From 7876ebed97694ef59a87bc324cf72ddf255862db Mon Sep 17 00:00:00 2001
From: Matthias Bernt <bernt.matthias@gmail.com>
Date: Wed, 23 Oct 2024 18:43:10 +0200
Subject: [PATCH 01/28] quota: do not complain on no-change of default

also no message
---
 lib/galaxy/managers/quotas.py | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/lib/galaxy/managers/quotas.py b/lib/galaxy/managers/quotas.py
index 8b91b94a94a8..3c7c6e361b43 100644
--- a/lib/galaxy/managers/quotas.py
+++ b/lib/galaxy/managers/quotas.py
@@ -184,27 +184,25 @@ def set_quota_default(self, quota, params) -> str:
             if params.default != "no":
                 self.quota_agent.set_default_quota(params.default, quota)
                 message = f"Quota '{quota.name}' is now the default for {params.default} users."
+            elif quota.default:
+                message = f"Quota '{quota.name}' is no longer the default for {quota.default[0].type} users."
+                for dqa in quota.default:
+                    self.sa_session.delete(dqa)
+                with transaction(self.sa_session):
+                    self.sa_session.commit()
             else:
-                if quota.default:
-                    message = f"Quota '{quota.name}' is no longer the default for {quota.default[0].type} users."
-                    for dqa in quota.default:
-                        self.sa_session.delete(dqa)
-                    with transaction(self.sa_session):
-                        self.sa_session.commit()
-                else:
-                    message = f"Quota '{quota.name}' is not a default."
+                message = ""
             return message
 
     def unset_quota_default(self, quota, params=None) -> str:
-        if not quota.default:
-            raise ActionInputError(f"Quota '{quota.name}' is not a default.")
-        else:
+        message = ""
+        if quota.default:
             message = f"Quota '{quota.name}' is no longer the default for {quota.default[0].type} users."
             for dqa in quota.default:
                 self.sa_session.delete(dqa)
             with transaction(self.sa_session):
                 self.sa_session.commit()
-            return message
+        return message
 
     def delete_quota(self, quota, params=None) -> str:
         quotas = util.listify(quota)

From 2666c2c0b00c1a7126cadf7f13f422f61fca0386 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 7 Dec 2024 20:57:56 +0000
Subject: [PATCH 02/28] Prefer our package index server

when running tests with tox that install dependencies from
requirements.txt files.

Workaround for https://github.com/astral-sh/uv/issues/7496 .
---
 tox.ini | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tox.ini b/tox.ini
index bf7909a66f1c..ab1153917d2e 100644
--- a/tox.ini
+++ b/tox.ini
@@ -46,6 +46,8 @@ setenv =
     first_startup: GALAXY_CONFIG_DATABASE_AUTO_MIGRATE=true
     mulled: marker=external_dependency_management
     mulled,unit: GALAXY_VIRTUAL_ENV={envdir}
+    mypy,test_galaxy_packages,test_galaxy_packages_for_pulsar: PIP_INDEX_URL=https://wheels.galaxyproject.org/simple
+    mypy,test_galaxy_packages,test_galaxy_packages_for_pulsar: PIP_EXTRA_INDEX_URL=https://pypi.python.org/simple
     unit: GALAXY_ENABLE_BETA_COMPRESSED_GENBANK_SNIFFING=1
     unit: marker=not external_dependency_management
 deps =

From 9220710a8255e9375eb874abfe71d48c77e8238b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 11 Dec 2024 10:47:30 +0100
Subject: [PATCH 03/28] Fix multiselect being clipped by ToolForm header

---
 client/src/style/scss/multiselect.scss | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/client/src/style/scss/multiselect.scss b/client/src/style/scss/multiselect.scss
index 05b4b3961220..55b70ab4f24c 100644
--- a/client/src/style/scss/multiselect.scss
+++ b/client/src/style/scss/multiselect.scss
@@ -95,3 +95,7 @@
         }
     }
 }
+
+.multiselect--active {
+    z-index: 1500; // Should be on top of everything
+}

From f06988107f0eb652578bc6601eff0ca701df20fa Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 11 Dec 2024 10:59:29 +0100
Subject: [PATCH 04/28] Adjust modal height to accommodate selector in history
 operations

---
 .../CurrentHistory/HistoryOperations/SelectionOperations.vue     | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
index 59076e8063af..c723da9cb146 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
@@ -402,5 +402,6 @@ export default {
 <style>
 .modal-with-selector {
     overflow: initial;
+    height: 300px; /* To make room for the selector */
 }
 </style>

From 69f2c18febe449c9eb83fc213b41d8f18437918a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 11 Dec 2024 12:39:52 +0100
Subject: [PATCH 05/28] Fix import of previously-deleted TRS workflow

By returning latest, non-deleted workflow in
`get_workflow_by_trs_id_and_version`.

