From 9cae33ffa8bd7cdb700ede687d0ec178a6937926 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 26 Nov 2024 17:14:35 +0100
Subject: [PATCH 01/21] only match filters that are descendants or
 data/collection

otherwise action filters are also checked which results in an error
since there is not text content.
---
 lib/galaxy/tool_util/linters/output.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/linters/output.py b/lib/galaxy/tool_util/linters/output.py
index e9ab7c4aaf4..e42c797dca0 100644
--- a/lib/galaxy/tool_util/linters/output.py
+++ b/lib/galaxy/tool_util/linters/output.py
@@ -83,7 +83,7 @@ class OutputsFilterExpression(Linter):
         tool_xml = getattr(tool_source, "xml_tree", None)
         if not tool_xml:
             return
-        for filter in tool_xml.findall("./outputs//filter"):
+        for filter in tool_xml.findall("./outputs/*/filter"):
             try:
                 ast.parse(filter.text, mode="eval")
             except Exception as e:

From a587336eddf9c4fc19a349adf393a4747537c4b2 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 26 Nov 2024 17:18:44 +0100
Subject: [PATCH 02/21] strip text

otherwise the parser gives an indentation error

also: we strip the text alo in the application
---
 lib/galaxy/tool_util/linters/output.py   | 2 +-
 test/unit/tool_util/test_tool_linters.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/linters/output.py b/lib/galaxy/tool_util/linters/output.py
index e42c797dca0..b1d48fd2a60 100644
--- a/lib/galaxy/tool_util/linters/output.py
+++ b/lib/galaxy/tool_util/linters/output.py
@@ -85,7 +85,7 @@ class OutputsFilterExpression(Linter):
             return
         for filter in tool_xml.findall("./outputs/*/filter"):
             try:
-                ast.parse(filter.text, mode="eval")
+                ast.parse(filter.text.strip(), mode="eval")
             except Exception as e:
                 lint_ctx.warn(
                     f"Filter '{filter.text}' is no valid expression: {str(e)}",
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index ea7f4cd8d5d..867e85dc2ba 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -656,7 +656,7 @@ OUTPUTS_FILTER_EXPRESSION = """
     <outputs>
         <data name="another_valid_name" format="fasta" label="a label">
             <filter>an invalid condition</filter>
-            <filter>an and condition</filter>
+            <filter> an and condition </filter>
         </data>
         <collection name="yet_another_valid_name" type="list" format="fasta" label="another label">
             <filter>another invalid condition</filter>

From a3c1d272005703a44a3d3c79605dfbba570d0fc3 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Mon, 2 Dec 2024 20:06:32 +0300
Subject: [PATCH 03/21] Update visualization package versions

---
 config/plugins/visualizations/cytoscape/config/cytoscape.xml   | 2 +-
 config/plugins/visualizations/ngl/config/ngl.xml               | 2 +-
 config/plugins/visualizations/openlayers/config/openlayers.xml | 2 +-
 config/plugins/visualizations/venn/config/venn.xml             | 2 +-
 config/plugins/visualizations/vizarr/config/vizarr.xml         | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/config/plugins/visualizations/cytoscape/config/cytoscape.xml b/config/plugins/visualizations/cytoscape/config/cytoscape.xml
index 9cd91fdeb45..79de685142f 100644
--- a/config/plugins/visualizations/cytoscape/config/cytoscape.xml
+++ b/config/plugins/visualizations/cytoscape/config/cytoscape.xml
@@ -14,7 +14,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.2" package="@galaxyproject/cytoscape"/>
+        <requirement type="npm" version="0.0.3" package="@galaxyproject/cytoscape"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
diff --git a/config/plugins/visualizations/ngl/config/ngl.xml b/config/plugins/visualizations/ngl/config/ngl.xml
index 817f94e217c..18607ed2c42 100644
--- a/config/plugins/visualizations/ngl/config/ngl.xml
+++ b/config/plugins/visualizations/ngl/config/ngl.xml
@@ -13,7 +13,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.8" package="@galaxyproject/ngl"/>
+        <requirement type="npm" version="0.0.11" package="@galaxyproject/ngl"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
diff --git a/config/plugins/visualizations/openlayers/config/openlayers.xml b/config/plugins/visualizations/openlayers/config/openlayers.xml
index 71c36fb1fe1..2fb0ae6ca42 100644
--- a/config/plugins/visualizations/openlayers/config/openlayers.xml
+++ b/config/plugins/visualizations/openlayers/config/openlayers.xml
@@ -14,7 +14,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.2" package="galaxy-openlayers"/>
+        <requirement type="npm" version="0.0.0" package="@galaxyproject/openlayers"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
diff --git a/config/plugins/visualizations/venn/config/venn.xml b/config/plugins/visualizations/venn/config/venn.xml
index 25e140440fa..1e9140135ea 100644
--- a/config/plugins/visualizations/venn/config/venn.xml
+++ b/config/plugins/visualizations/venn/config/venn.xml
@@ -14,7 +14,7 @@
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
     <requirements>
-        <requirement type="npm" version="0.0.2" package="@galaxyproject/venn"/>
+        <requirement type="npm" version="0.0.3" package="@galaxyproject/venn"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <tracks>
diff --git a/config/plugins/visualizations/vizarr/config/vizarr.xml b/config/plugins/visualizations/vizarr/config/vizarr.xml
index 5b4b20ffe1a..a6bc313c20d 100644
--- a/config/plugins/visualizations/vizarr/config/vizarr.xml
+++ b/config/plugins/visualizations/vizarr/config/vizarr.xml
@@ -3,7 +3,7 @@
 <visualization name="Vizarr Viewer">
     <description>Basic visualization for Zarr-based images like OME-Zarr</description>
     <requirements>
-        <requirement type="npm" version="0.1.5" package="@galaxyproject/vizarr"/>
+        <requirement type="npm" version="0.1.6" package="@galaxyproject/vizarr"/>
     </requirements>
     <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <data_sources>

From 91660b9d5eff9320d2faaa36d49aff859f827bba Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 10 Dec 2024 18:54:07 +0100
Subject: [PATCH 04/21] Fix target_type in auto-conversion context

which means we collect and store the converted dataset as the job input.

We don't need to wait for the galaxy.json collection, we know the exact
target type already. That fixes the retrieval in
`get_converted_files_by_type`.

I believe this was always the intention and is how it works if the
dataset already exists (i.e. on a re-run), and for all converters that
don't use galaxy.json The converter records the dataset that the user
chose, so there's no gap in the provenance either.

This somewhat addresses
https://github.com/galaxyproject/total-perspective-vortex/issues/141
so you can (reliably) differetiate your rules on the input datatype
and filesize combination.
---
 lib/galaxy/datatypes/data.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 05f5adbad6b..f5d15fa406a 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -847,7 +847,11 @@ class Data(metaclass=DataMeta):
         job, converted_datasets, *_ = converter.execute(
             trans, incoming=params, set_output_hid=visible, history=history, flush_job=False
         )
+        # We should only have a single converted output, but let's be defensive here
+        n_converted_datasets = len(converted_datasets)
         for converted_dataset in converted_datasets.values():
+            if converted_dataset.extension == "auto" and n_converted_datasets == 1:
+                converted_dataset.extension = target_type
             original_dataset.attach_implicitly_converted_dataset(trans.sa_session, converted_dataset, target_type)
         trans.app.job_manager.enqueue(job, tool=converter)
         if len(params) > 0:

From a75bca59b45777b6df4769791bab6badc2267bb6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 11 Dec 2024 12:18:14 +0100
Subject: [PATCH 05/21] Add test

---
 lib/galaxy_test/api/test_tools.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index 56fea13f828..4547e7d1331 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -2511,6 +2511,24 @@ class TestToolsApi(ApiTestCase, TestsTools):
                 exception_raised = e
             assert exception_raised, "Expected invalid column selection to fail job"
 
+    @skip_without_tool("implicit_conversion_format_input")
+    def test_implicit_conversion_input_dataset_tracking(self):
+        with self.dataset_populator.test_history() as history_id:
+            compressed_path = self.test_data_resolver.get_filename("1.fastqsanger.gz")
+            with open(compressed_path, "rb") as fh:
+                dataset = self.dataset_populator.new_dataset(
+                    history_id, content=fh, file_type="fastqsanger.gz", wait=True
+                )
+            outputs = self._run(
+                "Grep1", history_id=history_id, inputs={"data": {"src": "hda", "id": dataset["id"]}}, assert_ok=True
+            )
+            job_details = self.dataset_populator.get_job_details(outputs["jobs"][0]["id"], full=True).json()
+            assert job_details["inputs"]["input"]["id"] != dataset["id"]
+            converted_input = self.dataset_populator.get_history_dataset_details(
+                history_id=history_id, content_id=job_details["inputs"]["input"]["id"]
+            )
+            assert converted_input["extension"] == "fastqsanger"
+
     @skip_without_tool("column_multi_param")
     def test_implicit_conversion_and_reduce(self):
         with self.dataset_populator.test_history() as history_id:

From 5229449c95039d7e5e92a16a2017dec5f3317af6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 22 Dec 2024 12:43:00 -0500
Subject: [PATCH 06/21] Refactor collection name input out of
 CollectionCreator.

