text_model", "title": "Assert Has Json Property With Text"}}, "required": ["has_json_property_with_text"], "title": "Assert Has Json Property With Text (Nested)", "type": "object"}, "has_json_property_with_value_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified JSON value.\n\n```xml\n<has_json_property_with_value property=\"skipped_columns\" value=\"[1, 3, 5]\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}, "that": {"const": "has_json_property_with_value", "default": "has_json_property_with_value", "title": "That", "type": "string"}}, "required": ["property", "value"], "title": "Assert Has Json Property With Value", "type": "object"}, "has_json_property_with_value_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_value": {"$ref": "#/$defs/base_has_json_property_with_value_model", "title": "Assert Has Json Property With Value"}}, "required": ["has_json_property_with_value"], "title": "Assert Has Json Property With Value (Nested)", "type": "object"}, "has_line_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains a line matching the\nregular expression specified by the argument expression. If n is given\nthe assertion checks for exactly n occurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line_matching", "default": "has_line_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Line Matching", "type": "object"}, "has_line_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line_matching": {"$ref": "#/$defs/base_has_line_matching_model", "title": "Assert Has Line Matching"}}, "required": ["has_line_matching"], "title": "Assert Has Line Matching (Nested)", "type": "object"}, "has_line_model": {"additionalProperties": false, "description": "Asserts the specified output contains the line specified by the\nargument line. The exact number of occurrences can be optionally\nspecified by the argument n", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line", "default": "has_line", "title": "That", "type": "string"}}, "required": ["line"], "title": "Assert Has Line", "type": "object"}, "has_line_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line": {"$ref": "#/$defs/base_has_line_model", "title": "Assert Has Line"}}, "required": ["has_line"], "title": "Assert Has Line (Nested)", "type": "object"}, "has_n_columns_model": {"additionalProperties": false, "description": "Asserts tabular output  contains the specified\nnumber (``n``) of columns.\n\nFor instance, ``<has_n_columns n=\"3\"/>``. The assertion tests only the first line.\nNumber of columns can optionally also be specified with ``delta``. Alternatively the\nrange of expected occurrences can be specified by ``min`` and/or ``max``.\n\nOptionally a column separator (``sep``, default is ``       ``) `and comment character(s)\ncan be specified (``comment``, default is empty string). The first non-comment\nline is used for determining the number of columns.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_columns", "default": "has_n_columns", "title": "That", "type": "string"}}, "title": "Assert Has N Columns", "type": "object"}, "has_n_columns_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_columns": {"$ref": "#/$defs/base_has_n_columns_model", "title": "Assert Has N Columns"}}, "required": ["has_n_columns"], "title": "Assert Has N Columns (Nested)", "type": "object"}, "has_n_elements_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or\ntags) with the specified XPath-like ``path``.\n\nFor example:\n\n```xml\n<has_n_elements_with_path n=\"9\" path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num\" />\n```\n\nAlternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes\ncan be used to specify the range of the expected number of occurrences.\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_elements_with_path", "default": "has_n_elements_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has N Elements With Path", "type": "object"}, "has_n_elements_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_elements_with_path": {"$ref": "#/$defs/base_has_n_elements_with_path_model", "title": "Assert Has N Elements With Path"}}, "required": ["has_n_elements_with_path"], "title": "Assert Has N Elements With Path (Nested)", "type": "object"}, "has_n_lines_model": {"additionalProperties": false, "description": "Asserts the specified output contains ``n`` lines allowing\nfor a difference in the number of lines (delta)\nor relative differebce in the number of lines", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_lines", "default": "has_n_lines", "title": "That", "type": "string"}}, "title": "Assert Has N Lines", "type": "object"}, "has_n_lines_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_lines": {"$ref": "#/$defs/base_has_n_lines_model", "title": "Assert Has N Lines"}}, "required": ["has_n_lines"], "title": "Assert Has N Lines (Nested)", "type": "object"}, "has_size_model": {"additionalProperties": false, "description": "Asserts the specified output has a size of the specified value\n\nAttributes size and value or synonyms though value is considered deprecated.\nThe size optionally allows for absolute (``delta``) difference.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_size", "default": "has_size", "title": "That", "type": "string"}}, "title": "Assert Has Size", "type": "object"}, "has_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_size": {"$ref": "#/$defs/base_has_size_model", "title": "Assert Has Size"}}, "required": ["has_size"], "title": "Assert Has Size (Nested)", "type": "object"}, "has_text_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains text matching the\nregular expression specified by the argument expression.\nIf n is given the assertion checks for exactly n (nonoverlapping)\noccurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text_matching", "default": "has_text_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Text Matching", "type": "object"}, "has_text_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text_matching": {"$ref": "#/$defs/base_has_text_matching_model", "title": "Assert Has Text Matching"}}, "required": ["has_text_matching"], "title": "Assert Has Text Matching (Nested)", "type": "object"}, "has_text_model": {"additionalProperties": false, "description": "Asserts specified output contains the substring specified by\nthe argument text. The exact number of occurrences can be\noptionally specified by the argument n", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text", "default": "has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Has Text", "type": "object"}, "has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text": {"$ref": "#/$defs/base_has_text_model", "title": "Assert Has Text"}}, "required": ["has_text"], "title": "Assert Has Text (Nested)", "type": "object"}, "is_valid_xml_model": {"additionalProperties": false, "description": "Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).", "properties": {"that": {"const": "is_valid_xml", "default": "is_valid_xml", "title": "That", "type": "string"}}, "title": "Assert Is Valid Xml", "type": "object"}, "is_valid_xml_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"is_valid_xml": {"$ref": "#/$defs/base_is_valid_xml_model", "title": "Assert Is Valid Xml"}}, "required": ["is_valid_xml"], "title": "Assert Is Valid Xml (Nested)", "type": "object"}, "not_has_text_model": {"additionalProperties": false, "description": "Asserts specified output does not contain the substring\nspecified by the argument text", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "that": {"const": "not_has_text", "default": "not_has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Not Has Text", "type": "object"}, "not_has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"not_has_text": {"$ref": "#/$defs/base_not_has_text_model", "title": "Assert Not Has Text"}}, "required": ["not_has_text"], "title": "Assert Not Has Text (Nested)", "type": "object"}, "xml_element_model": {"additionalProperties": false, "description": "Assert if the XML file contains element(s) or tag(s) with the specified\n[XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``\nor ``min`` and ``max`` are given also the number of occurrences is checked.\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem\"/>\n  <xml_element path=\"./elem/more[2]\"/>\n  <xml_element path=\".//more\" n=\"3\" delta=\"1\"/>\n</assert_contents>\n```\n\nWith ``negate=\"true\"`` the outcome of the assertions wrt the presence and number\nof ``path`` can be negated. If there are any sub assertions then check them against\n\n- the content of the attribute ``attribute``\n- the element's text if no attribute is given\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem/more[2]\" attribute=\"name\">\n    <has_text_matching expression=\"foo$\"/>\n  </xml_element>\n</assert_contents>\n```\n\nSub-assertions are not subject to the ``negate`` attribute of ``xml_element``.\nIf ``all`` is ``true`` then the sub assertions are checked for all occurrences.\n\nNote that all other XML assertions can be expressed by this assertion (Galaxy\nalso implements the other assertions by calling this one).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "xml_element", "default": "xml_element", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Xml Element", "type": "object"}, "xml_element_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"xml_element": {"$ref": "#/$defs/base_xml_element_model", "title": "Assert Xml Element"}}, "required": ["xml_element"], "title": "Assert Xml Element (Nested)", "type": "object"}}, "additionalProperties": false, "description": "Full unprivileged tool source, including the optional ``tests`` block.\n\nThis is the model persisted and validated on the API surface\n(``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring\nuses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added\nback here so direct authors and stored rows can still carry tests.", "properties": {"id": {"anyOf": [{"maxLength": 255, "minLength": 3, "pattern": "^[a-z][a-z0-9_-]*$", "type": "string"}, {"type": "null"}], "default": null, "description": "Unique identifier for the tool. Lowercase, must start with a letter, may contain letters, digits, '_' and '-'.", "examples": ["my-cool-tool"], "title": "id"}, "version": {"description": "Version for the tool.", "examples": ["0.1.0"], "title": "version", "type": "string"}, "name": {"description": "The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.", "minLength": 5, "title": "name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The description is displayed in the tool menu immediately following the hyperlink for the tool.", "title": "description"}, "configfiles": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTemplateConfigFile"}, "type": "array"}, {"type": "null"}], "default": null, "description": "A list of config files for this tool.", "title": "configfiles"}, "requirements": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/JavascriptRequirement"}, {"$ref": "#/$defs/ResourceRequirement"}, {"$ref": "#/$defs/ContainerRequirement"}]}, "type": "array"}, {"type": "null"}], "default": [], "description": "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.", "title": "requirements"}, "shell_command": {"description": "A string that contains the command to be executed. Parameters can be referenced inside $().", "examples": ["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"], "title": "shell_command", "type": "string"}, "inputs": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "inputs", "type": "array"}, "outputs": {"default": [], "items": {"discriminator": {"mapping": {"boolean": "#/$defs/IncomingToolOutputBoolean", "collection": "#/$defs/IncomingToolOutputCollection", "data": "#/$defs/IncomingToolOutputDataset", "float": "#/$defs/IncomingToolOutputFloat", "integer": "#/$defs/IncomingToolOutputInteger", "text": "#/$defs/IncomingToolOutputText"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/IncomingToolOutputDataset"}, {"$ref": "#/$defs/IncomingToolOutputCollection"}, {"$ref": "#/$defs/IncomingToolOutputText"}, {"$ref": "#/$defs/IncomingToolOutputInteger"}, {"$ref": "#/$defs/IncomingToolOutputFloat"}, {"$ref": "#/$defs/IncomingToolOutputBoolean"}]}, "title": "outputs", "type": "array"}, "citations": {"anyOf": [{"items": {"$ref": "#/$defs/Citation"}, "type": "array"}, {"type": "null"}], "default": null, "title": "citations"}, "license": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.", "examples": ["MIT"], "title": "license"}, "edam_operations": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_operations"}, "edam_topics": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_topics"}, "xrefs": {"anyOf": [{"items": {"$ref": "#/$defs/XrefDict"}, "type": "array"}, {"type": "null"}], "default": null, "title": "xrefs"}, "profile": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "profile"}, "help": {"anyOf": [{"$ref": "#/$defs/HelpContent"}, {"type": "null"}], "default": null, "description": "Help text shown below the tool interface.", "title": "help"}, "class": {"const": "GalaxyUserTool", "title": "class_", "type": "string"}, "container": {"description": "Container image to use for this tool.", "examples": ["quay.io/biocontainers/python:3.13"], "title": "container", "type": "string"}, "tests": {"anyOf": [{"items": {"$ref": "#/$defs/YamlToolTest"}, "type": "array"}, {"type": "null"}], "default": null, "title": "tests"}}, "required": ["version", "name", "shell_command", "class", "container"], "title": "UserToolSource", "type": "object"}
\ No newline at end of file

From 6cf97ad3e8fd581d5fbbda090082d6c6e7e12ed2 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 18 Jun 2026 14:28:18 -0400
Subject: [PATCH 251/256] Include hidden intermediates in workflow extraction
 summary (#22967)

__summarize scanned visible_contents, dropping hidden intermediate
datasets IWC-style workflows produce - their creating jobs vanished from
the extraction form. Switch to new History.all_contents (no visibility
filter). Guard against minting spurious per-element steps: prefetch
collection-element HDA ids, skip hidden HDAs that are collection members
(represented by their collection, not standalone).

Tests: model-level all_contents view, unit include/skip branches, API
hidden-intermediate + no-spurious-mapover-rows.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/galaxy/model/__init__.py                  | 10 ++++
 lib/galaxy/workflow/extract.py                | 27 ++++++++++-
 .../api/test_workflow_extraction.py           | 43 +++++++++++++++++
 test/unit/data/model/db/test_misc.py          | 15 ++++++
 test/unit/workflows/test_extract_summary.py   | 46 ++++++++++++++++++-
 5 files changed, 138 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 747c312104b..bd68f19dc87 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -4241,6 +4241,16 @@ class History(Base, HasTags, UsesAnnotations, HasName, Serializable, UsesCreateA
     def visible_contents(self):
         return self.contents_iter(types=["dataset", "dataset_collection"], visible=True)
 
+    @property
+    def all_contents(self):
+        """Return every content (hidden, deleted and purged included) ordered by hid.
+
+        Workflow extraction reconstructs provenance from the jobs behind history
+        items, so it needs the hidden intermediates IWC-style workflows produce -
+        not just the visible outputs.
+        """
+        return self.contents_iter(types=["dataset", "dataset_collection"])
+
     def contents_iter(self, **kwds):
         """
         Fetch filtered list of contents of history.
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 80081853dfb..bfbcde409be 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -11,6 +11,8 @@ from typing import (
     Optional,
 )
 
+from sqlalchemy import select
+
 from galaxy import (
     exceptions,
     model,
@@ -18,6 +20,7 @@ from galaxy import (
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.managers.jobs import JobManager
 from galaxy.model import (
+    DatasetCollectionElement,
     History,
     HistoryDatasetAssociation,
     HistoryDatasetCollectionAssociation,
@@ -314,8 +317,25 @@ class WorkflowSummary(BaseWorkflowSummary):
         self.hda_hid_in_history: dict[int, int] = {}
         self.hdca_hid_in_history: dict[int, int] = {}
 
+        self.collection_element_hda_ids: set[int] = self.__collection_element_hda_ids()
+
         self.__summarize()
 
+    def __collection_element_hda_ids(self) -> set[int]:
+        """Ids of this history's HDAs that are elements of some collection.
+
+        Hidden contents now reach summarization (see History.all_contents), but a
+        collection's element datasets are represented by their collection during
+        extraction - "the collection or nothing" - so the hidden ones must be
+        skipped to avoid minting spurious per-element steps (e.g. one per map-over
+        element). Fetched once rather than per-dataset."""
+        stmt = (
+            select(HistoryDatasetAssociation.id)
+            .join(DatasetCollectionElement, DatasetCollectionElement.hda_id == HistoryDatasetAssociation.id)
+            .where(HistoryDatasetAssociation.history_id == self.history.id)
+        )
+        return set(self.trans.sa_session.scalars(stmt).all())
+
     def hid(self, content: HistoryItem) -> int:
         if content.history_content_type == "dataset_collection":
             if content.id in self.hdca_hid_in_history:
@@ -343,7 +363,7 @@ class WorkflowSummary(BaseWorkflowSummary):
         # just grab the implicitly mapped jobs and handle in second pass. Second pass is
         # needed because cannot allow selection of individual datasets from an implicit
         # mapping during extraction - you get the collection or nothing.
-        for content in self.history.visible_contents:
+        for content in self.history.all_contents:
             self.__summarize_content(content)
 
     def __summarize_content(self, content: HistoryItem) -> None:
@@ -416,6 +436,11 @@ class WorkflowSummary(BaseWorkflowSummary):
             self.jobs[DatasetCollectionCreationJob(dataset_collection)] = [(None, dataset_collection)]
 
     def __summarize_dataset(self, dataset: HistoryDatasetAssociation) -> None:
+        if not dataset.visible and dataset.id in self.collection_element_hda_ids:
+            # Hidden element of a collection - represented by its collection, not
+            # as a standalone step. Visible collection members are left alone so
+            # behavior matches the prior visible-only scan.
+            return
         if not self._check_state(dataset):
             return
 
diff --git a/lib/galaxy_test/api/test_workflow_extraction.py b/lib/galaxy_test/api/test_workflow_extraction.py
index 392d44099de..9de4235b9b5 100644
--- a/lib/galaxy_test/api/test_workflow_extraction.py
+++ b/lib/galaxy_test/api/test_workflow_extraction.py
@@ -1379,5 +1379,48 @@ class TestWorkflowExtractionSummaryApi(_ExtractionHelpersMixin, BaseWorkflowsApi
                 assert isinstance(job["checked"], bool)
                 assert isinstance(job["outputs"], list)
 
+    @skip_without_tool("cat1")
+    def test_extraction_summary_includes_hidden_intermediate(self):
+        # Histories produced by IWC-style workflows hide their intermediate
+        # datasets. The summary must still surface the jobs behind those hidden
+        # intermediates so the whole provenance graph can be extracted - not
+        # just the chain of visible outputs.
+        with self.dataset_populator.test_history() as history_id:
+            hda1 = self.dataset_populator.new_dataset(history_id, content="foo\nbar", wait=True)
+            first_run = self.dataset_populator.run_tool(
+                "cat1", {"input1": {"src": "hda", "id": hda1["id"]}}, history_id
+            )
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            intermediate = first_run["outputs"][0]
+            self.dataset_populator.hide_dataset(intermediate["id"])
+
+            self.dataset_populator.run_tool("cat1", {"input1": {"src": "hda", "id": intermediate["id"]}}, history_id)
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+
+            summary = self._get_extraction_summary(history_id)
+            tool_jobs = [j for j in summary["jobs"] if j["step_type"] == "tool"]
+            # Both cat1 jobs must appear even though the dataset bridging them is
+            # hidden; before the fix only the job behind the visible output did.
+            assert len(tool_jobs) == 2, summary["jobs"]
+            assert all(j["checked"] for j in tool_jobs), summary["jobs"]
+
+    @skip_without_tool("random_lines1")
+    def test_extraction_summary_no_spurious_rows_for_mapover_elements(self):
+        # Map-over hides each per-element output dataset. Surfacing hidden contents
+        # must not turn those elements into their own job cards - the mapped step
+        # (its implicit collection) represents them; otherwise a pair yields a
+        # spurious extra card per element.
+        with self.dataset_populator.test_history() as history_id:
+            hdca = self.dataset_collection_populator.create_pair_in_history(
+                history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"], wait=True
+            ).json()["outputs"][0]
+            inputs = {"input": {"batch": True, "values": [{"src": "hdca", "id": hdca["id"]}]}, "num_lines": 1}
+            self._run_tool_get_collection_and_job_id(history_id, "random_lines1", inputs)
+
+            summary = self._get_extraction_summary(history_id)
+            tool_jobs = [j for j in summary["jobs"] if j["step_type"] == "tool"]
+            assert len(tool_jobs) == 1, summary["jobs"]
+            assert tool_jobs[0]["implicit_collection_jobs_id"] is not None, tool_jobs[0]
+
 
 RunJobsSummary = namedtuple("RunJobsSummary", ["history_id", "workflow_id", "inputs", "jobs"])
diff --git a/test/unit/data/model/db/test_misc.py b/test/unit/data/model/db/test_misc.py
index 9dadda4c326..f38495360ab 100644
--- a/test/unit/data/model/db/test_misc.py
+++ b/test/unit/data/model/db/test_misc.py
@@ -226,6 +226,21 @@ def test_history_contents(session, make_history, make_hda):
     assert contents_iter_names(ids=[d1.id, d3.id]) == ["1", "3"]
 
 
+def test_history_content_views(session, make_history, make_hda):
+    h1 = make_history()
+    make_hda(history=h1, name="1")  # visible, active
+    make_hda(history=h1, name="2", visible=False, create_dataset=True, sa_session=session)  # hidden, active
+    make_hda(history=h1, name="3", deleted=True, create_dataset=True, sa_session=session)  # visible, deleted
+    make_hda(history=h1, name="4", visible=False, deleted=True)  # hidden, deleted
+
+    history = session.get(m.History, h1.id)
+    assert [c.name for c in history.active_contents] == ["1"]
+    assert [c.name for c in history.visible_contents] == ["1", "3"]
+    # all_contents (used by workflow extraction) must include the hidden
+    # intermediate "2" that visible_contents drops.
+    assert [c.name for c in history.all_contents] == ["1", "2", "3", "4"]
+
+
 def test_current_galaxy_session(make_user, make_galaxy_session):
     user = make_user()
     galaxy_session = make_galaxy_session(user=user)
diff --git a/test/unit/workflows/test_extract_summary.py b/test/unit/workflows/test_extract_summary.py
index fc477ee28db..e198b2fc320 100644
--- a/test/unit/workflows/test_extract_summary.py
+++ b/test/unit/workflows/test_extract_summary.py
@@ -122,6 +122,25 @@ class TestWorkflowExtractSummary(TestCase):
         job = next(iter(job_dict.keys()))
         assert job is creating_job
 
+    def test_includes_hidden_standalone_intermediate(self):
+        # A hidden dataset that is not a collection element (e.g. an intermediate
+        # an IWC workflow hid) must still yield a job - the regression this fixes.
+        hda = MockHda(visible=False)
+        self.history.active_datasets.append(hda)
+        job_dict, warnings = self._summarize()
+        assert not warnings
+        assert len(job_dict) == 1
+
+    def test_skips_hidden_collection_element(self):
+        # A hidden dataset that IS a collection element is represented by its
+        # collection, so it must not become a standalone job.
+        element = MockHda(visible=False, id=555)
+        self.history.active_datasets.append(element)
+        self.trans.sa_session.collection_element_hda_ids = [element.id]
+        job_dict, warnings = self._summarize()
+        assert not warnings
+        assert len(job_dict) == 0
+
     def test_warns_and_skips_datasets_if_not_finished(self):
         hda = MockHda(state="queued")
         self.history.active_datasets.append(hda)
@@ -140,6 +159,7 @@ class MockJobToOutputDatasetAssociation:
 
 class MockHistory:
     def __init__(self):
+        self.id = 1
         self.active_datasets = []
 