Fixes https://github.com/galaxyproject/galaxy/issues/19263
---
 lib/galaxy/managers/workflows.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 20354c029198..c55d64067370 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -2083,6 +2083,7 @@ def to_json(column, keys: List[str]):
             .join(model.Workflow, model.Workflow.id == model.StoredWorkflow.latest_workflow_id)
             .filter(
                 and_(
+                    model.StoredWorkflow.deleted == false(),
                     to_json(model.Workflow.source_metadata, ["trs_tool_id"]) == trs_id,
                     to_json(model.Workflow.source_metadata, ["trs_version_id"]) == trs_version,
                 )
@@ -2094,7 +2095,7 @@ def to_json(column, keys: List[str]):
             )
         else:
             stmnt = stmnt.filter(model.StoredWorkflow.importable == true())
-        return sa_session.execute(stmnt).scalar()
+        return sa_session.execute(stmnt.order_by(model.StoredWorkflow.id.desc()).limit(1)).scalar()
 
 
 class RefactorRequest(RefactorActions):

From 722b7c407fa3678f0f38b7cd7e7a546efdca9b86 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 11 Dec 2024 12:55:59 +0100
Subject: [PATCH 06/28] Don't show published workflows in workflow activity of
 workflow editor

If we want to do this we need to separate owned and published, then make
a new copy or reference as we insert the public workflow. As it
stands you won't be finding your own workflows, since the public
workflows are far more numerous then any one user's workflows.

Fixes https://github.com/galaxyproject/galaxy/issues/19265
---
 client/src/components/Panels/WorkflowPanel.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Panels/WorkflowPanel.vue b/client/src/components/Panels/WorkflowPanel.vue
index d5e56f332d5c..b16b1cf1d16b 100644
--- a/client/src/components/Panels/WorkflowPanel.vue
+++ b/client/src/components/Panels/WorkflowPanel.vue
@@ -52,7 +52,7 @@ const loadWorkflowsOptions = {
     sortBy: "update_time",
     sortDesc: true,
     limit: 20,
-    showPublished: true,
+    showPublished: false,
     skipStepCounts: false,
 } as const;
 

From 151612c2c2bd5582dc09fa8fe084945cf986bc32 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 11 Dec 2024 19:46:23 +0100
Subject: [PATCH 07/28] Use min-height for selector accommodation

---
 .../CurrentHistory/HistoryOperations/SelectionOperations.vue    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
index c723da9cb146..7873e6c4bb2c 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
@@ -402,6 +402,6 @@ export default {
 <style>
 .modal-with-selector {
     overflow: initial;
-    height: 300px; /* To make room for the selector */
+    min-height: 300px; /* To make room for the selector */
 }
 </style>

From f2eca1b5534015db4f16f7401eb58aeebcf357bd Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 11 Dec 2024 12:59:54 -0500
Subject: [PATCH 08/28] Fix activity-bar-id handling

---
 client/src/components/ActivityBar/ActivityBar.vue            | 3 +++
 client/src/components/ActivityBar/Items/InteractiveItem.vue  | 5 +++--
 client/src/components/ActivityBar/Items/NotificationItem.vue | 3 ++-
 client/src/components/ActivityBar/Items/UploadItem.vue       | 3 ++-
 4 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/client/src/components/ActivityBar/ActivityBar.vue b/client/src/components/ActivityBar/ActivityBar.vue
index aee942c40ee9..dd2f0bbffc09 100644
--- a/client/src/components/ActivityBar/ActivityBar.vue
+++ b/client/src/components/ActivityBar/ActivityBar.vue
@@ -230,6 +230,7 @@ defineExpose({
                                 v-if="activity.id === 'upload'"
                                 :id="`${activity.id}`"
                                 :key="activity.id"
+                                :activity-bar-id="props.activityBarId"
                                 :icon="activity.icon"
                                 :title="activity.title"
                                 :tooltip="activity.tooltip" />
@@ -237,6 +238,7 @@ defineExpose({
                                 v-else-if="activity.to && activity.id === 'interactivetools'"
                                 :id="`${activity.id}`"
                                 :key="activity.id"
+                                :activity-bar-id="props.activityBarId"
                                 :icon="activity.icon"
                                 :is-active="isActiveRoute(activity.to)"
                                 :title="activity.title"
@@ -274,6 +276,7 @@ defineExpose({
                 <NotificationItem
                     v-if="isConfigLoaded && config.enable_notification_system"
                     id="notifications"
+                    :activity-bar-id="props.activityBarId"
                     :icon="faBell"
                     :is-active="isActiveSideBar('notifications') || isActiveRoute('/user/notifications')"
                     title="Notifications"
diff --git a/client/src/components/ActivityBar/Items/InteractiveItem.vue b/client/src/components/ActivityBar/Items/InteractiveItem.vue
index e9e4756344a9..6b14104c74ab 100644
--- a/client/src/components/ActivityBar/Items/InteractiveItem.vue
+++ b/client/src/components/ActivityBar/Items/InteractiveItem.vue
@@ -17,6 +17,7 @@ export interface Props {
     icon: IconDefinition;
     isActive: boolean;
     to: string;
+    activityBarId: string;
 }
 