---
 .../Collections/common/CollectionCreator.vue  | 20 ++------
 .../common/CollectionNameInput.vue            | 47 +++++++++++++++++++
 2 files changed, 52 insertions(+), 15 deletions(-)
 create mode 100644 client/src/components/Collections/common/CollectionNameInput.vue

diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index c60e80099fd..2fd13b20517 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -1,7 +1,7 @@
 <script setup lang="ts">
 import { faChevronDown, faChevronUp, faPlus, faUpload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton, BFormCheckbox, BFormGroup, BFormInput, BLink, BTab, BTabs } from "bootstrap-vue";
+import { BAlert, BButton, BFormCheckbox, BFormGroup, BLink, BTab, BTabs } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
 
@@ -13,6 +13,7 @@ import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
 import { orList } from "@/utils/strings";
 
+import CollectionNameInput from "./CollectionNameInput.vue";
 import HelpText from "@/components/Help/HelpText.vue";
 import DefaultBox from "@/components/Upload/DefaultBox.vue";
 
@@ -227,20 +228,9 @@ watch(
                                     </BFormCheckbox>
                                 </div>
                             </BFormGroup>
-
-                            <BFormGroup
-                                class="flex-gapx-1 d-flex align-items-center w-50 inputs-form-group"
-                                :label="localize('Name:')"
-                                label-for="collection-name">
-                                <BFormInput
-                                    id="collection-name"
-                                    v-model="collectionName"
-                                    class="collection-name"
-                                    :placeholder="localize('Enter a name for your new ' + shortWhatIsBeingCreated)"
-                                    size="sm"
-                                    required
-                                    :state="!collectionName ? false : null" />
-                            </BFormGroup>
+                            <CollectionNameInput
+                                v-model="collectionName"
+                                :short-what-is-being-created="shortWhatIsBeingCreated" />
                         </div>
                     </div>
 
diff --git a/client/src/components/Collections/common/CollectionNameInput.vue b/client/src/components/Collections/common/CollectionNameInput.vue
new file mode 100644
index 00000000000..7f299899efb
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionNameInput.vue
@@ -0,0 +1,47 @@
+<script setup lang="ts">
+import { BFormGroup, BFormInput } from "bootstrap-vue";
+import { ref, watch } from "vue";
+
+import localize from "@/utils/localization";
+
+interface Props {
+    value: string;
+    shortWhatIsBeingCreated: string;
+}
+
+const props = defineProps<Props>();
+
+const name = ref(props.value);
+
+const emit = defineEmits<{
+    (e: "input", value: string): void;
+}>();
+
+// Watch for external updates to value and sync with innerValue
+watch(
+    () => props.value,
+    (newValue) => {
+        name.value = newValue;
+    }
+);
+
+watch(name, (newValue) => {
+    emit("input", newValue);
+});
+</script>
+
+<template>
+    <BFormGroup
+        class="flex-gapx-1 d-flex align-items-center w-50 inputs-form-group"
+        :label="localize('Name:')"
+        label-for="collection-name">
+        <BFormInput
+            id="collection-name"
+            v-model="name"
+            class="collection-name"
+            :placeholder="localize('Enter a name for your new ' + shortWhatIsBeingCreated)"
+            size="sm"
+            required
+            :state="!name ? false : null" />
+    </BFormGroup>
+</template>

From e6742ed4e168286355efceb0de701b72e62d2566 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 22 Dec 2024 12:56:31 -0500
Subject: [PATCH 07/21] Refactor the source options out of collection creator.

---
 .../Collections/common/CollectionCreator.vue  | 30 ++++------
 .../common/CollectionCreatorSourceOptions.vue | 56 +++++++++++++++++++
 2 files changed, 67 insertions(+), 19 deletions(-)
 create mode 100644 client/src/components/Collections/common/CollectionCreatorSourceOptions.vue

diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index 2fd13b20517..b0331452916 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -1,7 +1,7 @@
 <script setup lang="ts">
 import { faChevronDown, faChevronUp, faPlus, faUpload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton, BFormCheckbox, BFormGroup, BLink, BTab, BTabs } from "bootstrap-vue";
+import { BAlert, BButton, BLink, BTab, BTabs } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
 
@@ -13,6 +13,7 @@ import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
 import { orList } from "@/utils/strings";
 
+import CollectionCreatorSourceOptions from "./CollectionCreatorSourceOptions.vue";
 import CollectionNameInput from "./CollectionNameInput.vue";
 import HelpText from "@/components/Help/HelpText.vue";
 import DefaultBox from "@/components/Upload/DefaultBox.vue";
@@ -132,6 +133,10 @@ function cancelCreate() {
     props.oncancel();
 }
 
+function removeExtensionsToggle() {
+    emit("remove-extensions-toggle");
+}
+
 async function loadExtensions() {
     listExtensions.value = await getUploadDatatypes(false, AUTO_EXTENSION);
     extensionsSet.value = true;
@@ -210,24 +215,11 @@ watch(
                         </div>
 
                         <div class="d-flex align-items-center justify-content-between">
-                            <BFormGroup class="inputs-form-group">
-                                <BFormCheckbox
-                                    v-if="renderExtensionsToggle"
-                                    name="remove-extensions"
-                                    switch
-                                    :checked="extensionsToggle"
-                                    @input="emit('remove-extensions-toggle')">
-                                    {{ localize("Remove file extensions?") }}
-                                </BFormCheckbox>
-
-                                <div data-description="hide original elements">
-                                    <BFormCheckbox v-model="localHideSourceItems" name="hide-originals" switch>
-                                        <HelpText
-                                            uri="galaxy.collections.collectionBuilder.hideOriginalElements"
-                                            :text="localize('Hide original elements')" />
-                                    </BFormCheckbox>
-                                </div>
-                            </BFormGroup>
+                            <CollectionCreatorSourceOptions
+                                v-model="localHideSourceItems"
+                                :render-extensions-toggle="renderExtensionsToggle"
+                                :extensions-toggle="extensionsToggle"
+                                @remove-extensions-toggle="removeExtensionsToggle" />
                             <CollectionNameInput
                                 v-model="collectionName"
                                 :short-what-is-being-created="shortWhatIsBeingCreated" />
diff --git a/client/src/components/Collections/common/CollectionCreatorSourceOptions.vue b/client/src/components/Collections/common/CollectionCreatorSourceOptions.vue
new file mode 100644
index 00000000000..c35c4bd7e77
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorSourceOptions.vue
@@ -0,0 +1,56 @@
+<script setup lang="ts">
+import { BFormCheckbox, BFormGroup } from "bootstrap-vue";
+import { ref, watch } from "vue";
+
+import localize from "@/utils/localization";
+
+import HelpText from "@/components/Help/HelpText.vue";
+
+interface Props {
+    value: boolean;
+    extensionsToggle?: boolean;
+    renderExtensionsToggle?: boolean;
+}
+
+const props = defineProps<Props>();
+
+const localHideSourceItems = ref(props.value);
+
+const emit = defineEmits<{
+    (e: "input", value: boolean): void;
+    (e: "remove-extensions-toggle"): void;
+}>();
+
+// Watch for external updates to value and sync with innerValue
+watch(
+    () => props.value,
+    (newValue) => {
+        localHideSourceItems.value = newValue;
+    }
+);
+
+watch(localHideSourceItems, (newValue) => {
+    emit("input", newValue);
+});
+</script>
+
+<template>
+    <BFormGroup class="inputs-form-group">
+        <BFormCheckbox
+            v-if="renderExtensionsToggle"
+            name="remove-extensions"
+            switch
+            :checked="extensionsToggle"
+            @input="emit('remove-extensions-toggle')">
+            {{ localize("Remove file extensions?") }}
+        </BFormCheckbox>
+
+        <div data-description="hide original elements">
+            <BFormCheckbox v-model="localHideSourceItems" name="hide-originals" switch>
+                <HelpText
+                    uri="galaxy.collections.collectionBuilder.hideOriginalElements"
+                    :text="localize('Hide original elements')" />
+            </BFormCheckbox>
+        </div>
+    </BFormGroup>
+</template>

From 40eb1d9aab5126d3e74360d432551166357a0d03 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 22 Dec 2024 13:32:05 -0500
Subject: [PATCH 08/21] Refactor collection creator help out to simplify.