     @property
@@ -150,19 +170,41 @@ class MockHistory:
     def visible_contents(self):
         return self.active_contents
 
+    @property
+    def all_contents(self):
+        return self.active_contents
+
+
+class MockScalarResult:
+    def __init__(self, values):
+        self._values = values
+
+    def all(self):
+        return self._values
+
+
+class MockSession:
+    def __init__(self):
+        self.collection_element_hda_ids: list[int] = []
+
+    def scalars(self, statement):
+        return MockScalarResult(self.collection_element_hda_ids)
+
 
 class MockTrans:
     def __init__(self, history):
         self.history = history
+        self.sa_session = MockSession()
 
     def get_history(self):
         return self.history
 
 
 class MockHda:
-    def __init__(self, state="ok", output_name="out1", job=None):
+    def __init__(self, state="ok", output_name="out1", job=None, visible=True, id=123):
         self.hid = 1
-        self.id = 123
+        self.id = id
+        self.visible = visible
         self.state = state
         self.copied_from_history_dataset_association = None
         self.copied_from_library_dataset_dataset_association = None

From 0146e85d2daa22aa4a15f10a9adf8a5e4ebe4692 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 18 Jun 2026 19:43:09 -0400
Subject: [PATCH 252/256] Cap the tool recommendation agent's tool calls so it
 stops looping

The tool recommendation agent never bounded its tool calls, so on a wordy query it would keep re-searching tools and workflows until it tripped pydantic-ai's default request_limit of 50 and the whole turn errored out -- I hit this about one in three times asking it to recommend an IWC workflow. Give it the same soft budget the GTN agent already uses: after 8 data-gathering calls each search tool hands back a "stop searching, answer now" message instead of more data, so the model recommends from what it already found. A stubborn model still loops a little but recovers and returns the right workflow now instead of crashing.
---
 lib/galaxy/agents/tools.py   | 46 ++++++++++++++++++++++++++++++++++++
 test/unit/app/test_agents.py | 15 ++++++++++++
 2 files changed, 61 insertions(+)

diff --git a/lib/galaxy/agents/tools.py b/lib/galaxy/agents/tools.py
index 1539dfc71a3..7bc760264b0 100644
--- a/lib/galaxy/agents/tools.py
+++ b/lib/galaxy/agents/tools.py
@@ -71,6 +71,37 @@ class ToolRecommendationAgent(BaseGalaxyAgent):
 
     agent_type = AgentType.TOOL_RECOMMENDATION
 
+    # The model can keep re-searching tools and workflows long after it has
+    # enough to recommend from. Left unbounded it eventually trips pydantic-ai's
+    # default request_limit (50) and the whole turn errors out. Cap the number of
+    # data-gathering tool calls and, once spent, hand back a terminal instruction
+    # so the model produces its recommendation from what it already found.
+    MAX_TOOL_CALLS = 8
+    # Name the search tools to avoid rather than saying "no tools" -- the
+    # structured recommendation is itself delivered via an output tool call, so a
+    # blanket "no tools" instruction makes the model emit prose that fails
+    # structured-output validation.
+    _TOOL_BUDGET_MESSAGE = (
+        "SEARCH BUDGET REACHED. You already have enough information to recommend. "
+        "Do NOT call search_galaxy_tools, get_galaxy_tool_details, "
+        "get_galaxy_tool_categories, search_iwc_workflows, or "
+        "get_iwc_workflow_details again. Produce your final structured "
+        "recommendation now from the tools and workflows already found above. If "
+        "nothing is a strong match, say so and recommend the closest option."
+    )
+
+    def __init__(self, deps: GalaxyAgentDependencies):
+        super().__init__(deps)
+        self._tool_calls = 0
+
+    def _charge_tool_budget(self) -> Optional[str]:
+        """Count a data-gathering tool call; once over budget return a stop
+        message instead of more data so the model recommends from what it has."""
+        self._tool_calls += 1
+        if self._tool_calls > self.MAX_TOOL_CALLS:
+            return self._TOOL_BUDGET_MESSAGE
+        return None
+
     def _create_agent(self) -> Agent[GalaxyAgentDependencies, Any]:
         if self._supports_structured_output():
             agent = Agent(
@@ -95,6 +126,9 @@ class ToolRecommendationAgent(BaseGalaxyAgent):
             Use this to find real tool IDs for tools you want to recommend.
             Returns tool id, name, description, and category for matching tools.
             """
+            over_budget = self._charge_tool_budget()
+            if over_budget:
+                return over_budget
             results = await self.search_tools(query)
             if not results:
                 return f"No tools found matching '{query}'"
@@ -113,6 +147,9 @@ class ToolRecommendationAgent(BaseGalaxyAgent):
             Use this after searching to get more details about a tool you want to recommend,
             including input/output formats, version, and requirements.
             """
+            over_budget = self._charge_tool_budget()
+            if over_budget:
+                return over_budget
             details = await self.get_tool_details(tool_id)
             if "error" in details:
                 return f"Error: {details['error']}"
@@ -139,6 +176,9 @@ class ToolRecommendationAgent(BaseGalaxyAgent):
 
             Use this to understand what kinds of tools are available before searching.
             """
+            over_budget = self._charge_tool_budget()
+            if over_budget:
+                return over_budget
             categories = await self.get_tool_categories()
             if not categories:
                 return "No tool categories found"
@@ -153,6 +193,9 @@ class ToolRecommendationAgent(BaseGalaxyAgent):
             single tool. Returns ranked workflow entries with trsID, name,
             description, step count, and the tools each workflow uses.
             """
+            over_budget = self._charge_tool_budget()
+            if over_budget:
+                return over_budget
             results = await self.search_iwc_workflows(query, limit=limit)
             if not results:
                 return f"No IWC workflows found matching '{query}'"
@@ -172,6 +215,9 @@ class ToolRecommendationAgent(BaseGalaxyAgent):
             Use after search_iwc_workflows to get the complete tool list,
             authors, categories, and readme summary before recommending.
             """
+            over_budget = self._charge_tool_budget()
+            if over_budget:
+                return over_budget
             details = await self.get_iwc_workflow_details(trs_id)
             if details is None:
                 return f"No IWC workflow found with trsID {trs_id}"
diff --git a/test/unit/app/test_agents.py b/test/unit/app/test_agents.py
index 8336d12199b..a57d00c08f9 100644
--- a/test/unit/app/test_agents.py
+++ b/test/unit/app/test_agents.py
@@ -1341,6 +1341,21 @@ class TestAgentUnitMocked:
         assert suggestion.parameters["name"] == "RNA-seq"
         assert suggestion.priority == 1  # promoted when no tool comes back
 
+    def test_tool_rec_tool_budget_caps_then_returns_stop_message(self):
+        # Past MAX_TOOL_CALLS the budget hands back a terminal "stop searching"
+        # message instead of more data, so the model answers from what it already
+        # found rather than looping until pydantic-ai's request_limit trips and
+        # the whole turn errors out.
+        agent = ToolRecommendationAgent.__new__(ToolRecommendationAgent)
+        agent._tool_calls = 0
+
+        allowed = [agent._charge_tool_budget() for _ in range(agent.MAX_TOOL_CALLS)]
+        assert allowed == [None] * agent.MAX_TOOL_CALLS
+
+        over_budget = agent._charge_tool_budget()
+        assert over_budget is not None
+        assert "SEARCH BUDGET REACHED" in over_budget
+
     def test_tool_rec_workflow_suggestion_demoted_when_tool_present(self):
         agent = self._make_tool_rec_agent()
         # Stub _verify_tool_exists so the tool path produces a TOOL_RUN.

From d1280a8af32219a9f672b8dfb726e5f63ad8bc6b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 19 Jun 2026 10:21:02 +0200
Subject: [PATCH 253/256] Make discover_datasets reject under-specified
 descriptors

The discovery-descriptor defaults left ToolProvidedMetadataDatasetCollection
with zero required fields, so a bare {}, a pattern-less {format: ...}, or a
typo'd {patern: ...} silently validated as tool_provided_metadata instead of
erroring -- the tool lints clean but, writing no galaxy.json, collects nothing.
(The XML parser's default discover_via is "pattern", so the YAML path also
inverted the default.)

- Require `discover_via` on the metadata arm (no default) so an under-specified
  descriptor must say so explicitly; pattern discovery still works from a bare
  {pattern: ...}.
- Add extra="forbid" to the descriptors so a misspelled key is rejected rather
  than absorbed.

XML-safe: the legacy parser builds these models via to_model(), which passed
`dbkey` (both arms) and `sort_by` (file pattern) -- not fields on the models and
silently dropped before. Drop those kwargs so extra="forbid" doesn't reject
them; model_dump() output is unchanged.
---
 .../tool_util/parser/output_collection_def.py |  8 ++--
 lib/galaxy/tool_util_models/tool_outputs.py   | 12 ++++-
 test/unit/tool_util/test_yaml_parameters.py   | 29 ++++++++++++
 .../user_tool_source_validation_cases.yml     | 47 +++++++++++++++++++
 4 files changed, 92 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/output_collection_def.py b/lib/galaxy/tool_util/parser/output_collection_def.py
index bde4d22c00d..5e2f2ddd7bf 100644
--- a/lib/galaxy/tool_util/parser/output_collection_def.py
+++ b/lib/galaxy/tool_util/parser/output_collection_def.py
@@ -140,9 +140,10 @@ class ToolProvidedMetadataDatasetCollection(DatasetCollectionDescription):
     discover_via = "tool_provided_metadata"
 
     def to_model(self) -> ToolProvidedMetadataDatasetCollectionModel:
+        # ``dbkey`` is not part of the pydantic discovery model (it was silently
+        # dropped before; the model now forbids extras), so don't pass it.
         return ToolProvidedMetadataDatasetCollectionModel(
             discover_via=self.discover_via,
-            dbkey=self.default_dbkey,
             format=self.default_ext,
             visible=self.default_visible,
             assign_primary_output=self.assign_primary_output,
@@ -191,9 +192,11 @@ class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
             self.sort_comp = sort_comp
 
     def to_model(self) -> FilePatternDatasetCollectionDescriptionModel:
+        # ``dbkey`` and ``sort_by`` are not fields on the pydantic model (sort info is
+        # carried by sort_key/sort_comp/sort_reverse); they were silently dropped
+        # before and the model now forbids extras, so don't pass them.
         return FilePatternDatasetCollectionDescriptionModel(
             discover_via=self.discover_via,
-            dbkey=self.default_dbkey,
             format=self.default_ext,
             visible=self.default_visible,
             assign_primary_output=self.assign_primary_output,
@@ -203,7 +206,6 @@ class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
             sort_key=self.sort_key,
             sort_comp=self.sort_comp,
             pattern=self.pattern,
-            sort_by=self.sort_by,
             sort_reverse=self.sort_reverse,
         )
 
diff --git a/lib/galaxy/tool_util_models/tool_outputs.py b/lib/galaxy/tool_util_models/tool_outputs.py
index 868761ebf43..b044f84e0a3 100644
--- a/lib/galaxy/tool_util_models/tool_outputs.py
+++ b/lib/galaxy/tool_util_models/tool_outputs.py
@@ -15,6 +15,7 @@ from typing import (
 )
 
 from pydantic import (
+    ConfigDict,
     Field,
     model_validator,
 )
@@ -54,6 +55,10 @@ SortCompT = Literal["lexical", "numeric"]
 # (or an LLM) only needs to supply ``pattern``. Requiring all of them in the model is
 # the friction that makes ``discover_datasets`` nearly impossible to author by hand.
 class DatasetCollectionDescription(ToolSourceBaseModel):
+    # extra="forbid" so a typo'd key (e.g. ``patern``) is rejected rather than silently
+    # absorbed by the metadata arm below (which would otherwise collect nothing).
+    model_config = ConfigDict(extra="forbid")
+
     discover_via: DiscoverViaT
     format: Optional[str] = None
     visible: bool = False
@@ -64,7 +69,12 @@ class DatasetCollectionDescription(ToolSourceBaseModel):
 
 
 class ToolProvidedMetadataDatasetCollection(DatasetCollectionDescription):
-    discover_via: Literal["tool_provided_metadata"] = "tool_provided_metadata"
+    # ``discover_via`` is required (no default) so an under-specified descriptor
+    # ({} / {format: ...} / a typo'd pattern) does NOT silently resolve to
+    # tool_provided_metadata -- it must say so explicitly. Pattern discovery (the
+    # default in the XML parser) is opt-out only via the ``FilePattern`` arm, which
+    # still requires a real ``pattern``.
+    discover_via: Literal["tool_provided_metadata"]
 
 
 class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
diff --git a/test/unit/tool_util/test_yaml_parameters.py b/test/unit/tool_util/test_yaml_parameters.py
index 52d45148943..a6a334ba9ae 100644
--- a/test/unit/tool_util/test_yaml_parameters.py
+++ b/test/unit/tool_util/test_yaml_parameters.py
@@ -392,6 +392,35 @@ def test_collection_discovery_only_requires_pattern():
     assert (d.sort_key, d.sort_comp) == ("filename", "lexical")
 
 
+def test_collection_discovery_rejects_underspecified_descriptors():
+    """An under-specified or typo'd discovery descriptor must error -- it must NOT
+    silently resolve to tool_provided_metadata (which lints clean but, with no
+    galaxy.json written, collects nothing). `discover_via` is required on the metadata
+    arm and `extra="forbid"` catches typos; explicit pattern / tool_provided_metadata
+    forms still validate."""
+    from galaxy.tool_util_models.tool_outputs import (
+        FilePatternDatasetCollectionDescription,
+        IncomingToolOutputCollection,
+        ToolProvidedMetadataDatasetCollection,
+    )
+
+    def first(descriptor):
+        out = IncomingToolOutputCollection.model_validate(
+            {"type": "collection", "name": "o", "collection_type": "list", "discover_datasets": [descriptor]}
+        )
+        assert out.discover_datasets is not None
+        return out.discover_datasets[0]
+
+    # Explicit forms resolve to the right arm.
+    assert isinstance(first({"pattern": "x"}), FilePatternDatasetCollectionDescription)
+    assert isinstance(first({"discover_via": "tool_provided_metadata"}), ToolProvidedMetadataDatasetCollection)
+
+    # Under-specified / typo'd descriptors error instead of becoming tool_provided_metadata.
+    for bad in ({}, {"format": "fasta"}, {"patern": "x"}):
+        with pytest.raises(ValidationError):
+            first(bad)
+
+
 def test_simple_outputs_require_name_but_not_hidden_in_authoring_schema():
     """Regression: text/integer/float/boolean outputs must require `name` (a value
     output with no name can never be referenced) but must NOT require `hidden`.
diff --git a/test/unit/tool_util/user_tool_source_validation_cases.yml b/test/unit/tool_util/user_tool_source_validation_cases.yml
index d3ad5936fb1..61e9e9ad6bc 100644
--- a/test/unit/tool_util/user_tool_source_validation_cases.yml
+++ b/test/unit/tool_util/user_tool_source_validation_cases.yml
@@ -158,6 +158,53 @@ cases:
       - code: dynamic_tool.output_unclaimed
         msg_contains: discover_datasets
 
+  - name: collection_discover_underspecified_rejected
+    # A discovery descriptor with no usable pattern must NOT silently resolve to
+    # tool_provided_metadata (which lints clean but, writing no galaxy.json, collects
+    # nothing). discover_via is required on the metadata arm, so this errors.
+    doc:
+      outputs:
+        - type: collection
+          name: outs
+          collection_type: list
+          discover_datasets:
+            - {}
+    expected_errors:
+      - code: missing
+
+  - name: collection_discover_typo_rejected
+    # extra="forbid" on the descriptor catches a misspelled key instead of letting
+    # the metadata arm absorb it.
+    doc:
+      outputs:
+        - type: collection
+          name: outs
+          collection_type: list
+          discover_datasets:
+            - {patern: "*.txt"}
+    expected_errors:
+      - code: extra_forbidden
+
+  - name: collection_discover_pattern_accepted
+    doc:
+      outputs:
+        - type: collection
+          name: outs
+          collection_type: list
+          discover_datasets:
+            - {pattern: "*.txt"}
+    valid: true
+
+  - name: collection_discover_tool_provided_accepted
+    doc:
+      outputs:
+        - type: collection
+          name: outs
+          collection_type: list
+          discover_datasets:
+            - {discover_via: tool_provided_metadata}
+    valid: true
+
   - name: invalid_doi_citation
     doc:
       citations:

From 47104e4dfac8172a6a6fb21813cfc5ab494b929f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 19 Jun 2026 10:37:42 +0200
Subject: [PATCH 254/256] Drop min/max from user-defined-tool data parameters

`min`/`max` on a data parameter bound the number of *selected datasets* and are
only meaningful for a `multiple` input (the runtime DataToolParameter rejects
them on a single one, and enforces them at submission only for multiple). In
practice authors and the tool-generating agent reach for `min: 1` to mean
"required" -- which a data input already is -- and the tool then fails at build
time.

Remove the fields from the YAML authoring surface (YamlDataParameter). With
extra="forbid", a tool that sets `min`/`max` on a data input now gets a clear
authoring-time error instead of a build-time crash. The internal model and XML
tools keep min/max.

