From c6e700b7c5d7ec3cfa548984406bf4341ce4619c Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 24 Jan 2023 14:35:25 +0100
Subject: [PATCH 01/40] Disable add button when nothing is selected

---
 client/src/components/History/Modals/SelectorModal.vue | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/Modals/SelectorModal.vue b/client/src/components/History/Modals/SelectorModal.vue
index 76dded0a196..60771b6d37a 100644
--- a/client/src/components/History/Modals/SelectorModal.vue
+++ b/client/src/components/History/Modals/SelectorModal.vue
@@ -31,7 +31,9 @@
         </b-table>
         <template v-slot:modal-footer>
             <b-pagination v-model="currentPage" :total-rows="totalRows" :per-page="perPage" />
-            <b-button v-if="multiple" variant="primary" @click="addSelected">Add Selected</b-button>
+            <b-button v-if="multiple" :disabled="isEmptySelection" variant="primary" @click="addSelected">
+                Add Selected
+            </b-button>
         </template>
     </b-modal>
 </template>
@@ -77,6 +79,9 @@ export default {
                 return item;
             });
         },
+        isEmptySelection() {
+            return this.selectedHistories.length === 0;
+        },
     },
     watch: {
         histories(newVal) {

From a30beb4da541d6160037ad67855961d5a999bdc9 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 24 Jan 2023 14:43:52 +0100
Subject: [PATCH 02/40] Update row variant conditionally

The current history will be still highlighted differently when is not explicitly selected.
---
 client/src/components/History/Modals/SelectorModal.vue | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/Modals/SelectorModal.vue b/client/src/components/History/Modals/SelectorModal.vue
index 60771b6d37a..4776ed30dd5 100644
--- a/client/src/components/History/Modals/SelectorModal.vue
+++ b/client/src/components/History/Modals/SelectorModal.vue
@@ -74,7 +74,10 @@ export default {
         formattedItems() {
             return this.histories.map((item) => {
                 if (item.id === this.currentHistoryId) {
-                    item._rowVariant = "info";
+                    const isCurrentSelected = this.selectedHistories.some(
+                        (history) => history.id === this.currentHistoryId
+                    );
+                    item._rowVariant = isCurrentSelected ? "success" : "info";
                 }
                 return item;
             });

From 67a5e81d51fcf2e04207733bf6e6c328b1b123cc Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 24 Jan 2023 15:16:55 +0100
Subject: [PATCH 03/40] Add jest test for current history highlight

---
 .../History/Modals/SelectorModal.test.js      | 62 +++++++++++++------
 1 file changed, 44 insertions(+), 18 deletions(-)

diff --git a/client/src/components/History/Modals/SelectorModal.test.js b/client/src/components/History/Modals/SelectorModal.test.js
index bc026247c84..8aa8b281aed 100644
--- a/client/src/components/History/Modals/SelectorModal.test.js
+++ b/client/src/components/History/Modals/SelectorModal.test.js
@@ -5,7 +5,7 @@ import SelectorModal from "./SelectorModal";
 
 const localVue = getLocalVue();
 
-const SELECTED_HISTORY_ID = "COOL_ID";
+const CURRENT_HISTORY_ID = "COOL_ID";
 const getFakeHistorySummaries = (num, selectedIndex = 0) => {
     const result = Array.from({ length: num }, (_, index) => ({
         id: `ID-${index}`,
@@ -13,11 +13,11 @@ const getFakeHistorySummaries = (num, selectedIndex = 0) => {
         tags: [],
         update_time: new Date().toISOString(),
     }));
-    result[selectedIndex].id = SELECTED_HISTORY_ID;
+    result[selectedIndex].id = CURRENT_HISTORY_ID;
     return result;
 };
 const PROPS_WITH_10_HISTORIES = {
-    currentHistoryId: SELECTED_HISTORY_ID,
+    currentHistoryId: CURRENT_HISTORY_ID,
     histories: getFakeHistorySummaries(10),
     perPage: 3,
     static: true, // Force the modal visible for testing
@@ -27,6 +27,9 @@ const PROPS_WITH_10_HISTORY_MULTIPLE_SELECT = {
     multiple: true,
 };
 
+const CURRENT_HISTORY_HIGHLIGHT_CLASS = ".table-info";
+const SELECTED_HISTORY_HIGHLIGHT_CLASS = ".table-success";
+
 describe("History SelectorModal.vue", () => {
     let wrapper;
 
@@ -41,9 +44,9 @@ describe("History SelectorModal.vue", () => {
     it("should highlight the currently selected history", async () => {
         await mountWith(PROPS_WITH_10_HISTORIES);
 
-        const selectedRows = wrapper.findAll(".table-info");
+        const selectedRows = wrapper.findAll(CURRENT_HISTORY_HIGHLIGHT_CLASS);
         expect(selectedRows.length).toBe(1);
-        expect(selectedRows.at(0).attributes("data-pk")).toBe(SELECTED_HISTORY_ID);
+        expect(selectedRows.at(0).attributes("data-pk")).toBe(CURRENT_HISTORY_ID);
     });
 
     it("paginates the histories", async () => {
@@ -67,25 +70,48 @@ describe("History SelectorModal.vue", () => {
         expect(wrapper.emitted()["selectHistory"][0][0].id).toBe(targetHistoryId);
     });
 
-    it("select multiple histories", async () => {
-        await mountWith(PROPS_WITH_10_HISTORY_MULTIPLE_SELECT);
+    describe("Multi-selection Mode", () => {
+        it("should select multiple histories", async () => {
+            await mountWith(PROPS_WITH_10_HISTORY_MULTIPLE_SELECT);
 
-        expect(wrapper.emitted()["selectHistories"]).toBeUndefined();
+            expect(wrapper.emitted()["selectHistories"]).toBeUndefined();
 
-        const targetHistoryId1 = "ID-1";
-        const targetRow1 = wrapper.find(`[data-pk="${targetHistoryId1}"]`);
-        await targetRow1.trigger("click");
+            const targetHistoryId1 = "ID-1";
+            const targetRow1 = wrapper.find(`[data-pk="${targetHistoryId1}"]`);
+            await targetRow1.trigger("click");
 
-        const targetHistoryId2 = "ID-2";
-        const targetRow2 = wrapper.find(`[data-pk="${targetHistoryId2}"]`);
-        await targetRow2.trigger("click");
+            const targetHistoryId2 = "ID-2";
+            const targetRow2 = wrapper.find(`[data-pk="${targetHistoryId2}"]`);
+            await targetRow2.trigger("click");
 
-        expect(wrapper.vm.selectedHistories.length).toBe(2);
+            expect(wrapper.vm.selectedHistories.length).toBe(2);
 
-        const button = wrapper.find(".btn-primary");
+            const button = wrapper.find(".btn-primary");
 
-        await button.trigger("click");
+            await button.trigger("click");
 
-        expect(wrapper.emitted()["selectHistories"][0][0][0].id).toBe(targetHistoryId1);
+            expect(wrapper.emitted()["selectHistories"][0][0][0].id).toBe(targetHistoryId1);
+
+            console.debug(wrapper.html());
+        });
+
+        it("should highlight the current history differently by default but equally when selected", async () => {
+            await mountWith(PROPS_WITH_10_HISTORY_MULTIPLE_SELECT);
+
+            let selectedRows = wrapper.findAll(CURRENT_HISTORY_HIGHLIGHT_CLASS);
+            expect(selectedRows.length).toBe(1);
+            expect(selectedRows.at(0).attributes("data-pk")).toBe(CURRENT_HISTORY_ID);
+
+            const targetRow = wrapper.find(`[data-pk="${CURRENT_HISTORY_ID}"]`);
+            await targetRow.trigger("click");
+
+            // No longer highlighted as current
+            selectedRows = wrapper.findAll(CURRENT_HISTORY_HIGHLIGHT_CLASS);
+            expect(selectedRows.length).toBe(0);
+
+            // Highlighted as normal selection
+            selectedRows = wrapper.findAll(SELECTED_HISTORY_HIGHLIGHT_CLASS);
+            expect(selectedRows.length).toBe(1);
+        });
     });
 });

From 6f99f8aa281c6f2caf6002c4597030e7b6ee9936 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 24 Jan 2023 19:12:25 +0100
Subject: [PATCH 04/40] Indicate current history without color highlight

---
 .../History/Modals/SelectorModal.test.js      | 29 +++----------------
 .../History/Modals/SelectorModal.vue          | 16 +++-------
 2 files changed, 8 insertions(+), 37 deletions(-)

diff --git a/client/src/components/History/Modals/SelectorModal.test.js b/client/src/components/History/Modals/SelectorModal.test.js
index 8aa8b281aed..121e911f63b 100644
--- a/client/src/components/History/Modals/SelectorModal.test.js
+++ b/client/src/components/History/Modals/SelectorModal.test.js
@@ -27,8 +27,7 @@ const PROPS_WITH_10_HISTORY_MULTIPLE_SELECT = {
     multiple: true,
 };
 
-const CURRENT_HISTORY_HIGHLIGHT_CLASS = ".table-info";
-const SELECTED_HISTORY_HIGHLIGHT_CLASS = ".table-success";
+const CURRENT_HISTORY_INDICATION_TEXT = "(Current)";
 
 describe("History SelectorModal.vue", () => {
     let wrapper;
@@ -41,12 +40,11 @@ describe("History SelectorModal.vue", () => {
         await flushPromises();
     }
 
-    it("should highlight the currently selected history", async () => {
+    it("should indicate the currently selected history", async () => {
         await mountWith(PROPS_WITH_10_HISTORIES);
 