---
 .../Collections/common/CollectionCreator.vue  | 45 ++---------------
 .../common/CollectionCreatorHelpHeader.vue    | 50 +++++++++++++++++++
 2 files changed, 55 insertions(+), 40 deletions(-)
 create mode 100644 client/src/components/Collections/common/CollectionCreatorHelpHeader.vue

diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index b0331452916..b076d4f3b81 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faChevronDown, faChevronUp, faPlus, faUpload } from "@fortawesome/free-solid-svg-icons";
+import { faPlus, faUpload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert, BButton, BLink, BTab, BTabs } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
@@ -13,6 +13,7 @@ import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
 import { orList } from "@/utils/strings";
 
+import CollectionCreatorHelpHeader from "./CollectionCreatorHelpHeader.vue";
 import CollectionCreatorSourceOptions from "./CollectionCreatorSourceOptions.vue";
 import CollectionNameInput from "./CollectionNameInput.vue";
 import HelpText from "@/components/Help/HelpText.vue";
@@ -58,7 +59,6 @@ const emit = defineEmits<{
     (e: "add-uploaded-files", value: HDASummary[]): void;
 }>();
 
-const isExpanded = ref(false);
 const currentTab = ref(Tabs.create);
 const collectionName = ref(props.suggestedName);
 const localHideSourceItems = ref(props.hideSourceItems);
@@ -124,11 +124,6 @@ function addUploadedFiles(value: HDASummary[]) {
     emit("add-uploaded-files", value);
 }
 
-function clickForHelp() {
-    isExpanded.value = !isExpanded.value;
-    return isExpanded.value;
-}
-
 function cancelCreate() {
     props.oncancel();
 }
@@ -165,39 +160,9 @@ watch(
                 </BAlert>
             </div>
             <div v-else>
-                <div class="header flex-row no-flex">
-                    <div class="main-help well clear" :class="{ expanded: isExpanded }">
-                        <a
-                            class="more-help"
-                            href="javascript:void(0);"
-                            role="button"
-                            :title="localize('Expand or Close Help')"
-                            @click="clickForHelp">
-                            <div v-if="!isExpanded">
-                                <FontAwesomeIcon :icon="faChevronDown" />
-                                <span class="sr-only">{{ localize("Expand Help") }}</span>
-                            </div>
-                            <div v-else>
-                                <FontAwesomeIcon :icon="faChevronUp" />
-                                <span class="sr-only">{{ localize("Close Help") }}</span>
-                            </div>
-                        </a>
-
-                        <div class="help-content">
-                            <!-- each collection that extends this will add their own help content -->
-                            <slot name="help-content"></slot>
-
-                            <a
-                                class="more-help"
-                                href="javascript:void(0);"
-                                role="button"
-                                :title="localize('Expand or Close Help')"
-                                @click="clickForHelp">
-                                <span class="sr-only">{{ localize("Expand Help") }}</span>
-                            </a>
-                        </div>
-                    </div>
-                </div>
+                <CollectionCreatorHelpHeader>
+                    <slot name="help-content"></slot>
+                </CollectionCreatorHelpHeader>
 
                 <div class="middle flex-row flex-row-container">
                     <slot name="middle-content"></slot>
diff --git a/client/src/components/Collections/common/CollectionCreatorHelpHeader.vue b/client/src/components/Collections/common/CollectionCreatorHelpHeader.vue
new file mode 100644
index 00000000000..2564230253d
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorHelpHeader.vue
@@ -0,0 +1,50 @@
+<script setup lang="ts">
+import { faChevronDown, faChevronUp } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { ref } from "vue";
+
+import localize from "@/utils/localization";
+
+const isExpanded = ref(false);
+
+function clickForHelp() {
+    isExpanded.value = !isExpanded.value;
+    return isExpanded.value;
+}
+</script>
+
+<template>
+    <div class="header flex-row no-flex">
+        <div class="main-help well clear" :class="{ expanded: isExpanded }">
+            <a
+                class="more-help"
+                href="javascript:void(0);"
+                role="button"
+                :title="localize('Expand or Close Help')"
+                @click="clickForHelp">
+                <div v-if="!isExpanded">
+                    <FontAwesomeIcon :icon="faChevronDown" />
+                    <span class="sr-only">{{ localize("Expand Help") }}</span>
+                </div>
+                <div v-else>
+                    <FontAwesomeIcon :icon="faChevronUp" />
+                    <span class="sr-only">{{ localize("Close Help") }}</span>
+                </div>
+            </a>
+
+            <div class="help-content">
+                <!-- each collection that extends this will add their own help content -->
+                <slot></slot>
+
+                <a
+                    class="more-help"
+                    href="javascript:void(0);"
+                    role="button"
+                    :title="localize('Expand or Close Help')"
+                    @click="clickForHelp">
+                    <span class="sr-only">{{ localize("Expand Help") }}</span>
+                </a>
+            </div>
+        </div>
+    </div>
+</template>

From df0336185277d4c0b3c7d604c7bf6d0c91c4ee5d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 22 Dec 2024 14:05:25 -0500
Subject: [PATCH 09/21] Refactor showing of extensions into own component.

---
 .../Collections/common/CollectionCreator.vue  | 10 ++------
 .../CollectionCreatorShowExtensions.vue       | 25 +++++++++++++++++++
 2 files changed, 27 insertions(+), 8 deletions(-)
 create mode 100644 client/src/components/Collections/common/CollectionCreatorShowExtensions.vue

diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index b076d4f3b81..81c1eea4191 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -14,6 +14,7 @@ import localize from "@/utils/localization";
 import { orList } from "@/utils/strings";
 
 import CollectionCreatorHelpHeader from "./CollectionCreatorHelpHeader.vue";
+import CollectionCreatorShowExtensions from "./CollectionCreatorShowExtensions.vue";
 import CollectionCreatorSourceOptions from "./CollectionCreatorSourceOptions.vue";
 import CollectionNameInput from "./CollectionNameInput.vue";
 import HelpText from "@/components/Help/HelpText.vue";
@@ -170,14 +171,7 @@ watch(
 
                 <div class="footer flex-row">
                     <div class="vertically-spaced">
-                        <div class="d-flex align-items-center justify-content-between">
-                            <BAlert v-if="extensions?.length" class="w-100 py-0" variant="secondary" show>
-                                <HelpText
-                                    uri="galaxy.collections.collectionBuilder.filteredExtensions"
-                                    :text="localize('Filtered extensions: ')" />
-                                <strong>{{ orList(extensions) }}</strong>
-                            </BAlert>
-                        </div>
+                        <CollectionCreatorShowExtensions :extensions="extensions" />
 
                         <div class="d-flex align-items-center justify-content-between">
                             <CollectionCreatorSourceOptions
diff --git a/client/src/components/Collections/common/CollectionCreatorShowExtensions.vue b/client/src/components/Collections/common/CollectionCreatorShowExtensions.vue
new file mode 100644
index 00000000000..45a99b22eef
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorShowExtensions.vue
@@ -0,0 +1,25 @@
+<script setup lang="ts">
+import { BAlert } from "bootstrap-vue";
+
+import localize from "@/utils/localization";
+import { orList } from "@/utils/strings";
+
+import HelpText from "@/components/Help/HelpText.vue";
+
+interface Props {
+    extensions?: string[];
+}
+
+defineProps<Props>();
+</script>
+
+<template>
+    <div class="d-flex align-items-center justify-content-between">
+        <BAlert v-if="extensions?.length" class="w-100 py-0" variant="secondary" show>
+            <HelpText
+                uri="galaxy.collections.collectionBuilder.filteredExtensions"
+                :text="localize('Filtered extensions: ')" />
+            <strong>{{ orList(extensions) }}</strong>
+        </BAlert>
+    </div>
+</template>

From d20672096cd1bbafedf8435d1773b2d04e63a3c6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 22 Dec 2024 14:11:57 -0500
Subject: [PATCH 10/21] Refactor collection creator footer buttons into a
 component.