Regenerate ToolSourceSchema.json (via rebuild.py) and the api-client / tool_shed
TypeScript schemas; the latter also pick up the discover_via default removal
from the previous commit.
---
 .../packages/api-client/src/schema/schema.ts  | 11 --------
 .../src/components/Tool/ToolSourceSchema.json |  2 +-
 .../tool_util_models/yaml_parameters.py       | 28 +++++--------------
 .../webapp/frontend/src/schema/schema.ts      |  1 -
 test/unit/tool_util/test_yaml_parameters.py   | 10 +++++++
 5 files changed, 18 insertions(+), 34 deletions(-)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index a15dd3f7bb9..4a1f6812337 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -24300,7 +24300,6 @@ export interface components {
             directory?: string | null;
             /**
              * Discover Via
-             * @default tool_provided_metadata
              * @constant
              */
             discover_via: "tool_provided_metadata";
@@ -27274,16 +27273,6 @@ export interface components {
             help?: string | null;
             /** Label */
             label?: string | null;
-            /**
-             * Max
-             * @description Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; leave unset for a single-dataset input.
-             */
-            max?: number | null;
-            /**
-             * Min
-             * @description Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. Do NOT set this for a single-dataset input -- a data input is already required by default, so leave 'min' unset unless the input accepts multiple datasets.
-             */
-            min?: number | null;
             /**
              * Multiple
              * @description Set true to accept several datasets (a list) for this input instead of one.
diff --git a/client/src/components/Tool/ToolSourceSchema.json b/client/src/components/Tool/ToolSourceSchema.json
index 02eee957129..8ba24a6e022 100644
--- a/client/src/components/Tool/ToolSourceSchema.json
+++ b/client/src/components/Tool/ToolSourceSchema.json
@@ -1 +1 @@
-{"$defs": {"Citation": {"properties": {"type": {"title": "Type", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["type", "content"], "title": "Citation", "type": "object"}, "CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "Container": {"properties": {"type": {"enum": ["docker", "singularity"], "title": "Type", "type": "string"}, "container_id": {"title": "Container Id", "type": "string"}}, "required": ["type", "container_id"], "title": "Container", "type": "object"}, "ContainerRequirement": {"properties": {"type": {"const": "container", "title": "Type", "type": "string"}, "container": {"$ref": "#/$defs/Container"}}, "required": ["type", "container"], "title": "ContainerRequirement", "type": "object"}, "EmptyFieldParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "empty_field", "default": "empty_field", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "EmptyFieldParameterValidatorModel", "type": "object"}, "FilePatternDatasetCollectionDescription": {"properties": {"discover_via": {"const": "pattern", "default": "pattern", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}, "sort_key": {"default": "filename", "enum": ["filename", "name", "designation", "dbkey"], "title": "Sort Key", "type": "string"}, "sort_comp": {"default": "lexical", "enum": ["lexical", "numeric"], "title": "Sort Comp", "type": "string"}, "sort_reverse": {"default": false, "title": "Sort Reverse", "type": "boolean"}, "pattern": {"title": "Pattern", "type": "string"}}, "required": ["pattern"], "title": "FilePatternDatasetCollectionDescription", "type": "object"}, "HelpContent": {"properties": {"format": {"enum": ["restructuredtext", "plain_text", "markdown"], "title": "Format", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["format", "content"], "title": "HelpContent", "type": "object"}, "InRangeParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "in_range", "default": "in_range", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "exclude_min": {"default": false, "title": "Exclude Min", "type": "boolean"}, "exclude_max": {"default": false, "title": "Exclude Max", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "InRangeParameterValidatorModel", "type": "object"}, "IncomingToolOutputBoolean": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "boolean", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputBoolean", "type": "object"}, "IncomingToolOutputCollection": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "collection_type_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type Source"}, "collection_type_from_rules": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type From Rules"}, "structured_like": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Structured Like"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}}, "required": ["type"], "title": "IncomingToolOutputCollection", "type": "object"}, "IncomingToolOutputDataset": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The short name for the output datatype.", "title": "Format"}, "format_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.", "title": "Format Source"}, "metadata_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This copies the metadata information from the tool\u2019s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.", "title": "Metadata Source"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}, "from_work_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Relative path to a file produced by the tool in its working directory. Output\u2019s contents are set to this file\u2019s contents.", "title": "from_work_dir"}, "precreate_directory": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Precreate Directory"}}, "required": ["type"], "title": "IncomingToolOutputDataset", "type": "object"}, "IncomingToolOutputFloat": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "float", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputFloat", "type": "object"}, "IncomingToolOutputInteger": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "integer", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputInteger", "type": "object"}, "IncomingToolOutputText": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "text", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputText", "type": "object"}, "JavascriptRequirement": {"properties": {"type": {"const": "javascript", "title": "Type", "type": "string"}, "expression_lib": {"anyOf": [{"items": {"description": "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.", "examples": ["function pickValue() {\n    if (inputs.conditional_parameter.test_parameter == \"a\") {\n        return inputs.conditional_parameter.integer_parameter\n    } else {\n        return inputs.conditional_parameter.boolean_parameter\n    }\n}"], "title": "expression_lib", "type": "string"}, "type": "array"}, {"type": "null"}], "title": "Expression Lib"}}, "required": ["type", "expression_lib"], "title": "JavascriptRequirement", "type": "object"}, "LengthParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "length", "default": "length", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "LengthParameterValidatorModel", "type": "object"}, "NoOptionsParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "no_options", "default": "no_options", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "NoOptionsParameterValidatorModel", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RegexParameterValidatorModel": {"additionalProperties": false, "description": "Check if a regular expression **matches** the value, i.e. appears\nat the beginning of the value. To enforce a match of the complete value use\n``$`` at the end of the expression. The expression is given is the content\nof the validator tag. Note that for ``selects`` each option is checked\nseparately.", "properties": {"type": {"const": "regex", "default": "regex", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}, "expression": {"title": "Expression", "type": "string"}}, "required": ["expression"], "title": "RegexParameterValidatorModel", "type": "object"}, "ResourceRequirement": {"properties": {"type": {"const": "resource", "title": "Type", "type": "string"}, "cores_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 1, "description": "Minimum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Min"}, "cores_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Max"}, "ram_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 256, "description": "Minimum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Min"}, "ram_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Max"}, "tmpdir_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Min"}, "tmpdir_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Max"}, "cuda_version_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Version Min"}, "cuda_compute_capability": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Compute Capability"}, "gpu_memory_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Gpu Memory Min"}, "cuda_device_count_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Min"}, "cuda_device_count_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Max"}, "shm_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Shm Size"}, "timelimit": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum time in seconds the tool is allowed to run. Job will be terminated if exceeded.", "title": "Timelimit"}}, "required": ["type"], "title": "ResourceRequirement", "type": "object"}, "TestCollectionCollectionElementAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}}, "title": "TestCollectionCollectionElementAssertions", "type": "object"}, "TestCollectionDatasetElementAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestCollectionDatasetElementAssertions", "type": "object"}, "TestCollectionOutputAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}, "element_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Element Count"}, "attributes": {"anyOf": [{"$ref": "#/$defs/CollectionAttributes"}, {"type": "null"}], "default": null, "title": "Attributes"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "TestCollectionOutputAssertions", "type": "object"}, "TestDataOutputAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestDataOutputAssertions", "type": "object"}, "ToolProvidedMetadataDatasetCollection": {"properties": {"discover_via": {"const": "tool_provided_metadata", "default": "tool_provided_metadata", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}}, "title": "ToolProvidedMetadataDatasetCollection", "type": "object"}, "XrefDict": {"additionalProperties": false, "properties": {"value": {"title": "value", "type": "string"}, "type": {"title": "type", "type": "string"}}, "required": ["value", "type"], "title": "XrefDict", "type": "object"}, "YamlBooleanParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "boolean", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Value"}}, "required": ["name", "type"], "title": "YamlBooleanParameter", "type": "object"}, "YamlColorParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "color", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}}, "required": ["name", "type"], "title": "YamlColorParameter", "type": "object"}, "YamlConditionalParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "conditional", "title": "Type", "type": "string"}, "test_parameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "select": "#/$defs/YamlSelectParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}], "title": "Test Parameter"}, "whens": {"items": {"$ref": "#/$defs/YamlConditionalWhen"}, "minItems": 1, "title": "Whens", "type": "array"}}, "required": ["name", "type", "test_parameter", "whens"], "title": "YamlConditionalParameter", "type": "object"}, "YamlConditionalWhen": {"additionalProperties": false, "properties": {"discriminator": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "title": "Discriminator"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["discriminator"], "title": "YamlConditionalWhen", "type": "object"}, "YamlDataCollectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data_collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}}, "required": ["name", "type"], "title": "YamlDataCollectionParameter", "type": "object"}, "YamlDataParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}, "multiple": {"default": false, "description": "Set true to accept several datasets (a list) for this input instead of one.", "title": "Multiple", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. Do NOT set this for a single-dataset input -- a data input is already required by default, so leave 'min' unset unless the input accepts multiple datasets.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; leave unset for a single-dataset input.", "title": "Max"}}, "required": ["name", "type"], "title": "YamlDataParameter", "type": "object"}, "YamlFloatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "float", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlFloatParameter", "type": "object"}, "YamlGalaxyToolParameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "color": "#/$defs/YamlColorParameter", "conditional": "#/$defs/YamlConditionalParameter", "data": "#/$defs/YamlDataParameter", "data_collection": "#/$defs/YamlDataCollectionParameter", "float": "#/$defs/YamlFloatParameter", "integer": "#/$defs/YamlIntegerParameter", "repeat": "#/$defs/YamlRepeatParameter", "section": "#/$defs/YamlSectionParameter", "select": "#/$defs/YamlSelectParameter", "text": "#/$defs/YamlTextParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlIntegerParameter"}, {"$ref": "#/$defs/YamlFloatParameter"}, {"$ref": "#/$defs/YamlTextParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}, {"$ref": "#/$defs/YamlColorParameter"}, {"$ref": "#/$defs/YamlDataParameter"}, {"$ref": "#/$defs/YamlDataCollectionParameter"}, {"$ref": "#/$defs/YamlConditionalParameter"}, {"$ref": "#/$defs/YamlRepeatParameter"}, {"$ref": "#/$defs/YamlSectionParameter"}], "title": "YamlGalaxyToolParameter"}, "YamlIntegerParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "integer", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlIntegerParameter", "type": "object"}, "YamlLabelValue": {"description": "YAML-friendly option model \u2014 ``selected`` defaults to ``False``.", "properties": {"label": {"title": "Label", "type": "string"}, "value": {"title": "Value", "type": "string"}, "selected": {"default": false, "title": "Selected", "type": "boolean"}}, "required": ["label", "value"], "title": "YamlLabelValue", "type": "object"}, "YamlRepeatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "repeat", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}}, "required": ["name", "type"], "title": "YamlRepeatParameter", "type": "object"}, "YamlSectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "section", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["name", "type"], "title": "YamlSectionParameter", "type": "object"}, "YamlSelectParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "select", "title": "Type", "type": "string"}, "options": {"items": {"$ref": "#/$defs/YamlLabelValue"}, "minItems": 1, "title": "Options", "type": "array"}, "multiple": {"default": false, "title": "Multiple", "type": "boolean"}, "validators": {"default": [], "items": {"$ref": "#/$defs/NoOptionsParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type", "options"], "title": "YamlSelectParameter", "type": "object"}, "YamlTemplateConfigFile": {"properties": {"content": {"title": "Content", "type": "string"}, "name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Name"}, "filename": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Filename"}, "eval_engine": {"const": "ecmascript", "default": "ecmascript", "title": "Eval Engine", "type": "string"}}, "required": ["content"], "title": "YamlTemplateConfigFile", "type": "object"}, "YamlTestCredential": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credentials group.", "title": "Name", "type": "string"}, "variables": {"default": [], "description": "Variables exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Variables", "type": "array"}, "secrets": {"default": [], "description": "Secrets exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Secrets", "type": "array"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Version of the credential definition.", "title": "Version"}}, "required": ["name"], "title": "YamlTestCredential", "type": "object"}, "YamlTestCredentialValue": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credential variable or secret.", "title": "Name", "type": "string"}, "value": {"description": "Value of the credential variable or secret.", "title": "Value", "type": "string"}}, "required": ["name", "value"], "title": "YamlTestCredentialValue", "type": "object"}, "YamlTextParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "text", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}, "area": {"default": false, "title": "Area", "type": "boolean"}, "validators": {"default": [], "items": {"anyOf": [{"$ref": "#/$defs/LengthParameterValidatorModel"}, {"$ref": "#/$defs/RegexParameterValidatorModel"}, {"$ref": "#/$defs/EmptyFieldParameterValidatorModel"}]}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlTextParameter", "type": "object"}, "YamlToolTest": {"additionalProperties": false, "description": "In-tool test case as authored in YAML tool fixtures.", "properties": {"doc": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Human-readable description of this test case.", "title": "Doc"}, "inputs": {"anyOf": [{"additionalProperties": {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}, {"items": {}, "type": "array"}, {"additionalProperties": true, "type": "object"}]}, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of input parameter names to test values.", "title": "Inputs"}, "outputs": {"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionOutputAssertions"}, {"$ref": "#/$defs/TestDataOutputAssertions"}, {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}]}]}, "default": {}, "description": "Mapping of output names to expected values or assertions.", "title": "Outputs", "type": "object"}, "assert_stdout": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard output.", "title": "Assert Stdout"}, "assert_stderr": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard error.", "title": "Assert Stderr"}, "command": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the executed command line.", "title": "Command"}, "expect_exit_code": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected process exit code.", "title": "Expect Exit Code"}, "expect_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the tool is expected to produce an error.", "title": "Expect Failure"}, "expect_test_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the test itself is expected to fail.", "title": "Expect Test Failure"}, "credentials": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTestCredential"}, "type": "array"}, {"type": "null"}], "default": null, "description": "Credentials to inject for this test case.", "title": "Credentials"}}, "title": "YamlToolTest", "type": "object"}, "assertion_dict": {"additionalProperties": false, "properties": {"has_line": {"anyOf": [{"$ref": "#/$defs/base_has_line_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line"}, "has_line_matching": {"anyOf": [{"$ref": "#/$defs/base_has_line_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line Matching"}, "has_n_lines": {"anyOf": [{"$ref": "#/$defs/base_has_n_lines_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Lines"}, "has_text": {"anyOf": [{"$ref": "#/$defs/base_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text"}, "has_text_matching": {"anyOf": [{"$ref": "#/$defs/base_has_text_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text Matching"}, "not_has_text": {"anyOf": [{"$ref": "#/$defs/base_not_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Not Has Text"}, "has_n_columns": {"anyOf": [{"$ref": "#/$defs/base_has_n_columns_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Columns"}, "attribute_is": {"anyOf": [{"$ref": "#/$defs/base_attribute_is_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Is"}, "attribute_matches": {"anyOf": [{"$ref": "#/$defs/base_attribute_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Matches"}, "element_text": {"anyOf": [{"$ref": "#/$defs/base_element_text_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text"}, "element_text_is": {"anyOf": [{"$ref": "#/$defs/base_element_text_is_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Is"}, "element_text_matches": {"anyOf": [{"$ref": "#/$defs/base_element_text_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Matches"}, "has_element_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_element_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has Element With Path"}, "has_n_elements_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_n_elements_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Elements With Path"}, "is_valid_xml": {"anyOf": [{"$ref": "#/$defs/base_is_valid_xml_model"}, {"type": "null"}], "default": null, "title": "Assert Is Valid Xml"}, "xml_element": {"anyOf": [{"$ref": "#/$defs/base_xml_element_model"}, {"type": "null"}], "default": null, "title": "Assert Xml Element"}, "has_json_property_with_text": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Text"}, "has_json_property_with_value": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_value_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Value"}, "has_h5_attribute": {"anyOf": [{"$ref": "#/$defs/base_has_h5_attribute_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Attribute"}, "has_h5_keys": {"anyOf": [{"$ref": "#/$defs/base_has_h5_keys_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Keys"}, "has_archive_member": {"anyOf": [{"$ref": "#/$defs/base_has_archive_member_model"}, {"type": "null"}], "default": null, "title": "Assert Has Archive Member"}, "has_size": {"anyOf": [{"$ref": "#/$defs/base_has_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Size"}, "has_image_center_of_mass": {"anyOf": [{"$ref": "#/$defs/base_has_image_center_of_mass_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Center Of Mass"}, "has_image_channels": {"anyOf": [{"$ref": "#/$defs/base_has_image_channels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Channels"}, "has_image_depth": {"anyOf": [{"$ref": "#/$defs/base_has_image_depth_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Depth"}, "has_image_frames": {"anyOf": [{"$ref": "#/$defs/base_has_image_frames_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Frames"}, "has_image_height": {"anyOf": [{"$ref": "#/$defs/base_has_image_height_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Height"}, "has_image_mean_intensity": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_intensity_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Intensity"}, "has_image_mean_object_size": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_object_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Object Size"}, "has_image_n_labels": {"anyOf": [{"$ref": "#/$defs/base_has_image_n_labels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image N Labels"}, "has_image_width": {"anyOf": [{"$ref": "#/$defs/base_has_image_width_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Width"}}, "title": "assertion_dict", "type": "object"}, "assertion_list": {"items": {"anyOf": [{"discriminator": {"mapping": {"attribute_is": "#/$defs/attribute_is_model", "attribute_matches": "#/$defs/attribute_matches_model", "element_text": "#/$defs/element_text_model", "element_text_is": "#/$defs/element_text_is_model", "element_text_matches": "#/$defs/element_text_matches_model", "has_archive_member": "#/$defs/has_archive_member_model", "has_element_with_path": "#/$defs/has_element_with_path_model", "has_h5_attribute": "#/$defs/has_h5_attribute_model", "has_h5_keys": "#/$defs/has_h5_keys_model", "has_image_center_of_mass": "#/$defs/has_image_center_of_mass_model", "has_image_channels": "#/$defs/has_image_channels_model", "has_image_depth": "#/$defs/has_image_depth_model", "has_image_frames": "#/$defs/has_image_frames_model", "has_image_height": "#/$defs/has_image_height_model", "has_image_mean_intensity": "#/$defs/has_image_mean_intensity_model", "has_image_mean_object_size": "#/$defs/has_image_mean_object_size_model", "has_image_n_labels": "#/$defs/has_image_n_labels_model", "has_image_width": "#/$defs/has_image_width_model", "has_json_property_with_text": "#/$defs/has_json_property_with_text_model", "has_json_property_with_value": "#/$defs/has_json_property_with_value_model", "has_line": "#/$defs/has_line_model", "has_line_matching": "#/$defs/has_line_matching_model", "has_n_columns": "#/$defs/has_n_columns_model", "has_n_elements_with_path": "#/$defs/has_n_elements_with_path_model", "has_n_lines": "#/$defs/has_n_lines_model", "has_size": "#/$defs/has_size_model", "has_text": "#/$defs/has_text_model", "has_text_matching": "#/$defs/has_text_matching_model", "is_valid_xml": "#/$defs/is_valid_xml_model", "not_has_text": "#/$defs/not_has_text_model", "xml_element": "#/$defs/xml_element_model"}, "propertyName": "that"}, "oneOf": [{"$ref": "#/$defs/has_line_model"}, {"$ref": "#/$defs/has_line_matching_model"}, {"$ref": "#/$defs/has_n_lines_model"}, {"$ref": "#/$defs/has_text_model"}, {"$ref": "#/$defs/has_text_matching_model"}, {"$ref": "#/$defs/not_has_text_model"}, {"$ref": "#/$defs/has_n_columns_model"}, {"$ref": "#/$defs/attribute_is_model"}, {"$ref": "#/$defs/attribute_matches_model"}, {"$ref": "#/$defs/element_text_model"}, {"$ref": "#/$defs/element_text_is_model"}, {"$ref": "#/$defs/element_text_matches_model"}, {"$ref": "#/$defs/has_element_with_path_model"}, {"$ref": "#/$defs/has_n_elements_with_path_model"}, {"$ref": "#/$defs/is_valid_xml_model"}, {"$ref": "#/$defs/xml_element_model"}, {"$ref": "#/$defs/has_json_property_with_text_model"}, {"$ref": "#/$defs/has_json_property_with_value_model"}, {"$ref": "#/$defs/has_h5_attribute_model"}, {"$ref": "#/$defs/has_h5_keys_model"}, {"$ref": "#/$defs/has_archive_member_model"}, {"$ref": "#/$defs/has_size_model"}, {"$ref": "#/$defs/has_image_center_of_mass_model"}, {"$ref": "#/$defs/has_image_channels_model"}, {"$ref": "#/$defs/has_image_depth_model"}, {"$ref": "#/$defs/has_image_frames_model"}, {"$ref": "#/$defs/has_image_height_model"}, {"$ref": "#/$defs/has_image_mean_intensity_model"}, {"$ref": "#/$defs/has_image_mean_object_size_model"}, {"$ref": "#/$defs/has_image_n_labels_model"}, {"$ref": "#/$defs/has_image_width_model"}]}, {"$ref": "#/$defs/has_line_model_nested"}, {"$ref": "#/$defs/has_line_matching_model_nested"}, {"$ref": "#/$defs/has_n_lines_model_nested"}, {"$ref": "#/$defs/has_text_model_nested"}, {"$ref": "#/$defs/has_text_matching_model_nested"}, {"$ref": "#/$defs/not_has_text_model_nested"}, {"$ref": "#/$defs/has_n_columns_model_nested"}, {"$ref": "#/$defs/attribute_is_model_nested"}, {"$ref": "#/$defs/attribute_matches_model_nested"}, {"$ref": "#/$defs/element_text_model_nested"}, {"$ref": "#/$defs/element_text_is_model_nested"}, {"$ref": "#/$defs/element_text_matches_model_nested"}, {"$ref": "#/$defs/has_element_with_path_model_nested"}, {"$ref": "#/$defs/has_n_elements_with_path_model_nested"}, {"$ref": "#/$defs/is_valid_xml_model_nested"}, {"$ref": "#/$defs/xml_element_model_nested"}, {"$ref": "#/$defs/has_json_property_with_text_model_nested"}, {"$ref": "#/$defs/has_json_property_with_value_model_nested"}, {"$ref": "#/$defs/has_h5_attribute_model_nested"}, {"$ref": "#/$defs/has_h5_keys_model_nested"}, {"$ref": "#/$defs/has_archive_member_model_nested"}, {"$ref": "#/$defs/has_size_model_nested"}, {"$ref": "#/$defs/has_image_center_of_mass_model_nested"}, {"$ref": "#/$defs/has_image_channels_model_nested"}, {"$ref": "#/$defs/has_image_depth_model_nested"}, {"$ref": "#/$defs/has_image_frames_model_nested"}, {"$ref": "#/$defs/has_image_height_model_nested"}, {"$ref": "#/$defs/has_image_mean_intensity_model_nested"}, {"$ref": "#/$defs/has_image_mean_object_size_model_nested"}, {"$ref": "#/$defs/has_image_n_labels_model_nested"}, {"$ref": "#/$defs/has_image_width_model_nested"}]}, "title": "assertion_list", "type": "array"}, "attribute_is_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` is the specified ``text``.\n\nFor example:\n\n```xml\n<attribute_is path=\"outerElement/innerElement1\" attribute=\"foo\" text=\"bar\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_is", "default": "attribute_is", "title": "That", "type": "string"}}, "required": ["path", "attribute", "text"], "title": "Assert Attribute Is", "type": "object"}, "attribute_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_is": {"$ref": "#/$defs/base_attribute_is_model", "title": "Assert Attribute Is"}}, "required": ["attribute_is"], "title": "Assert Attribute Is (Nested)", "type": "object"}, "attribute_matches_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` matches the regular expression specified by ``expression``.\n\nFor example:\n\n```xml\n<attribute_matches path=\"outerElement/innerElement2\" attribute=\"foo2\" expression=\"bar\\d+\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_matches", "default": "attribute_matches", "title": "That", "type": "string"}}, "required": ["path", "attribute", "expression"], "title": "Assert Attribute Matches", "type": "object"}, "attribute_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_matches": {"$ref": "#/$defs/base_attribute_matches_model", "title": "Assert Attribute Matches"}}, "required": ["attribute_matches"], "title": "Assert Attribute Matches (Nested)", "type": "object"}, "base_attribute_is_model": {"additionalProperties": false, "description": "base model for attribute_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "text"], "title": "base_attribute_is_model", "type": "object"}, "base_attribute_matches_model": {"additionalProperties": false, "description": "base model for attribute_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "expression"], "title": "base_attribute_matches_model", "type": "object"}, "base_element_text_is_model": {"additionalProperties": false, "description": "base model for element_text_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "text"], "title": "base_element_text_is_model", "type": "object"}, "base_element_text_matches_model": {"additionalProperties": false, "description": "base model for element_text_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "expression"], "title": "base_element_text_matches_model", "type": "object"}, "base_element_text_model": {"additionalProperties": false, "description": "base model for element_text describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_element_text_model", "type": "object"}, "base_has_archive_member_model": {"additionalProperties": false, "description": "base model for has_archive_member describing attributes.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_has_archive_member_model", "type": "object"}, "base_has_element_with_path_model": {"additionalProperties": false, "description": "base model for has_element_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_element_with_path_model", "type": "object"}, "base_has_h5_attribute_model": {"additionalProperties": false, "description": "base model for has_h5_attribute describing attributes.", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}}, "required": ["key", "value"], "title": "base_has_h5_attribute_model", "type": "object"}, "base_has_h5_keys_model": {"additionalProperties": false, "description": "base model for has_h5_keys describing attributes.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}}, "required": ["keys"], "title": "base_has_h5_keys_model", "type": "object"}, "base_has_image_center_of_mass_model": {"additionalProperties": false, "description": "base model for has_image_center_of_mass describing attributes.", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}}, "required": ["center_of_mass"], "title": "base_has_image_center_of_mass_model", "type": "object"}, "base_has_image_channels_model": {"additionalProperties": false, "description": "base model for has_image_channels describing attributes.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_channels_model", "type": "object"}, "base_has_image_depth_model": {"additionalProperties": false, "description": "base model for has_image_depth describing attributes.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_depth_model", "type": "object"}, "base_has_image_frames_model": {"additionalProperties": false, "description": "base model for has_image_frames describing attributes.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_frames_model", "type": "object"}, "base_has_image_height_model": {"additionalProperties": false, "description": "base model for has_image_height describing attributes.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_height_model", "type": "object"}, "base_has_image_mean_intensity_model": {"additionalProperties": false, "description": "base model for has_image_mean_intensity describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}}, "title": "base_has_image_mean_intensity_model", "type": "object"}, "base_has_image_mean_object_size_model": {"additionalProperties": false, "description": "base model for has_image_mean_object_size describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}}, "title": "base_has_image_mean_object_size_model", "type": "object"}, "base_has_image_n_labels_model": {"additionalProperties": false, "description": "base model for has_image_n_labels describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_n_labels_model", "type": "object"}, "base_has_image_width_model": {"additionalProperties": false, "description": "base model for has_image_width describing attributes.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_width_model", "type": "object"}, "base_has_json_property_with_text_model": {"additionalProperties": false, "description": "base model for has_json_property_with_text describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}}, "required": ["property", "text"], "title": "base_has_json_property_with_text_model", "type": "object"}, "base_has_json_property_with_value_model": {"additionalProperties": false, "description": "base model for has_json_property_with_value describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}}, "required": ["property", "value"], "title": "base_has_json_property_with_value_model", "type": "object"}, "base_has_line_matching_model": {"additionalProperties": false, "description": "base model for has_line_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_line_matching_model", "type": "object"}, "base_has_line_model": {"additionalProperties": false, "description": "base model for has_line describing attributes.", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["line"], "title": "base_has_line_model", "type": "object"}, "base_has_n_columns_model": {"additionalProperties": false, "description": "base model for has_n_columns describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_columns_model", "type": "object"}, "base_has_n_elements_with_path_model": {"additionalProperties": false, "description": "base model for has_n_elements_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_n_elements_with_path_model", "type": "object"}, "base_has_n_lines_model": {"additionalProperties": false, "description": "base model for has_n_lines describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_lines_model", "type": "object"}, "base_has_size_model": {"additionalProperties": false, "description": "base model for has_size describing attributes.