 defineProps<Props>();
@@ -27,7 +28,7 @@ const emit = defineEmits<{
 
 const tooltip = computed(() =>
     totalCount.value === 1
-        ? `You currently have 1 active interactive tool`
+        ? "You currently have 1 active interactive tool"
         : `You currently have ${totalCount.value} active interactive tools`
 );
 </script>
@@ -36,7 +37,7 @@ const tooltip = computed(() =>
     <ActivityItem
         v-if="totalCount > 0"
         :id="id"
-        :activity-bar-id="id"
+        :activity-bar-id="activityBarId"
         :icon="icon"
         :indicator="totalCount"
         :is-active="isActive"
diff --git a/client/src/components/ActivityBar/Items/NotificationItem.vue b/client/src/components/ActivityBar/Items/NotificationItem.vue
index 1f1dde9110e3..d72136402dc2 100644
--- a/client/src/components/ActivityBar/Items/NotificationItem.vue
+++ b/client/src/components/ActivityBar/Items/NotificationItem.vue
@@ -11,6 +11,7 @@ const { totalUnreadCount } = storeToRefs(useNotificationsStore());
 
 export interface Props {
     id: string;
+    activityBarId: string;
     title: string;
     icon: IconDefinition;
     isActive: boolean;
@@ -32,7 +33,7 @@ const tooltip = computed(() =>
 <template>
     <ActivityItem
         :id="id"
-        :activity-bar-id="'notifications'"
+        :activity-bar-id="activityBarId"
         :icon="icon"
         :indicator="totalUnreadCount"
         :is-active="isActive"
diff --git a/client/src/components/ActivityBar/Items/UploadItem.vue b/client/src/components/ActivityBar/Items/UploadItem.vue
index 6d5a6df9da64..9b1c5a0f8e11 100644
--- a/client/src/components/ActivityBar/Items/UploadItem.vue
+++ b/client/src/components/ActivityBar/Items/UploadItem.vue
@@ -14,6 +14,7 @@ export interface Props {
     title: string;
     icon: IconDefinition;
     tooltip: string;
+    activityBarId: string;
 }
 
 defineProps<Props>();
@@ -40,7 +41,7 @@ function onUploadModal() {
 <template>
     <ActivityItem
         :id="id"
-        :activity-bar-id="id"
+        :activity-bar-id="activityBarId"
         :title="title"
         :tooltip="tooltip"
         :icon="icon"

From 79f663c8d1543aa19376b21981e42e75ffc0ace8 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 11 Dec 2024 23:43:08 +0100
Subject: [PATCH 09/28] fix initial value overwrite

---
 client/src/composables/userLocalStorage.ts | 5 ++++-
 client/src/stores/activityStore.ts         | 5 +----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/src/composables/userLocalStorage.ts b/client/src/composables/userLocalStorage.ts
index f0787732a12d..619bbe88bfa0 100644
--- a/client/src/composables/userLocalStorage.ts
+++ b/client/src/composables/userLocalStorage.ts
@@ -13,9 +13,11 @@ import { useHashedUserId } from "./hashedUserId";
 export function useUserLocalStorage<T>(key: string, initialValue: T, user?: Ref<AnyUser>) {
     const { hashedUserId } = useHashedUserId(user);
 
+    let refSyncedRawValue = initialValue;
+
     const storedRef = computed(() => {
         if (hashedUserId.value) {
-            return useLocalStorage(`${key}-${hashedUserId.value}`, initialValue);
+            return useLocalStorage(`${key}-${hashedUserId.value}`, refSyncedRawValue);
         } else {
             return ref(initialValue);
         }
@@ -28,6 +30,7 @@ export function useUserLocalStorage<T>(key: string, initialValue: T, user?: Ref<
         },
         set(newValue) {
             storedRef.value.value = newValue;
+            refSyncedRawValue = newValue as T;
             trigger();
         },
     }));
diff --git a/client/src/stores/activityStore.ts b/client/src/stores/activityStore.ts
index 466ee226bf00..b74a66286f4d 100644
--- a/client/src/stores/activityStore.ts
+++ b/client/src/stores/activityStore.ts
@@ -127,10 +127,7 @@ export const useActivityStore = defineScopedStore("activityStore", (scope) => {
             }
         });
 
-        // update activities stored in local cache only if changes were applied
-        if (JSON.stringify(activities.value) !== JSON.stringify(newActivities)) {
-            activities.value = newActivities;
-        }
+        activities.value = newActivities;
 
         // if toggled side-bar does not exist, choose the first option
         if (toggledSideBar.value !== "") {

From ff0d12b23018c1317e9d52d6f64f384fdf6524ed Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 6 Dec 2024 22:41:17 +0100
Subject: [PATCH 10/28] add create new workflow activity