---
 .../Collections/common/CollectionCreator.vue  | 21 +++++----------
 .../common/CollectionCreatorFooterButtons.vue | 27 +++++++++++++++++++
 2 files changed, 34 insertions(+), 14 deletions(-)
 create mode 100644 client/src/components/Collections/common/CollectionCreatorFooterButtons.vue

diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index 81c1eea4191..cb51fe28faa 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -1,7 +1,7 @@
 <script setup lang="ts">
 import { faPlus, faUpload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton, BLink, BTab, BTabs } from "bootstrap-vue";
+import { BAlert, BLink, BTab, BTabs } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
 
@@ -13,6 +13,7 @@ import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
 import { orList } from "@/utils/strings";
 
+import CollectionCreatorFooterButtons from "./CollectionCreatorFooterButtons.vue";
 import CollectionCreatorHelpHeader from "./CollectionCreatorHelpHeader.vue";
 import CollectionCreatorShowExtensions from "./CollectionCreatorShowExtensions.vue";
 import CollectionCreatorSourceOptions from "./CollectionCreatorSourceOptions.vue";
@@ -185,19 +186,11 @@ watch(
                         </div>
                     </div>
 
-                    <div class="actions vertically-spaced d-flex justify-content-between">
-                        <BButton tabindex="-1" @click="cancelCreate">
-                            {{ localize("Cancel") }}
-                        </BButton>
-
-                        <BButton
-                            class="create-collection"
-                            variant="primary"
-                            :disabled="!validInput"
-                            @click="emit('clicked-create', collectionName)">
-                            {{ localize("Create " + shortWhatIsBeingCreated) }}
-                        </BButton>
-                    </div>
+                    <CollectionCreatorFooterButtons
+                        :short-what-is-being-created="shortWhatIsBeingCreated"
+                        :valid-input="validInput"
+                        @clicked-cancel="cancelCreate"
+                        @clicked-create="emit('clicked-create', collectionName)" />
                 </div>
             </div>
         </BTab>
diff --git a/client/src/components/Collections/common/CollectionCreatorFooterButtons.vue b/client/src/components/Collections/common/CollectionCreatorFooterButtons.vue
new file mode 100644
index 00000000000..3137ade35ad
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorFooterButtons.vue
@@ -0,0 +1,27 @@
+<script setup lang="ts">
+import localize from "@/utils/localization";
+
+interface Props {
+    validInput: boolean;
+    shortWhatIsBeingCreated: string;
+}
+
+defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "clicked-create"): void;
+    (e: "clicked-cancel"): void;
+}>();
+</script>
+
+<template>
+    <div class="actions vertically-spaced d-flex justify-content-between">
+        <BButton tabindex="-1" @click="emit('clicked-cancel')">
+            {{ localize("Cancel") }}
+        </BButton>
+
+        <BButton class="create-collection" variant="primary" :disabled="!validInput" @click="emit('clicked-create')">
+            {{ localize("Create " + shortWhatIsBeingCreated) }}
+        </BButton>
+    </div>
+</template>

From 1bbe39c57ac19163469538a2c8dae00c5631aef9 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 22 Dec 2024 14:17:26 -0500
Subject: [PATCH 11/21] Refactor no items message out of collection creator for
 reuse.

---
 .../Collections/common/CollectionCreator.vue   | 11 +++--------
 .../common/CollectionCreatorNoItemsMessage.vue | 18 ++++++++++++++++++
 2 files changed, 21 insertions(+), 8 deletions(-)
 create mode 100644 client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue

diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index cb51fe28faa..06e2ec892ee 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -1,7 +1,7 @@
 <script setup lang="ts">
 import { faPlus, faUpload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BLink, BTab, BTabs } from "bootstrap-vue";
+import { BAlert, BTab, BTabs } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
 
@@ -15,6 +15,7 @@ import { orList } from "@/utils/strings";
 
 import CollectionCreatorFooterButtons from "./CollectionCreatorFooterButtons.vue";
 import CollectionCreatorHelpHeader from "./CollectionCreatorHelpHeader.vue";
+import CollectionCreatorNoItemsMessage from "./CollectionCreatorNoItemsMessage.vue";
 import CollectionCreatorShowExtensions from "./CollectionCreatorShowExtensions.vue";
 import CollectionCreatorSourceOptions from "./CollectionCreatorSourceOptions.vue";
 import CollectionNameInput from "./CollectionNameInput.vue";
@@ -153,13 +154,7 @@ watch(
     <BTabs v-model="currentTab" fill justified>
         <BTab class="collection-creator" :title="localize('Create Collection')">
             <div v-if="props.noItems">
-                <BAlert variant="info" show>
-                    {{ localize("No items available to create a collection.") }}
-                    {{ localize("Exit and change your current history, or") }}
-                    <BLink class="text-decoration-none" @click.stop.prevent="currentTab = Tabs.upload">
-                        {{ localize("Upload some datasets.") }}
-                    </BLink>
-                </BAlert>
+                <CollectionCreatorNoItemsMessage @click-upload="currentTab = Tabs.upload" />
             </div>
             <div v-else>
                 <CollectionCreatorHelpHeader>
diff --git a/client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue b/client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue
new file mode 100644
index 00000000000..b525f3a2836
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue
@@ -0,0 +1,18 @@
+<script setup lang="ts">
+import { BAlert, BLink } from "bootstrap-vue";
+
+import localize from "@/utils/localization";
+
+const emit = defineEmits<{
+    (e: "clicked-upload"): void;
+}>();
+</script>
+<template>
+    <BAlert variant="info" show>
+        {{ localize("No items available to create a collection.") }}
+        {{ localize("Exit and change your current history, or") }}
+        <BLink class="text-decoration-none" @click.stop.prevent="emit('clicked-upload')">
+            {{ localize("Upload some datasets.") }}
+        </BLink>
+    </BAlert>
+</template>

From b2e2053431717d20aec5600c2e15493055a23939 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 22 Dec 2024 14:28:23 -0500
Subject: [PATCH 12/21] Don't show upload files option when selecting datasets.

---
 .../Collections/ListCollectionCreator.vue     |   1 +
 .../Collections/PairCollectionCreator.vue     |   1 +
 .../PairedListCollectionCreator.vue           |   1 +
 .../Collections/common/CollectionCreator.vue  | 118 ++++++++++++------
 4 files changed, 82 insertions(+), 39 deletions(-)