-        const selectedRows = wrapper.findAll(CURRENT_HISTORY_HIGHLIGHT_CLASS);
-        expect(selectedRows.length).toBe(1);
-        expect(selectedRows.at(0).attributes("data-pk")).toBe(CURRENT_HISTORY_ID);
+        const currentHistoryRow = wrapper.find(`[data-pk="${CURRENT_HISTORY_ID}"]`);
+        expect(currentHistoryRow.html()).toContain(CURRENT_HISTORY_INDICATION_TEXT);
     });
 
     it("paginates the histories", async () => {
@@ -94,24 +92,5 @@ describe("History SelectorModal.vue", () => {
 
             console.debug(wrapper.html());
         });
-
-        it("should highlight the current history differently by default but equally when selected", async () => {
-            await mountWith(PROPS_WITH_10_HISTORY_MULTIPLE_SELECT);
-
-            let selectedRows = wrapper.findAll(CURRENT_HISTORY_HIGHLIGHT_CLASS);
-            expect(selectedRows.length).toBe(1);
-            expect(selectedRows.at(0).attributes("data-pk")).toBe(CURRENT_HISTORY_ID);
-
-            const targetRow = wrapper.find(`[data-pk="${CURRENT_HISTORY_ID}"]`);
-            await targetRow.trigger("click");
-
-            // No longer highlighted as current
-            selectedRows = wrapper.findAll(CURRENT_HISTORY_HIGHLIGHT_CLASS);
-            expect(selectedRows.length).toBe(0);
-
-            // Highlighted as normal selection
-            selectedRows = wrapper.findAll(SELECTED_HISTORY_HIGHLIGHT_CLASS);
-            expect(selectedRows.length).toBe(1);
-        });
     });
 });
diff --git a/client/src/components/History/Modals/SelectorModal.vue b/client/src/components/History/Modals/SelectorModal.vue
index 4776ed30dd5..5fdd0440798 100644
--- a/client/src/components/History/Modals/SelectorModal.vue
+++ b/client/src/components/History/Modals/SelectorModal.vue
@@ -11,7 +11,7 @@
             primary-key="id"
             :fields="fields"
             :filter="filter"
-            :items="formattedItems"
+            :items="histories"
             :per-page="perPage"
             :current-page="currentPage"
             :selectable="true"
@@ -22,6 +22,9 @@
             selected-variant="success"
             @row-selected="rowSelected"
             @filtered="onFiltered">
+            <template v-slot:cell(name)="row">
+                {{ row.item.name }} <i v-if="row.item.id === currentHistoryId"><b>(Current)</b></i>
+            </template>
             <template v-slot:cell(tags)="row">
                 <stateless-tags :value="row.item.tags" :disabled="true" />
             </template>
@@ -71,17 +74,6 @@ export default {
         };
     },
     computed: {
-        formattedItems() {
-            return this.histories.map((item) => {
-                if (item.id === this.currentHistoryId) {
-                    const isCurrentSelected = this.selectedHistories.some(
-                        (history) => history.id === this.currentHistoryId
-                    );
-                    item._rowVariant = isCurrentSelected ? "success" : "info";
-                }
-                return item;
-            });
-        },
         isEmptySelection() {
             return this.selectedHistories.length === 0;
         },

From bf1938b1075633b2827aded350a5199a621a0289 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 26 Jan 2023 15:03:07 -0500
Subject: [PATCH 05/40] Hide metadata auto-detection option if dataset is in
 improper state

---
 .../src/components/DatasetInformation/DatasetAttributes.vue   | 4 ++--
 lib/galaxy/webapps/galaxy/controllers/dataset.py              | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index dd942966dd0..fbb1aa44e52 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -20,12 +20,12 @@
                                 @click="submit('attribute', 'attributes')">
                                 <font-awesome-icon icon="save" class="mr-1" />{{ "Save" | l }}
                             </b-button>
-                            <b-button @click="submit('attribute', 'autodetect')">
+                            <b-button v-if="!result['metadata_disable']" @click="submit('attribute', 'autodetect')">
                                 <font-awesome-icon icon="redo" class="mr-1" />{{ "Auto-detect" | l }}
                             </b-button>
                         </div>
                     </b-tab>
-                    <b-tab v-if="!result['conversion_disable'] || !result['datatype_disable']">
+                    <b-tab v-if="(!result['conversion_disable'] || !result['datatype_disable']) && !result['metadata_disable']">
                         <template v-slot:title>
                             <span v-if="!result['conversion_disable']">
                                 <font-awesome-icon icon="cog" class="mr-1" />{{ "Convert" | l }}
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 0473f7d2a1f..c496a8aedeb 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -291,6 +291,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             if data.missing_meta():
                 message = 'Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.'
                 status = "warning"
+            metadata_disable = data.state not in [trans.model.Dataset.states.OK, trans.model.Dataset.states.FAILED_METADATA]
             # datatype conversion
             conversion_options = [
                 (f"{convert_id} (using '{convert_name}')", convert_id)
@@ -369,6 +370,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 "message": message,
                 "status": status,
                 "dataset_id": dataset_id,
+                "metadata_disable": metadata_disable,
                 "attribute_inputs": attribute_inputs,
                 "conversion_inputs": conversion_inputs,
                 "conversion_disable": conversion_disable,

From ec7b8b01401e2eb3b4cfb74d4120e95efca8ddbd Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 26 Jan 2023 15:09:09 -0500
Subject: [PATCH 06/40] Fix linting

---
 .../src/components/DatasetInformation/DatasetAttributes.vue | 6 +++++-
 client/src/components/Workflow/Editor/modules/terminals.ts  | 4 ++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index fbb1aa44e52..73874c5f601 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -25,7 +25,11 @@
                             </b-button>
                         </div>
                     </b-tab>
-                    <b-tab v-if="(!result['conversion_disable'] || !result['datatype_disable']) && !result['metadata_disable']">
+                    <b-tab
+                        v-if="
+                            (!result['conversion_disable'] || !result['datatype_disable']) &&
+                            !result['metadata_disable']
+                        ">
                         <template v-slot:title>
                             <span v-if="!result['conversion_disable']">
                                 <font-awesome-icon icon="cog" class="mr-1" />{{ "Convert" | l }}
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 1e354149ffa..9b145699bed 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -490,10 +490,10 @@ export class InputParameterTerminal extends BaseInputTerminal {
         const effectiveThisType = this.effectiveType(this.type);
         const otherType = ("type" in other && other.type) || "data";
         const effectiveOtherType = this.effectiveType(otherType);
-        const canAccept = effectiveThisType === effectiveOtherType
+        const canAccept = effectiveThisType === effectiveOtherType;
         return new ConnectionAcceptable(
             canAccept,
-            canAccept ? null: `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
+            canAccept ? null : `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
         );
     }
 }

From d71472f07143b712c85ca1005c129ebca4007b55 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 26 Jan 2023 15:49:27 -0500
Subject: [PATCH 07/40] Fix python linting

---
 lib/galaxy/webapps/galaxy/controllers/dataset.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index c496a8aedeb..95bdbb1632d 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -291,6 +291,10 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             if data.missing_meta():
                 message = 'Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.'
                 status = "warning"
+            metadata_disable = data.state not in [
+                trans.model.Dataset.states.OK,
+                trans.model.Dataset.states.FAILED_METADATA,
+            ]
             metadata_disable = data.state not in [trans.model.Dataset.states.OK, trans.model.Dataset.states.FAILED_METADATA]
             # datatype conversion
             conversion_options = [

From 4ed173a0fc38675c916166a4eeafb2dd76121d13 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 26 Jan 2023 15:34:24 -0800
Subject: [PATCH 08/40] move loading indicator and supress it for non-initial
 load

---
 client/src/components/LoadingSpan.vue          | 9 +++++++--
 client/src/components/Workflow/Editor/Node.vue | 6 ++++--
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/client/src/components/LoadingSpan.vue b/client/src/components/LoadingSpan.vue
index 85e79a25c7e..c4c3b9d26b5 100644
--- a/client/src/components/LoadingSpan.vue
+++ b/client/src/components/LoadingSpan.vue
@@ -1,7 +1,7 @@
 <template>
     <span>
-        <span :class="spinnerClasses"></span>
-        <span class="loading-message">{{ message }}.<span class="blinking">..</span></span>
+        <span :class="spinnerClasses" title="loading"></span>
+        <span v-if="!spinnerOnly" class="loading-message">{{ message }}.<span class="blinking">..</span></span>
     </span>
 </template>
 <script>
@@ -16,6 +16,11 @@ export default {
             type: String,
             default: "Loading",
         },
+        spinnerOnly: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
     },
     computed: {
         spinnerClasses() {
diff --git a/client/src/components/Workflow/Editor/Node.vue b/client/src/components/Workflow/Editor/Node.vue
index 3a475c5ceb2..af5fec39f87 100644
--- a/client/src/components/Workflow/Editor/Node.vue
+++ b/client/src/components/Workflow/Editor/Node.vue
@@ -11,8 +11,8 @@
         @move="onMoveTo"
         @pan-by="onPanBy">
         <div class="node-header unselectable clearfix" @click="makeActive" @keyup.enter="makeActive">
-            <loading-span v-if="isLoading" message="Loading details" />
             <b-button-group class="float-right">
+                <loading-span v-if="isLoading" spinner-only />
                 <b-button
                     v-if="canClone"
                     v-b-tooltip.hover
@@ -175,7 +175,9 @@ const workflowOutputs = computed(() => props.step.workflow_outputs || []);
 const connectionStore = useConnectionStore();
 const stateStore = useWorkflowStateStore();
 const stepStore = useWorkflowStepStore();
-const isLoading = computed(() => Boolean(stateStore.getStepLoadingState(props.id)?.loading));
+const isLoading = computed(() =>
+    Boolean(stateStore.getStepLoadingState(props.id)?.loading && props.step.outputs.length === 0)
+);
 useNodePosition(el, props.id, stateStore);
 const title = computed(() => props.step.label || props.step.name);
 const idString = computed(() => `wf-node-step-${props.id}`);

From b0187d6670659b5e82aa808d04bc5e6e536dd2fa Mon Sep 17 00:00:00 2001
From: Martin Cech <emulatorer@gmail.com>
Date: Fri, 27 Jan 2023 00:47:51 +0100
Subject: [PATCH 09/40] drop duplicated statement

---
 lib/galaxy/webapps/galaxy/controllers/dataset.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 95bdbb1632d..fe1578907b9 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -295,7 +295,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 trans.model.Dataset.states.OK,
                 trans.model.Dataset.states.FAILED_METADATA,
             ]
-            metadata_disable = data.state not in [trans.model.Dataset.states.OK, trans.model.Dataset.states.FAILED_METADATA]
             # datatype conversion
             conversion_options = [
                 (f"{convert_id} (using '{convert_name}')", convert_id)

From 93c2835aeffa034e0eda30c21327da2fcebf29c7 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Fri, 27 Jan 2023 18:46:02 +0100
Subject: [PATCH 10/40] do no t limit loading indicator to initial load

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 client/src/components/Workflow/Editor/Node.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Editor/Node.vue b/client/src/components/Workflow/Editor/Node.vue
index af5fec39f87..d6a11e5a1e2 100644
--- a/client/src/components/Workflow/Editor/Node.vue
+++ b/client/src/components/Workflow/Editor/Node.vue
@@ -176,7 +176,7 @@ const connectionStore = useConnectionStore();
 const stateStore = useWorkflowStateStore();
 const stepStore = useWorkflowStepStore();
 const isLoading = computed(() =>
-    Boolean(stateStore.getStepLoadingState(props.id)?.loading && props.step.outputs.length === 0)
+    Boolean(stateStore.getStepLoadingState(props.id)?.loading)
 );
 useNodePosition(el, props.id, stateStore);
 const title = computed(() => props.step.label || props.step.name);

From 0375df7c70a343f2eb4d5ea8ccb778dc52cc1602 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Fri, 27 Jan 2023 10:00:20 -0800
Subject: [PATCH 11/40] pretify

---
 client/src/components/Workflow/Editor/Node.vue | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/client/src/components/Workflow/Editor/Node.vue b/client/src/components/Workflow/Editor/Node.vue
index d6a11e5a1e2..0d7abe9abd6 100644
--- a/client/src/components/Workflow/Editor/Node.vue
+++ b/client/src/components/Workflow/Editor/Node.vue
@@ -175,9 +175,7 @@ const workflowOutputs = computed(() => props.step.workflow_outputs || []);
 const connectionStore = useConnectionStore();
 const stateStore = useWorkflowStateStore();
 const stepStore = useWorkflowStepStore();
-const isLoading = computed(() =>
-    Boolean(stateStore.getStepLoadingState(props.id)?.loading)
-);
+const isLoading = computed(() => Boolean(stateStore.getStepLoadingState(props.id)?.loading));
 useNodePosition(el, props.id, stateStore);
 const title = computed(() => props.step.label || props.step.name);
 const idString = computed(() => `wf-node-step-${props.id}`);