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_size_model", "type": "object"}, "base_has_text_matching_model": {"additionalProperties": false, "description": "base model for has_text_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_text_matching_model", "type": "object"}, "base_has_text_model": {"additionalProperties": false, "description": "base model for has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["text"], "title": "base_has_text_model", "type": "object"}, "base_is_valid_xml_model": {"additionalProperties": false, "description": "base model for is_valid_xml describing attributes.", "properties": {}, "title": "base_is_valid_xml_model", "type": "object"}, "base_not_has_text_model": {"additionalProperties": false, "description": "base model for not_has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}}, "required": ["text"], "title": "base_not_has_text_model", "type": "object"}, "base_xml_element_model": {"additionalProperties": false, "description": "base model for xml_element describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_xml_element_model", "type": "object"}, "element_text_is_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path`` is\nthe specified ``text``.\n\nFor example:\n\n```xml\n<element_text_is path=\"BlastOutput_program\" text=\"blastp\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_is", "default": "element_text_is", "title": "That", "type": "string"}}, "required": ["path", "text"], "title": "Assert Element Text Is", "type": "object"}, "element_text_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_is": {"$ref": "#/$defs/base_element_text_is_model", "title": "Assert Element Text Is"}}, "required": ["element_text_is"], "title": "Assert Element Text Is (Nested)", "type": "object"}, "element_text_matches_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path``\nmatches the regular expression defined by ``expression``.\n\nFor example:\n\n```xml\n<element_text_matches path=\"BlastOutput_version\" expression=\"BLASTP\\s+2\\.2.*\"/>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_matches", "default": "element_text_matches", "title": "That", "type": "string"}}, "required": ["path", "expression"], "title": "Assert Element Text Matches", "type": "object"}, "element_text_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_matches": {"$ref": "#/$defs/base_element_text_matches_model", "title": "Assert Element Text Matches"}}, "required": ["element_text_matches"], "title": "Assert Element Text Matches (Nested)", "type": "object"}, "element_text_model": {"additionalProperties": false, "description": "This tag allows the developer to recurisively specify additional assertions as\nchild elements about just the text contained in the element specified by the\nXPath-like ``path``, e.g.\n\n```xml\n<element_text path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def\">\n  <not_has_text text=\"EDK72998.1\" />\n</element_text>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the implicit assertions can be inverted.\nThe sub-assertions, which have their own ``negate`` attribute, are not affected\nby ``negate``.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "element_text", "default": "element_text", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Element Text", "type": "object"}, "element_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text": {"$ref": "#/$defs/base_element_text_model", "title": "Assert Element Text"}}, "required": ["element_text"], "title": "Assert Element Text (Nested)", "type": "object"}, "has_archive_member_model": {"additionalProperties": false, "description": "This tag allows to check if ``path`` is contained in a compressed file.\n\nThe path is a regular expression that is matched against the full paths of the objects in\nthe compressed file (remember that \"matching\" means it is checked if a prefix of\nthe full path of an archive member is described by the regular expression).\nValid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that\ndepending on the archive creation method:\n\n- full paths of the members may be prefixed with ``./``\n- directories may be treated as empty files\n\n```xml\n<has_archive_member path=\"./path/to/my-file.txt\"/>\n```\n\nWith ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of\narchive members matching ``path`` can be expressed. The following could be used,\ne.g., to assert an archive containing n&plusmn;1 elements out of which at least\n4 need to have a ``txt`` extension.\n\n```xml\n<has_archive_member path=\".*\" n=\"10\" delta=\"1\"/>\n<has_archive_member path=\".*\\.txt\" min=\"4\"/>\n```\n\nIn addition the tag can contain additional assertions as child elements about\nthe first member in the archive matching the regular expression ``path``. For\ninstance\n\n```xml\n<has_archive_member path=\".*/my-file.txt\">\n  <not_has_text text=\"EDK72998.1\"/>\n</has_archive_member>\n```\n\nIf the ``all`` attribute is set to ``true`` then all archive members are subject\nto the assertions. Note that, archive members matching the ``path`` are sorted\nalphabetically.\n\nThe ``negate`` attribute of the ``has_archive_member`` assertion only affects\nthe asserts on the presence and number of matching archive members, but not any\nsub-assertions (which can offer the ``negate`` attribute on their own).  The\ncheck if the file is an archive at all, which is also done by the function, is\nnot affected.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "has_archive_member", "default": "has_archive_member", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Archive Member", "type": "object"}, "has_archive_member_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_archive_member": {"$ref": "#/$defs/base_has_archive_member_model", "title": "Assert Has Archive Member"}}, "required": ["has_archive_member"], "title": "Assert Has Archive Member (Nested)", "type": "object"}, "has_element_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains at least one element (or tag) with the specified\nXPath-like ``path``, e.g.\n\n```xml\n<has_element_with_path path=\"BlastOutput_param/Parameters/Parameters_matrix\" />\n```\n\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_element_with_path", "default": "has_element_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Element With Path", "type": "object"}, "has_element_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_element_with_path": {"$ref": "#/$defs/base_has_element_with_path_model", "title": "Assert Has Element With Path"}}, "required": ["has_element_with_path"], "title": "Assert Has Element With Path (Nested)", "type": "object"}, "has_h5_attribute_model": {"additionalProperties": false, "description": "Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.\n\n```xml\n<has_h5_attribute key=\"nchroms\" value=\"15\" />\n```", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}, "that": {"const": "has_h5_attribute", "default": "has_h5_attribute", "title": "That", "type": "string"}}, "required": ["key", "value"], "title": "Assert Has H5 Attribute", "type": "object"}, "has_h5_attribute_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_attribute": {"$ref": "#/$defs/base_has_h5_attribute_model", "title": "Assert Has H5 Attribute"}}, "required": ["has_h5_attribute"], "title": "Assert Has H5 Attribute (Nested)", "type": "object"}, "has_h5_keys_model": {"additionalProperties": false, "description": "Asserts the specified HDF5 output has the given keys.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}, "that": {"const": "has_h5_keys", "default": "has_h5_keys", "title": "That", "type": "string"}}, "required": ["keys"], "title": "Assert Has H5 Keys", "type": "object"}, "has_h5_keys_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_keys": {"$ref": "#/$defs/base_has_h5_keys_model", "title": "Assert Has H5 Keys"}}, "required": ["has_h5_keys"], "title": "Assert Has H5 Keys (Nested)", "type": "object"}, "has_image_center_of_mass_model": {"additionalProperties": false, "description": "Asserts the specified output is an image and has the specified center of mass.\n\nAsserts the output is an image and has a specific center of mass,\nor has an Euclidean distance of ``eps`` or less to that point (e.g.,\n``<has_image_center_of_mass center_of_mass=\"511.07, 223.34\" />``).", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}, "that": {"const": "has_image_center_of_mass", "default": "has_image_center_of_mass", "title": "That", "type": "string"}}, "required": ["center_of_mass"], "title": "Assert Has Image Center Of Mass", "type": "object"}, "has_image_center_of_mass_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_center_of_mass": {"$ref": "#/$defs/base_has_image_center_of_mass_model", "title": "Assert Has Image Center Of Mass"}}, "required": ["has_image_center_of_mass"], "title": "Assert Has Image Center Of Mass (Nested)", "type": "object"}, "has_image_channels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of channels.\n\nThe number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels=\"3\" />``).\n\nAlternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_channels", "default": "has_image_channels", "title": "That", "type": "string"}}, "title": "Assert Has Image Channels", "type": "object"}, "has_image_channels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_channels": {"$ref": "#/$defs/base_has_image_channels_model", "title": "Assert Has Image Channels"}}, "required": ["has_image_channels"], "title": "Assert Has Image Channels (Nested)", "type": "object"}, "has_image_depth_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific depth (number of slices).\n\nThe depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected depth can be specified by ``min`` and/or ``max``.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_depth", "default": "has_image_depth", "title": "That", "type": "string"}}, "title": "Assert Has Image Depth", "type": "object"}, "has_image_depth_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_depth": {"$ref": "#/$defs/base_has_image_depth_model", "title": "Assert Has Image Depth"}}, "required": ["has_image_depth"], "title": "Assert Has Image Depth (Nested)", "type": "object"}, "has_image_frames_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of frames (number of time steps).\n\nThe number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_frames", "default": "has_image_frames", "title": "That", "type": "string"}}, "title": "Assert Has Image Frames", "type": "object"}, "has_image_frames_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_frames": {"$ref": "#/$defs/base_has_image_frames_model", "title": "Assert Has Image Frames"}}, "required": ["has_image_frames"], "title": "Assert Has Image Frames (Nested)", "type": "object"}, "has_image_height_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific height (in pixels).\n\nThe height is plus/minus ``delta`` (e.g., ``<has_image_height height=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected height can be specified by ``min`` and/or ``max``.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_height", "default": "has_image_height", "title": "That", "type": "string"}}, "title": "Assert Has Image Height", "type": "object"}, "has_image_height_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_height": {"$ref": "#/$defs/base_has_image_height_model", "title": "Assert Has Image Height"}}, "required": ["has_image_height"], "title": "Assert Has Image Height (Nested)", "type": "object"}, "has_image_mean_intensity_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific mean intensity value.\n\nThe mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity=\"0.83\" />``).\nAlternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}, "that": {"const": "has_image_mean_intensity", "default": "has_image_mean_intensity", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Intensity", "type": "object"}, "has_image_mean_intensity_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_intensity": {"$ref": "#/$defs/base_has_image_mean_intensity_model", "title": "Assert Has Image Mean Intensity"}}, "required": ["has_image_mean_intensity"], "title": "Assert Has Image Mean Intensity (Nested)", "type": "object"}, "has_image_mean_object_size_model": {"additionalProperties": false, "description": "Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),\n\nThe mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size=\"111.87\" exclude_labels=\"0\" />``).\n\nThe labels must be unique.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}, "that": {"const": "has_image_mean_object_size", "default": "has_image_mean_object_size", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Object Size", "type": "object"}, "has_image_mean_object_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_object_size": {"$ref": "#/$defs/base_has_image_mean_object_size_model", "title": "Assert Has Image Mean Object Size"}}, "required": ["has_image_mean_object_size"], "title": "Assert Has Image Mean Object Size (Nested)", "type": "object"}, "has_image_n_labels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has the specified labels.\n\nLabels can be a number of labels or unique values (e.g.,\n``<has_image_n_labels n=\"187\" exclude_labels=\"0\" />``).\n\nThe primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_n_labels", "default": "has_image_n_labels", "title": "That", "type": "string"}}, "title": "Assert Has Image N Labels", "type": "object"}, "has_image_n_labels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_n_labels": {"$ref": "#/$defs/base_has_image_n_labels_model", "title": "Assert Has Image N Labels"}}, "required": ["has_image_n_labels"], "title": "Assert Has Image N Labels (Nested)", "type": "object"}, "has_image_width_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific width (in pixels).\n\nThe width is plus/minus ``delta`` (e.g., ``<has_image_width width=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected width can be specified by ``min`` and/or ``max``.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_width", "default": "has_image_width", "title": "That", "type": "string"}}, "title": "Assert Has Image Width", "type": "object"}, "has_image_width_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_width": {"$ref": "#/$defs/base_has_image_width_model", "title": "Assert Has Image Width"}}, "required": ["has_image_width"], "title": "Assert Has Image Width (Nested)", "type": "object"}, "has_json_property_with_text_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified text (i.e. string) value.\n\n```xml\n<has_json_property_with_text property=\"color\" text=\"red\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}, "that": {"const": "has_json_property_with_text", "default": "has_json_property_with_text", "title": "That", "type": "string"}}, "required": ["property", "text"], "title": "Assert Has Json Property With Text", "type": "object"}, "has_json_property_with_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_text": {"$ref": "#/$defs/base_has_json_property_with_text_model", "title": "Assert Has Json Property With Text"}}, "required": ["has_json_property_with_text"], "title": "Assert Has Json Property With Text (Nested)", "type": "object"}, "has_json_property_with_value_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified JSON value.\n\n```xml\n<has_json_property_with_value property=\"skipped_columns\" value=\"[1, 3, 5]\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}, "that": {"const": "has_json_property_with_value", "default": "has_json_property_with_value", "title": "That", "type": "string"}}, "required": ["property", "value"], "title": "Assert Has Json Property With Value", "type": "object"}, "has_json_property_with_value_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_value": {"$ref": "#/$defs/base_has_json_property_with_value_model", "title": "Assert Has Json Property With Value"}}, "required": ["has_json_property_with_value"], "title": "Assert Has Json Property With Value (Nested)", "type": "object"}, "has_line_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains a line matching the\nregular expression specified by the argument expression. If n is given\nthe assertion checks for exactly n occurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line_matching", "default": "has_line_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Line Matching", "type": "object"}, "has_line_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line_matching": {"$ref": "#/$defs/base_has_line_matching_model", "title": "Assert Has Line Matching"}}, "required": ["has_line_matching"], "title": "Assert Has Line Matching (Nested)", "type": "object"}, "has_line_model": {"additionalProperties": false, "description": "Asserts the specified output contains the line specified by the\nargument line. The exact number of occurrences can be optionally\nspecified by the argument n", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line", "default": "has_line", "title": "That", "type": "string"}}, "required": ["line"], "title": "Assert Has Line", "type": "object"}, "has_line_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line": {"$ref": "#/$defs/base_has_line_model", "title": "Assert Has Line"}}, "required": ["has_line"], "title": "Assert Has Line (Nested)", "type": "object"}, "has_n_columns_model": {"additionalProperties": false, "description": "Asserts tabular output  contains the specified\nnumber (``n``) of columns.\n\nFor instance, ``<has_n_columns n=\"3\"/>``. The assertion tests only the first line.\nNumber of columns can optionally also be specified with ``delta``. Alternatively the\nrange of expected occurrences can be specified by ``min`` and/or ``max``.\n\nOptionally a column separator (``sep``, default is ``       ``) `and comment character(s)\ncan be specified (``comment``, default is empty string). The first non-comment\nline is used for determining the number of columns.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_columns", "default": "has_n_columns", "title": "That", "type": "string"}}, "title": "Assert Has N Columns", "type": "object"}, "has_n_columns_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_columns": {"$ref": "#/$defs/base_has_n_columns_model", "title": "Assert Has N Columns"}}, "required": ["has_n_columns"], "title": "Assert Has N Columns (Nested)", "type": "object"}, "has_n_elements_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or\ntags) with the specified XPath-like ``path``.\n\nFor example:\n\n```xml\n<has_n_elements_with_path n=\"9\" path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num\" />\n```\n\nAlternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes\ncan be used to specify the range of the expected number of occurrences.\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_elements_with_path", "default": "has_n_elements_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has N Elements With Path", "type": "object"}, "has_n_elements_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_elements_with_path": {"$ref": "#/$defs/base_has_n_elements_with_path_model", "title": "Assert Has N Elements With Path"}}, "required": ["has_n_elements_with_path"], "title": "Assert Has N Elements With Path (Nested)", "type": "object"}, "has_n_lines_model": {"additionalProperties": false, "description": "Asserts the specified output contains ``n`` lines allowing\nfor a difference in the number of lines (delta)\nor relative differebce in the number of lines", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_lines", "default": "has_n_lines", "title": "That", "type": "string"}}, "title": "Assert Has N Lines", "type": "object"}, "has_n_lines_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_lines": {"$ref": "#/$defs/base_has_n_lines_model", "title": "Assert Has N Lines"}}, "required": ["has_n_lines"], "title": "Assert Has N Lines (Nested)", "type": "object"}, "has_size_model": {"additionalProperties": false, "description": "Asserts the specified output has a size of the specified value\n\nAttributes size and value or synonyms though value is considered deprecated.\nThe size optionally allows for absolute (``delta``) difference.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_size", "default": "has_size", "title": "That", "type": "string"}}, "title": "Assert Has Size", "type": "object"}, "has_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_size": {"$ref": "#/$defs/base_has_size_model", "title": "Assert Has Size"}}, "required": ["has_size"], "title": "Assert Has Size (Nested)", "type": "object"}, "has_text_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains text matching the\nregular expression specified by the argument expression.\nIf n is given the assertion checks for exactly n (nonoverlapping)\noccurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text_matching", "default": "has_text_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Text Matching", "type": "object"}, "has_text_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text_matching": {"$ref": "#/$defs/base_has_text_matching_model", "title": "Assert Has Text Matching"}}, "required": ["has_text_matching"], "title": "Assert Has Text Matching (Nested)", "type": "object"}, "has_text_model": {"additionalProperties": false, "description": "Asserts specified output contains the substring specified by\nthe argument text. The exact number of occurrences can be\noptionally specified by the argument n", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text", "default": "has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Has Text", "type": "object"}, "has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text": {"$ref": "#/$defs/base_has_text_model", "title": "Assert Has Text"}}, "required": ["has_text"], "title": "Assert Has Text (Nested)", "type": "object"}, "is_valid_xml_model": {"additionalProperties": false, "description": "Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).", "properties": {"that": {"const": "is_valid_xml", "default": "is_valid_xml", "title": "That", "type": "string"}}, "title": "Assert Is Valid Xml", "type": "object"}, "is_valid_xml_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"is_valid_xml": {"$ref": "#/$defs/base_is_valid_xml_model", "title": "Assert Is Valid Xml"}}, "required": ["is_valid_xml"], "title": "Assert Is Valid Xml (Nested)", "type": "object"}, "not_has_text_model": {"additionalProperties": false, "description": "Asserts specified output does not contain the substring\nspecified by the argument text", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "that": {"const": "not_has_text", "default": "not_has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Not Has Text", "type": "object"}, "not_has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"not_has_text": {"$ref": "#/$defs/base_not_has_text_model", "title": "Assert Not Has Text"}}, "required": ["not_has_text"], "title": "Assert Not Has Text (Nested)", "type": "object"}, "xml_element_model": {"additionalProperties": false, "description": "Assert if the XML file contains element(s) or tag(s) with the specified\n[XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``\nor ``min`` and ``max`` are given also the number of occurrences is checked.\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem\"/>\n  <xml_element path=\"./elem/more[2]\"/>\n  <xml_element path=\".//more\" n=\"3\" delta=\"1\"/>\n</assert_contents>\n```\n\nWith ``negate=\"true\"`` the outcome of the assertions wrt the presence and number\nof ``path`` can be negated. If there are any sub assertions then check them against\n\n- the content of the attribute ``attribute``\n- the element's text if no attribute is given\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem/more[2]\" attribute=\"name\">\n    <has_text_matching expression=\"foo$\"/>\n  </xml_element>\n</assert_contents>\n```\n\nSub-assertions are not subject to the ``negate`` attribute of ``xml_element``.\nIf ``all`` is ``true`` then the sub assertions are checked for all occurrences.\n\nNote that all other XML assertions can be expressed by this assertion (Galaxy\nalso implements the other assertions by calling this one).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "xml_element", "default": "xml_element", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Xml Element", "type": "object"}, "xml_element_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"xml_element": {"$ref": "#/$defs/base_xml_element_model", "title": "Assert Xml Element"}}, "required": ["xml_element"], "title": "Assert Xml Element (Nested)", "type": "object"}}, "additionalProperties": false, "description": "Full unprivileged tool source, including the optional ``tests`` block.\n\nThis is the model persisted and validated on the API surface\n(``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring\nuses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added\nback here so direct authors and stored rows can still carry tests.", "properties": {"id": {"anyOf": [{"maxLength": 255, "minLength": 3, "pattern": "^[a-z][a-z0-9_-]*$", "type": "string"}, {"type": "null"}], "default": null, "description": "Unique identifier for the tool. Lowercase, must start with a letter, may contain letters, digits, '_' and '-'.", "examples": ["my-cool-tool"], "title": "id"}, "version": {"description": "Version for the tool.", "examples": ["0.1.0"], "title": "version", "type": "string"}, "name": {"description": "The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.", "minLength": 5, "title": "name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The description is displayed in the tool menu immediately following the hyperlink for the tool.", "title": "description"}, "configfiles": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTemplateConfigFile"}, "type": "array"}, {"type": "null"}], "default": null, "description": "A list of config files for this tool.", "title": "configfiles"}, "requirements": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/JavascriptRequirement"}, {"$ref": "#/$defs/ResourceRequirement"}, {"$ref": "#/$defs/ContainerRequirement"}]}, "type": "array"}, {"type": "null"}], "default": [], "description": "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.", "title": "requirements"}, "shell_command": {"description": "A string that contains the command to be executed. Parameters can be referenced inside $().", "examples": ["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"], "title": "shell_command", "type": "string"}, "inputs": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "inputs", "type": "array"}, "outputs": {"default": [], "items": {"discriminator": {"mapping": {"boolean": "#/$defs/IncomingToolOutputBoolean", "collection": "#/$defs/IncomingToolOutputCollection", "data": "#/$defs/IncomingToolOutputDataset", "float": "#/$defs/IncomingToolOutputFloat", "integer": "#/$defs/IncomingToolOutputInteger", "text": "#/$defs/IncomingToolOutputText"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/IncomingToolOutputDataset"}, {"$ref": "#/$defs/IncomingToolOutputCollection"}, {"$ref": "#/$defs/IncomingToolOutputText"}, {"$ref": "#/$defs/IncomingToolOutputInteger"}, {"$ref": "#/$defs/IncomingToolOutputFloat"}, {"$ref": "#/$defs/IncomingToolOutputBoolean"}]}, "title": "outputs", "type": "array"}, "citations": {"anyOf": [{"items": {"$ref": "#/$defs/Citation"}, "type": "array"}, {"type": "null"}], "default": null, "title": "citations"}, "license": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.", "examples": ["MIT"], "title": "license"}, "edam_operations": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_operations"}, "edam_topics": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_topics"}, "xrefs": {"anyOf": [{"items": {"$ref": "#/$defs/XrefDict"}, "type": "array"}, {"type": "null"}], "default": null, "title": "xrefs"}, "profile": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "profile"}, "help": {"anyOf": [{"$ref": "#/$defs/HelpContent"}, {"type": "null"}], "default": null, "description": "Help text shown below the tool interface.", "title": "help"}, "class": {"const": "GalaxyUserTool", "title": "class_", "type": "string"}, "container": {"description": "Container image to use for this tool.", "examples": ["quay.io/biocontainers/python:3.13"], "title": "container", "type": "string"}, "tests": {"anyOf": [{"items": {"$ref": "#/$defs/YamlToolTest"}, "type": "array"}, {"type": "null"}], "default": null, "title": "tests"}}, "required": ["version", "name", "shell_command", "class", "container"], "title": "UserToolSource", "type": "object"}
\ No newline at end of file
+{"$defs": {"Citation": {"properties": {"type": {"title": "Type", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["type", "content"], "title": "Citation", "type": "object"}, "CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "Container": {"properties": {"type": {"enum": ["docker", "singularity"], "title": "Type", "type": "string"}, "container_id": {"title": "Container Id", "type": "string"}}, "required": ["type", "container_id"], "title": "Container", "type": "object"}, "ContainerRequirement": {"properties": {"type": {"const": "container", "title": "Type", "type": "string"}, "container": {"$ref": "#/$defs/Container"}}, "required": ["type", "container"], "title": "ContainerRequirement", "type": "object"}, "EmptyFieldParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "empty_field", "default": "empty_field", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "EmptyFieldParameterValidatorModel", "type": "object"}, "FilePatternDatasetCollectionDescription": {"additionalProperties": false, "properties": {"discover_via": {"const": "pattern", "default": "pattern", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}, "sort_key": {"default": "filename", "enum": ["filename", "name", "designation", "dbkey"], "title": "Sort Key", "type": "string"}, "sort_comp": {"default": "lexical", "enum": ["lexical", "numeric"], "title": "Sort Comp", "type": "string"}, "sort_reverse": {"default": false, "title": "Sort Reverse", "type": "boolean"}, "pattern": {"title": "Pattern", "type": "string"}}, "required": ["pattern"], "title": "FilePatternDatasetCollectionDescription", "type": "object"}, "HelpContent": {"properties": {"format": {"enum": ["restructuredtext", "plain_text", "markdown"], "title": "Format", "type": "string"}, "content": {"title": "Content", "type": "string"}}, "required": ["format", "content"], "title": "HelpContent", "type": "object"}, "InRangeParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "in_range", "default": "in_range", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "exclude_min": {"default": false, "title": "Exclude Min", "type": "boolean"}, "exclude_max": {"default": false, "title": "Exclude Max", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "InRangeParameterValidatorModel", "type": "object"}, "IncomingToolOutputBoolean": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "boolean", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputBoolean", "type": "object"}, "IncomingToolOutputCollection": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "collection_type_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type Source"}, "collection_type_from_rules": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type From Rules"}, "structured_like": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Structured Like"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}}, "required": ["type"], "title": "IncomingToolOutputCollection", "type": "object"}, "IncomingToolOutputDataset": {"properties": {"name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The short name for the output datatype.", "title": "Format"}, "format_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.", "title": "Format Source"}, "metadata_source": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "This copies the metadata information from the tool\u2019s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.", "title": "Metadata Source"}, "discover_datasets": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/FilePatternDatasetCollectionDescription"}, {"$ref": "#/$defs/ToolProvidedMetadataDatasetCollection"}]}, "type": "array"}, {"type": "null"}], "default": null, "title": "Discover Datasets"}, "from_work_dir": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Relative path to a file produced by the tool in its working directory. Output\u2019s contents are set to this file\u2019s contents.", "title": "from_work_dir"}, "precreate_directory": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Precreate Directory"}}, "required": ["type"], "title": "IncomingToolOutputDataset", "type": "object"}, "IncomingToolOutputFloat": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "float", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputFloat", "type": "object"}, "IncomingToolOutputInteger": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "integer", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputInteger", "type": "object"}, "IncomingToolOutputText": {"properties": {"name": {"description": "Parameter name. Used when referencing parameter in workflows.", "title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Output label. Will be used as dataset name in history.", "title": "Label"}, "hidden": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the output will not be shown in the history.", "title": "Hidden"}, "type": {"const": "text", "title": "Type", "type": "string"}}, "required": ["name", "type"], "title": "IncomingToolOutputText", "type": "object"}, "JavascriptRequirement": {"properties": {"type": {"const": "javascript", "title": "Type", "type": "string"}, "expression_lib": {"anyOf": [{"items": {"description": "Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.", "examples": ["function pickValue() {\n    if (inputs.conditional_parameter.test_parameter == \"a\") {\n        return inputs.conditional_parameter.integer_parameter\n    } else {\n        return inputs.conditional_parameter.boolean_parameter\n    }\n}"], "title": "expression_lib", "type": "string"}, "type": "array"}, {"type": "null"}], "title": "Expression Lib"}}, "required": ["type", "expression_lib"], "title": "JavascriptRequirement", "type": "object"}, "LengthParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "length", "default": "length", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "LengthParameterValidatorModel", "type": "object"}, "NoOptionsParameterValidatorModel": {"additionalProperties": false, "properties": {"type": {"const": "no_options", "default": "no_options", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}}, "title": "NoOptionsParameterValidatorModel", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RegexParameterValidatorModel": {"additionalProperties": false, "description": "Check if a regular expression **matches** the value, i.e. appears\nat the beginning of the value. To enforce a match of the complete value use\n``$`` at the end of the expression. The expression is given is the content\nof the validator tag. Note that for ``selects`` each option is checked\nseparately.", "properties": {"type": {"const": "regex", "default": "regex", "title": "Type", "type": "string"}, "message": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Message"}, "implicit": {"default": false, "title": "Implicit", "type": "boolean"}, "negate": {"default": false, "title": "Negate", "type": "boolean"}, "expression": {"title": "Expression", "type": "string"}}, "required": ["expression"], "title": "RegexParameterValidatorModel", "type": "object"}, "ResourceRequirement": {"properties": {"type": {"const": "resource", "title": "Type", "type": "string"}, "cores_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 1, "description": "Minimum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Min"}, "cores_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved number of CPU cores.\nMay be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\nThe reported number of CPU cores reserved for the process is a non-zero integer calculated by rounding up the cores request to the next whole number.\n", "title": "Cores Max"}, "ram_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": 256, "description": "Minimum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Min"}, "ram_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum reserved RAM in mebibytes (2**20).