diff --git a/client/src/components/Collections/ListCollectionCreator.vue b/client/src/components/Collections/ListCollectionCreator.vue
index ca9e25aec41..d33f98927d8 100644
--- a/client/src/components/Collections/ListCollectionCreator.vue
+++ b/client/src/components/Collections/ListCollectionCreator.vue
@@ -414,6 +414,7 @@ function renameElement(element: any, name: string) {
                 :extensions="extensions"
                 collection-type="list"
                 :no-items="props.initialElements.length == 0 && !props.fromSelection"
+                :show-upload="!fromSelection"
                 @add-uploaded-files="addUploadedFiles"
                 @on-update-datatype-toggle="changeDatatypeFilter"
                 @onUpdateHideSourceItems="onUpdateHideSourceItems"
diff --git a/client/src/components/Collections/PairCollectionCreator.vue b/client/src/components/Collections/PairCollectionCreator.vue
index 1d3e5922f31..c00c2c0f9b1 100644
--- a/client/src/components/Collections/PairCollectionCreator.vue
+++ b/client/src/components/Collections/PairCollectionCreator.vue
@@ -376,6 +376,7 @@ function _naiveStartingAndEndingLCS(s1: string, s2: string) {
                 :extensions-toggle="removeExtensions"
                 collection-type="paired"
                 :no-items="props.initialElements.length == 0 && !props.fromSelection"
+                :show-upload="!fromSelection"
                 @add-uploaded-files="addUploadedFiles"
                 @onUpdateHideSourceItems="onUpdateHideSourceItems"
                 @clicked-create="clickedCreate"
diff --git a/client/src/components/Collections/PairedListCollectionCreator.vue b/client/src/components/Collections/PairedListCollectionCreator.vue
index 620252f7c28..1f831e66a79 100644
--- a/client/src/components/Collections/PairedListCollectionCreator.vue
+++ b/client/src/components/Collections/PairedListCollectionCreator.vue
@@ -881,6 +881,7 @@ function _naiveStartingAndEndingLCS(s1: string, s2: string) {
                 :extensions="extensions"
                 collection-type="list:paired"
                 :no-items="props.initialElements.length == 0 && !props.fromSelection"
+                :show-upload="!fromSelection"
                 @add-uploaded-files="addUploadedFiles"
                 @onUpdateHideSourceItems="hideSourceItems = $event"
                 @clicked-create="clickedCreate"
diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index 06e2ec892ee..b43bbd5574d 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -46,12 +46,14 @@ interface Props {
     extensionsToggle?: boolean;
     noItems?: boolean;
     collectionType?: string;
+    showUpload: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
     suggestedName: "",
     extensions: undefined,
     extensionsToggle: false,
+    showUpload: true,
 });
 
 const emit = defineEmits<{
@@ -151,8 +153,8 @@ watch(
 </script>
 
 <template>
-    <BTabs v-model="currentTab" fill justified>
-        <BTab class="collection-creator" :title="localize('Create Collection')">
+    <span>
+        <span v-if="!showUpload" class="collection-creator">
             <div v-if="props.noItems">
                 <CollectionCreatorNoItemsMessage @click-upload="currentTab = Tabs.upload" />
             </div>
@@ -188,45 +190,83 @@ watch(
                         @clicked-create="emit('clicked-create', collectionName)" />
                 </div>
             </div>
-        </BTab>
-        <BTab>
-            <template v-slot:title>
-                <FontAwesomeIcon :icon="faUpload" fixed-width />
-                <span>{{ localize("Upload Files to Add to Collection") }}</span>
-            </template>
-            <!-- TODO: This is incomplete; need to return uploadValues to parent -->
-            <DefaultBox
-                v-if="configOptions && extensionsSet"
-                :chunk-upload-size="configOptions.chunkUploadSize"
-                :default-db-key="configOptions.defaultDbKey"
-                :default-extension="defaultExtension"
-                :effective-extensions="props.extensions?.length ? validExtensions : listExtensions"
-                :file-sources-configured="configOptions.fileSourcesConfigured"
-                :ftp-upload-site="ftpUploadSite"
-                :has-callback="false"
-                :history-id="historyId"
-                :list-db-keys="[]"
-                disable-footer
-                emit-uploaded
-                @uploaded="addUploadedFiles"
-                @dismiss="currentTab = Tabs.create">
-                <template v-slot:footer>
-                    <div class="d-flex align-items-center justify-content-between mt-2">
-                        <BAlert v-if="extensions?.length" class="w-100 py-0" variant="secondary" show>
-                            <HelpText
-                                uri="galaxy.collections.collectionBuilder.requiredUploadExtensions"
-                                :text="localize('Required extensions: ')" />
-                            <strong>{{ orList(extensions) }}</strong>
-                        </BAlert>
+        </span>
+        <BTabs v-else v-model="currentTab" fill justified>
+            <BTab class="collection-creator" :title="localize('Create Collection')">
+                <div v-if="props.noItems">
+                    <CollectionCreatorNoItemsMessage @click-upload="currentTab = Tabs.upload" />
+                </div>
+                <div v-else>
+                    <CollectionCreatorHelpHeader>
+                        <slot name="help-content"></slot>
+                    </CollectionCreatorHelpHeader>
+
+                    <div class="middle flex-row flex-row-container">
+                        <slot name="middle-content"></slot>
                     </div>
+
+                    <div class="footer flex-row">
+                        <div class="vertically-spaced">
+                            <CollectionCreatorShowExtensions :extensions="extensions" />
+
+                            <div class="d-flex align-items-center justify-content-between">
+                                <CollectionCreatorSourceOptions
+                                    v-model="localHideSourceItems"
+                                    :render-extensions-toggle="renderExtensionsToggle"
+                                    :extensions-toggle="extensionsToggle" />
+                                <CollectionNameInput
+                                    v-model="collectionName"
+                                    :short-what-is-being-created="shortWhatIsBeingCreated" />
+                            </div>
+                        </div>
+
+                        <CollectionCreatorFooterButtons
+                            :short-what-is-being-created="shortWhatIsBeingCreated"
+                            :valid-input="validInput"
+                            @clicked-cancel="cancelCreate"
+                            @clicked-create="emit('clicked-create', collectionName)" />
+                    </div>
+                </div>
+            </BTab>
+            <BTab>
+                <template v-slot:title>
+                    <FontAwesomeIcon :icon="faUpload" fixed-width />
+                    <span>{{ localize("Upload Files to Add to Collection") }}</span>
                 </template>
-                <template v-slot:emit-btn-txt>
-                    <FontAwesomeIcon :icon="faPlus" fixed-width />
-                    {{ localize("Add Uploaded") }}
-                </template>
-            </DefaultBox>
-        </BTab>
-    </BTabs>
+                <!-- TODO: This is incomplete; need to return uploadValues to parent -->
+                <DefaultBox
+                    v-if="configOptions && extensionsSet"
+                    :chunk-upload-size="configOptions.chunkUploadSize"
+                    :default-db-key="configOptions.defaultDbKey"
+                    :default-extension="defaultExtension"
+                    :effective-extensions="props.extensions?.length ? validExtensions : listExtensions"
+                    :file-sources-configured="configOptions.fileSourcesConfigured"
+                    :ftp-upload-site="ftpUploadSite"
+                    :has-callback="false"
+                    :history-id="historyId"
+                    :list-db-keys="[]"
+                    disable-footer
+                    emit-uploaded
+                    @uploaded="addUploadedFiles"
+                    @dismiss="currentTab = Tabs.create">
+                    <template v-slot:footer>
+                        <div class="d-flex align-items-center justify-content-between mt-2">
+                            <BAlert v-if="extensions?.length" class="w-100 py-0" variant="secondary" show>
+                                <HelpText
+                                    uri="galaxy.collections.collectionBuilder.requiredUploadExtensions"
+                                    :text="localize('Required extensions: ')" />
+                                <strong>{{ orList(extensions) }}</strong>
+                            </BAlert>
+                        </div>
+                    </template>
+                    <template v-slot:emit-btn-txt>
+                        <FontAwesomeIcon :icon="faPlus" fixed-width />
+                        {{ localize("Add Uploaded") }}
+                    </template>
+                </DefaultBox>
+            </BTab>
+        </BTabs>
+    </span>
 </template>
 
 <style lang="scss">

From 22bae10ec34b17f7efa7e2f509bd58fcf551fe43 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 7 Jan 2025 12:18:03 -0500
Subject: [PATCH 13/21] Fixes for console logging.