From b33b48561785cebbe4c62f6378f286251295646a Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 26 Jan 2023 13:30:44 -0500
Subject: [PATCH 12/40] Prevent posting changes when initializing tool forms in
 workflow editor

---
 client/src/components/Workflow/Editor/Forms/FormTool.vue | 9 ++++++++-
 client/src/components/Workflow/Editor/Index.vue          | 1 +
 .../src/components/Workflow/Editor/modules/terminals.ts  | 4 ++--
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Workflow/Editor/Forms/FormTool.vue b/client/src/components/Workflow/Editor/Forms/FormTool.vue
index 609447c15a9..2d8e70e2972 100644
--- a/client/src/components/Workflow/Editor/Forms/FormTool.vue
+++ b/client/src/components/Workflow/Editor/Forms/FormTool.vue
@@ -163,9 +163,16 @@ export default {
         onLabel(newLabel) {
             this.$emit("onLabel", this.stepId, newLabel);
         },
+        /**
+         * Change event is triggered on component creation and input changes.
+         * @param { Object } values contains flat key-value pairs `prefixed-name=value`
+         */
         onChange(values) {
+            const initialRequest = Object.keys(this.mainValues).length === 0;
             this.mainValues = values;
-            this.postChanges();
+            if (!initialRequest) {
+                this.postChanges();
+            }
         },
         onChangePostJobActions(postJobActions) {
             this.$emit("onChangePostJobActions", this.stepId, postJobActions);
diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index 92ee4af0680..3f5f8e3fd41 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -108,6 +108,7 @@
                             <div>
                                 <FormTool
                                     v-if="hasActiveNodeTool"
+                                    :key="activeStep.id"
                                     :step="activeStep"
                                     :datatypes="datatypes"
                                     @onChangePostJobActions="onChangePostJobActions"
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 1e354149ffa..9b145699bed 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -490,10 +490,10 @@ export class InputParameterTerminal extends BaseInputTerminal {
         const effectiveThisType = this.effectiveType(this.type);
         const otherType = ("type" in other && other.type) || "data";
         const effectiveOtherType = this.effectiveType(otherType);
-        const canAccept = effectiveThisType === effectiveOtherType
+        const canAccept = effectiveThisType === effectiveOtherType;
         return new ConnectionAcceptable(
             canAccept,
-            canAccept ? null: `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
+            canAccept ? null : `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
         );
     }
 }

From f0e09031f4a194f0d1f9c1656eb53d1f1681e9a9 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 27 Jan 2023 19:30:44 -0500
Subject: [PATCH 13/40] Adjust test to ensure that onSetData is not fired on
 initialization

---
 .../Workflow/Editor/Forms/FormTool.test.js          | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/client/src/components/Workflow/Editor/Forms/FormTool.test.js b/client/src/components/Workflow/Editor/Forms/FormTool.test.js
index 2db5af07c0e..01bdcfb973c 100644
--- a/client/src/components/Workflow/Editor/Forms/FormTool.test.js
+++ b/client/src/components/Workflow/Editor/Forms/FormTool.test.js
@@ -11,9 +11,7 @@ import { createTestingPinia } from "@pinia/testing";
 const localVue = getLocalVue();
 
 describe("FormTool", () => {
-    let wrapper;
-
-    beforeEach(() => {
+    function mountTarget() {
         const store = new Vuex.Store({
             modules: {
                 user: mockModule(userStore),
@@ -21,7 +19,7 @@ describe("FormTool", () => {
             },
         });
 
-        wrapper = mount(FormTool, {
+        return mount(FormTool, {
             propsData: {
                 id: "input",
                 datatypes: [],
@@ -32,7 +30,7 @@ describe("FormTool", () => {
                         name: "tool_name",
                         version: "1.0",
                         description: "description",
-                        inputs: [],
+                        inputs: [{ name: "input", label: "input", type: "text", value: "value" }],
                         help: "help_text",
                         versions: ["1.0", "2.0", "3.0"],
                         citations: false,
@@ -46,15 +44,16 @@ describe("FormTool", () => {
             stubs: {
                 CurrentUser: MockCurrentUser({ id: "fakeuser" }),
                 ConfigProvider: MockConfigProvider({ id: "fakeconfig" }),
-                FormElement: { template: "<div>form-element</div>" },
                 ToolFooter: { template: "<div>tool-footer</div>" },
             },
             pinia: createTestingPinia(),
             provide: { store },
         });
-    });
+    }
 
     it("changes between different versions", async () => {
+        const wrapper = mountTarget();
+
         const dropdowns = wrapper.findAll(".tool-versions .dropdown-item");
         let version = dropdowns.at(1);
         expect(version.text()).toBe("Switch to 2.0");

From 63d0e5c14984265eb78db36b8635c84dccd7f8b0 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sat, 28 Jan 2023 23:26:48 +0500
Subject: [PATCH 14/40] Add name+description ToolSearch

---
 client/src/components/Panels/Common/ToolSearch.vue | 2 +-
 client/src/components/Panels/utilities.js          | 7 ++++++-
 client/src/components/Panels/utilities.test.js     | 6 ++++++
 3 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Panels/Common/ToolSearch.vue b/client/src/components/Panels/Common/ToolSearch.vue
index dd2a5303020..167659c2870 100644
--- a/client/src/components/Panels/Common/ToolSearch.vue
+++ b/client/src/components/Panels/Common/ToolSearch.vue
@@ -109,7 +109,7 @@ export default {
                     this.$emit("onResults", this.favoritesResults);
                 } else {
                     // keys with sorting order
-                    const keys = { exact: 2, name: 1, description: 0 };
+                    const keys = { exact: 3, name: 2, description: 1, combined: 0 };
                     this.$emit("onResults", searchToolsByKeys(this.toolsList, keys, q));
                 }
             } else {
diff --git a/client/src/components/Panels/utilities.js b/client/src/components/Panels/utilities.js
index 8431e0828c1..900e32079ba 100644
--- a/client/src/components/Panels/utilities.js
+++ b/client/src/components/Panels/utilities.js
@@ -89,7 +89,12 @@ export function searchToolsByKeys(tools, keys, query) {
     const returnedTools = [];
     for (const tool of tools) {
         for (const key of Object.keys(keys)) {
-            const actualValue = tool[key] ? tool[key].toLowerCase() : "";
+            let actualValue = "";
+            if (key === "combined") {
+                actualValue = tool.name.toLowerCase() + " " + tool.description.toLowerCase();
+            } else {
+                actualValue = tool[key] ? tool[key].toLowerCase() : "";
+            }
             const queryLowerCase = query.toLowerCase();
             if (actualValue.match(queryLowerCase)) {
                 // do we care for exact matches && is it an exact match ?
diff --git a/client/src/components/Panels/utilities.test.js b/client/src/components/Panels/utilities.test.js
index eb6fdadad6f..976c43e1a47 100644
--- a/client/src/components/Panels/utilities.test.js
+++ b/client/src/components/Panels/utilities.test.js
@@ -37,6 +37,12 @@ describe("test helpers in tool searching utilities", () => {
         keys = { description: 0, name: 1 };
         results = searchToolsByKeys(normalizeTools(toolsList), keys, q);
         expect(results).toEqual(expectedResults);
+
+        q = "filter empty datasets";
+        expectedResults = ["__FILTER_EMPTY_DATASETS__"];
+        keys = { description: 1, name: 2, combined: 0 };
+        results = searchToolsByKeys(normalizeTools(toolsList), keys, q);
+        expect(results).toEqual(expectedResults);
     });
 
     it("test tool filtering helpers on toolsList given list of ids", async () => {

From e14d68bfda5888819a41201b4e07e5a3db9632f2 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sat, 28 Jan 2023 23:31:52 +0500
Subject: [PATCH 15/40] name+description ToolSearch: change constant to let

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

diff --git a/client/src/components/Panels/utilities.test.js b/client/src/components/Panels/utilities.test.js
index 976c43e1a47..05697266a11 100644
--- a/client/src/components/Panels/utilities.test.js
+++ b/client/src/components/Panels/utilities.test.js
@@ -17,7 +17,7 @@ describe("test helpers in tool searching utilities", () => {
     });
 
     it("test tool search helper that searches for tools given keys", async () => {
-        const q = "collection";
+        let q = "collection";
         let expectedResults = [
             "__FILTER_FAILED_DATASETS__",
             "__FILTER_EMPTY_DATASETS__",

From adc425c6569ff5b5d839db3f2e9db9128897fccd Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sun, 29 Jan 2023 00:45:32 +0500
Subject: [PATCH 16/40] ToolBoxWorkflow only include and search for compatible
 tools

---
 client/src/components/Panels/Common/Tool.vue     |  4 ++--
 client/src/components/Panels/ToolBoxWorkflow.vue | 10 +++++++---
 client/src/components/Panels/utilities.js        | 16 ++++++++++++++++
 3 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Panels/Common/Tool.vue b/client/src/components/Panels/Common/Tool.vue
index be926ec04ed..7da41962ca2 100644
--- a/client/src/components/Panels/Common/Tool.vue
+++ b/client/src/components/Panels/Common/Tool.vue
@@ -59,9 +59,9 @@ export default {
     computed: {
         targetClass() {
             if (this.toolKey) {
-                return `tool-menu-item-${this.tool[this.toolKey]} title-link`;
+                return `tool-menu-item-${this.tool[this.toolKey]} title-link cursor-pointer`;
             } else {
-                return `title-link`;
+                return `title-link cursor-pointer`;
             }
         },
     },
diff --git a/client/src/components/Panels/ToolBoxWorkflow.vue b/client/src/components/Panels/ToolBoxWorkflow.vue
index 95e2dab6d48..bcb26c53f60 100644
--- a/client/src/components/Panels/ToolBoxWorkflow.vue
+++ b/client/src/components/Panels/ToolBoxWorkflow.vue
@@ -18,7 +18,7 @@
             <tool-search
                 :current-panel-view="currentPanelView"
                 placeholder="search tools"
-                :toolbox="toolbox"
+                :toolbox="workflowTools"
                 :query="query"
                 @onQuery="onQuery"
                 @onResults="onResults" />
@@ -74,7 +74,7 @@
 import _l from "utils/localization";
 import ToolSection from "./Common/ToolSection";
 import ToolSearch from "./Common/ToolSearch";
-import { filterToolSections } from "./utilities";
+import { filterToolSections, removeDisabledTools } from "./utilities";
 import PanelViewButton from "./Buttons/PanelViewButton";
 
 export default {
@@ -140,12 +140,13 @@ export default {
             };
         },
         sections() {
-            return filterToolSections(this.toolsLayout, this.results);
+            return filterToolSections(this.workflowTools, this.results);
         },
         toolsLayout() {
             return this.toolbox.map((section) => {
                 return {
                     ...section,
+                    disabled: !section.elems && !section.is_workflow_compatible,
                     elems:
                         section.elems &&
                         section.elems.map((el) => {
@@ -155,6 +156,9 @@ export default {
                 };
             });
         },
+        workflowTools() {
+            return removeDisabledTools(this.toolsLayout);
+        },
     },
     methods: {
         onQuery(query) {
diff --git a/client/src/components/Panels/utilities.js b/client/src/components/Panels/utilities.js
index 8431e0828c1..434f1005d81 100644
--- a/client/src/components/Panels/utilities.js
+++ b/client/src/components/Panels/utilities.js
@@ -109,6 +109,22 @@ export function normalizeTools(tools) {
     return tools;
 }
 