---
 client/src/components/Workflow/Editor/Index.vue       |  8 ++++++++
 .../components/Workflow/Editor/modules/activities.ts  | 11 +++++++++++
 2 files changed, 19 insertions(+)

diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index 357482638c78..b974a4e824fa 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -738,6 +738,10 @@ export default {
         onSaveAs() {
             this.showSaveAsModal = true;
         },
+        async createNewWorkflow() {
+            await this.saveOrCreate();
+            this.$router.push("/workflows/edit");
+        },
         async saveOrCreate() {
             if (this.hasInvalidConnections) {
                 const confirmed = await this.confirm(
@@ -788,6 +792,10 @@ export default {
             if (activityId === "save-workflow-as") {
                 this.onSaveAs();
             }
+
+            if (activityId === "workflow-create") {
+                this.createNewWorkflow();
+            }
         },
         onAnnotation(nodeId, newAnnotation) {
             this.stepActions.setAnnotation(this.steps[nodeId], newAnnotation);
diff --git a/client/src/components/Workflow/Editor/modules/activities.ts b/client/src/components/Workflow/Editor/modules/activities.ts
index 5a5534a4af0e..365bbba411d3 100644
--- a/client/src/components/Workflow/Editor/modules/activities.ts
+++ b/client/src/components/Workflow/Editor/modules/activities.ts
@@ -6,6 +6,7 @@ import {
     faMagic,
     faPencilAlt,
     faPlay,
+    faPlus,
     faRecycle,
     faSave,
     faSignOutAlt,
@@ -126,6 +127,16 @@ export const workflowEditorActivities = [
         click: true,
         optional: true,
     },
+    {
+        description: "Save this workflow and create a new workflow.",
+        icon: faPlus,
+        title: "Create new",
+        id: "workflow-create",
+        tooltip: "Save this workflow and create a new one",
+        visible: true,
+        click: true,
+        optional: true,
+    },
     {
         description: "Exit the workflow editor and return to the start screen.",
         icon: faSignOutAlt,

From f58ba5cc9ddb0e0415c558ef69d9ed0fc773c55e Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 6 Dec 2024 22:53:58 +0100
Subject: [PATCH 11/28] add create button to activity panel

---
 .../src/components/Panels/ActivityPanel.vue   |  6 +++--
 .../src/components/Panels/WorkflowPanel.vue   | 24 +++++++++++++++++++
 .../src/components/Workflow/Editor/Index.vue  |  3 ++-
 3 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Panels/ActivityPanel.vue b/client/src/components/Panels/ActivityPanel.vue
index d97512c24cc5..e0d3dd646ab8 100644
--- a/client/src/components/Panels/ActivityPanel.vue
+++ b/client/src/components/Panels/ActivityPanel.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { BButton } from "bootstrap-vue";
+import { BButton, BButtonGroup } from "bootstrap-vue";
 import { computed } from "vue";
 
 interface Props {
@@ -26,7 +26,9 @@ const hasGoToAll = computed(() => props.goToAllTitle && props.href);
             <nav unselectable="on" class="activity-panel-header-top">
                 <h2 id="activity-panel-heading" v-localize class="activity-panel-heading h-sm">{{ props.title }}</h2>
 
-                <slot name="header-buttons" />
+                <BButtonGroup>
+                    <slot name="header-buttons" />
+                </BButtonGroup>
             </nav>
 
             <slot name="header" class="activity-panel-header-description" />
diff --git a/client/src/components/Panels/WorkflowPanel.vue b/client/src/components/Panels/WorkflowPanel.vue
index b16b1cf1d16b..c596363d7fe3 100644
--- a/client/src/components/Panels/WorkflowPanel.vue
+++ b/client/src/components/Panels/WorkflowPanel.vue
@@ -1,5 +1,8 @@
 <script setup lang="ts">
+import { faPlus } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { useMemoize, watchImmediate } from "@vueuse/core";
+import { BButton } from "bootstrap-vue";
 import { computed, ref, watch } from "vue";
 
 import { loadWorkflows, type Workflow } from "@/components/Workflow/workflows.services";
@@ -19,6 +22,7 @@ const props = defineProps<{
 const emit = defineEmits<{
     (e: "insertWorkflow", id: string, name: string): void;
     (e: "insertWorkflowSteps", id: string, stepCount: number): void;
+    (e: "createWorkflow"): void;
 }>();
 
 const scrollable = ref<HTMLDivElement | null>(null);
@@ -138,11 +142,26 @@ watch(
 function scrollToTop() {
     scrollable.value?.scrollTo({ top: 0, behavior: "smooth" });
 }
+
+function createNew(event: Event) {
+    event.preventDefault();
+    emit("createWorkflow");
+}
 </script>
 
 <template>
     <ActivityPanel title="Workflows">
         <template v-slot:header-buttons>
+            <BButton
+                v-b-tooltip.hover.top.noninteractive
+                size="sm"
+                variant="link"
+                class="create-button"
+                title="Create new workflow"
+                href="/workflows/edit"
+                @click="createNew">
+                <FontAwesomeIcon :icon="faPlus" />
+            </BButton>
             <FavoritesButton v-model="showFavorites" tooltip="Show bookmarked" />
         </template>
 