---
 client/src/components/JobInformation/JobInformation.vue | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/client/src/components/JobInformation/JobInformation.vue b/client/src/components/JobInformation/JobInformation.vue
index 22871692e6f..8e63e8dea2e 100644
--- a/client/src/components/JobInformation/JobInformation.vue
+++ b/client/src/components/JobInformation/JobInformation.vue
@@ -39,11 +39,15 @@ const stderr_position = computed(() => stderr_text.value.length);
 const runTime = computed(() => getJobDuration(job.value));
 
 function jobStateIsTerminal(jobState) {
-    return jobState && !NON_TERMINAL_STATES.includes(job.value.state);
+    return jobState && !NON_TERMINAL_STATES.includes(jobState);
+}
+
+function jobStateIsRunning(jobState) {
+    return jobState == "running";
 }
 
 const jobIsTerminal = computed(() => jobStateIsTerminal(job?.value?.state));
-
+const jobIsRunning = computed(() => jobStateIsRunning(job?.value?.state));
 const routeToInvocation = computed(() => `/workflows/invocations/${invocationId.value}`);
 
 const metadataDetail = ref({
@@ -127,6 +131,7 @@ watch(
     <div>
         <JobDetailsProvider auto-refresh :job-id="props.job_id" @update:result="updateJob" />
         <JobConsoleOutputProvider
+            v-if="jobIsRunning"
             auto-refresh
             :job-id="props.job_id"
             :stdout_position="stdout_position"

From 05ede4ab0e11048a542e1ec8dd5fa4daaad40b91 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Jan 2025 12:18:55 +0200
Subject: [PATCH 14/21] Fix planemo timeout handling

Planemo calls `verify_tool` with a maxseconds value,
and then sets `tool_test_dict.setdefault("maxseconds", maxseconds)`,
which fails, since we are serializing and already setting the default
maxseconds while parsing the test dict.

Fixes the IUC tool test timeouts not working when testing against 24.2.
Broken in
https://github.com/galaxyproject/galaxy/commit/9695ccc3c45a14b36beccfbaac69036a5ac65c21#diff-06835be1d1943ebce8373e2cd1f8e86c7b7813b720398850c978b734dd29e2daR1390
(maxseconds was prviously not serialized at all in
`ToolTestDescription.to_dict`)
---
 lib/galaxy/tool_util/verify/interactor.py     | 58 +++++++++----------
 .../tool_util/test_test_definition_parsing.py | 15 +++++
 2 files changed, 42 insertions(+), 31 deletions(-)

diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index ca186d823eb..91e7de7483b 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -1688,7 +1688,7 @@ def adapt_tool_source_dict(processed_dict: ToolTestDict) -> ToolTestDescriptionD
 
     if not error_in_test_definition:
         processed_test_dict = cast(ValidToolTestDict, processed_dict)
-        maxseconds = _get_maxseconds(processed_test_dict)
+        maxseconds = processed_test_dict.get("maxseconds")
         output_collections = processed_test_dict.get("output_collections", [])
         if "num_outputs" in processed_test_dict and processed_test_dict["num_outputs"]:
             num_outputs = int(processed_test_dict["num_outputs"])
@@ -1750,10 +1750,6 @@ def _get_test_name(test_dict: Union[ToolTestDict, ToolTestDescriptionDict], test
     return name
 
 
-def _get_maxseconds(test_dict: Union[ToolTestDict, ToolTestDescriptionDict]) -> int:
-    return int(cast(Union[str, int], test_dict.get("maxseconds") or DEFAULT_TOOL_TEST_WAIT or 86400))
-
-
 def expanded_inputs_from_json(expanded_inputs_json: ExpandedToolInputsJsonified) -> ExpandedToolInputs:
     loaded_inputs: ExpandedToolInputs = {}
     for key, value in expanded_inputs_json.items():
@@ -1829,7 +1825,7 @@ class ToolTestDescription:
         self.inputs = expanded_inputs_from_json(json_dict.get("inputs", {}))
         self.tool_id = json_dict["tool_id"]
         self.tool_version = json_dict.get("tool_version")
-        self.maxseconds = _get_maxseconds(json_dict)
+        self.maxseconds = json_dict.get("maxseconds")
 
     def test_data(self):
         """
@@ -1839,31 +1835,31 @@ class ToolTestDescription:
 
     def to_dict(self) -> ToolTestDescriptionDict:
         inputs = expanded_inputs_to_json(self.inputs)
-        return ToolTestDescriptionDict(
-            {
-                "inputs": inputs,
-                "outputs": self.outputs,
-                "output_collections": [_.to_dict() for _ in self.output_collections],
-                "num_outputs": self.num_outputs,
-                "command_line": self.command_line,
-                "command_version": self.command_version,
-                "stdout": self.stdout,
-                "stderr": self.stderr,
-                "expect_exit_code": self.expect_exit_code,
-                "expect_failure": self.expect_failure,
-                "expect_test_failure": self.expect_test_failure,
-                "name": self.name,
-                "test_index": self.test_index,
-                "tool_id": self.tool_id,
-                "tool_version": self.tool_version,
-                "required_files": self.required_files,
-                "required_data_tables": self.required_data_tables,
-                "required_loc_files": self.required_loc_files,
-                "error": self.error,
-                "exception": self.exception,
-                "maxseconds": self.maxseconds,
-            }
-        )
+        test_description_def: ToolTestDescriptionDict = {
+            "inputs": inputs,
+            "outputs": self.outputs,
+            "output_collections": [_.to_dict() for _ in self.output_collections],
+            "num_outputs": self.num_outputs,
+            "command_line": self.command_line,
+            "command_version": self.command_version,
+            "stdout": self.stdout,
+            "stderr": self.stderr,
+            "expect_exit_code": self.expect_exit_code,
+            "expect_failure": self.expect_failure,
+            "expect_test_failure": self.expect_test_failure,
+            "name": self.name,
+            "test_index": self.test_index,
+            "tool_id": self.tool_id,
+            "tool_version": self.tool_version,
+            "required_files": self.required_files,
+            "required_data_tables": self.required_data_tables,
+            "required_loc_files": self.required_loc_files,
+            "error": self.error,
+            "exception": self.exception,
+        }
+        if self.maxseconds is not None:
+            test_description_def["maxseconds"] = self.maxseconds
+        return ToolTestDescriptionDict(**test_description_def)
 
 
 def test_data_iter(required_files):
diff --git a/test/unit/tool_util/test_test_definition_parsing.py b/test/unit/tool_util/test_test_definition_parsing.py
index 6576660c3b0..ed5fbdaaee9 100644
--- a/test/unit/tool_util/test_test_definition_parsing.py
+++ b/test/unit/tool_util/test_test_definition_parsing.py
@@ -68,6 +68,21 @@ class TestTestParsing(TestCase):
         tool_source = get_tool_source(path)
         self.tool_source = tool_source
 
+    def test_maxseconds_not_filled_with_default(self):
+        self._init_tool_for_path(functional_test_tool_path("simple_constructs.xml"))
+        test_dicts = list(self._parse_tests())
+        assert test_dicts[0].maxseconds is None
+        assert "maxseconds" not in test_dicts[0].to_dict()
+
+    def test_maxseconds_parsed(self):
+        self._init_tool_for_path(functional_test_tool_path("maxseconds.xml"))
+        test_def = next(iter(self._parse_tests()))
+        assert test_def.maxseconds == 5
+        test_dict = test_def.to_dict()
+        print(test_dict)
+        assert "maxseconds" in test_dict
+        assert test_dict["maxseconds"] == 5
+
     def test_simple_state_parsing(self):
         self._init_tool_for_path(functional_test_tool_path("simple_constructs.xml"))
         test_dicts = self._parse_tests()

From c717b3ed028a5a838efe5b412e2940e5da4ee77f Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Jan 2025 13:46:21 -0500
Subject: [PATCH 15/21] Fix for empty string in regex validator message.

xref https://github.com/galaxyproject/galaxy/issues/19386
---
 lib/galaxy/tool_util/parser/parameter_validators.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/parameter_validators.py b/lib/galaxy/tool_util/parser/parameter_validators.py
index 29af9494b0b..f850e0acce8 100644
--- a/lib/galaxy/tool_util/parser/parameter_validators.py
+++ b/lib/galaxy/tool_util/parser/parameter_validators.py
@@ -668,9 +668,9 @@ def raise_error_if_valiation_fails(
         raise AssertionError("Validator logic problem - computed validation value must be boolean")
     if message is None:
         message = validator.message
-    if message is None:
+    if not message:
         message = DEFAULT_VALIDATOR_MESSAGE
-    assert message
+    assert message is not None
     if value_to_show and "%s" in message:
         message = message % value_to_show
     negate = validator.negate

From 97de7f3bfe7d2662ca00c4cc9a69aae9978a42fe Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Jan 2025 22:55:09 -0500
Subject: [PATCH 16/21] Refactor chat prompts loading to check for OpenAI API
 key configuration

---
 lib/galaxy/config/__init__.py | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 909df2ba148..267f7209279 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -1093,8 +1093,9 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
         self._process_celery_config()
 