+export function removeDisabledTools(tools) {
+    return tools.filter((section) => {
+        if (section.model_class === "ToolSectionLabel") {
+            return true;
+        } else if (!section.elems && section.disabled) {
+            return false;
+        } else if (section.elems) {
+            section.elems = section.elems.filter((el) => !el.disabled);
+            if (!section.elems.length) {
+                return false;
+            }
+        }
+        return true;
+    });
+}
+
 function flattenToolsSection(section) {
     const flattenTools = [];
     if (section.elems) {

From c2bd9df6218a6e7fe45a9b11cd3d4d0570854192 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 25 Jan 2023 14:43:01 +0100
Subject: [PATCH 17/40] Disable Switch histories for anonymous users

---
 .../components/History/CurrentHistory/HistoryNavigation.vue    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index 9d73f41cf6a..1e4cfba5873 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -23,7 +23,8 @@
                     data-description="switch to another history"
                     size="sm"
                     variant="link"
-                    title="Switch to history">
+                    :disabled="currentUser.isAnonymous"
+                    :title="userTitle('Switch to history')">
                     <Icon fixed-width icon="exchange-alt" />
                 </b-button>
 

From ba4907cb897530c2629c3862fd46ae0db4ce9761 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 25 Jan 2023 14:43:31 +0100
Subject: [PATCH 18/40] Disable creating histories for anonymous users

---
 .../components/History/CurrentHistory/HistoryNavigation.vue    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index 1e4cfba5873..adc4d45a35e 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -12,7 +12,8 @@
                     data-description="create new history"
                     size="sm"
                     variant="link"
-                    title="Create new history"
+                    :disabled="currentUser.isAnonymous"
+                    :title="userTitle('Create new history')"
                     @click="$emit('createNewHistory')">
                     <Icon fixed-width icon="plus" />
                 </b-button>

From 66464d201c9454db75821f500d007d8bd1bb7ce1 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 25 Jan 2023 17:06:55 +0100
Subject: [PATCH 19/40] Add tests for buttons availability

---
 .../History/CurrentHistory/HistoryNavigation.test.js  | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.test.js b/client/src/components/History/CurrentHistory/HistoryNavigation.test.js
index e0486579328..3fffa8e50ec 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.test.js
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.test.js
@@ -56,6 +56,11 @@ describe("History Navigation", () => {
             provide: { store },
         });
 
+        const createButton = wrapper.find("*[data-description='create new history']");
+        expect(createButton.attributes().disabled).toBeFalsy();
+        const switchButton = wrapper.find("*[data-description='switch to another history']");
+        expect(switchButton.attributes().disabled).toBeFalsy();
+
         const dropDown = wrapper.find("*[data-description='history options']");
         const optionElements = dropDown.findAll("b-dropdown-item-stub");
         const optionTexts = optionElements.wrappers.map((el) => el.text());
@@ -76,8 +81,12 @@ describe("History Navigation", () => {
             provide: { store },
         });
 
-        const dropDown = wrapper.find("*[data-description='history options']");
+        const createButton = wrapper.find("*[data-description='create new history']");
+        expect(createButton.attributes().disabled).toBeTruthy();
+        const switchButton = wrapper.find("*[data-description='switch to another history']");
+        expect(switchButton.attributes().disabled).toBeTruthy();
 
+        const dropDown = wrapper.find("*[data-description='history options']");
         const enabledOptionElements = dropDown.findAll("b-dropdown-item-stub:not([disabled])");
         const enabledOptionTexts = enabledOptionElements.wrappers.map((el) => el.text());
         expect(enabledOptionTexts).toStrictEqual(anonymousOptions);

From 4d57cd820bbd99ccb32deeebc6f7db589fd750c2 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 26 Jan 2023 16:18:03 +0100
Subject: [PATCH 20/40] Adapt Window Manager tour

Instead of auto-creating a new history, make it a requirement.
---
 config/plugins/tours/core.windows.yaml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/config/plugins/tours/core.windows.yaml b/config/plugins/tours/core.windows.yaml
index 226150dadf6..d2318ce3c5d 100644
--- a/config/plugins/tours/core.windows.yaml
+++ b/config/plugins/tours/core.windows.yaml
@@ -6,15 +6,14 @@ tags:
   - "UI"
   - "visualization"
 
+requirements:
+  - new_history
+
 steps:
     - content: "This short tour will walk you through <b>Galaxy's Window Manager</b> feature"
 
-    - element: "#current-history-panel .create-hist-btn"
-      intro: "Before using the Window Manager, we will create a new history for this tour."
-      postclick: true
-
     - element: "#tool-panel-upload-button"
-      intro: "Now, we will upload some tabular data into our new history."
+      intro: "First, we will upload some tabular data into our new history."
       postclick: true
 
     - element: "#btn-new"
@@ -78,7 +77,7 @@ steps:
 
     - element: "#right"
       intro: "This is your history. It contains our two tables being uploaded."
-    
+
     - component: history_panel.item(hid=1,state=ok).display_button
       intro: "Clicking the eye-icon usually displays a dataset in the center panel."
       postclick: true

From 1997c7d8abc74b3b0c9527cf5efb2e46e5153eb1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 30 Jan 2023 11:18:01 +0100
Subject: [PATCH 21/40] Adjust to bleach.ALLOWED_PROTOCOLS being frozenset

---
 lib/galaxy/util/sanitize_html.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/util/sanitize_html.py b/lib/galaxy/util/sanitize_html.py
index cdfe5229168..d915a80a7a1 100644
--- a/lib/galaxy/util/sanitize_html.py
+++ b/lib/galaxy/util/sanitize_html.py
@@ -252,5 +252,5 @@ _acceptable_attributes = [
 def sanitize_html(htmlSource, allow_data_urls=False):
     kwd = dict(tags=_acceptable_elements, attributes=_acceptable_attributes, strip=True)
     if allow_data_urls:
-        kwd["protocols"] = bleach.ALLOWED_PROTOCOLS + ["data"]
+        kwd["protocols"] = list(bleach.ALLOWED_PROTOCOLS) + ["data"]
     return bleach.clean(unicodify(htmlSource), **kwd)

From 911bf26078fb0f004704f527447c4fd9257fdf2c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 27 Jan 2023 11:24:07 +0100
Subject: [PATCH 22/40] Determine collection type when collection_type_source
 is given

And make sure mapOver doesn't "flicker" when combining different
effective mapOver types.
---
 .../Editor/composables/useUniqueLabelError.ts |  2 +-
 .../Workflow/Editor/modules/terminals.test.ts | 41 ++++++--
 .../Workflow/Editor/modules/terminals.ts      | 51 +++++++++-
 .../Editor/test-data/parameter_steps.json     | 94 +++++++++++++++++++
 client/src/stores/workflowStepStore.ts        |  8 +-
 5 files changed, 180 insertions(+), 16 deletions(-)

diff --git a/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts b/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts
index db69f9e509e..50916494f52 100644
--- a/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts
+++ b/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts
@@ -3,7 +3,7 @@ import { ref } from "vue";
 
 export function useUniqueLabelError(
     workflowStateStore: ReturnType<typeof useWorkflowStepStore>,
-    label: string | undefined
+    label: string | null | undefined
 ) {
     const error = ref("");
     if (label && workflowStateStore.workflowOutputs[label]) {
diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index f71de5dabbf..16bd273d6d6 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -1,6 +1,6 @@
 import { setActivePinia, createPinia } from "pinia";
 
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
+import { useWorkflowStepStore, type TerminalSource } from "@/stores/workflowStepStore";
 import {
     terminalFactory,
     InputCollectionTerminal,
@@ -15,7 +15,11 @@ import {
 import { testDatatypesMapper } from "@/components/Datatypes/test_fixtures";
 import { useConnectionStore } from "@/stores/workflowConnectionStore";
 import type { DataOutput, Steps } from "@/stores/workflowStepStore";
-import { NULL_COLLECTION_TYPE_DESCRIPTION } from "./collectionTypeDescription";
+import {
+    ANY_COLLECTION_TYPE_DESCRIPTION,
+    CollectionTypeDescription,
+    NULL_COLLECTION_TYPE_DESCRIPTION,
+} from "./collectionTypeDescription";
 import { simpleSteps, advancedSteps } from "../test_fixtures";
 
 function setupAdvanced() {
@@ -35,6 +39,17 @@ function setupAdvanced() {
     return terminals;
 }
 
+function rebuildTerminal<T extends ReturnType<typeof terminalFactory>>(terminal: T): T {
+    let terminalSource: TerminalSource;
+    const step = terminal.stepStore.getStep(terminal.stepId);
+    if (terminal.terminalType === "input") {
+        terminalSource = step.inputs.find((input) => input.name == terminal.name)!;
+    } else {
+        terminalSource = step.outputs.find((output) => output.name == terminal.name)!;
+    }
+    return terminalFactory(terminal.stepId, terminalSource, testDatatypesMapper) as T;
+}
+
 describe("terminalFactory", () => {
     let terminals: { [index: string]: { [index: string]: ReturnType<typeof terminalFactory> } } = {};
     beforeEach(() => {
@@ -64,6 +79,8 @@ describe("terminalFactory", () => {
         expect(terminals["any collection"]["output"]).toBeInstanceOf(OutputCollectionTerminal);
         expect(terminals["multi data"]["advanced|advanced_threshold"]).toBeInstanceOf(InputParameterTerminal);
         expect(terminals["list collection input"]["input1"]).toBeInstanceOf(InputCollectionTerminal);
+        expect(terminals["filter_failed"]["input"]).toBeInstanceOf(InputCollectionTerminal);
+        expect(terminals["filter_failed"]["output"]).toBeInstanceOf(OutputCollectionTerminal);
     });
     it("throws error on invalid terminalSource", () => {
         const invalidFactory = () => terminalFactory(1, {} as any, testDatatypesMapper);
@@ -281,11 +298,7 @@ describe("canAccept", () => {
         dataInTwo.disconnect(dataOut);
         // terminal isn't a reactive class in any way (worth a thought doing, but difficult!), the following happens when a new terminal is built
         // in useTerminal.ts
-        const rebuiltDataIn = terminalFactory(
-            dataIn.stepId,
-            advancedSteps[dataIn.stepId].inputs[0],
-            testDatatypesMapper
-        );
+        const rebuiltDataIn = rebuildTerminal(dataIn);
         expect(rebuiltDataIn.localMapOver.isCollection).toBe(false);
         expect(rebuiltDataIn.canAccept(simpleDataOut).canAccept).toBe(true);
     });
@@ -459,6 +472,20 @@ describe("canAccept", () => {
             "Effective output data type(s) [tabular] do not appear to match input type(s) [ab1]."
         );
     });
+    it("resolves collection type source", () => {
+        const filterFailedInput = terminals["filter_failed"]["input"] as InputCollectionTerminal;
+        const filterFailedOutput = terminals["filter_failed"]["output"] as OutputCollectionTerminal;
+        expect(filterFailedOutput.collectionType).toBe(ANY_COLLECTION_TYPE_DESCRIPTION);
+        const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
+        filterFailedInput.connect(collectionOut);
+        expect(rebuildTerminal(filterFailedOutput).collectionType).toStrictEqual(new CollectionTypeDescription("list"));
+        filterFailedInput.disconnect(collectionOut);
+        const listPairedOutput = terminals["list:paired input"]["output"] as OutputCollectionTerminal;
+        filterFailedInput.connect(listPairedOutput);
+        expect(rebuildTerminal(filterFailedOutput).collectionType).toStrictEqual(
+            new CollectionTypeDescription("list:paired")
+        );
+    });
 });
 