@@ -189,4 +208,9 @@ function scrollToTop() {
     color: $text-light;
     margin: 0.5rem;
 }
+
+.create-button:hover {
+    background-color: #c8cfd6;
+    border-color: #c1c9d0;
+}
 </style>
diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index b974a4e824fa..dec4617e26d4 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -77,7 +77,8 @@
                     v-else-if="isActiveSideBar('workflow-editor-workflows')"
                     :current-workflow-id="id"
                     @insertWorkflow="onInsertWorkflow"
-                    @insertWorkflowSteps="onInsertWorkflowSteps" />
+                    @insertWorkflowSteps="onInsertWorkflowSteps"
+                    @createWorkflow="createNewWorkflow" />
                 <WorkflowAttributes
                     v-else-if="isActiveSideBar('workflow-editor-attributes')"
                     :id="id"

From 8315a04259ada0977bc684c7cdd0854b1a900aeb Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 6 Dec 2024 23:08:26 +0100
Subject: [PATCH 12/28] reload if window is navigated to/from new workflow

---
 client/src/entry/analysis/modules/WorkflowEditor.vue | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/client/src/entry/analysis/modules/WorkflowEditor.vue b/client/src/entry/analysis/modules/WorkflowEditor.vue
index 67634f4a3842..c3010426c026 100644
--- a/client/src/entry/analysis/modules/WorkflowEditor.vue
+++ b/client/src/entry/analysis/modules/WorkflowEditor.vue
@@ -25,6 +25,7 @@ export default {
             version: null,
             editorConfig: null,
             editorReloadKey: 0,
+            previousHistoryLength: 0,
         };
     },
     watch: {
@@ -39,14 +40,18 @@ export default {
         async getEditorConfig() {
             let reloadEditor = true;
 
+            const noStoredIds = !this.storedWorkflowId && !this.workflowId;
+            const historyNavigatedForwards = window.history.length > this.previousHistoryLength;
+
             // this will only be the case the first time the route updates from a new workflow
-            if (!this.storedWorkflowId && !this.workflowId) {
+            if (noStoredIds && historyNavigatedForwards) {
                 reloadEditor = false;
             }
 
             this.storedWorkflowId = Query.get("id");
             this.workflowId = Query.get("workflow_id");
             this.version = Query.get("version");
+            this.previousHistoryLength = window.history.length;
 
             const params = {};
 

From 7bd81453d86d8b1f2be95df6caaa450507ee0575 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 11 Dec 2024 10:27:40 +0100
Subject: [PATCH 13/28] add custom persistentRef fix type import

---
 client/src/components/Panels/utilities.ts     |  7 +--
 client/src/composables/hashedUserId.ts        |  5 +-
 client/src/composables/persistentRef.ts       | 59 +++++++++++++++++++
 client/src/composables/userLocalStorage.ts    |  2 +-
 client/src/onload/console.js                  |  5 +-
 .../src/stores/workflowNodeInspectorStore.ts  |  6 +-
 6 files changed, 70 insertions(+), 14 deletions(-)
 create mode 100644 client/src/composables/persistentRef.ts

diff --git a/client/src/components/Panels/utilities.ts b/client/src/components/Panels/utilities.ts
index 27dde0d1cf86..38f7f4d335fe 100644
--- a/client/src/components/Panels/utilities.ts
+++ b/client/src/components/Panels/utilities.ts
@@ -4,12 +4,7 @@
  */
 import { orderBy } from "lodash";
 
-import {
-    type FilterSettings as ToolFilters,
-    type Tool,
-    type ToolSection,
-    type ToolSectionLabel,
-} from "@/stores/toolStore";
+import type { FilterSettings as ToolFilters, Tool, ToolSection, ToolSectionLabel } from "@/stores/toolStore";
 import levenshteinDistance from "@/utils/levenshtein";
 
 const FILTER_KEYS = {
diff --git a/client/src/composables/hashedUserId.ts b/client/src/composables/hashedUserId.ts
index 5d86b2dd8c42..a7f651a3c628 100644
--- a/client/src/composables/hashedUserId.ts
+++ b/client/src/composables/hashedUserId.ts
@@ -1,10 +1,11 @@
-import { useLocalStorage } from "@vueuse/core";
 import { storeToRefs } from "pinia";
 import { computed, type Ref, ref, watch } from "vue";
 
 import { type AnyUser } from "@/api";
 import { useUserStore } from "@/stores/userStore";
 
+import { usePersistentRef } from "./persistentRef";
+
 async function hash32(value: string): Promise<string> {
     const valueUtf8 = new TextEncoder().encode(value);
     const hashBuffer = await crypto.subtle.digest("SHA-256", valueUtf8);
@@ -43,7 +44,7 @@ export function useHashedUserId(user?: Ref<AnyUser>) {
     }
 