-        # load in the chat_prompts if openai is enabled
-        self._load_chat_prompts()
+        # load in the chat_prompts if openai api key is configured
+        if self.openai_api_key:
+            self._load_chat_prompts()
 
         self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
         try:
@@ -1257,21 +1258,20 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             self.file_source_temp_dir = os.path.abspath(self.file_source_temp_dir)
 
     def _load_chat_prompts(self):
-        if self.openai_api_key:
-            current_dir = os.path.dirname(os.path.abspath(__file__))
-            chat_prompts_path = os.path.join(current_dir, "chat_prompts.json")
+        current_dir = os.path.dirname(os.path.abspath(__file__))
+        chat_prompts_path = os.path.join(current_dir, "chat_prompts.json")
 
-            if os.path.exists(chat_prompts_path):
-                try:
-                    with open(chat_prompts_path, encoding="utf-8") as file:
-                        data = json.load(file)
-                        self.chat_prompts = data.get("prompts", {})
-                except json.JSONDecodeError as e:
-                    log.error(f"JSON decoding error in chat prompts file: {e}")
-                except Exception as e:
-                    log.error(f"An error occurred while reading chat prompts file: {e}")
-            else:
-                log.warning(f"Chat prompts file not found at {chat_prompts_path}")
+        if os.path.exists(chat_prompts_path):
+            try:
+                with open(chat_prompts_path, encoding="utf-8") as file:
+                    data = json.load(file)
+                    self.chat_prompts = data.get("prompts", {})
+            except json.JSONDecodeError as e:
+                log.error(f"JSON decoding error in chat prompts file: {e}")
+            except Exception as e:
+                log.error(f"An error occurred while reading chat prompts file: {e}")
+        else:
+            log.warning(f"Chat prompts file not found at {chat_prompts_path}")
 
     def _process_celery_config(self):
         if self.celery_conf and self.celery_conf.get("result_backend") is None:

From 2ed796a2271f2a8f470bfbab06ffafe1d9bbda9c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Jan 2025 23:16:03 -0500
Subject: [PATCH 17/21] Add 'llm_api_configured' key to config serializer

---
 lib/galaxy/managers/configuration.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index d0ccfa8d53c..f30118d2fbf 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -229,6 +229,7 @@ class ConfigSerializer(base.ModelSerializer):
             "fixed_delegated_auth": _defaults_to(False),
             "help_forum_api_url": _use_config,
             "enable_help_forum_tool_panel_integration": _use_config,
+            "llm_api_configured": lambda item, key, **context: bool(item.openai_api_key),
         }
 
 

From 1349d27610df9c18bdc66358af88af83418317c2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 8 Jan 2025 23:20:32 -0500
Subject: [PATCH 18/21] Only show error wizard when llm api is configured

---
 .../DatasetInformation/DatasetError.vue       | 35 +++++++++++--------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index cbe9f3e4018..22a807219ae 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -9,6 +9,7 @@ import { computed, onMounted, ref } from "vue";
 import { GalaxyApi, type HDADetailed } from "@/api";
 import { fetchDatasetDetails } from "@/api/datasets";
 import { type JobDetails, type JobInputSummary } from "@/api/jobs";
+import { useConfig } from "@/composables/config";
 import { useMarkdown } from "@/composables/markdown";
 import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
@@ -30,6 +31,7 @@ const userStore = useUserStore();
 const { currentUser } = storeToRefs(userStore);
 
 const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
+const { config, isConfigLoaded } = useConfig();
 
 const message = ref("");
 const jobLoading = ref(true);
@@ -47,6 +49,8 @@ const showForm = computed(() => {
     return noResult || hasError;
 });
 
+const showWizard = computed(() => isConfigLoaded && config.value?.llm_api_configured);
+
 async function getDatasetDetails() {
     datasetLoading.value = true;
     try {
@@ -154,21 +158,22 @@ onMounted(async () => {
                 <b id="dataset-error-tool-id" class="text-break">{{ jobDetails.tool_id }}</b
                 >.
             </p>
-
-            <h4 class="mb-3 h-md">Possible Causes</h4>
-            <p>
-                <span>
-                    We can use AI to analyze the issue and suggest possible fixes. Please note that the diagnosis may
-                    not always be accurate.
-                </span>
-            </p>
-            <BCard class="mb-2">
-                <GalaxyWizard
-                    view="error"
-                    :query="jobDetails.tool_stderr"
-                    context="tool_error"
-                    :job-id="jobDetails.id" />
-            </BCard>
+            <template v-if="showWizard">
+                <h4 class="mb-3 h-md">Possible Causes</h4>
+                <p>
+                    <span>
+                        We can use AI to analyze the issue and suggest possible fixes. Please note that the diagnosis
+                        may not always be accurate.
+                    </span>
+                </p>
+                <BCard class="mb-2">
+                    <GalaxyWizard
+                        view="error"
+                        :query="jobDetails.tool_stderr"
+                        context="tool_error"
+                        :job-id="jobDetails.id" />
+                </BCard>
+            </template>
 
             <DatasetErrorDetails
                 :tool-stderr="jobDetails.tool_stderr"

From 01e912ae3cc96878bae421de531a85f167d5635f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 9 Jan 2025 10:56:39 +0200
Subject: [PATCH 19/21] Adjust client unit tests to conditional console
 rendering

---
 client/src/components/JobInformation/JobInformation.test.js  | 5 +++--
 .../JobInformation/testData/jobInformationResponse.json      | 3 ++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/client/src/components/JobInformation/JobInformation.test.js b/client/src/components/JobInformation/JobInformation.test.js
index 68602a1b6ff..29f3f8d604b 100644
--- a/client/src/components/JobInformation/JobInformation.test.js
+++ b/client/src/components/JobInformation/JobInformation.test.js
@@ -67,8 +67,8 @@ describe("JobInformation/JobInformation.vue", () => {
         // table should exist
         expect(jobInfoTable).toBeTruthy();
         const rows = jobInfoTable.findAll("tr");
-        // should contain 9 rows
-        expect(rows.length).toBe(9);
+        // should contain 10 rows
+        expect(rows.length).toBe(10);
     });
 
     it("stdout and stderr should be rendered", async () => {
@@ -96,5 +96,6 @@ describe("JobInformation/JobInformation.vue", () => {
             { id: "encoded-copied-from-job-id", backend_key: "copied_from_job_id" },
         ];
         verifyValues(rendered_entries, jobInfoTable, jobResponse);
+        expect(wrapper.find('td[data-description="galaxy-job-state"]').exists()).toBe(true);
     });
 });
diff --git a/client/src/components/JobInformation/testData/jobInformationResponse.json b/client/src/components/JobInformation/testData/jobInformationResponse.json
index a53d9efa910..4a74f832272 100644
--- a/client/src/components/JobInformation/testData/jobInformationResponse.json
+++ b/client/src/components/JobInformation/testData/jobInformationResponse.json
@@ -7,5 +7,6 @@
     "command_line": "commandline",
     "job_messages": ["test-msg1", "test-msg2", "test-msg3", "test-msg4"],
     "id": "test_id",
-    "copied_from_job_id": "test_copied_from_job_id"
+    "copied_from_job_id": "test_copied_from_job_id",
+    "state": "running"
 }

From 9023ef3aed54813f0acb08d5db243445cf140449 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 9 Jan 2025 09:39:33 -0500
Subject: [PATCH 20/21] Update
 client/src/components/Collections/common/CollectionCreator.vue

Co-authored-by: Ahmed Hamid Awan <qe66653@umbc.edu>
---
 client/src/components/Collections/common/CollectionCreator.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index b43bbd5574d..6947a1d592f 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -233,7 +233,6 @@ watch(
                     <FontAwesomeIcon :icon="faUpload" fixed-width />
                     <span>{{ localize("Upload Files to Add to Collection") }}</span>
                 </template>
-                <!-- TODO: This is incomplete; need to return uploadValues to parent -->
                 <DefaultBox
                     v-if="configOptions && extensionsSet"
                     :chunk-upload-size="configOptions.chunkUploadSize"

From e61121acab065ffa355ad024689b12cc3afd1682 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 10 Jan 2025 12:28:51 +0000
Subject: [PATCH 21/21] Use `id` entity attribute when setting `exampleOfWork`
 property