 describe("Input terminal", () => {
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 9b145699bed..2e3eb87d539 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -97,6 +97,7 @@ class Terminal extends EventEmitter {
         this.resetMappingIfNeeded(connection);
     }
     setMapOver(val: CollectionTypeDescriptor) {
+        // we use this method to determine the map over status based on all terminals connected to this step
         let outputVal = val;
         if (this.multiple) {
             // emulate list input
@@ -112,7 +113,12 @@ class Terminal extends EventEmitter {
             this.stepStore.changeStepInputMapOver(this.stepId, this.name, effectiveMapOver);
             this.localMapOver = effectiveMapOver;
         }
-        if (!this.mapOver.equal(effectiveMapOver)) {
+        if (
+            !this.mapOver.equal(effectiveMapOver) &&
+            Object.values(this.stepStore.stepInputMapOver[this.stepId]).some((mapOver) =>
+                mapOver.equal(effectiveMapOver)
+            )
+        ) {
             this.stepStore.changeStepMapOver(this.stepId, effectiveMapOver);
         }
     }
@@ -672,19 +678,56 @@ interface OutputCollectionTerminalArgs extends BaseOutputTerminalArgs {
 }
 
 export class OutputCollectionTerminal extends BaseOutputTerminal {
+    collectionTypeSource: string | null;
+
     constructor(attr: OutputCollectionTerminalArgs) {
         super(attr);
+        this.collectionTypeSource = null;
         if (attr.collection_type) {
             this.collectionType = new CollectionTypeDescription(attr.collection_type);
         } else {
-            const collectionTypeSource = attr.collection_type_source;
-            if (!collectionTypeSource) {
+            this.collectionTypeSource = attr.collection_type_source;
+            if (!this.collectionTypeSource) {
                 console.log("Warning: No collection type or collection type source defined.");
             }
-            this.collectionType = ANY_COLLECTION_TYPE_DESCRIPTION;
+            this.collectionType = this.getCollectionTypeFromInput() || ANY_COLLECTION_TYPE_DESCRIPTION;
         }
         this.isCollection = true;
     }
+
+    getCollectionTypeFromInput() {
+        const connection = this.connectionStore.connections.find(
+            (connection) =>
+                connection.input.name === this.collectionTypeSource && connection.input.stepId === this.stepId
+        );
+        if (connection) {
+            const outputStep = this.stepStore.getStep(connection.output.stepId);
+            const inputStep = this.stepStore.getStep(this.stepId);
+            if (outputStep) {
+                const stepOutput = outputStep.outputs.find((output) => output.name == connection.output.name);
+                const stepInput = inputStep.inputs.find((input) => input.name === this.collectionTypeSource);
+                if (stepInput && stepOutput) {
+                    const outputTerminal = terminalFactory(connection.output.stepId, stepOutput, this.datatypesMapper);
+                    const inputTerminal = terminalFactory(connection.output.stepId, stepInput, this.datatypesMapper);
+                    // otherCollectionType is the mapped over output collection as it would appear at the input terminal
+                    const otherCollectionType = inputTerminal._otherCollectionType(outputTerminal);
+                    // we need to find which of the possible input collection types is connected
+                    if ("collectionTypes" in inputTerminal) {
+                        // collection_type_source must point at input collection terminal
+                        const connectedCollectionType = inputTerminal.collectionTypes.find(
+                            (collectionType) =>
+                                otherCollectionType.canMatch(collectionType) ||
+                                otherCollectionType.canMapOver(collectionType)
+                        );
+                        if (connectedCollectionType) {
+                            return connectedCollectionType;
+                        }
+                    }
+                }
+            }
+        }
+        return ANY_COLLECTION_TYPE_DESCRIPTION;
+    }
 }
 
 interface OutputParameterTerminalArgs extends Omit<BaseOutputTerminalArgs, "datatypes"> {
diff --git a/client/src/components/Workflow/Editor/test-data/parameter_steps.json b/client/src/components/Workflow/Editor/test-data/parameter_steps.json
index fb9a9ed0f02..d3cff2cf8d9 100644
--- a/client/src/components/Workflow/Editor/test-data/parameter_steps.json
+++ b/client/src/components/Workflow/Editor/test-data/parameter_steps.json
@@ -812,5 +812,99 @@
       "left": 70.45245361328125,
       "top": 316.3525695800781
     }
+  },
+  "17": {
+    "id": 17,
+    "type": "tool",
+    "label": "filter_failed",
+    "content_id": "__FILTER_FAILED_DATASETS__",
+    "name": "Filter failed datasets",
+    "tool_state": {
+      "input": "{\"__class__\": \"RuntimeValue\"}",
+      "__page__": null,
+      "__rerun_remap_job_id__": null
+    },
+    "errors": null,
+    "inputs": [
+      {
+        "name": "input",
+        "label": "Input Collection",
+        "multiple": false,
+        "input_type": "dataset_collection",
+        "collection_types": [
+          "list",
+          "list:paired"
+        ],
+        "optional": false,
+        "extensions": [
+          "data"
+        ]
+      }
+    ],
+    "outputs": [
+      {
+        "name": "output",
+        "extensions": [
+          "input"
+        ],
+        "type": "collection",
+        "optional": false,
+        "collection": true,
+        "collection_type": null,
+        "collection_type_source": "input",
+        "label": "input dataset(s) (filtered failed datasets)"
+      }
+    ],
+    "annotation": "",
+    "post_job_actions": {},
+    "uuid": "f5de18b9-b08e-4160-b71b-54768a4e5208",
+    "when": null,
+    "workflow_outputs": [
+      {
+        "output_name": "output",
+        "uuid": "3774e554-b7d1-41ba-9acd-ee82ba9fbf54",
+        "label": null
+      }
+    ],
+    "input_connections": {},
+    "position": {
+      "left": 0,
+      "top": 0
+    }
+  },
+  "18": {
+    "id": 18,
+    "type": "data_collection_input",
+    "label": "list:paired input",
+    "content_id": null,
+    "name": "Input dataset collection",
+    "tool_state": {
+      "collection_type": "\"list:paired\"",
+      "optional": "\"false\"",
+      "tag": "\"\"",
+      "__page__": null,
+      "__rerun_remap_job_id__": null
+    },
+    "errors": null,
+    "inputs": [],
+    "outputs": [
+      {
+        "name": "output",
+        "extensions": [
+          "input"
+        ],
+        "collection": true,
+        "collection_type": "list:paired",
+        "optional": false
+      }
+    ],
+    "annotation": "",
+    "post_job_actions": {},
+    "workflow_outputs": [],
+    "input_connections": {},
+    "position": {
+      "left": 12.8729248046875,
+      "top": 501.7839660644531
+    }
   }
 }
diff --git a/client/src/stores/workflowStepStore.ts b/client/src/stores/workflowStepStore.ts
index 655f6735c7d..113f8f8ba01 100644
--- a/client/src/stores/workflowStepStore.ts
+++ b/client/src/stores/workflowStepStore.ts
@@ -85,8 +85,8 @@ export type TerminalSource = InputTerminalSource | OutputTerminalSource;
 
 interface WorkflowOutput {
     output_name: string;
-    label?: string;
-    uuid?: string;
+    label?: string | null;
+    uuid?: string | null;
 }
 
 export interface NewStep {
@@ -97,7 +97,7 @@ export interface NewStep {
     errors?: string[] | null;
     input_connections: StepInputConnection;
     inputs: Array<InputTerminalSource>;
-    label?: string;
+    label?: string | null;
     name: string;
     outputs: Array<OutputTerminalSource>;
     position?: StepPosition;
@@ -106,7 +106,7 @@ export interface NewStep {
     tooltip?: string;
     type: "tool" | "data_input" | "data_collection_input" | "subworkflow" | "parameter_input" | "pause";
     uuid?: string;
-    when?: string;
+    when?: string | null;
     workflow_outputs?: WorkflowOutput[];
 }
 

From 85ee4c3c1fde08d0bc004491614881749ad9b62a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 27 Jan 2023 14:48:03 +0100
Subject: [PATCH 23/40] Fix isMappedOver for all types of input terminals

It previously only worked for non-collection, non-parameter inputs.
---
 .../components/Workflow/Editor/modules/terminals.test.ts | 2 ++
 .../src/components/Workflow/Editor/modules/terminals.ts  | 9 +++++----
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index 16bd273d6d6..e3f6bcd5cc2 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -402,7 +402,9 @@ describe("canAccept", () => {
         const collectionOut = terminals["list:list input"]["output"] as OutputCollectionTerminal;
         const collectionIn = terminals["list collection input"]["input1"] as InputCollectionTerminal;
         expect(collectionIn.canAccept(collectionOut).canAccept).toBe(true);
+        expect(collectionIn.isMappedOver()).toBe(false);
         collectionIn.connect(collectionOut);
+        expect(collectionIn.isMappedOver()).toBe(true);
         expect(collectionIn.mapOver).toEqual({ collectionType: "list", isCollection: true, rank: 1 });
         const intermediateOut = terminals["list collection input"]["out_file1"] as OutputCollectionTerminal;
         const otherListIn = terminals["list collection input 2"]["input1"] as InputCollectionTerminal;
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 2e3eb87d539..f1b4b1ec474 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -248,6 +248,11 @@ class BaseInputTerminal extends Terminal {
         }
         return null;
     }
+
+    isMappedOver(): boolean {
+        return Boolean(this.localMapOver.isCollection);
+    }
+
     connected() {
         return Boolean(this._getFirstOutputTerminal());
     }
@@ -406,10 +411,6 @@ export class InputTerminal extends BaseInputTerminal {
         this.getStepMapOver();
     }
 
-    isMappedOver(): boolean {
-        return Boolean(this.localMapOver.isCollection);
-    }
-
     attachable(other: BaseOutputTerminal) {
         const otherCollectionType = this._otherCollectionType(other);
         const mapOver = this.mapOver;

From a78ca90b7187e2eec4a0830614a30a8cca7f8b97 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 29 Jan 2023 11:01:25 +0100
Subject: [PATCH 24/40] Infer subworkflow input step if index is not given
 explicitly Seems to be used at least by the refactor action.