\nMay be a fractional value. If so, the actual RAM request is rounded up to the next whole number. The reported amount of RAM reserved for the process is a non-zero integer.", "title": "Ram Max"}, "tmpdir_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Min"}, "tmpdir_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Tmpdir Max"}, "cuda_version_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Version Min"}, "cuda_compute_capability": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Compute Capability"}, "gpu_memory_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Gpu Memory Min"}, "cuda_device_count_min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Min"}, "cuda_device_count_max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Cuda Device Count Max"}, "shm_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "title": "Shm Size"}, "timelimit": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "string"}, {"type": "null"}], "default": null, "description": "Maximum time in seconds the tool is allowed to run. Job will be terminated if exceeded.", "title": "Timelimit"}}, "required": ["type"], "title": "ResourceRequirement", "type": "object"}, "TestCollectionCollectionElementAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}}, "title": "TestCollectionCollectionElementAssertions", "type": "object"}, "TestCollectionDatasetElementAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestCollectionDatasetElementAssertions", "type": "object"}, "TestCollectionOutputAssertions": {"additionalProperties": false, "properties": {"class": {"anyOf": [{"const": "Collection", "type": "string"}, {"type": "null"}], "default": "Collection", "title": "Class"}, "elements": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Elements"}, "element_tests": {"anyOf": [{"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionDatasetElementAssertions"}, {"$ref": "#/$defs/TestCollectionCollectionElementAssertions"}]}, "type": "object"}, {"type": "null"}], "default": null, "title": "Element Tests"}, "element_count": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Element Count"}, "attributes": {"anyOf": [{"$ref": "#/$defs/CollectionAttributes"}, {"type": "null"}], "default": null, "title": "Attributes"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "TestCollectionOutputAssertions", "type": "object"}, "TestDataOutputAssertions": {"additionalProperties": false, "properties": {"file": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Name of the output file stored in the target `test-data` directory that will be used to compare against the results of executing the tool via the functional test framework.", "title": "File"}, "path": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Filesystem path to a local output file used for comparison.", "title": "Path"}, "location": {"anyOf": [{"format": "uri", "minLength": 1, "type": "string"}, {"type": "null"}], "default": null, "description": "URL that points to a remote output file that will be downloaded and used for output comparison. Use only when the file cannot be included in the `test-data` folder. May be combined with `file` (downloads when missing on disk) or used alone (filename inferred from the URL). A `checksum` is also used to verify the download when provided.", "title": "Location"}, "ftype": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "If specified, this value is checked against the corresponding output's data type. If these do not match, the test will fail.", "title": "File Type"}, "sort": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "Applies only if `compare` is `diff`, `re_match` or `re_match_multiline`. Sorts the lines of the history data set before comparison; for `diff` and `re_match` the local file is also sorted. Useful for non-deterministic output.", "title": "Sort"}, "compare": {"anyOf": [{"$ref": "#/$defs/OutputCompareType"}, {"type": "null"}], "default": null, "description": "Comparison mode used when matching the output against the reference file.", "title": "Compare"}, "checksum": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The target output's checksum should match the value specified here, in the form `hash_type$hash_value` (e.g. `sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041`). Useful for large static files where uploading the whole file is inconvenient.", "title": "Checksum"}, "metadata": {"anyOf": [{"additionalProperties": true, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of metadata keys to expected values for this output.", "title": "Metadata"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions about the content of the output.", "title": "Asserts"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed absolute size difference (in bytes) between the generated data set and the reference file in `test-data/`. Default is 10000 bytes. Can be combined with `delta_frac`.", "title": "Delta"}, "delta_frac": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "description": "If `compare` is set to `sim_size`, the maximum allowed relative size difference between the generated data set and the reference file in `test-data/`. 0.1 means the generated file can differ by at most 10%. Default is not to check for relative size difference. Can be combined with `delta`.", "title": "Delta Frac"}, "lines_diff": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Applies when `compare` is set to `diff`, `re_match`, or `contains`. For `diff`, the number of lines of difference to allow (a modified line counts as two: one added, one removed).", "title": "Lines Diff"}, "decompress": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, decompress files before comparison. Applies to assertions expressed with `assert_contents` or `compare` set to anything but `sim_size`. Useful for testing compressed outputs that are non-deterministic despite having deterministic decompressed contents. By default, only files compressed with bz2, gzip and zip are automatically decompressed.", "title": "Decompress"}, "class": {"anyOf": [{"const": "File", "type": "string"}, {"type": "null"}], "default": "File", "title": "Class"}}, "title": "TestDataOutputAssertions", "type": "object"}, "ToolProvidedMetadataDatasetCollection": {"additionalProperties": false, "properties": {"discover_via": {"const": "tool_provided_metadata", "title": "Discover Via", "type": "string"}, "format": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Format"}, "visible": {"default": false, "title": "Visible", "type": "boolean"}, "assign_primary_output": {"default": false, "title": "Assign Primary Output", "type": "boolean"}, "directory": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Directory"}, "recurse": {"default": false, "title": "Recurse", "type": "boolean"}, "match_relative_path": {"default": false, "title": "Match Relative Path", "type": "boolean"}}, "required": ["discover_via"], "title": "ToolProvidedMetadataDatasetCollection", "type": "object"}, "XrefDict": {"additionalProperties": false, "properties": {"value": {"title": "value", "type": "string"}, "type": {"title": "type", "type": "string"}}, "required": ["value", "type"], "title": "XrefDict", "type": "object"}, "YamlBooleanParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "boolean", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": false, "title": "Value"}}, "required": ["name", "type"], "title": "YamlBooleanParameter", "type": "object"}, "YamlColorParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "color", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}}, "required": ["name", "type"], "title": "YamlColorParameter", "type": "object"}, "YamlConditionalParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "conditional", "title": "Type", "type": "string"}, "test_parameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "select": "#/$defs/YamlSelectParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}], "title": "Test Parameter"}, "whens": {"items": {"$ref": "#/$defs/YamlConditionalWhen"}, "minItems": 1, "title": "Whens", "type": "array"}}, "required": ["name", "type", "test_parameter", "whens"], "title": "YamlConditionalParameter", "type": "object"}, "YamlConditionalWhen": {"additionalProperties": false, "properties": {"discriminator": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "title": "Discriminator"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["discriminator"], "title": "YamlConditionalWhen", "type": "object"}, "YamlDataCollectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data_collection", "title": "Type", "type": "string"}, "collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}}, "required": ["name", "type"], "title": "YamlDataCollectionParameter", "type": "object"}, "YamlDataParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "data", "title": "Type", "type": "string"}, "format": {"default": ["data"], "items": {"type": "string"}, "title": "Format", "type": "array"}, "multiple": {"default": false, "description": "Set true to accept several datasets (a list) for this input instead of one.", "title": "Multiple", "type": "boolean"}}, "required": ["name", "type"], "title": "YamlDataParameter", "type": "object"}, "YamlFloatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "float", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlFloatParameter", "type": "object"}, "YamlGalaxyToolParameter": {"discriminator": {"mapping": {"boolean": "#/$defs/YamlBooleanParameter", "color": "#/$defs/YamlColorParameter", "conditional": "#/$defs/YamlConditionalParameter", "data": "#/$defs/YamlDataParameter", "data_collection": "#/$defs/YamlDataCollectionParameter", "float": "#/$defs/YamlFloatParameter", "integer": "#/$defs/YamlIntegerParameter", "repeat": "#/$defs/YamlRepeatParameter", "section": "#/$defs/YamlSectionParameter", "select": "#/$defs/YamlSelectParameter", "text": "#/$defs/YamlTextParameter"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/YamlBooleanParameter"}, {"$ref": "#/$defs/YamlIntegerParameter"}, {"$ref": "#/$defs/YamlFloatParameter"}, {"$ref": "#/$defs/YamlTextParameter"}, {"$ref": "#/$defs/YamlSelectParameter"}, {"$ref": "#/$defs/YamlColorParameter"}, {"$ref": "#/$defs/YamlDataParameter"}, {"$ref": "#/$defs/YamlDataCollectionParameter"}, {"$ref": "#/$defs/YamlConditionalParameter"}, {"$ref": "#/$defs/YamlRepeatParameter"}, {"$ref": "#/$defs/YamlSectionParameter"}], "title": "YamlGalaxyToolParameter"}, "YamlIntegerParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "integer", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Value"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}, "validators": {"default": [], "items": {"$ref": "#/$defs/InRangeParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlIntegerParameter", "type": "object"}, "YamlLabelValue": {"description": "YAML-friendly option model \u2014 ``selected`` defaults to ``False``.", "properties": {"label": {"title": "Label", "type": "string"}, "value": {"title": "Value", "type": "string"}, "selected": {"default": false, "title": "Selected", "type": "boolean"}}, "required": ["label", "value"], "title": "YamlLabelValue", "type": "object"}, "YamlRepeatParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "repeat", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "title": "Max"}}, "required": ["name", "type"], "title": "YamlRepeatParameter", "type": "object"}, "YamlSectionParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "section", "title": "Type", "type": "string"}, "parameters": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "Parameters", "type": "array"}}, "required": ["name", "type"], "title": "YamlSectionParameter", "type": "object"}, "YamlSelectParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "select", "title": "Type", "type": "string"}, "options": {"items": {"$ref": "#/$defs/YamlLabelValue"}, "minItems": 1, "title": "Options", "type": "array"}, "multiple": {"default": false, "title": "Multiple", "type": "boolean"}, "validators": {"default": [], "items": {"$ref": "#/$defs/NoOptionsParameterValidatorModel"}, "title": "Validators", "type": "array"}}, "required": ["name", "type", "options"], "title": "YamlSelectParameter", "type": "object"}, "YamlTemplateConfigFile": {"properties": {"content": {"title": "Content", "type": "string"}, "name": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Name"}, "filename": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Filename"}, "eval_engine": {"const": "ecmascript", "default": "ecmascript", "title": "Eval Engine", "type": "string"}}, "required": ["content"], "title": "YamlTemplateConfigFile", "type": "object"}, "YamlTestCredential": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credentials group.", "title": "Name", "type": "string"}, "variables": {"default": [], "description": "Variables exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Variables", "type": "array"}, "secrets": {"default": [], "description": "Secrets exposed to the tool environment.", "items": {"$ref": "#/$defs/YamlTestCredentialValue"}, "title": "Secrets", "type": "array"}, "version": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Version of the credential definition.", "title": "Version"}}, "required": ["name"], "title": "YamlTestCredential", "type": "object"}, "YamlTestCredentialValue": {"additionalProperties": false, "properties": {"name": {"description": "Name of the credential variable or secret.", "title": "Name", "type": "string"}, "value": {"description": "Value of the credential variable or secret.", "title": "Value", "type": "string"}}, "required": ["name", "value"], "title": "YamlTestCredentialValue", "type": "object"}, "YamlTextParameter": {"additionalProperties": false, "properties": {"name": {"title": "Name", "type": "string"}, "label": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Label"}, "help": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Help"}, "optional": {"default": false, "title": "Optional", "type": "boolean"}, "type": {"const": "text", "title": "Type", "type": "string"}, "value": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Value"}, "area": {"default": false, "title": "Area", "type": "boolean"}, "validators": {"default": [], "items": {"anyOf": [{"$ref": "#/$defs/LengthParameterValidatorModel"}, {"$ref": "#/$defs/RegexParameterValidatorModel"}, {"$ref": "#/$defs/EmptyFieldParameterValidatorModel"}]}, "title": "Validators", "type": "array"}}, "required": ["name", "type"], "title": "YamlTextParameter", "type": "object"}, "YamlToolTest": {"additionalProperties": false, "description": "In-tool test case as authored in YAML tool fixtures.", "properties": {"doc": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "Human-readable description of this test case.", "title": "Doc"}, "inputs": {"anyOf": [{"additionalProperties": {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}, {"items": {}, "type": "array"}, {"additionalProperties": true, "type": "object"}]}, "type": "object"}, {"type": "null"}], "default": null, "description": "Mapping of input parameter names to test values.", "title": "Inputs"}, "outputs": {"additionalProperties": {"oneOf": [{"$ref": "#/$defs/TestCollectionOutputAssertions"}, {"$ref": "#/$defs/TestDataOutputAssertions"}, {"anyOf": [{"type": "boolean"}, {"type": "integer"}, {"type": "number"}, {"type": "string"}]}]}, "default": {}, "description": "Mapping of output names to expected values or assertions.", "title": "Outputs", "type": "object"}, "assert_stdout": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard output.", "title": "Assert Stdout"}, "assert_stderr": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the tool's standard error.", "title": "Assert Stderr"}, "command": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"$ref": "#/$defs/assertion_dict"}, {"type": "null"}], "default": null, "description": "Assertions to apply against the executed command line.", "title": "Command"}, "expect_exit_code": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected process exit code.", "title": "Expect Exit Code"}, "expect_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the tool is expected to produce an error.", "title": "Expect Failure"}, "expect_test_failure": {"anyOf": [{"type": "boolean"}, {"type": "null"}], "default": null, "description": "If true, the test itself is expected to fail.", "title": "Expect Test Failure"}, "credentials": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTestCredential"}, "type": "array"}, {"type": "null"}], "default": null, "description": "Credentials to inject for this test case.", "title": "Credentials"}}, "title": "YamlToolTest", "type": "object"}, "assertion_dict": {"additionalProperties": false, "properties": {"has_line": {"anyOf": [{"$ref": "#/$defs/base_has_line_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line"}, "has_line_matching": {"anyOf": [{"$ref": "#/$defs/base_has_line_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Line Matching"}, "has_n_lines": {"anyOf": [{"$ref": "#/$defs/base_has_n_lines_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Lines"}, "has_text": {"anyOf": [{"$ref": "#/$defs/base_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text"}, "has_text_matching": {"anyOf": [{"$ref": "#/$defs/base_has_text_matching_model"}, {"type": "null"}], "default": null, "title": "Assert Has Text Matching"}, "not_has_text": {"anyOf": [{"$ref": "#/$defs/base_not_has_text_model"}, {"type": "null"}], "default": null, "title": "Assert Not Has Text"}, "has_n_columns": {"anyOf": [{"$ref": "#/$defs/base_has_n_columns_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Columns"}, "attribute_is": {"anyOf": [{"$ref": "#/$defs/base_attribute_is_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Is"}, "attribute_matches": {"anyOf": [{"$ref": "#/$defs/base_attribute_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Attribute Matches"}, "element_text": {"anyOf": [{"$ref": "#/$defs/base_element_text_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text"}, "element_text_is": {"anyOf": [{"$ref": "#/$defs/base_element_text_is_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Is"}, "element_text_matches": {"anyOf": [{"$ref": "#/$defs/base_element_text_matches_model"}, {"type": "null"}], "default": null, "title": "Assert Element Text Matches"}, "has_element_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_element_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has Element With Path"}, "has_n_elements_with_path": {"anyOf": [{"$ref": "#/$defs/base_has_n_elements_with_path_model"}, {"type": "null"}], "default": null, "title": "Assert Has N Elements With Path"}, "is_valid_xml": {"anyOf": [{"$ref": "#/$defs/base_is_valid_xml_model"}, {"type": "null"}], "default": null, "title": "Assert Is Valid Xml"}, "xml_element": {"anyOf": [{"$ref": "#/$defs/base_xml_element_model"}, {"type": "null"}], "default": null, "title": "Assert Xml Element"}, "has_json_property_with_text": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_text_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Text"}, "has_json_property_with_value": {"anyOf": [{"$ref": "#/$defs/base_has_json_property_with_value_model"}, {"type": "null"}], "default": null, "title": "Assert Has Json Property With Value"}, "has_h5_attribute": {"anyOf": [{"$ref": "#/$defs/base_has_h5_attribute_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Attribute"}, "has_h5_keys": {"anyOf": [{"$ref": "#/$defs/base_has_h5_keys_model"}, {"type": "null"}], "default": null, "title": "Assert Has H5 Keys"}, "has_archive_member": {"anyOf": [{"$ref": "#/$defs/base_has_archive_member_model"}, {"type": "null"}], "default": null, "title": "Assert Has Archive Member"}, "has_size": {"anyOf": [{"$ref": "#/$defs/base_has_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Size"}, "has_image_center_of_mass": {"anyOf": [{"$ref": "#/$defs/base_has_image_center_of_mass_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Center Of Mass"}, "has_image_channels": {"anyOf": [{"$ref": "#/$defs/base_has_image_channels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Channels"}, "has_image_depth": {"anyOf": [{"$ref": "#/$defs/base_has_image_depth_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Depth"}, "has_image_frames": {"anyOf": [{"$ref": "#/$defs/base_has_image_frames_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Frames"}, "has_image_height": {"anyOf": [{"$ref": "#/$defs/base_has_image_height_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Height"}, "has_image_mean_intensity": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_intensity_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Intensity"}, "has_image_mean_object_size": {"anyOf": [{"$ref": "#/$defs/base_has_image_mean_object_size_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Mean Object Size"}, "has_image_n_labels": {"anyOf": [{"$ref": "#/$defs/base_has_image_n_labels_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image N Labels"}, "has_image_width": {"anyOf": [{"$ref": "#/$defs/base_has_image_width_model"}, {"type": "null"}], "default": null, "title": "Assert Has Image Width"}}, "title": "assertion_dict", "type": "object"}, "assertion_list": {"items": {"anyOf": [{"discriminator": {"mapping": {"attribute_is": "#/$defs/attribute_is_model", "attribute_matches": "#/$defs/attribute_matches_model", "element_text": "#/$defs/element_text_model", "element_text_is": "#/$defs/element_text_is_model", "element_text_matches": "#/$defs/element_text_matches_model", "has_archive_member": "#/$defs/has_archive_member_model", "has_element_with_path": "#/$defs/has_element_with_path_model", "has_h5_attribute": "#/$defs/has_h5_attribute_model", "has_h5_keys": "#/$defs/has_h5_keys_model", "has_image_center_of_mass": "#/$defs/has_image_center_of_mass_model", "has_image_channels": "#/$defs/has_image_channels_model", "has_image_depth": "#/$defs/has_image_depth_model", "has_image_frames": "#/$defs/has_image_frames_model", "has_image_height": "#/$defs/has_image_height_model", "has_image_mean_intensity": "#/$defs/has_image_mean_intensity_model", "has_image_mean_object_size": "#/$defs/has_image_mean_object_size_model", "has_image_n_labels": "#/$defs/has_image_n_labels_model", "has_image_width": "#/$defs/has_image_width_model", "has_json_property_with_text": "#/$defs/has_json_property_with_text_model", "has_json_property_with_value": "#/$defs/has_json_property_with_value_model", "has_line": "#/$defs/has_line_model", "has_line_matching": "#/$defs/has_line_matching_model", "has_n_columns": "#/$defs/has_n_columns_model", "has_n_elements_with_path": "#/$defs/has_n_elements_with_path_model", "has_n_lines": "#/$defs/has_n_lines_model", "has_size": "#/$defs/has_size_model", "has_text": "#/$defs/has_text_model", "has_text_matching": "#/$defs/has_text_matching_model", "is_valid_xml": "#/$defs/is_valid_xml_model", "not_has_text": "#/$defs/not_has_text_model", "xml_element": "#/$defs/xml_element_model"}, "propertyName": "that"}, "oneOf": [{"$ref": "#/$defs/has_line_model"}, {"$ref": "#/$defs/has_line_matching_model"}, {"$ref": "#/$defs/has_n_lines_model"}, {"$ref": "#/$defs/has_text_model"}, {"$ref": "#/$defs/has_text_matching_model"}, {"$ref": "#/$defs/not_has_text_model"}, {"$ref": "#/$defs/has_n_columns_model"}, {"$ref": "#/$defs/attribute_is_model"}, {"$ref": "#/$defs/attribute_matches_model"}, {"$ref": "#/$defs/element_text_model"}, {"$ref": "#/$defs/element_text_is_model"}, {"$ref": "#/$defs/element_text_matches_model"}, {"$ref": "#/$defs/has_element_with_path_model"}, {"$ref": "#/$defs/has_n_elements_with_path_model"}, {"$ref": "#/$defs/is_valid_xml_model"}, {"$ref": "#/$defs/xml_element_model"}, {"$ref": "#/$defs/has_json_property_with_text_model"}, {"$ref": "#/$defs/has_json_property_with_value_model"}, {"$ref": "#/$defs/has_h5_attribute_model"}, {"$ref": "#/$defs/has_h5_keys_model"}, {"$ref": "#/$defs/has_archive_member_model"}, {"$ref": "#/$defs/has_size_model"}, {"$ref": "#/$defs/has_image_center_of_mass_model"}, {"$ref": "#/$defs/has_image_channels_model"}, {"$ref": "#/$defs/has_image_depth_model"}, {"$ref": "#/$defs/has_image_frames_model"}, {"$ref": "#/$defs/has_image_height_model"}, {"$ref": "#/$defs/has_image_mean_intensity_model"}, {"$ref": "#/$defs/has_image_mean_object_size_model"}, {"$ref": "#/$defs/has_image_n_labels_model"}, {"$ref": "#/$defs/has_image_width_model"}]}, {"$ref": "#/$defs/has_line_model_nested"}, {"$ref": "#/$defs/has_line_matching_model_nested"}, {"$ref": "#/$defs/has_n_lines_model_nested"}, {"$ref": "#/$defs/has_text_model_nested"}, {"$ref": "#/$defs/has_text_matching_model_nested"}, {"$ref": "#/$defs/not_has_text_model_nested"}, {"$ref": "#/$defs/has_n_columns_model_nested"}, {"$ref": "#/$defs/attribute_is_model_nested"}, {"$ref": "#/$defs/attribute_matches_model_nested"}, {"$ref": "#/$defs/element_text_model_nested"}, {"$ref": "#/$defs/element_text_is_model_nested"}, {"$ref": "#/$defs/element_text_matches_model_nested"}, {"$ref": "#/$defs/has_element_with_path_model_nested"}, {"$ref": "#/$defs/has_n_elements_with_path_model_nested"}, {"$ref": "#/$defs/is_valid_xml_model_nested"}, {"$ref": "#/$defs/xml_element_model_nested"}, {"$ref": "#/$defs/has_json_property_with_text_model_nested"}, {"$ref": "#/$defs/has_json_property_with_value_model_nested"}, {"$ref": "#/$defs/has_h5_attribute_model_nested"}, {"$ref": "#/$defs/has_h5_keys_model_nested"}, {"$ref": "#/$defs/has_archive_member_model_nested"}, {"$ref": "#/$defs/has_size_model_nested"}, {"$ref": "#/$defs/has_image_center_of_mass_model_nested"}, {"$ref": "#/$defs/has_image_channels_model_nested"}, {"$ref": "#/$defs/has_image_depth_model_nested"}, {"$ref": "#/$defs/has_image_frames_model_nested"}, {"$ref": "#/$defs/has_image_height_model_nested"}, {"$ref": "#/$defs/has_image_mean_intensity_model_nested"}, {"$ref": "#/$defs/has_image_mean_object_size_model_nested"}, {"$ref": "#/$defs/has_image_n_labels_model_nested"}, {"$ref": "#/$defs/has_image_width_model_nested"}]}, "title": "assertion_list", "type": "array"}, "attribute_is_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` is the specified ``text``.\n\nFor example:\n\n```xml\n<attribute_is path=\"outerElement/innerElement1\" attribute=\"foo\" text=\"bar\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_is", "default": "attribute_is", "title": "That", "type": "string"}}, "required": ["path", "attribute", "text"], "title": "Assert Attribute Is", "type": "object"}, "attribute_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_is": {"$ref": "#/$defs/base_attribute_is_model", "title": "Assert Attribute Is"}}, "required": ["attribute_is"], "title": "Assert Attribute Is (Nested)", "type": "object"}, "attribute_matches_model": {"additionalProperties": false, "description": "Asserts the XML ``attribute`` for the element (or tag) with the specified\nXPath-like ``path`` matches the regular expression specified by ``expression``.\n\nFor example:\n\n```xml\n<attribute_matches path=\"outerElement/innerElement2\" attribute=\"foo2\" expression=\"bar\\d+\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "attribute_matches", "default": "attribute_matches", "title": "That", "type": "string"}}, "required": ["path", "attribute", "expression"], "title": "Assert Attribute Matches", "type": "object"}, "attribute_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"attribute_matches": {"$ref": "#/$defs/base_attribute_matches_model", "title": "Assert Attribute Matches"}}, "required": ["attribute_matches"], "title": "Assert Attribute Matches (Nested)", "type": "object"}, "base_attribute_is_model": {"additionalProperties": false, "description": "base model for attribute_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "text": {"description": "The expected attribute value to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "text"], "title": "base_attribute_is_model", "type": "object"}, "base_attribute_matches_model": {"additionalProperties": false, "description": "base model for attribute_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"description": "The XML attribute name to test against from the target XML element.", "title": "Attribute", "type": "string"}, "expression": {"description": "The regular expressions to apply against the named attribute on the target XML element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "attribute", "expression"], "title": "base_attribute_matches_model", "type": "object"}, "base_element_text_is_model": {"additionalProperties": false, "description": "base model for element_text_is describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "text"], "title": "base_element_text_is_model", "type": "object"}, "base_element_text_matches_model": {"additionalProperties": false, "description": "base model for element_text_matches describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path", "expression"], "title": "base_element_text_matches_model", "type": "object"}, "base_element_text_model": {"additionalProperties": false, "description": "base model for element_text describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_element_text_model", "type": "object"}, "base_has_archive_member_model": {"additionalProperties": false, "description": "base model for has_archive_member describing attributes.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_has_archive_member_model", "type": "object"}, "base_has_element_with_path_model": {"additionalProperties": false, "description": "base model for has_element_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_element_with_path_model", "type": "object"}, "base_has_h5_attribute_model": {"additionalProperties": false, "description": "base model for has_h5_attribute describing attributes.", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}}, "required": ["key", "value"], "title": "base_has_h5_attribute_model", "type": "object"}, "base_has_h5_keys_model": {"additionalProperties": false, "description": "base model for has_h5_keys describing attributes.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}}, "required": ["keys"], "title": "base_has_h5_keys_model", "type": "object"}, "base_has_image_center_of_mass_model": {"additionalProperties": false, "description": "base model for has_image_center_of_mass describing attributes.", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}}, "required": ["center_of_mass"], "title": "base_has_image_center_of_mass_model", "type": "object"}, "base_has_image_channels_model": {"additionalProperties": false, "description": "base model for has_image_channels describing attributes.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_channels_model", "type": "object"}, "base_has_image_depth_model": {"additionalProperties": false, "description": "base model for has_image_depth describing attributes.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_depth_model", "type": "object"}, "base_has_image_frames_model": {"additionalProperties": false, "description": "base model for has_image_frames describing attributes.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_frames_model", "type": "object"}, "base_has_image_height_model": {"additionalProperties": false, "description": "base model for has_image_height describing attributes.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_height_model", "type": "object"}, "base_has_image_mean_intensity_model": {"additionalProperties": false, "description": "base model for has_image_mean_intensity describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}}, "title": "base_has_image_mean_intensity_model", "type": "object"}, "base_has_image_mean_object_size_model": {"additionalProperties": false, "description": "base model for has_image_mean_object_size describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}}, "title": "base_has_image_mean_object_size_model", "type": "object"}, "base_has_image_n_labels_model": {"additionalProperties": false, "description": "base model for has_image_n_labels describing attributes.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_n_labels_model", "type": "object"}, "base_has_image_width_model": {"additionalProperties": false, "description": "base model for has_image_width describing attributes.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_image_width_model", "type": "object"}, "base_has_json_property_with_text_model": {"additionalProperties": false, "description": "base model for has_json_property_with_text describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}}, "required": ["property", "text"], "title": "base_has_json_property_with_text_model", "type": "object"}, "base_has_json_property_with_value_model": {"additionalProperties": false, "description": "base model for has_json_property_with_value describing attributes.", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}}, "required": ["property", "value"], "title": "base_has_json_property_with_value_model", "type": "object"}, "base_has_line_matching_model": {"additionalProperties": false, "description": "base model for has_line_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_line_matching_model", "type": "object"}, "base_has_line_model": {"additionalProperties": false, "description": "base model for has_line describing attributes.", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["line"], "title": "base_has_line_model", "type": "object"}, "base_has_n_columns_model": {"additionalProperties": false, "description": "base model for has_n_columns describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_columns_model", "type": "object"}, "base_has_n_elements_with_path_model": {"additionalProperties": false, "description": "base model for has_n_elements_with_path describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["path"], "title": "base_has_n_elements_with_path_model", "type": "object"}, "base_has_n_lines_model": {"additionalProperties": false, "description": "base model for has_n_lines describing attributes.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_n_lines_model", "type": "object"}, "base_has_size_model": {"additionalProperties": false, "description": "base model for has_size describing attributes.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "title": "base_has_size_model", "type": "object"}, "base_has_text_matching_model": {"additionalProperties": false, "description": "base model for has_text_matching describing attributes.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["expression"], "title": "base_has_text_matching_model", "type": "object"}, "base_has_text_model": {"additionalProperties": false, "description": "base model for has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}}, "required": ["text"], "title": "base_has_text_model", "type": "object"}, "base_is_valid_xml_model": {"additionalProperties": false, "description": "base model for is_valid_xml describing attributes.", "properties": {}, "title": "base_is_valid_xml_model", "type": "object"}, "base_not_has_text_model": {"additionalProperties": false, "description": "base model for not_has_text describing attributes.", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}}, "required": ["text"], "title": "base_not_has_text_model", "type": "object"}, "base_xml_element_model": {"additionalProperties": false, "description": "base model for xml_element describing attributes.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}}, "required": ["path"], "title": "base_xml_element_model", "type": "object"}, "element_text_is_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path`` is\nthe specified ``text``.\n\nFor example:\n\n```xml\n<element_text_is path=\"BlastOutput_program\" text=\"blastp\" />\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the equality) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "text": {"description": "The expected element text (body of the XML tag) to test against on the target XML element", "title": "Text", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_is", "default": "element_text_is", "title": "That", "type": "string"}}, "required": ["path", "text"], "title": "Assert Element Text Is", "type": "object"}, "element_text_is_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_is": {"$ref": "#/$defs/base_element_text_is_model", "title": "Assert Element Text Is"}}, "required": ["element_text_is"], "title": "Assert Element Text Is (Nested)", "type": "object"}, "element_text_matches_model": {"additionalProperties": false, "description": "Asserts the text of the XML element with the specified XPath-like ``path``\nmatches the regular expression defined by ``expression``.\n\nFor example:\n\n```xml\n<element_text_matches path=\"BlastOutput_version\" expression=\"BLASTP\\s+2\\.2.*\"/>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the assertion (on the matching) can be inverted (the\nimplicit assertion on the existence of the path is not affected).