     // salt the local store, to make a user untraceable by id across different clients
-    const localStorageSalt = useLocalStorage("local-storage-salt", createSalt());
+    const localStorageSalt = usePersistentRef("local-storage-salt", createSalt());
 
     watch(
         () => currentUser.value,
diff --git a/client/src/composables/persistentRef.ts b/client/src/composables/persistentRef.ts
new file mode 100644
index 000000000000..98c9e3542029
--- /dev/null
+++ b/client/src/composables/persistentRef.ts
@@ -0,0 +1,59 @@
+/*
+   vueuse local storage has some strange, buggy side-effects,
+   so were re-implementing just the parts we need here
+*/
+
+import { type Ref, ref, watch } from "vue";
+
+import { match } from "@/utils/utils";
+
+function stringify(value: unknown): string {
+    if (typeof value !== "object") {
+        return `${value}`;
+    } else {
+        return JSON.stringify(value);
+    }
+}
+
+function parse<T>(value: string, type: "string" | "number" | "boolean" | "object"): T {
+    return match(type, {
+        string: () => value as T,
+        number: () => parseFloat(value) as T,
+        boolean: () => (value.toLowerCase().trim() === "true" ? true : false) as T,
+        object: () => JSON.parse(value),
+    });
+}
+
+export function usePersistentRef(key: string, defaultValue: string): Ref<string>;
+export function usePersistentRef(key: string, defaultValue: number): Ref<number>;
+export function usePersistentRef<T>(key: string, defaultValue: T): Ref<T>;
+export function usePersistentRef<T extends string | number | boolean | object | null>(
+    key: string,
+    defaultValue: T
+): Ref<T> {
+    const storageSyncedRef = ref(defaultValue) as Ref<T>;
+
+    const stored = window?.localStorage?.getItem(key);
+
+    if (stored) {
+        try {
+            storageSyncedRef.value = parse(stored, typeof defaultValue as "string" | "number" | "boolean" | "object");
+        } catch (e) {
+            console.error(`Failed to parse value "${stored}" from local storage key "${key}". Resetting key`);
+            window?.localStorage?.removeItem(key);
+        }
+    } else {
+        const stringified = stringify(storageSyncedRef.value);
+        window?.localStorage?.setItem(key, stringified);
+    }
+
+    watch(
+        () => storageSyncedRef.value,
+        () => {
+            const stringified = stringify(storageSyncedRef.value);
+            window?.localStorage?.setItem(key, stringified);
+        }
+    );
+
+    return storageSyncedRef;
+}
diff --git a/client/src/composables/userLocalStorage.ts b/client/src/composables/userLocalStorage.ts
index 619bbe88bfa0..2f179d66dc74 100644
--- a/client/src/composables/userLocalStorage.ts
+++ b/client/src/composables/userLocalStorage.ts
@@ -1,9 +1,9 @@
-import { useLocalStorage } from "@vueuse/core";
 import { computed, customRef, type Ref, ref } from "vue";
 
 import { type AnyUser } from "@/api";
 
 import { useHashedUserId } from "./hashedUserId";
+import { usePersistentRef } from "./persistentRef";
 
 /**
  * Local storage composable specific to current user.
diff --git a/client/src/onload/console.js b/client/src/onload/console.js
index 3cc2afb908d9..de552ac937c0 100644
--- a/client/src/onload/console.js
+++ b/client/src/onload/console.js
@@ -4,9 +4,10 @@
  * using the global functions
  * enableDebugging() and disableDebugging()
  */
-import { useLocalStorage } from "@vueuse/core";
 import { watch } from "vue";
 
+import { usePersistentRef } from "@/composables/persistentRef";
+
 export function overrideProductionConsole() {
     let defaultEnabled = true;
 
@@ -14,7 +15,7 @@ export function overrideProductionConsole() {
         defaultEnabled = false;
     }
 
-    const isEnabled = useLocalStorage("console-debugging-enabled", defaultEnabled);
+    const isEnabled = usePersistentRef("console-debugging-enabled", defaultEnabled);
 
     let storedConsole = null;
 
diff --git a/client/src/stores/workflowNodeInspectorStore.ts b/client/src/stores/workflowNodeInspectorStore.ts
index 6591baf1c8bb..e92683ac853d 100644
--- a/client/src/stores/workflowNodeInspectorStore.ts
+++ b/client/src/stores/workflowNodeInspectorStore.ts
@@ -1,7 +1,7 @@
-import { useLocalStorage } from "@vueuse/core";
 import { defineStore } from "pinia";
 import { computed, del, ref, set } from "vue";
 
+import { usePersistentRef } from "@/composables/persistentRef";
 import { ensureDefined } from "@/utils/assertions";
 import { getShortToolId } from "@/utils/tool";
 import { match } from "@/utils/utils";
@@ -26,10 +26,10 @@ function getContentId(step: Step) {
 
 export const useWorkflowNodeInspectorStore = defineStore("workflowNodeInspectorStore", () => {
     /** width of the node inspector if no other width is stored */
-    const generalWidth = useLocalStorage("workflowNodeInspectorGeneralWidth", 300);
+    const generalWidth = usePersistentRef("workflowNodeInspectorGeneralWidth", 300);
     /** maximized state of the node inspector if no other value is stored */
     const generalMaximized = ref(false);
-    const storedSizes = useLocalStorage<Record<string, StoredSize>>("workflowNodeInspectorStoredSizes", {});
+    const storedSizes = usePersistentRef<Record<string, StoredSize>>("workflowNodeInspectorStoredSizes", {});
 
     const isStored = computed(() => (step: Step) => {
         const id = getContentId(step);