---
 lib/galaxy/model/__init__.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index bda53e4dc96..6063ad4ad17 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7163,8 +7163,20 @@ class WorkflowStep(Base, RepresentById):
         conn.output_name = output_name
         add_object_to_object_session(conn, output_step)
         conn.output_step = output_step
-        if input_subworkflow_step_index is not None:
-            input_subworkflow_step = self.subworkflow.step_by_index(input_subworkflow_step_index)
+        if self.subworkflow:
+            if input_subworkflow_step_index is not None:
+                input_subworkflow_step = self.subworkflow.step_by_index(input_subworkflow_step_index)
+            else:
+                input_subworkflow_steps = [step for step in self.subworkflow.input_steps if step.label == input_name]
+                if not input_subworkflow_steps:
+                    inferred_order_index = input_name.split(":", 1)[0]
+                    if inferred_order_index.isdigit():
+                        input_subworkflow_steps = [self.subworkflow.step_by_index(int(inferred_order_index))]
+                if len(input_subworkflow_steps) != 1:
+                    raise galaxy.exceptions.MessageException(
+                        f"Invalid subworkflow connection at step index {self.order_index + 1}"
+                    )
+                input_subworkflow_step = input_subworkflow_steps[0]
             conn.input_subworkflow_step = input_subworkflow_step
         return conn
 

From 62715c998de64113c139292f2052a3aa6be97715 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 29 Jan 2023 15:35:26 +0100
Subject: [PATCH 25/40] Fix test description typo

---
 client/src/components/Workflow/Editor/modules/terminals.test.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index e3f6bcd5cc2..154477afb7f 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -274,7 +274,7 @@ describe("canAccept", () => {
             "Can't map over this input with output collection type - this step has outputs defined constraining the mapping of this tool. Disconnect outputs and retry."
         );
     });
-    it("rejects attaching non-collection outputs to mapper over inputs", () => {
+    it("rejects attaching non-collection outputs to mapped-over inputs", () => {
         const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
         const simpleDataOut = terminals["data input"]["output"] as OutputTerminal;
         const dataIn = terminals["simple data"]["input"] as InputTerminal;

From 6847a94b35f8dae54a5304363edfaeb95d20f4ce Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 29 Jan 2023 15:38:42 +0100
Subject: [PATCH 26/40] Fix resetting mapOver

Reset to null only if no input terminal is mapped over.
If a terminal is mapped over and another is not this
could lead to an infinite update cycle.
---
 client/src/components/Workflow/Editor/modules/terminals.ts | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index f1b4b1ec474..f6f4cc149cb 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -115,9 +115,8 @@ class Terminal extends EventEmitter {
         }
         if (
             !this.mapOver.equal(effectiveMapOver) &&
-            Object.values(this.stepStore.stepInputMapOver[this.stepId]).some((mapOver) =>
-                mapOver.equal(effectiveMapOver)
-            )
+            (effectiveMapOver.isCollection ||
+                !Object.values(this.stepStore.stepInputMapOver[this.stepId]).find((mapOver) => mapOver.isCollection))
         ) {
             this.stepStore.changeStepMapOver(this.stepId, effectiveMapOver);
         }

From fbebbb13c44ed917b79c81dee302fcc4b750bc2f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 29 Jan 2023 15:49:31 +0100
Subject: [PATCH 27/40] Reset stores when receiving refactor action response

---
 client/src/components/Workflow/Editor/Index.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index 3f5f8e3fd41..a4be41fab7b 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -409,6 +409,7 @@ export default {
             hide_modal(); // hide other modals created in utilities also...
         },
         async onRefactor(response) {
+            this.resetStores();
             await fromSimple(response.workflow);
             this._loadEditorData(response.workflow);
         },

From 63b59f26cc0a0bb168b97ade5dcffdf3a3ef2df3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 29 Jan 2023 15:51:53 +0100
Subject: [PATCH 28/40] Track input subworkflow step id

---
 client/src/stores/workflowConnectionStore.ts |  1 +
 client/src/stores/workflowStepStore.ts       | 20 +++++++++++++++++---
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/client/src/stores/workflowConnectionStore.ts b/client/src/stores/workflowConnectionStore.ts
index 7748a417e77..cacd54e14f6 100644
--- a/client/src/stores/workflowConnectionStore.ts
+++ b/client/src/stores/workflowConnectionStore.ts
@@ -34,6 +34,7 @@ export interface BaseTerminal {
 
 export interface InputTerminal extends BaseTerminal {
     connectorType: "input";
+    input_subworkflow_step_id?: number;
 }
 
 export interface OutputTerminal extends BaseTerminal {
diff --git a/client/src/stores/workflowStepStore.ts b/client/src/stores/workflowStepStore.ts
index 113f8f8ba01..20057d984f1 100644
--- a/client/src/stores/workflowStepStore.ts
+++ b/client/src/stores/workflowStepStore.ts
@@ -63,6 +63,7 @@ interface BaseStepInput {
     extensions: string[];
     optional: boolean;
     input_type: string;
+    input_subworkflow_step_id?: number;
 }
 
 export interface DataStepInput extends BaseStepInput {
@@ -125,6 +126,7 @@ export interface StepInputConnection {
 export interface ConnectionOutputLink {
     output_name: string;
     id: number;
+    input_subworkflow_step_id?: number;
 }
 
 interface WorkflowOutputs {
@@ -231,11 +233,19 @@ export const useWorkflowStepStore = defineStore("workflowStepStore", {
         },
         addConnection(connection: Connection) {
             const inputStep = this.getStep(connection.input.stepId);
+            const input = inputStep.inputs.find((input) => input.name === connection.input.name);
+            const connectionLink: ConnectionOutputLink = {
+                output_name: connection.output.name,
+                id: connection.output.stepId,
+            };
+            if (input && "input_subworkflow_step_id" in input && input.input_subworkflow_step_id !== undefined) {
+                connectionLink["input_subworkflow_step_id"] = input.input_subworkflow_step_id;
+            }
             const updatedStep = {
                 ...inputStep,
                 input_connections: {
                     ...inputStep.input_connections,
-                    [connection.input.name]: { output_name: connection.output.name, id: connection.output.stepId },
+                    [connection.input.name]: connectionLink,
                 },
             };
             this.updateStep(updatedStep);
@@ -258,7 +268,7 @@ export const useWorkflowStepStore = defineStore("workflowStepStore", {
 export function stepToConnections(step: Step): Connection[] {
     const connections: Connection[] = [];
     if (step.input_connections) {
-        Object.entries(step?.input_connections).forEach(([input_name, outputArray]) => {
+        Object.entries(step?.input_connections).forEach(([inputName, outputArray]) => {
             if (outputArray === undefined) {
                 return;
             }
@@ -269,7 +279,7 @@ export function stepToConnections(step: Step): Connection[] {
                 const connection = new Connection(
                     {
                         stepId: step.id,
-                        name: input_name,
+                        name: inputName,
                         connectorType: "input",
                     },
                     {
@@ -278,6 +288,10 @@ export function stepToConnections(step: Step): Connection[] {
                         connectorType: "output",
                     }
                 );
+                const connectionInput = step.inputs.find((input) => input.name == inputName);
+                if (connectionInput && "input_subworkflow_step_id" in connectionInput) {
+                    connection.input.input_subworkflow_step_id = connectionInput.input_subworkflow_step_id;
+                }
                 connections.push(connection);
             });
         });

From 1edefe8b3db3b34811d26f27d221b16a955bdd4b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 30 Jan 2023 10:39:41 +0100
Subject: [PATCH 29/40] Fix test workflow input definitions

---
 lib/galaxy_test/api/test_workflows.py     | 3 +++
 lib/galaxy_test/base/workflow_fixtures.py | 1 +
 2 files changed, 4 insertions(+)

diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index 4f5e1553325..92bbd17a2aa 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -2051,6 +2051,8 @@ steps:
       inputs:
         some_file:
           type: data
+        should_run:
+          type: boolean
       steps:
         a_tool_step:
           tool_id: cat1
@@ -2154,6 +2156,7 @@ steps:
       class: GalaxyWorkflow
       inputs:
         boolean_input_file: data
+        should_run: boolean
       steps:
         consume_expression_parameter:
           tool_id: cat1
diff --git a/lib/galaxy_test/base/workflow_fixtures.py b/lib/galaxy_test/base/workflow_fixtures.py
index 0178e935dae..0f164c087b0 100644
--- a/lib/galaxy_test/base/workflow_fixtures.py
+++ b/lib/galaxy_test/base/workflow_fixtures.py
@@ -1012,6 +1012,7 @@ steps:
       class: GalaxyWorkflow
       inputs:
         boolean_input_file: data
+        should_run: boolean
       steps:
         create_more_inputs:
           tool_id: collection_creates_dynamic_nested

From f624f188cbcb91f63b5a2f36038ffdf93b94820f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 30 Jan 2023 12:44:05 +0100
Subject: [PATCH 30/40] Replace manual step watcher with step store
 subscription

---
 client/src/components/Workflow/Editor/Index.vue | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index a4be41fab7b..34362b5f2ff 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -254,6 +254,10 @@ export default {
         const hasChanges = ref(false);
         const hasInvalidConnections = computed(() => Object.keys(connectionsStore.invalidConnections).length > 0);
 
+        stepStore.$subscribe((mutation, state) => {
+            hasChanges.value = true;
+        });
+
         function resetStores() {
             connectionsStore.$reset();
             stepStore.$reset();
@@ -342,9 +346,6 @@ export default {
                 this.hasChanges = true;
             }
         },
-        steps(newSteps, oldSteps) {
-            this.hasChanges = true;
-        },
         hasChanges() {
             this.$emit("update:confirmation", this.hasChanges);
         },
@@ -357,7 +358,6 @@ export default {
     methods: {
         onUpdateStep(step) {
             this.stepStore.updateStep(step);
-            this.hasChanges = true;
         },
         onUpdateStepPosition(stepId, position) {
             const step = { ...this.steps[stepId], position };

From 4cac7c216ead1e3131a887416713a08b7a0ea522 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 30 Jan 2023 12:59:19 +0100
Subject: [PATCH 31/40] Extend selenium tests and make sure
 input_subworkflow_step_id is passed