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "expression": {"description": "The regular expressions to apply against the target element.", "title": "Expression", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "element_text_matches", "default": "element_text_matches", "title": "That", "type": "string"}}, "required": ["path", "expression"], "title": "Assert Element Text Matches", "type": "object"}, "element_text_matches_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text_matches": {"$ref": "#/$defs/base_element_text_matches_model", "title": "Assert Element Text Matches"}}, "required": ["element_text_matches"], "title": "Assert Element Text Matches (Nested)", "type": "object"}, "element_text_model": {"additionalProperties": false, "description": "This tag allows the developer to recurisively specify additional assertions as\nchild elements about just the text contained in the element specified by the\nXPath-like ``path``, e.g.\n\n```xml\n<element_text path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def\">\n  <not_has_text text=\"EDK72998.1\" />\n</element_text>\n```\n\nThe assertion implicitly also asserts that an element matching ``path`` exists.\nWith ``negate`` the result of the implicit assertions can be inverted.\nThe sub-assertions, which have their own ``negate`` attribute, are not affected\nby ``negate``.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "element_text", "default": "element_text", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Element Text", "type": "object"}, "element_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"element_text": {"$ref": "#/$defs/base_element_text_model", "title": "Assert Element Text"}}, "required": ["element_text"], "title": "Assert Element Text (Nested)", "type": "object"}, "has_archive_member_model": {"additionalProperties": false, "description": "This tag allows to check if ``path`` is contained in a compressed file.\n\nThe path is a regular expression that is matched against the full paths of the objects in\nthe compressed file (remember that \"matching\" means it is checked if a prefix of\nthe full path of an archive member is described by the regular expression).\nValid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that\ndepending on the archive creation method:\n\n- full paths of the members may be prefixed with ``./``\n- directories may be treated as empty files\n\n```xml\n<has_archive_member path=\"./path/to/my-file.txt\"/>\n```\n\nWith ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of\narchive members matching ``path`` can be expressed. The following could be used,\ne.g., to assert an archive containing n&plusmn;1 elements out of which at least\n4 need to have a ``txt`` extension.\n\n```xml\n<has_archive_member path=\".*\" n=\"10\" delta=\"1\"/>\n<has_archive_member path=\".*\\.txt\" min=\"4\"/>\n```\n\nIn addition the tag can contain additional assertions as child elements about\nthe first member in the archive matching the regular expression ``path``. For\ninstance\n\n```xml\n<has_archive_member path=\".*/my-file.txt\">\n  <not_has_text text=\"EDK72998.1\"/>\n</has_archive_member>\n```\n\nIf the ``all`` attribute is set to ``true`` then all archive members are subject\nto the assertions. Note that, archive members matching the ``path`` are sorted\nalphabetically.\n\nThe ``negate`` attribute of the ``has_archive_member`` assertion only affects\nthe asserts on the presence and number of matching archive members, but not any\nsub-assertions (which can offer the ``negate`` attribute on their own).  The\ncheck if the file is an archive at all, which is also done by the function, is\nnot affected.", "properties": {"path": {"description": "The regular expression specifying the archive member.", "title": "Path", "type": "string"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "has_archive_member", "default": "has_archive_member", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Archive Member", "type": "object"}, "has_archive_member_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_archive_member": {"$ref": "#/$defs/base_has_archive_member_model", "title": "Assert Has Archive Member"}}, "required": ["has_archive_member"], "title": "Assert Has Archive Member (Nested)", "type": "object"}, "has_element_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains at least one element (or tag) with the specified\nXPath-like ``path``, e.g.\n\n```xml\n<has_element_with_path path=\"BlastOutput_param/Parameters/Parameters_matrix\" />\n```\n\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_element_with_path", "default": "has_element_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has Element With Path", "type": "object"}, "has_element_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_element_with_path": {"$ref": "#/$defs/base_has_element_with_path_model", "title": "Assert Has Element With Path"}}, "required": ["has_element_with_path"], "title": "Assert Has Element With Path (Nested)", "type": "object"}, "has_h5_attribute_model": {"additionalProperties": false, "description": "Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.\n\n```xml\n<has_h5_attribute key=\"nchroms\" value=\"15\" />\n```", "properties": {"key": {"description": "HDF5 attribute to check value of.", "title": "Key", "type": "string"}, "value": {"description": "Expected value of HDF5 attribute to check.", "title": "Value", "type": "string"}, "that": {"const": "has_h5_attribute", "default": "has_h5_attribute", "title": "That", "type": "string"}}, "required": ["key", "value"], "title": "Assert Has H5 Attribute", "type": "object"}, "has_h5_attribute_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_attribute": {"$ref": "#/$defs/base_has_h5_attribute_model", "title": "Assert Has H5 Attribute"}}, "required": ["has_h5_attribute"], "title": "Assert Has H5 Attribute (Nested)", "type": "object"}, "has_h5_keys_model": {"additionalProperties": false, "description": "Asserts the specified HDF5 output has the given keys.", "properties": {"keys": {"description": "HDF5 attributes to check value of as a comma-separated string.", "title": "Keys", "type": "string"}, "that": {"const": "has_h5_keys", "default": "has_h5_keys", "title": "That", "type": "string"}}, "required": ["keys"], "title": "Assert Has H5 Keys", "type": "object"}, "has_h5_keys_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_h5_keys": {"$ref": "#/$defs/base_has_h5_keys_model", "title": "Assert Has H5 Keys"}}, "required": ["has_h5_keys"], "title": "Assert Has H5 Keys (Nested)", "type": "object"}, "has_image_center_of_mass_model": {"additionalProperties": false, "description": "Asserts the specified output is an image and has the specified center of mass.\n\nAsserts the output is an image and has a specific center of mass,\nor has an Euclidean distance of ``eps`` or less to that point (e.g.,\n``<has_image_center_of_mass center_of_mass=\"511.07, 223.34\" />``).", "properties": {"center_of_mass": {"description": "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).", "title": "Center Of Mass", "type": "string"}, "channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).", "title": "Eps"}, "that": {"const": "has_image_center_of_mass", "default": "has_image_center_of_mass", "title": "That", "type": "string"}}, "required": ["center_of_mass"], "title": "Assert Has Image Center Of Mass", "type": "object"}, "has_image_center_of_mass_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_center_of_mass": {"$ref": "#/$defs/base_has_image_center_of_mass_model", "title": "Assert Has Image Center Of Mass"}}, "required": ["has_image_center_of_mass"], "title": "Assert Has Image Center Of Mass (Nested)", "type": "object"}, "has_image_channels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of channels.\n\nThe number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels=\"3\" />``).\n\nAlternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.", "properties": {"channels": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of channels of the image.", "title": "Channels"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of channels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of channels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_channels", "default": "has_image_channels", "title": "That", "type": "string"}}, "title": "Assert Has Image Channels", "type": "object"}, "has_image_channels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_channels": {"$ref": "#/$defs/base_has_image_channels_model", "title": "Assert Has Image Channels"}}, "required": ["has_image_channels"], "title": "Assert Has Image Channels (Nested)", "type": "object"}, "has_image_depth_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific depth (number of slices).\n\nThe depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected depth can be specified by ``min`` and/or ``max``.", "properties": {"depth": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected depth of the image (number of slices).", "title": "Depth"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed depth of the image (number of slices).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed depth of the image (number of slices).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_depth", "default": "has_image_depth", "title": "That", "type": "string"}}, "title": "Assert Has Image Depth", "type": "object"}, "has_image_depth_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_depth": {"$ref": "#/$defs/base_has_image_depth_model", "title": "Assert Has Image Depth"}}, "required": ["has_image_depth"], "title": "Assert Has Image Depth (Nested)", "type": "object"}, "has_image_frames_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific number of frames (number of time steps).\n\nThe number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.", "properties": {"frames": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of frames in the image sequence (number of time steps).", "title": "Frames"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of frames in the image sequence (number of time steps).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of frames in the image sequence (number of time steps).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_frames", "default": "has_image_frames", "title": "That", "type": "string"}}, "title": "Assert Has Image Frames", "type": "object"}, "has_image_frames_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_frames": {"$ref": "#/$defs/base_has_image_frames_model", "title": "Assert Has Image Frames"}}, "required": ["has_image_frames"], "title": "Assert Has Image Frames (Nested)", "type": "object"}, "has_image_height_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific height (in pixels).\n\nThe height is plus/minus ``delta`` (e.g., ``<has_image_height height=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected height can be specified by ``min`` and/or ``max``.", "properties": {"height": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected height of the image (in pixels).", "title": "Height"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed height of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed height of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_height", "default": "has_image_height", "title": "That", "type": "string"}}, "title": "Assert Has Image Height", "type": "object"}, "has_image_height_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_height": {"$ref": "#/$defs/base_has_image_height_model", "title": "Assert Has Image Height"}}, "required": ["has_image_height"], "title": "Assert Has Image Height (Nested)", "type": "object"}, "has_image_mean_intensity_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific mean intensity value.\n\nThe mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity=\"0.83\" />``).\nAlternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "mean_intensity": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean value of the image intensities.", "title": "Mean Intensity"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean value of the image intensities.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean value of the image intensities.", "title": "Max"}, "that": {"const": "has_image_mean_intensity", "default": "has_image_mean_intensity", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Intensity", "type": "object"}, "has_image_mean_intensity_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_intensity": {"$ref": "#/$defs/base_has_image_mean_intensity_model", "title": "Assert Has Image Mean Intensity"}}, "required": ["has_image_mean_intensity"], "title": "Assert Has Image Mean Intensity (Nested)", "type": "object"}, "has_image_mean_object_size_model": {"additionalProperties": false, "description": "Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),\n\nThe mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size=\"111.87\" exclude_labels=\"0\" />``).\n\nThe labels must be unique.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "mean_object_size": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "The required mean size of the uniquely labeled objects.", "title": "Mean Object Size"}, "eps": {"anyOf": [{"type": "integer"}, {"type": "number"}], "default": 0.01, "description": "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.", "title": "Eps"}, "min": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "A lower bound of the required mean size of the uniquely labeled objects.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "number"}, {"type": "null"}], "default": null, "description": "An upper bound of the required mean size of the uniquely labeled objects.", "title": "Max"}, "that": {"const": "has_image_mean_object_size", "default": "has_image_mean_object_size", "title": "That", "type": "string"}}, "title": "Assert Has Image Mean Object Size", "type": "object"}, "has_image_mean_object_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_mean_object_size": {"$ref": "#/$defs/base_has_image_mean_object_size_model", "title": "Assert Has Image Mean Object Size"}}, "required": ["has_image_mean_object_size"], "title": "Assert Has Image Mean Object Size (Nested)", "type": "object"}, "has_image_n_labels_model": {"additionalProperties": false, "description": "Asserts the output is an image and has the specified labels.\n\nLabels can be a number of labels or unique values (e.g.,\n``<has_image_n_labels n=\"187\" exclude_labels=\"0\" />``).\n\nThe primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.", "properties": {"channel": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).", "title": "Channel"}, "slice": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).", "title": "Slice"}, "frame": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).", "title": "Frame"}, "labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.", "title": "Labels"}, "exclude_labels": {"anyOf": [{"items": {"anyOf": [{"type": "integer"}, {"type": "number"}]}, "type": "array"}, {"type": "null"}], "default": null, "description": "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.", "title": "Exclude Labels"}, "n": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected number of labels.", "title": "N"}, "delta": {"default": 0, "description": "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed number of labels.", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed number of labels.", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_n_labels", "default": "has_image_n_labels", "title": "That", "type": "string"}}, "title": "Assert Has Image N Labels", "type": "object"}, "has_image_n_labels_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_n_labels": {"$ref": "#/$defs/base_has_image_n_labels_model", "title": "Assert Has Image N Labels"}}, "required": ["has_image_n_labels"], "title": "Assert Has Image N Labels (Nested)", "type": "object"}, "has_image_width_model": {"additionalProperties": false, "description": "Asserts the output is an image and has a specific width (in pixels).\n\nThe width is plus/minus ``delta`` (e.g., ``<has_image_width width=\"512\" delta=\"2\" />``).\nAlternatively the range of the expected width can be specified by ``min`` and/or ``max``.", "properties": {"width": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Expected width of the image (in pixels).", "title": "Width"}, "delta": {"default": 0, "description": "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.", "title": "Delta", "type": "integer"}, "min": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum allowed width of the image (in pixels).", "title": "Min"}, "max": {"anyOf": [{"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum allowed width of the image (in pixels).", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_image_width", "default": "has_image_width", "title": "That", "type": "string"}}, "title": "Assert Has Image Width", "type": "object"}, "has_image_width_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_image_width": {"$ref": "#/$defs/base_has_image_width_model", "title": "Assert Has Image Width"}}, "required": ["has_image_width"], "title": "Assert Has Image Width (Nested)", "type": "object"}, "has_json_property_with_text_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified text (i.e. string) value.\n\n```xml\n<has_json_property_with_text property=\"color\" text=\"red\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "text": {"description": "The expected text value of the target JSON attribute.", "title": "Text", "type": "string"}, "that": {"const": "has_json_property_with_text", "default": "has_json_property_with_text", "title": "That", "type": "string"}}, "required": ["property", "text"], "title": "Assert Has Json Property With Text", "type": "object"}, "has_json_property_with_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_text": {"$ref": "#/$defs/base_has_json_property_with_text_model", "title": "Assert Has Json Property With Text"}}, "required": ["has_json_property_with_text"], "title": "Assert Has Json Property With Text (Nested)", "type": "object"}, "has_json_property_with_value_model": {"additionalProperties": false, "description": "Asserts the JSON document contains a property or key with the specified JSON value.\n\n```xml\n<has_json_property_with_value property=\"skipped_columns\" value=\"[1, 3, 5]\" />\n```", "properties": {"property": {"description": "The property name to search the JSON document for.", "title": "Property", "type": "string"}, "value": {"description": "The expected JSON value of the target JSON attribute (as a JSON encoded string).", "title": "Value", "type": "string"}, "that": {"const": "has_json_property_with_value", "default": "has_json_property_with_value", "title": "That", "type": "string"}}, "required": ["property", "value"], "title": "Assert Has Json Property With Value", "type": "object"}, "has_json_property_with_value_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_json_property_with_value": {"$ref": "#/$defs/base_has_json_property_with_value_model", "title": "Assert Has Json Property With Value"}}, "required": ["has_json_property_with_value"], "title": "Assert Has Json Property With Value (Nested)", "type": "object"}, "has_line_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains a line matching the\nregular expression specified by the argument expression. If n is given\nthe assertion checks for exactly n occurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line_matching", "default": "has_line_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Line Matching", "type": "object"}, "has_line_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line_matching": {"$ref": "#/$defs/base_has_line_matching_model", "title": "Assert Has Line Matching"}}, "required": ["has_line_matching"], "title": "Assert Has Line Matching (Nested)", "type": "object"}, "has_line_model": {"additionalProperties": false, "description": "Asserts the specified output contains the line specified by the\nargument line. The exact number of occurrences can be optionally\nspecified by the argument n", "properties": {"line": {"description": "The full line of text to search for in the output.", "title": "Line", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_line", "default": "has_line", "title": "That", "type": "string"}}, "required": ["line"], "title": "Assert Has Line", "type": "object"}, "has_line_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_line": {"$ref": "#/$defs/base_has_line_model", "title": "Assert Has Line"}}, "required": ["has_line"], "title": "Assert Has Line (Nested)", "type": "object"}, "has_n_columns_model": {"additionalProperties": false, "description": "Asserts tabular output  contains the specified\nnumber (``n``) of columns.\n\nFor instance, ``<has_n_columns n=\"3\"/>``. The assertion tests only the first line.\nNumber of columns can optionally also be specified with ``delta``. Alternatively the\nrange of expected occurrences can be specified by ``min`` and/or ``max``.\n\nOptionally a column separator (``sep``, default is ``       ``) `and comment character(s)\ncan be specified (``comment``, default is empty string). The first non-comment\nline is used for determining the number of columns.", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "sep": {"default": "\t", "description": "Separator defining columns, default: tab", "title": "Sep", "type": "string"}, "comment": {"default": "", "description": "Comment character(s) used to skip comment lines (which should not be used for counting columns)", "title": "Comment", "type": "string"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_columns", "default": "has_n_columns", "title": "That", "type": "string"}}, "title": "Assert Has N Columns", "type": "object"}, "has_n_columns_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_columns": {"$ref": "#/$defs/base_has_n_columns_model", "title": "Assert Has N Columns"}}, "required": ["has_n_columns"], "title": "Assert Has N Columns (Nested)", "type": "object"}, "has_n_elements_with_path_model": {"additionalProperties": false, "description": "Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or\ntags) with the specified XPath-like ``path``.\n\nFor example:\n\n```xml\n<has_n_elements_with_path n=\"9\" path=\"BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num\" />\n```\n\nAlternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes\ncan be used to specify the range of the expected number of occurrences.\nWith ``negate`` the result of the assertion can be inverted.", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_elements_with_path", "default": "has_n_elements_with_path", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Has N Elements With Path", "type": "object"}, "has_n_elements_with_path_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_elements_with_path": {"$ref": "#/$defs/base_has_n_elements_with_path_model", "title": "Assert Has N Elements With Path"}}, "required": ["has_n_elements_with_path"], "title": "Assert Has N Elements With Path (Nested)", "type": "object"}, "has_n_lines_model": {"additionalProperties": false, "description": "Asserts the specified output contains ``n`` lines allowing\nfor a difference in the number of lines (delta)\nor relative differebce in the number of lines", "properties": {"n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_n_lines", "default": "has_n_lines", "title": "That", "type": "string"}}, "title": "Assert Has N Lines", "type": "object"}, "has_n_lines_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_n_lines": {"$ref": "#/$defs/base_has_n_lines_model", "title": "Assert Has N Lines"}}, "required": ["has_n_lines"], "title": "Assert Has N Lines (Nested)", "type": "object"}, "has_size_model": {"additionalProperties": false, "description": "Asserts the specified output has a size of the specified value\n\nAttributes size and value or synonyms though value is considered deprecated.\nThe size optionally allows for absolute (``delta``) difference.", "properties": {"value": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Deprecated alias for `size`", "title": "Value"}, "size": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Size"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_size", "default": "has_size", "title": "That", "type": "string"}}, "title": "Assert Has Size", "type": "object"}, "has_size_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_size": {"$ref": "#/$defs/base_has_size_model", "title": "Assert Has Size"}}, "required": ["has_size"], "title": "Assert Has Size (Nested)", "type": "object"}, "has_text_matching_model": {"additionalProperties": false, "description": "Asserts the specified output contains text matching the\nregular expression specified by the argument expression.\nIf n is given the assertion checks for exactly n (nonoverlapping)\noccurrences.", "properties": {"expression": {"description": "The regular expressions to attempt match in the output.", "title": "Expression", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text_matching", "default": "has_text_matching", "title": "That", "type": "string"}}, "required": ["expression"], "title": "Assert Has Text Matching", "type": "object"}, "has_text_matching_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text_matching": {"$ref": "#/$defs/base_has_text_matching_model", "title": "Assert Has Text Matching"}}, "required": ["has_text_matching"], "title": "Assert Has Text Matching (Nested)", "type": "object"}, "has_text_model": {"additionalProperties": false, "description": "Asserts specified output contains the substring specified by\nthe argument text. The exact number of occurrences can be\noptionally specified by the argument n", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "that": {"const": "has_text", "default": "has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Has Text", "type": "object"}, "has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"has_text": {"$ref": "#/$defs/base_has_text_model", "title": "Assert Has Text"}}, "required": ["has_text"], "title": "Assert Has Text (Nested)", "type": "object"}, "is_valid_xml_model": {"additionalProperties": false, "description": "Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).", "properties": {"that": {"const": "is_valid_xml", "default": "is_valid_xml", "title": "That", "type": "string"}}, "title": "Assert Is Valid Xml", "type": "object"}, "is_valid_xml_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"is_valid_xml": {"$ref": "#/$defs/base_is_valid_xml_model", "title": "Assert Is Valid Xml"}}, "required": ["is_valid_xml"], "title": "Assert Is Valid Xml (Nested)", "type": "object"}, "not_has_text_model": {"additionalProperties": false, "description": "Asserts specified output does not contain the substring\nspecified by the argument text", "properties": {"text": {"description": "The text to search for in the output.", "title": "Text", "type": "string"}, "that": {"const": "not_has_text", "default": "not_has_text", "title": "That", "type": "string"}}, "required": ["text"], "title": "Assert Not Has Text", "type": "object"}, "not_has_text_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"not_has_text": {"$ref": "#/$defs/base_not_has_text_model", "title": "Assert Not Has Text"}}, "required": ["not_has_text"], "title": "Assert Not Has Text (Nested)", "type": "object"}, "xml_element_model": {"additionalProperties": false, "description": "Assert if the XML file contains element(s) or tag(s) with the specified\n[XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``\nor ``min`` and ``max`` are given also the number of occurrences is checked.\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem\"/>\n  <xml_element path=\"./elem/more[2]\"/>\n  <xml_element path=\".//more\" n=\"3\" delta=\"1\"/>\n</assert_contents>\n```\n\nWith ``negate=\"true\"`` the outcome of the assertions wrt the presence and number\nof ``path`` can be negated. If there are any sub assertions then check them against\n\n- the content of the attribute ``attribute``\n- the element's text if no attribute is given\n\n```xml\n<assert_contents>\n  <xml_element path=\"./elem/more[2]\" attribute=\"name\">\n    <has_text_matching expression=\"foo$\"/>\n  </xml_element>\n</assert_contents>\n```\n\nSub-assertions are not subject to the ``negate`` attribute of ``xml_element``.\nIf ``all`` is ``true`` then the sub assertions are checked for all occurrences.\n\nNote that all other XML assertions can be expressed by this assertion (Galaxy\nalso implements the other assertions by calling this one).", "properties": {"path": {"description": "The Python xpath-like expression to find the target element.", "title": "Path", "type": "string"}, "attribute": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The XML attribute name to test against from the target XML element.", "title": "Attribute"}, "all": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ", "title": "All"}, "n": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "N"}, "delta": {"anyOf": [{"type": "integer"}, {"type": "string"}], "default": 0, "description": "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Delta"}, "min": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Min"}, "max": {"anyOf": [{"type": "string"}, {"type": "integer"}, {"type": "null"}], "default": null, "description": "Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", "title": "Max"}, "negate": {"anyOf": [{"type": "boolean"}, {"type": "string"}], "default": false, "description": "A boolean that can be set to true to negate the outcome of the assertion.", "title": "Negate"}, "children": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Children"}, "asserts": {"anyOf": [{"$ref": "#/$defs/assertion_list"}, {"type": "null"}], "default": null, "title": "Asserts"}, "that": {"const": "xml_element", "default": "xml_element", "title": "That", "type": "string"}}, "required": ["path"], "title": "Assert Xml Element", "type": "object"}, "xml_element_model_nested": {"additionalProperties": false, "description": "Nested version of this assertion model.", "properties": {"xml_element": {"$ref": "#/$defs/base_xml_element_model", "title": "Assert Xml Element"}}, "required": ["xml_element"], "title": "Assert Xml Element (Nested)", "type": "object"}}, "additionalProperties": false, "description": "Full unprivileged tool source, including the optional ``tests`` block.\n\nThis is the model persisted and validated on the API surface\n(``DynamicUnprivilegedToolCreatePayload.representation``). LLM authoring\nuses the slimmer ``UserToolSourceAuthoringView`` parent; ``tests`` is added\nback here so direct authors and stored rows can still carry tests.", "properties": {"id": {"anyOf": [{"maxLength": 255, "minLength": 3, "pattern": "^[a-z][a-z0-9_-]*$", "type": "string"}, {"type": "null"}], "default": null, "description": "Unique identifier for the tool. Lowercase, must start with a letter, may contain letters, digits, '_' and '-'.", "examples": ["my-cool-tool"], "title": "id"}, "version": {"description": "Version for the tool.", "examples": ["0.1.0"], "title": "version", "type": "string"}, "name": {"description": "The name of the tool, displayed in the tool menu. This is not the same as the tool id, which is a unique identifier for the tool.", "minLength": 5, "title": "name", "type": "string"}, "description": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "The description is displayed in the tool menu immediately following the hyperlink for the tool.", "title": "description"}, "configfiles": {"anyOf": [{"items": {"$ref": "#/$defs/YamlTemplateConfigFile"}, "type": "array"}, {"type": "null"}], "default": null, "description": "A list of config files for this tool.", "title": "configfiles"}, "requirements": {"anyOf": [{"items": {"anyOf": [{"$ref": "#/$defs/JavascriptRequirement"}, {"$ref": "#/$defs/ResourceRequirement"}, {"$ref": "#/$defs/ContainerRequirement"}]}, "type": "array"}, {"type": "null"}], "default": [], "description": "A list of requirements needed to execute this tool. These can be javascript expressions, resource requirements or container images.", "title": "requirements"}, "shell_command": {"description": "A string that contains the command to be executed. Parameters can be referenced inside $().", "examples": ["head -n '$(inputs.num_lines)' '$(inputs.input_file.path)' > output.txt"], "title": "shell_command", "type": "string"}, "inputs": {"default": [], "items": {"$ref": "#/$defs/YamlGalaxyToolParameter"}, "title": "inputs", "type": "array"}, "outputs": {"default": [], "items": {"discriminator": {"mapping": {"boolean": "#/$defs/IncomingToolOutputBoolean", "collection": "#/$defs/IncomingToolOutputCollection", "data": "#/$defs/IncomingToolOutputDataset", "float": "#/$defs/IncomingToolOutputFloat", "integer": "#/$defs/IncomingToolOutputInteger", "text": "#/$defs/IncomingToolOutputText"}, "propertyName": "type"}, "oneOf": [{"$ref": "#/$defs/IncomingToolOutputDataset"}, {"$ref": "#/$defs/IncomingToolOutputCollection"}, {"$ref": "#/$defs/IncomingToolOutputText"}, {"$ref": "#/$defs/IncomingToolOutputInteger"}, {"$ref": "#/$defs/IncomingToolOutputFloat"}, {"$ref": "#/$defs/IncomingToolOutputBoolean"}]}, "title": "outputs", "type": "array"}, "citations": {"anyOf": [{"items": {"$ref": "#/$defs/Citation"}, "type": "array"}, {"type": "null"}], "default": null, "title": "citations"}, "license": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "description": "A full URI or a a short [SPDX](https://spdx.org/licenses/) identifier for a license for this tool wrapper. The tool wrapper license can be independent of the underlying tool license. This license covers the tool yaml and associated scripts shipped with the tool.", "examples": ["MIT"], "title": "license"}, "edam_operations": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_operations"}, "edam_topics": {"anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}], "default": null, "title": "edam_topics"}, "xrefs": {"anyOf": [{"items": {"$ref": "#/$defs/XrefDict"}, "type": "array"}, {"type": "null"}], "default": null, "title": "xrefs"}, "profile": {"anyOf": [{"type": "number"}, {"type": "null"}], "default": null, "title": "profile"}, "help": {"anyOf": [{"$ref": "#/$defs/HelpContent"}, {"type": "null"}], "default": null, "description": "Help text shown below the tool interface.", "title": "help"}, "class": {"const": "GalaxyUserTool", "title": "class_", "type": "string"}, "container": {"description": "Container image to use for this tool.", "examples": ["quay.io/biocontainers/python:3.13"], "title": "container", "type": "string"}, "tests": {"anyOf": [{"items": {"$ref": "#/$defs/YamlToolTest"}, "type": "array"}, {"type": "null"}], "default": null, "title": "tests"}}, "required": ["version", "name", "shell_command", "class", "container"], "title": "UserToolSource", "type": "object"}
\ No newline at end of file
diff --git a/lib/galaxy/tool_util_models/yaml_parameters.py b/lib/galaxy/tool_util_models/yaml_parameters.py
index 9feff67e411..efcc1774380 100644
--- a/lib/galaxy/tool_util_models/yaml_parameters.py
+++ b/lib/galaxy/tool_util_models/yaml_parameters.py
@@ -195,25 +195,13 @@ class YamlDataParameter(_YamlParamBase):
         bool,
         Field(description="Set true to accept several datasets (a list) for this input instead of one."),
     ] = False
-    min: Annotated[
-        Optional[int],
-        Field(
-            description=(
-                "Minimum number of datasets the user must select. ONLY valid when 'multiple' is true. "
-                "Do NOT set this for a single-dataset input -- a data input is already required by default, "
-                "so leave 'min' unset unless the input accepts multiple datasets."
-            )
-        ),
-    ] = None
-    max: Annotated[
-        Optional[int],
-        Field(
-            description=(
-                "Maximum number of datasets the user may select. ONLY valid when 'multiple' is true; "
-                "leave unset for a single-dataset input."
-            )
-        ),
-    ] = None
+    # NOTE: `min`/`max` (the min/max number of selected datasets) are intentionally
+    # NOT exposed here. They only have meaning for a `multiple` input and the runtime
+    # rejects them on a single one; in practice authors (and LLMs) reach for `min: 1`
+    # to mean "required" -- which a data input already is -- and then the tool fails
+    # at build time. Omitting the fields means such a tool is rejected up front with a
+    # clear `extra_forbidden` error instead. The internal model still supports them
+    # for XML tools.
 