From fd042d23359af1d0ba8da7f2c38281b766402a06 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 11 Dec 2024 23:09:23 +0100
Subject: [PATCH 14/28] fix wrong id passed to composable

---
 .../components/ActivityBar/Items/InteractiveItem.vue  |  6 +++---
 .../components/ActivityBar/Items/NotificationItem.vue |  4 ++--
 .../src/components/ActivityBar/Items/UploadItem.vue   |  6 +++---
 client/src/composables/persistentRef.ts               | 11 ++++++-----
 4 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/client/src/components/ActivityBar/Items/InteractiveItem.vue b/client/src/components/ActivityBar/Items/InteractiveItem.vue
index 6b14104c74ab..e6e80ea1d34d 100644
--- a/client/src/components/ActivityBar/Items/InteractiveItem.vue
+++ b/client/src/components/ActivityBar/Items/InteractiveItem.vue
@@ -13,14 +13,14 @@ const totalCount = computed(() => entryPoints.value.length);
 
 export interface Props {
     id: string;
+    activityBarId: string;
     title: string;
     icon: IconDefinition;
     isActive: boolean;
     to: string;
-    activityBarId: string;
 }
 
-defineProps<Props>();
+const props = defineProps<Props>();
 
 const emit = defineEmits<{
     (e: "click"): void;
@@ -37,7 +37,7 @@ const tooltip = computed(() =>
     <ActivityItem
         v-if="totalCount > 0"
         :id="id"
-        :activity-bar-id="activityBarId"
+        :activity-bar-id="props.activityBarId"
         :icon="icon"
         :indicator="totalCount"
         :is-active="isActive"
diff --git a/client/src/components/ActivityBar/Items/NotificationItem.vue b/client/src/components/ActivityBar/Items/NotificationItem.vue
index d72136402dc2..3bd5332c4528 100644
--- a/client/src/components/ActivityBar/Items/NotificationItem.vue
+++ b/client/src/components/ActivityBar/Items/NotificationItem.vue
@@ -17,7 +17,7 @@ export interface Props {
     isActive: boolean;
 }
 
-defineProps<Props>();
+const props = defineProps<Props>();
 
 const emit = defineEmits<{
     (e: "click"): void;
@@ -33,7 +33,7 @@ const tooltip = computed(() =>
 <template>
     <ActivityItem
         :id="id"
-        :activity-bar-id="activityBarId"
+        :activity-bar-id="props.activityBarId"
         :icon="icon"
         :indicator="totalUnreadCount"
         :is-active="isActive"
diff --git a/client/src/components/ActivityBar/Items/UploadItem.vue b/client/src/components/ActivityBar/Items/UploadItem.vue
index 9b1c5a0f8e11..c130c4965b21 100644
--- a/client/src/components/ActivityBar/Items/UploadItem.vue
+++ b/client/src/components/ActivityBar/Items/UploadItem.vue
@@ -11,13 +11,13 @@ import ActivityItem from "@/components/ActivityBar/ActivityItem.vue";
 
 export interface Props {
     id: string;
+    activityBarId: string;
     title: string;
     icon: IconDefinition;
     tooltip: string;
-    activityBarId: string;
 }
 
-defineProps<Props>();
+const props = defineProps<Props>();
 
 const emit = defineEmits<{
     (e: "click"): void;
@@ -41,7 +41,7 @@ function onUploadModal() {
 <template>
     <ActivityItem
         :id="id"
-        :activity-bar-id="activityBarId"
+        :activity-bar-id="props.activityBarId"
         :title="title"
         :tooltip="tooltip"
         :icon="icon"
diff --git a/client/src/composables/persistentRef.ts b/client/src/composables/persistentRef.ts
index 98c9e3542029..bd925f7965f7 100644
--- a/client/src/composables/persistentRef.ts
+++ b/client/src/composables/persistentRef.ts
@@ -33,26 +33,27 @@ export function usePersistentRef<T extends string | number | boolean | object |
 ): Ref<T> {
     const storageSyncedRef = ref(defaultValue) as Ref<T>;
 
-    const stored = window?.localStorage?.getItem(key);
+    const stored = window.localStorage.getItem(key);
 
     if (stored) {
         try {
             storageSyncedRef.value = parse(stored, typeof defaultValue as "string" | "number" | "boolean" | "object");
         } catch (e) {
             console.error(`Failed to parse value "${stored}" from local storage key "${key}". Resetting key`);
-            window?.localStorage?.removeItem(key);
+            window.localStorage.removeItem(key);
         }
     } else {
         const stringified = stringify(storageSyncedRef.value);
-        window?.localStorage?.setItem(key, stringified);
+        window.localStorage.setItem(key, stringified);
     }
 
     watch(
         () => storageSyncedRef.value,
         () => {
             const stringified = stringify(storageSyncedRef.value);
-            window?.localStorage?.setItem(key, stringified);
-        }
+            window.localStorage.setItem(key, stringified);
+        },
+        { deep: true }
     );
 
     return storageSyncedRef;

From 36de47d5b09ca2d4a89447a7be8d7ab331ca6160 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 11 Dec 2024 23:43:08 +0100
Subject: [PATCH 15/28] fix initial value overwrite