---
 lib/galaxy_test/selenium/test_workflow_editor.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index 9be68ab210c..eb40f60ff96 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -697,7 +697,10 @@ steps:
         workflow_populator.upload_yaml_workflow(WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION, name=child_workflow_name)
         parent_workflow_id = workflow_populator.upload_yaml_workflow(
             """class: GalaxyWorkflow
-inputs: []
+inputs:
+  input_collection:
+    type: collection
+    collection_type: "list"
 steps:
   - tool_id: multiple_versions
     tool_version: 0.1
@@ -716,10 +719,16 @@ steps:
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(parent_workflow_id)
-        subworkflow_step = workflow["steps"]["1"]
+        subworkflow_step = workflow["steps"]["2"]
         assert subworkflow_step["name"] == child_workflow_name
         assert subworkflow_step["type"] == "subworkflow"
         assert subworkflow_step["subworkflow"]["a_galaxy_workflow"] == "true"
+        self.workflow_editor_connect("input_collection#output", f"{child_workflow_name}#input1")
+        self.assert_connected("input_collection#output", f"{child_workflow_name}#input1")
+        self.assert_workflow_has_changes_and_save()
+        workflow = self.workflow_populator.download_workflow(parent_workflow_id)
+        subworkflow_step = workflow["steps"]["2"]
+        assert subworkflow_step["input_connections"]["input1"]["input_subworkflow_step_id"] == 0
 
     @selenium_test
     def test_editor_insert_steps(self):

From 32fc3b4b8bf63b6263bb2af8081a4df2749accab Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Mon, 30 Jan 2023 14:10:21 +0100
Subject: [PATCH 32/40] Import old screenshot generator

---
 .github/workflows/screenshot-producer.yml | 40 +++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 .github/workflows/screenshot-producer.yml

diff --git a/.github/workflows/screenshot-producer.yml b/.github/workflows/screenshot-producer.yml
new file mode 100644
index 00000000000..5f572473803
--- /dev/null
+++ b/.github/workflows/screenshot-producer.yml
@@ -0,0 +1,40 @@
+on: [push, pull_request]
+name: tests
+jobs:
+  screenshooter:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        galaxy_version: [release_21.01]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+
+      - name: create screenshots from ${{ matrix.galaxy_version }}
+        run: |
+          wget https://github.com/galaxyproject/galaxy/archive/${{ matrix.galaxy_version }}.tar.gz
+          tar xvzf ${{ matrix.galaxy_version }}.tar.gz | tail
+          cd galaxy-${{ matrix.galaxy_version }}
+          SCREENSHOTS_DIR=${{ github.workspace }}/screenshots
+          mkdir -p "$SCREENSHOTS_DIR"
+          GALAXY_TEST_SCREENSHOTS_DIRECTORY=$SCREENSHOTS_DIR ./run_tests.sh -selenium lib/galaxy_test/selenium -- -m gtn_screenshot -m local
+          echo "SCREENSHOTS_DIR=$SCREENSHOTS_DIR" >> $GITHUB_ENV
+
+      - name: Upload screenshots to S3
+        run: |
+          echo $SCREENSHOTS_DIR
+          aws configure set aws_access_key_id ${{ secrets.TESTS_AWS_ACCESS_KEY_ID }}
+          aws configure set aws_secret_access_key ${{ secrets.TESTS_AWS_SECRET_KEY_ID }}
+          aws configure set default.region us-east-2
+          aws s3 cp --recursive $SCREENSHOTS_DIR s3://galaxy-tests/galaxy-gtn-screenshots/local --acl public-read
+          aws s3 ls s3://galaxy-tests
+
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ${{ github.workspace }}/galaxy-${{ matrix.galaxy_version }}/.venv
+          key: pip-cache-${{ matrix.galaxy_version }}
\ No newline at end of file

From 58b1927b31408438d96c532119988eafa7e713e9 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 30 Jan 2023 14:17:43 +0100
Subject: [PATCH 33/40] Update to take current version of Galaxy

---
 .github/workflows/screenshot-producer.yml | 28 ++++++++---------------
 1 file changed, 10 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/screenshot-producer.yml b/.github/workflows/screenshot-producer.yml
index 5f572473803..def301c5ee3 100644
--- a/.github/workflows/screenshot-producer.yml
+++ b/.github/workflows/screenshot-producer.yml
@@ -3,26 +3,24 @@ name: tests
 jobs:
   screenshooter:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        galaxy_version: [release_21.01]
-
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.6
+          python-version: 3.10
 
-      - name: create screenshots from ${{ matrix.galaxy_version }}
+      - name: create screenshots from current version
         run: |
-          wget https://github.com/galaxyproject/galaxy/archive/${{ matrix.galaxy_version }}.tar.gz
-          tar xvzf ${{ matrix.galaxy_version }}.tar.gz | tail
-          cd galaxy-${{ matrix.galaxy_version }}
-          SCREENSHOTS_DIR=${{ github.workspace }}/screenshots
+          # Setup environment
+          export GALAXY_VERSION=$(cat lib/galaxy/version.py | grep '^VERSION_MAJOR' | cut -d'"' -f 2)
+          export SCREENSHOTS_DIR=/tmp/screenshots
+          echo "SCREENSHOTS_DIR=$SCREENSHOTS_DIR" >> $GITHUB_ENV
+          echo "GALAXY_VERSION=$GALAXY_VERSION" >> $GITHUB_ENV
+
+          # Take our screenshots
           mkdir -p "$SCREENSHOTS_DIR"
           GALAXY_TEST_SCREENSHOTS_DIRECTORY=$SCREENSHOTS_DIR ./run_tests.sh -selenium lib/galaxy_test/selenium -- -m gtn_screenshot -m local
-          echo "SCREENSHOTS_DIR=$SCREENSHOTS_DIR" >> $GITHUB_ENV
 
       - name: Upload screenshots to S3
         run: |
@@ -30,11 +28,5 @@ jobs:
           aws configure set aws_access_key_id ${{ secrets.TESTS_AWS_ACCESS_KEY_ID }}
           aws configure set aws_secret_access_key ${{ secrets.TESTS_AWS_SECRET_KEY_ID }}
           aws configure set default.region us-east-2
-          aws s3 cp --recursive $SCREENSHOTS_DIR s3://galaxy-tests/galaxy-gtn-screenshots/local --acl public-read
+          aws s3 cp --recursive $SCREENSHOTS_DIR s3://galaxy-tests/galaxy-gtn-screenshots/${GALAXY_VERSION}/ --acl public-read
           aws s3 ls s3://galaxy-tests
-
-      - name: Cache pip dir
-        uses: actions/cache@v2
-        with:
-          path: ${{ github.workspace }}/galaxy-${{ matrix.galaxy_version }}/.venv
-          key: pip-cache-${{ matrix.galaxy_version }}
\ No newline at end of file

From f28063c6fe0b1ab8c255d7b4734268189d448127 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 30 Jan 2023 14:19:39 +0100
Subject: [PATCH 34/40] Swap to cron, dispatch

---
 .github/workflows/screenshot-producer.yml | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/screenshot-producer.yml b/.github/workflows/screenshot-producer.yml
index def301c5ee3..672654887ac 100644
--- a/.github/workflows/screenshot-producer.yml
+++ b/.github/workflows/screenshot-producer.yml
@@ -1,10 +1,21 @@
-on: [push, pull_request]
-name: tests
+name: Autogenerate UI screenshots for GTN Tutorials
+
+on:
+  schedule:
+    # Run mondays at noon.
+    - cron:  '0 12 * * 1'
+  workflow_dispatch:
+
 jobs:
   screenshooter:
+    if: github.repository_owner == 'galaxyproject'
     runs-on: ubuntu-latest
     steps:
+      # Shallow should be fine here.
       - uses: actions/checkout@v2
+        with:
+          fetch-depth: 500
+
       - name: Set up Python
         uses: actions/setup-python@v2
         with:

From cba9140534ea684c10108201c788a114a028563b Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 30 Jan 2023 14:21:46 +0100
Subject: [PATCH 35/40] Only run on modern branches

---
 .github/workflows/screenshot-producer.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/screenshot-producer.yml b/.github/workflows/screenshot-producer.yml
index 672654887ac..37acd48ab8b 100644
--- a/.github/workflows/screenshot-producer.yml
+++ b/.github/workflows/screenshot-producer.yml
@@ -1,10 +1,12 @@
 name: Autogenerate UI screenshots for GTN Tutorials
 
 on:
-  schedule:
-    # Run mondays at noon.
-    - cron:  '0 12 * * 1'
   workflow_dispatch:
+  # Generate screenshots per release branch whenever they're updated
+  push:
+    branches:
+      - dev
+      - 'release_2*'
 
 jobs:
   screenshooter:

From 232a52e96c60410d045da873a1ae067997d42a66 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 30 Jan 2023 14:25:02 +0100
Subject: [PATCH 36/40] Revert "Only run on modern branches"

This reverts commit cba9140534ea684c10108201c788a114a028563b.
---
 .github/workflows/screenshot-producer.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/screenshot-producer.yml b/.github/workflows/screenshot-producer.yml
index 37acd48ab8b..672654887ac 100644
--- a/.github/workflows/screenshot-producer.yml
+++ b/.github/workflows/screenshot-producer.yml
@@ -1,12 +1,10 @@
 name: Autogenerate UI screenshots for GTN Tutorials
 
 on:
+  schedule:
+    # Run mondays at noon.
+    - cron:  '0 12 * * 1'
   workflow_dispatch:
-  # Generate screenshots per release branch whenever they're updated
-  push:
-    branches:
-      - dev
-      - 'release_2*'
 
 jobs:
   screenshooter:

From 3edf6335137cd976557007471c47d86356c4db71 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 30 Jan 2023 14:25:42 +0100
Subject: [PATCH 37/40] Revert "Swap to cron, dispatch"

This reverts commit f28063c6fe0b1ab8c255d7b4734268189d448127.
---
 .github/workflows/screenshot-producer.yml | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/screenshot-producer.yml b/.github/workflows/screenshot-producer.yml
index 672654887ac..def301c5ee3 100644
--- a/.github/workflows/screenshot-producer.yml
+++ b/.github/workflows/screenshot-producer.yml
@@ -1,21 +1,10 @@
-name: Autogenerate UI screenshots for GTN Tutorials
-
-on:
-  schedule:
-    # Run mondays at noon.
-    - cron:  '0 12 * * 1'
-  workflow_dispatch:
-
+on: [push, pull_request]
+name: tests
 jobs:
   screenshooter:
-    if: github.repository_owner == 'galaxyproject'
     runs-on: ubuntu-latest
     steps:
-      # Shallow should be fine here.
       - uses: actions/checkout@v2
-        with:
-          fetch-depth: 500
-
       - name: Set up Python
         uses: actions/setup-python@v2
         with:

From 14a30b3d014a0ef262d5f3c6c43cf0e58cacc8e1 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 30 Jan 2023 14:25:51 +0100
Subject: [PATCH 38/40] Revert "Update to take current version of Galaxy"

This reverts commit 58b1927b31408438d96c532119988eafa7e713e9.
---
 .github/workflows/screenshot-producer.yml | 28 +++++++++++++++--------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/screenshot-producer.yml b/.github/workflows/screenshot-producer.yml
index def301c5ee3..5f572473803 100644
--- a/.github/workflows/screenshot-producer.yml
+++ b/.github/workflows/screenshot-producer.yml
@@ -3,24 +3,26 @@ name: tests
 jobs:
   screenshooter:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        galaxy_version: [release_21.01]
+
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.10
+          python-version: 3.6
 