Fix the following error in 3 unit tests when using rocrate 0.13.0 :

```
______________________ test_export_invocation_to_ro_crate ______________________

tmp_path = PosixPath('/tmp/pytest-of-runner/pytest-5/test_export_invocation_to_ro_c0')

    def test_export_invocation_to_ro_crate(tmp_path):
        app = _mock_app()
        workflow_invocation = _setup_invocation(app)
        crate_directory = tmp_path / "crate"
        with store.ROCrateModelExportStore(crate_directory, app=app) as export_store:
            export_store.export_workflow_invocation(workflow_invocation)
>       validate_invocation_crate_directory(crate_directory)

tests/data/model/test_model_store.py:627:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/data/model/test_model_store.py:564: in validate_invocation_crate_directory
    validate_create_action(crate)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

ro_crate = <rocrate.rocrate.ROCrate object at 0x7fb4673c2520>

    def validate_create_action(ro_crate: ROCrate):
        workflow = ro_crate.mainEntity
        actions = [_ for _ in ro_crate.contextual_entities if "CreateAction" in _.type]
        assert len(actions) == 1
        wf_action = actions[0]
        assert wf_action["instrument"]
        assert wf_action["instrument"] is workflow
        wf_objects = wf_action["object"]
        wf_results = wf_action["result"]
        assert len(wf_objects) == 1
        assert len(wf_results) == 1
        for entity in wf_results:
            if entity.id.endswith(".txt"):
                assert "File" in entity.type
                wf_output_file = entity
                assert wf_output_file["encodingFormat"] == "text/plain"
>               assert wf_output_file["exampleOfWork"] is workflow["output"][0]
E               AssertionError: assert '#d2ed04ef-36f8-49ae-86ce-47cb03a856c0' is <d2ed04ef-36f8-49ae-86ce-47cb03a856c0 FormalParameter>

tests/data/model/test_model_store.py:540: AssertionError
```

Also:
- Remove unused `_add_step_tool_pv` method.
---
 lib/galaxy/model/store/ro_crate_utils.py | 64 +++++++++---------------
 1 file changed, 24 insertions(+), 40 deletions(-)

diff --git a/lib/galaxy/model/store/ro_crate_utils.py b/lib/galaxy/model/store/ro_crate_utils.py
index b6b583a57a7..33072d27baa 100644
--- a/lib/galaxy/model/store/ro_crate_utils.py
+++ b/lib/galaxy/model/store/ro_crate_utils.py
@@ -123,25 +123,27 @@ class WorkflowRunCrateProfileBuilder:
     def _add_files(self, crate: ROCrate):
         for wfda in self.invocation.input_datasets:
             if not self.file_entities.get(wfda.dataset.dataset.id):
-                properties = {
-                    "exampleOfWork": {"@id": f"#{wfda.dataset.dataset.uuid}"},
-                }
-                file_entity = self._add_file(wfda.dataset, properties, crate)
                 dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
                 crate.mainEntity.append_to("input", dataset_formal_param)
+                properties = {
+                    "exampleOfWork": {"@id": dataset_formal_param.id},
+                }
+                file_entity = self._add_file(wfda.dataset, properties, crate)
                 self.create_action.append_to("object", file_entity)
 
         for wfda in self.invocation.output_datasets:
             if not self.file_entities.get(wfda.dataset.dataset.id):
-                properties = {
-                    "exampleOfWork": {"@id": f"#{wfda.dataset.dataset.uuid}"},
-                }
-                file_entity = self._add_file(wfda.dataset, properties, crate)
                 dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
                 crate.mainEntity.append_to("output", dataset_formal_param)
+                properties = {
+                    "exampleOfWork": {"@id": dataset_formal_param.id},
+                }
+                file_entity = self._add_file(wfda.dataset, properties, crate)
                 self.create_action.append_to("result", file_entity)
 
-    def _add_collection(self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate) -> ContextEntity:
+    def _add_collection(
+        self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate, collection_formal_param: ContextEntity
+    ) -> ContextEntity:
         name = hdca.name
         dataset_ids = []
         for hda in hdca.dataset_instances:
@@ -158,7 +160,7 @@ class WorkflowRunCrateProfileBuilder:
             "@type": "Collection",
             "additionalType": self._get_collection_additional_type(hdca.collection.collection_type),
             "hasPart": dataset_ids,
-            "exampleOfWork": {"@id": f"#{hdca.type_id}-param"},
+            "exampleOfWork": {"@id": collection_formal_param.id},
         }
         collection_entity = crate.add(
             ContextEntity(
@@ -185,14 +187,14 @@ class WorkflowRunCrateProfileBuilder:
 
     def _add_collections(self, crate: ROCrate):
         for wfdca in self.invocation.input_dataset_collections:
-            collection_entity = self._add_collection(wfdca.dataset_collection, crate)
             collection_formal_param = self._add_collection_formal_parameter(wfdca.dataset_collection, crate)
+            collection_entity = self._add_collection(wfdca.dataset_collection, crate, collection_formal_param)
             crate.mainEntity.append_to("input", collection_formal_param)
             self.create_action.append_to("object", collection_entity)
 
         for wfdca in self.invocation.output_dataset_collections:
-            collection_entity = self._add_collection(wfdca.dataset_collection, crate)
             collection_formal_param = self._add_collection_formal_parameter(wfdca.dataset_collection, crate)
+            collection_entity = self._add_collection(wfdca.dataset_collection, crate, collection_formal_param)
             crate.mainEntity.append_to("output", collection_formal_param)
             self.create_action.append_to("result", collection_entity)
 
@@ -336,31 +338,14 @@ class WorkflowRunCrateProfileBuilder:
     def _add_parameters(self, crate: ROCrate):
         for step in self.invocation.steps:
             if step.workflow_step.type == "parameter_input":
-                property_value = self._add_step_parameter_pv(step, crate)
-                formal_param = self._add_step_parameter_fp(step, crate)
-                crate.mainEntity.append_to("input", formal_param)
+                property_value = self._add_step_parameter(step, crate)
                 self.create_action.append_to("object", property_value)
 
-    def _add_step_parameter_pv(self, step: WorkflowInvocationStep, crate: ROCrate):
-        param_id = step.workflow_step.label
-        return crate.add(
-            ContextEntity(
-                crate,
-                f"{param_id}-pv",
-                properties={
-                    "@type": "PropertyValue",
-                    "name": f"{param_id}",
-                    "value": step.output_value.value,
-                    "exampleOfWork": {"@id": f"#{param_id}-param"},
-                },
-            )
-        )
-
-    def _add_step_parameter_fp(self, step: WorkflowInvocationStep, crate: ROCrate):
+    def _add_step_parameter(self, step: WorkflowInvocationStep, crate: ROCrate) -> ContextEntity:
         param_id = step.workflow_step.label
         assert step.workflow_step.tool_inputs
         param_type = step.workflow_step.tool_inputs["parameter_type"]
-        return crate.add(
+        formal_param = crate.add(
             ContextEntity(
                 crate,
                 f"{param_id}-param",
@@ -373,19 +358,16 @@ class WorkflowRunCrateProfileBuilder:
                 },
             )
         )
-
-    def _add_step_tool_pv(self, step: WorkflowInvocationStep, tool_input: str, crate: ROCrate):
-        param_id = tool_input
-        assert step.workflow_step.tool_inputs
+        crate.mainEntity.append_to("input", formal_param)
         return crate.add(
             ContextEntity(
                 crate,
                 f"{param_id}-pv",
                 properties={
                     "@type": "PropertyValue",
-                    "name": f"{step.workflow_step.label}",
-                    "value": step.workflow_step.tool_inputs[tool_input],
-                    "exampleOfWork": {"@id": f"#{param_id}-param"},
+                    "name": f"{param_id}",
+                    "value": step.output_value.value,
+                    "exampleOfWork": {"@id": formal_param.id},
                 },
             )
         )
@@ -419,7 +401,9 @@ class WorkflowRunCrateProfileBuilder:
             )
         )
 
-    def _add_collection_formal_parameter(self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate):
+    def _add_collection_formal_parameter(
+        self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate
+    ) -> ContextEntity:
         return crate.add(
             ContextEntity(
                 crate,