     @field_validator("format", mode="before")
     @classmethod
@@ -225,8 +213,6 @@ class YamlDataParameter(_YamlParamBase):
             type="data",
             extensions=list(self.format),
             multiple=self.multiple,
-            min=self.min,
-            max=self.max,
             **_common_internal_kwargs(self),
         )
 
diff --git a/lib/tool_shed/webapp/frontend/src/schema/schema.ts b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
index 743d57f8967..d284f0cfd53 100644
--- a/lib/tool_shed/webapp/frontend/src/schema/schema.ts
+++ b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
@@ -3832,7 +3832,6 @@ export interface components {
             directory?: string | null
             /**
              * Discover Via
-             * @default tool_provided_metadata
              * @constant
              */
             discover_via: "tool_provided_metadata"
diff --git a/test/unit/tool_util/test_yaml_parameters.py b/test/unit/tool_util/test_yaml_parameters.py
index a6a334ba9ae..20de283c05d 100644
--- a/test/unit/tool_util/test_yaml_parameters.py
+++ b/test/unit/tool_util/test_yaml_parameters.py
@@ -181,6 +181,16 @@ def test_data_rejects_extensions_key():
         _validate({"name": "input1", "type": "data", "extensions": ["txt"]})
 
 
+@pytest.mark.parametrize("bound", [{"min": 1}, {"max": 5}, {"min": 1, "max": 5}])
+def test_data_rejects_min_max(bound):
+    # min/max (dataset-count bounds) are not part of the user-defined-tool data
+    # parameter -- they only apply to `multiple` inputs and authors misuse `min: 1`
+    # to mean "required". extra="forbid" rejects them up front rather than letting
+    # the tool fail at build time.
+    with pytest.raises(ValidationError):
+        _validate({"name": "input1", "type": "data", **bound})
+
+
 # ---------------------------------------------------------------------------
 # Green cases: structural groups
 # ---------------------------------------------------------------------------