-      - name: create screenshots from current version
+      - name: create screenshots from ${{ matrix.galaxy_version }}
         run: |
-          # Setup environment
-          export GALAXY_VERSION=$(cat lib/galaxy/version.py | grep '^VERSION_MAJOR' | cut -d'"' -f 2)
-          export SCREENSHOTS_DIR=/tmp/screenshots
-          echo "SCREENSHOTS_DIR=$SCREENSHOTS_DIR" >> $GITHUB_ENV
-          echo "GALAXY_VERSION=$GALAXY_VERSION" >> $GITHUB_ENV
-
-          # Take our screenshots
+          wget https://github.com/galaxyproject/galaxy/archive/${{ matrix.galaxy_version }}.tar.gz
+          tar xvzf ${{ matrix.galaxy_version }}.tar.gz | tail
+          cd galaxy-${{ matrix.galaxy_version }}
+          SCREENSHOTS_DIR=${{ github.workspace }}/screenshots
           mkdir -p "$SCREENSHOTS_DIR"
           GALAXY_TEST_SCREENSHOTS_DIRECTORY=$SCREENSHOTS_DIR ./run_tests.sh -selenium lib/galaxy_test/selenium -- -m gtn_screenshot -m local
+          echo "SCREENSHOTS_DIR=$SCREENSHOTS_DIR" >> $GITHUB_ENV
 
       - name: Upload screenshots to S3
         run: |
@@ -28,5 +30,11 @@ jobs:
           aws configure set aws_access_key_id ${{ secrets.TESTS_AWS_ACCESS_KEY_ID }}
           aws configure set aws_secret_access_key ${{ secrets.TESTS_AWS_SECRET_KEY_ID }}
           aws configure set default.region us-east-2
-          aws s3 cp --recursive $SCREENSHOTS_DIR s3://galaxy-tests/galaxy-gtn-screenshots/${GALAXY_VERSION}/ --acl public-read
+          aws s3 cp --recursive $SCREENSHOTS_DIR s3://galaxy-tests/galaxy-gtn-screenshots/local --acl public-read
           aws s3 ls s3://galaxy-tests
+
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ${{ github.workspace }}/galaxy-${{ matrix.galaxy_version }}/.venv
+          key: pip-cache-${{ matrix.galaxy_version }}
\ No newline at end of file

From 32fa9d50278b888889a862ce119bdf745bd18131 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 30 Jan 2023 14:26:01 +0100
Subject: [PATCH 39/40] Revert "Import old screenshot generator"

This reverts commit 32fc3b4b8bf63b6263bb2af8081a4df2749accab.
---
 .github/workflows/screenshot-producer.yml | 40 -----------------------
 1 file changed, 40 deletions(-)
 delete mode 100644 .github/workflows/screenshot-producer.yml

diff --git a/.github/workflows/screenshot-producer.yml b/.github/workflows/screenshot-producer.yml
deleted file mode 100644
index 5f572473803..00000000000
--- a/.github/workflows/screenshot-producer.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-on: [push, pull_request]
-name: tests
-jobs:
-  screenshooter:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        galaxy_version: [release_21.01]
-
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.6
-
-      - name: create screenshots from ${{ matrix.galaxy_version }}
-        run: |
-          wget https://github.com/galaxyproject/galaxy/archive/${{ matrix.galaxy_version }}.tar.gz
-          tar xvzf ${{ matrix.galaxy_version }}.tar.gz | tail
-          cd galaxy-${{ matrix.galaxy_version }}
-          SCREENSHOTS_DIR=${{ github.workspace }}/screenshots
-          mkdir -p "$SCREENSHOTS_DIR"
-          GALAXY_TEST_SCREENSHOTS_DIRECTORY=$SCREENSHOTS_DIR ./run_tests.sh -selenium lib/galaxy_test/selenium -- -m gtn_screenshot -m local
-          echo "SCREENSHOTS_DIR=$SCREENSHOTS_DIR" >> $GITHUB_ENV
-
-      - name: Upload screenshots to S3
-        run: |
-          echo $SCREENSHOTS_DIR
-          aws configure set aws_access_key_id ${{ secrets.TESTS_AWS_ACCESS_KEY_ID }}
-          aws configure set aws_secret_access_key ${{ secrets.TESTS_AWS_SECRET_KEY_ID }}
-          aws configure set default.region us-east-2
-          aws s3 cp --recursive $SCREENSHOTS_DIR s3://galaxy-tests/galaxy-gtn-screenshots/local --acl public-read
-          aws s3 ls s3://galaxy-tests
-
-      - name: Cache pip dir
-        uses: actions/cache@v2
-        with:
-          path: ${{ github.workspace }}/galaxy-${{ matrix.galaxy_version }}/.venv
-          key: pip-cache-${{ matrix.galaxy_version }}
\ No newline at end of file

From 118855d5705d79fa3b1b4d972772a663c1a8161e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 6 Dec 2021 15:59:03 +0100
Subject: [PATCH 40/40] Serialize tools via json, not pickle

I assume we don't need to maintain comments for this kind of
serialization.
---
 lib/galaxy/tool_util/cwl/parser.py | 67 +++++++++---------------------
 1 file changed, 20 insertions(+), 47 deletions(-)

diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
index 467c6070f66..5f0bd18563c 100644
--- a/lib/galaxy/tool_util/cwl/parser.py
+++ b/lib/galaxy/tool_util/cwl/parser.py
@@ -4,12 +4,10 @@ adapt cwltool to Galaxy features and abstract the library away from the rest
 of the framework.
 """
 
-import base64
 import copy
 import json
 import logging
 import os
-import pickle
 from abc import (
     ABCMeta,
     abstractmethod,
@@ -31,7 +29,6 @@ from galaxy.exceptions import MessageException
 from galaxy.util import (
     listify,
     safe_makedirs,
-    unicodify,
 )
 from galaxy.util.bunch import Bunch
 from .cwltool_deps import (
@@ -86,8 +83,6 @@ SUPPORTED_TOOL_REQUIREMENTS = [
 
 SUPPORTED_WORKFLOW_REQUIREMENTS = SUPPORTED_TOOL_REQUIREMENTS + []
 
-PERSISTED_REPRESENTATION = "cwl_tool_object"
-
 ToolStateType = Dict[str, Union[None, str, bool, Dict[str, str]]]
 
 
@@ -173,29 +168,29 @@ class ToolProxy(metaclass=ABCMeta):
     def to_persistent_representation(self):
         """Return a JSON representation of this tool. Not for serialization
         over the wire, but serialization in a database."""
-        # TODO: Replace this with some more readable serialization,
-        # I really don't like using pickle here.
-        if PERSISTED_REPRESENTATION == "cwl_tool_object":
-            persisted_obj = remove_pickle_problems(self._tool)
-        else:
-            persisted_obj = self._raw_process_reference
+        persisted_obj = self._tool.tool
+        persisted_obj["requirements"] = self.requirements
+        if not persisted_obj.get("cwlVersion"):
+            # This happens for any inline process, but getting it from metadata is correct for inline processes at least
+            persisted_obj["cwlVersion"] = self._tool.metadata["cwlVersion"]
         return {
             "class": self._class,
-            "pickle": unicodify(base64.b64encode(pickle.dumps(persisted_obj, pickle.HIGHEST_PROTOCOL))),
+            # Should maybe be yaml instead
+            "raw_process_reference": persisted_obj,
             "uuid": self.uuid,
         }
 
     @staticmethod
-    def from_persistent_representation(as_object) -> "ToolProxy":
+    def from_persistent_representation(as_object, strict_cwl_validation=True, tool_directory=None) -> "ToolProxy":
         """Recover an object serialized with to_persistent_representation."""
         if "class" not in as_object:
             raise Exception("Failed to deserialize tool proxy from JSON object - no class found.")
-        if "pickle" not in as_object:
-            raise Exception("Failed to deserialize tool proxy from JSON object - no pickle representation found.")
-        if "uuid" not in as_object:
-            raise Exception("Failed to deserialize tool proxy from JSON object - no uuid found.")
-        to_unpickle = base64.b64decode(as_object["pickle"])
-        loaded_object = pickle.loads(to_unpickle)
+        loaded_object = tool_proxy(
+            tool_object=as_object["raw_process_reference"],
+            strict_cwl_validation=strict_cwl_validation,
+            tool_directory=tool_directory,
+            uuid=as_object.get("uuid"),
+        )
         return loaded_object
 
     @property
@@ -743,14 +738,8 @@ def tool_proxy_from_persistent_representation(
 ) -> ToolProxy:
     """Load a ToolProxy from a previously persisted representation."""
     ensure_cwltool_available()
-    if PERSISTED_REPRESENTATION == "cwl_tool_object":
-        kwds = {"cwl_tool_object": ToolProxy.from_persistent_representation(persisted_tool)}
-    else:
-        raw_process_reference = persisted_tool  # ???
-        kwds = {"raw_process_reference": ToolProxy.from_persistent_representation(raw_process_reference)}
-    uuid = persisted_tool["uuid"]
-    return _to_cwl_tool_object(
-        uuid=uuid, strict_cwl_validation=strict_cwl_validation, tool_directory=tool_directory, **kwds
+    return ToolProxy.from_persistent_representation(
+        persisted_tool, strict_cwl_validation=strict_cwl_validation, tool_directory=tool_directory
     )
 
 
@@ -765,15 +754,10 @@ def load_job_proxy(job_directory, strict_cwl_validation=True) -> JobProxy:
     job_objects = json.load(open(job_objects_path))
     job_inputs = job_objects["job_inputs"]
     output_dict = job_objects["output_dict"]
-    # Any reason to retain older tool_path variant of this? Probably not?
-    if "tool_path" in job_objects:
-        tool_path = job_objects["tool_path"]
-        cwl_tool = tool_proxy(tool_path, strict_cwl_validation=strict_cwl_validation)
-    else:
-        persisted_tool = job_objects["tool_representation"]
-        cwl_tool = tool_proxy_from_persistent_representation(
-            persisted_tool=persisted_tool, strict_cwl_validation=strict_cwl_validation
-        )
+    persisted_tool = job_objects["tool_representation"]
+    cwl_tool = tool_proxy_from_persistent_representation(
+        persisted_tool=persisted_tool, strict_cwl_validation=strict_cwl_validation
+    )
     return cwl_tool.job_proxy(job_inputs, output_dict, job_directory=job_directory)
 
 
@@ -1107,17 +1091,6 @@ class SubworkflowStepProxy(BaseStepProxy):
         return self._subworkflow_proxy
 
 
-def remove_pickle_problems(obj):
-    """doc_loader does not pickle correctly"""
-    if hasattr(obj, "doc_loader"):
-        obj.doc_loader = None
-    if hasattr(obj, "embedded_tool"):
-        obj.embedded_tool = remove_pickle_problems(obj.embedded_tool)
-    if hasattr(obj, "steps"):
-        obj.steps = [remove_pickle_problems(s) for s in obj.steps]
-    return obj
-
-
 def _outer_field_to_input_instance(field):
     field_type = field_to_field_type(field)  # Must be a list if in here?
     if not isinstance(field_type, list):