From e8bf83bb5daf778f36d01a57908ba9b4af8c07ca Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 19 Jun 2026 10:59:47 +0200
Subject: [PATCH 255/256] Use typing.Dict for Python 3.8 compatibility in
 version_updates

---
 lib/galaxy/tool_util/version_updates.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/version_updates.py b/lib/galaxy/tool_util/version_updates.py
index 540589f507e..073fb9d45a7 100644
--- a/lib/galaxy/tool_util/version_updates.py
+++ b/lib/galaxy/tool_util/version_updates.py
@@ -6,6 +6,7 @@ tool definition for validation and state inspection.
 """
 
 from typing import (
+    Dict,
     NamedTuple,
     Optional,
 )
@@ -19,7 +20,7 @@ class safe_update(NamedTuple):
     current_version: AnyVersionT
 
 
-WORKFLOW_SAFE_TOOL_VERSION_UPDATES: dict[str, safe_update] = {
+WORKFLOW_SAFE_TOOL_VERSION_UPDATES: Dict[str, safe_update] = {
     "Filter1": safe_update(parse_version("1.1.0"), parse_version("1.1.1")),
     "__BUILD_LIST__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
     "__APPLY_RULES__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),

From 52d815392531d8df6297b7dec2588b93073056c0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 19 Jun 2026 11:30:37 +0200
Subject: [PATCH 256/256] Move chat agent-type attribution to ChatManager

The agent-type attribution logic (_responder_agent_type and the
exchange-message formatting) lived in galaxy.webapps.galaxy.api.chat, so
the new unit tests in test/unit/app/test_chat_manager.py imported it from
the web_apps layer. That test runs as part of the galaxy-app package
suite, which does not (and should not) depend on web_apps, so the import
pulled in a2wsgi and failed with ModuleNotFoundError.

Push the pure logic down to ChatManager.responder_agent_type and
ChatManager.get_exchange_messages, alongside the existing
_message_is_clarification / get_routing_history helpers that already parse
stored exchange messages. The API endpoint and history formatter now
delegate to the manager, and the tests import only app-layer code.
---
 lib/galaxy/managers/chat.py           | 58 +++++++++++++++++++++++++++
 lib/galaxy/webapps/galaxy/api/chat.py | 55 +------------------------
 test/unit/app/test_chat_manager.py    | 23 +++++------
 3 files changed, 69 insertions(+), 67 deletions(-)

diff --git a/lib/galaxy/managers/chat.py b/lib/galaxy/managers/chat.py
index 29d622ce568..e41f34d8c11 100644
--- a/lib/galaxy/managers/chat.py
+++ b/lib/galaxy/managers/chat.py
@@ -347,6 +347,64 @@ class ChatManager:
                 pydantic_messages.append(ModelResponse(parts=[TextPart(content=msg.message)]))
         return pydantic_messages
 
+    @staticmethod
+    def responder_agent_type(data: dict[str, Any]) -> str:
+        """Agent type that actually answered a stored turn.
+
+        Prefer the nested agent_response (the real responder, e.g. the specialist after a
+        router handoff) over the top-level agent_type, which records the *request* type
+        ("auto"). Older rows only stored the request type at the top level.
+        """
+        return (data.get("agent_response") or {}).get("agent_type") or data.get("agent_type", "unknown")
+
+    def get_exchange_messages(self, trans: ProvidesUserContext, exchange_id: int) -> list[dict[str, Any]]:
+        """Return all messages for an exchange as user/assistant dicts.
+
+        Each stored message holds one query/response turn as JSON; the assistant turn is
+        badged with the agent that actually responded (see ``responder_agent_type``).
+        """
+        exchange = self.get_exchange_by_id(trans, exchange_id)
+        if not exchange:
+            return []
+
+        messages: list[dict[str, Any]] = []
+        for msg in exchange.messages:
+            try:
+                # Parse JSON content to extract individual messages
+                data = json.loads(msg.message)
+                # Add both user query and assistant response
+                if "query" in data:
+                    messages.append(
+                        {
+                            "role": "user",
+                            "content": data["query"],
+                            "timestamp": msg.create_time.isoformat() if msg.create_time else None,
+                        }
+                    )
+                if "response" in data:
+                    messages.append(
+                        {
+                            "role": "assistant",
+                            "content": data["response"],
+                            "agent_type": self.responder_agent_type(data),
+                            "agent_response": data.get("agent_response"),
+                            "timestamp": msg.create_time.isoformat() if msg.create_time else None,
+                            "feedback": msg.feedback,
+                        }
+                    )
+            except (json.JSONDecodeError, AttributeError):
+                # Fallback for non-JSON messages
+                messages.append(
+                    {
+                        "role": "assistant",
+                        "content": msg.message,
+                        "timestamp": msg.create_time.isoformat() if msg.create_time else None,
+                        "feedback": msg.feedback,
+                    }
+                )
+
+        return messages
+
     @staticmethod
     def _message_is_clarification(message) -> bool:
         """Whether a stored message's response was a clarifying question (by ``agent_type``)."""
diff --git a/lib/galaxy/webapps/galaxy/api/chat.py b/lib/galaxy/webapps/galaxy/api/chat.py
index 57209a8ec7f..bc257eaf51a 100644
--- a/lib/galaxy/webapps/galaxy/api/chat.py
+++ b/lib/galaxy/webapps/galaxy/api/chat.py
@@ -106,16 +106,6 @@ JobIdPathParam = Annotated[
 ]
 
 
-def _responder_agent_type(data: dict[str, Any]) -> str:
-    """Agent type that actually answered a stored turn.
-
-    Prefer the nested agent_response (the real responder, e.g. the specialist after a
-    router handoff) over the top-level agent_type, which records the *request* type
-    ("auto"). Older rows only stored the request type at the top level.
-    """
-    return (data.get("agent_response") or {}).get("agent_type") or data.get("agent_type", "unknown")
-
-
 @router.cbv
 class ChatAPI:
     """Chat interface for AI agents.
@@ -481,48 +471,7 @@ class ChatAPI:
         user: User = DependsOnUser,
     ) -> list[dict[str, Any]]:
         """Get all messages for a specific chat exchange."""
-        exchange = self.chat_manager.get_exchange_by_id(trans, exchange_id)
-        if not exchange:
-            return []
-
-        messages = []
-
-        for msg in exchange.messages:
-            try:
-                # Parse JSON content to extract individual messages
-                data = json.loads(msg.message)
-                # Add both user query and assistant response
-                if "query" in data:
-                    messages.append(
-                        {
-                            "role": "user",
-                            "content": data["query"],
-                            "timestamp": msg.create_time.isoformat() if msg.create_time else None,
-                        }
-                    )
-                if "response" in data:
-                    messages.append(
-                        {
-                            "role": "assistant",
-                            "content": data["response"],
-                            "agent_type": _responder_agent_type(data),
-                            "agent_response": data.get("agent_response"),
-                            "timestamp": msg.create_time.isoformat() if msg.create_time else None,
-                            "feedback": msg.feedback,
-                        }
-                    )
-            except (json.JSONDecodeError, AttributeError):
-                # Fallback for non-JSON messages
-                messages.append(
-                    {
-                        "role": "assistant",
-                        "content": msg.message,
-                        "timestamp": msg.create_time.isoformat() if msg.create_time else None,
-                        "feedback": msg.feedback,
-                    }
-                )
-
-        return messages
+        return self.chat_manager.get_exchange_messages(trans, exchange_id)
 
     def _format_exchange_history(self, exchanges) -> list[ChatHistoryItemResponse]:
         """Convert a list of ChatExchange ORM objects into API response models."""
@@ -540,7 +489,7 @@ class ChatAPI:
                         id=exchange.id,
                         query=data.get("query", ""),
                         response=data.get("response", ""),
-                        agent_type=_responder_agent_type(data),
+                        agent_type=self.chat_manager.responder_agent_type(data),
                         agent_response=agent_response,
                         timestamp=message.create_time.isoformat() if message.create_time else None,
                         feedback=message.feedback,
diff --git a/test/unit/app/test_chat_manager.py b/test/unit/app/test_chat_manager.py
index d280f83d59c..036d46927bb 100644
--- a/test/unit/app/test_chat_manager.py
+++ b/test/unit/app/test_chat_manager.py
@@ -6,10 +6,6 @@ from unittest import mock
 import pytest
 
 from galaxy.managers.chat import ChatManager
-from galaxy.webapps.galaxy.api.chat import (
-    _responder_agent_type,
-    ChatAPI,
-)
 
 
 def _make_trans(user_id=1):
@@ -282,14 +278,14 @@ class TestResponderAgentType:
 
     def test_prefers_nested_response_agent_type(self):
         data = {"agent_type": "auto", "agent_response": {"agent_type": "error_analysis"}}
-        assert _responder_agent_type(data) == "error_analysis"
+        assert ChatManager.responder_agent_type(data) == "error_analysis"
 
     def test_falls_back_to_top_level_when_no_response(self):
         data = {"agent_type": "gtn_training", "agent_response": None}
-        assert _responder_agent_type(data) == "gtn_training"
+        assert ChatManager.responder_agent_type(data) == "gtn_training"
 
     def test_unknown_when_nothing_present(self):
-        assert _responder_agent_type({}) == "unknown"
+        assert ChatManager.responder_agent_type({}) == "unknown"
 
 
 class TestGetExchangeMessagesAttribution:
@@ -298,21 +294,20 @@ class TestGetExchangeMessagesAttribution:
     specialist that actually answered."""
 
     @staticmethod
-    def _api_for(message):
-        api = ChatAPI.__new__(ChatAPI)
+    def _exchange_for(message):
         msg = mock.Mock()
         msg.message = message
         msg.feedback = None
         msg.create_time = None
         exchange = _FakeChatExchange()
         exchange.messages = [msg]
-        api.chat_manager = mock.Mock()
-        api.chat_manager.get_exchange_by_id.return_value = exchange
-        return api
+        return exchange
 
     def _assistant_turn(self, message):
-        api = self._api_for(message)
-        messages = api.get_exchange_messages(exchange_id=1, trans=_make_trans(), user=mock.Mock())
+        mgr = ChatManager()
+        exchange = self._exchange_for(message)
+        with mock.patch.object(mgr, "get_exchange_by_id", return_value=exchange):
+            messages = mgr.get_exchange_messages(_make_trans(), exchange_id=1)
         assistant = [m for m in messages if m["role"] == "assistant"]
         assert len(assistant) == 1
         return assistant[0]