---
 client/src/composables/userLocalStorage.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/composables/userLocalStorage.ts b/client/src/composables/userLocalStorage.ts
index 2f179d66dc74..b0aa58b1a9ca 100644
--- a/client/src/composables/userLocalStorage.ts
+++ b/client/src/composables/userLocalStorage.ts
@@ -17,7 +17,7 @@ export function useUserLocalStorage<T>(key: string, initialValue: T, user?: Ref<
 
     const storedRef = computed(() => {
         if (hashedUserId.value) {
-            return useLocalStorage(`${key}-${hashedUserId.value}`, refSyncedRawValue);
+            return usePersistentRef(`${key}-${hashedUserId.value}`, refSyncedRawValue);
         } else {
             return ref(initialValue);
         }

From ba0f0d41654913258ba2fc0165e9f1deacfbf3f4 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Thu, 12 Dec 2024 01:27:58 +0100
Subject: [PATCH 16/28] remove computed side-effect and simplify user scoped
 ref allow to sync existing ref

---
 client/src/composables/persistentRef.ts    | 39 +++++++++++++---------
 client/src/composables/userLocalStorage.ts | 36 ++++++++------------
 2 files changed, 37 insertions(+), 38 deletions(-)

diff --git a/client/src/composables/persistentRef.ts b/client/src/composables/persistentRef.ts
index bd925f7965f7..ab511f74caaa 100644
--- a/client/src/composables/persistentRef.ts
+++ b/client/src/composables/persistentRef.ts
@@ -24,37 +24,44 @@ function parse<T>(value: string, type: "string" | "number" | "boolean" | "object
     });
 }
 
-export function usePersistentRef(key: string, defaultValue: string): Ref<string>;
-export function usePersistentRef(key: string, defaultValue: number): Ref<number>;
-export function usePersistentRef<T>(key: string, defaultValue: T): Ref<T>;
-export function usePersistentRef<T extends string | number | boolean | object | null>(
-    key: string,
-    defaultValue: T
-): Ref<T> {
-    const storageSyncedRef = ref(defaultValue) as Ref<T>;
-
+export function syncRefToLocalStorage<T>(key: string, refToSync: Ref<T>) {
     const stored = window.localStorage.getItem(key);
 
+    const sync = () => {
+        const stringified = stringify(refToSync.value);
+        window.localStorage.setItem(key, stringified);
+    };
+
     if (stored) {
         try {
-            storageSyncedRef.value = parse(stored, typeof defaultValue as "string" | "number" | "boolean" | "object");
+            refToSync.value = parse(stored, typeof refToSync.value as "string" | "number" | "boolean" | "object");
         } catch (e) {
             console.error(`Failed to parse value "${stored}" from local storage key "${key}". Resetting key`);
-            window.localStorage.removeItem(key);
+            sync();
         }
     } else {
-        const stringified = stringify(storageSyncedRef.value);
-        window.localStorage.setItem(key, stringified);
+        sync();
     }
 
     watch(
-        () => storageSyncedRef.value,
+        () => refToSync.value,
         () => {
-            const stringified = stringify(storageSyncedRef.value);
-            window.localStorage.setItem(key, stringified);
+            sync();
         },
         { deep: true }
     );
+}
+
+export function usePersistentRef(key: string, defaultValue: string): Ref<string>;
+export function usePersistentRef(key: string, defaultValue: number): Ref<number>;
+export function usePersistentRef<T>(key: string, defaultValue: T): Ref<T>;
+export function usePersistentRef<T extends string | number | boolean | object | null>(
+    key: string,
+    defaultValue: T
+): Ref<T> {
+    const storageSyncedRef = ref(defaultValue) as Ref<T>;
+
+    syncRefToLocalStorage(key, storageSyncedRef);
 
     return storageSyncedRef;
 }
diff --git a/client/src/composables/userLocalStorage.ts b/client/src/composables/userLocalStorage.ts
index b0aa58b1a9ca..d81dfda55e09 100644
--- a/client/src/composables/userLocalStorage.ts
+++ b/client/src/composables/userLocalStorage.ts
@@ -1,9 +1,10 @@
-import { computed, customRef, type Ref, ref } from "vue";
+import { watchImmediate } from "@vueuse/core";
+import { type Ref, ref } from "vue";
 
 import { type AnyUser } from "@/api";
 
 import { useHashedUserId } from "./hashedUserId";
-import { usePersistentRef } from "./persistentRef";
+import { syncRefToLocalStorage } from "./persistentRef";
 
 /**
  * Local storage composable specific to current user.
@@ -13,27 +14,18 @@ import { usePersistentRef } from "./persistentRef";
 export function useUserLocalStorage<T>(key: string, initialValue: T, user?: Ref<AnyUser>) {
     const { hashedUserId } = useHashedUserId(user);
 
-    let refSyncedRawValue = initialValue;
+    const refToSync = ref(initialValue);
+    let hasSynced = false;
 
-    const storedRef = computed(() => {
-        if (hashedUserId.value) {
-            return usePersistentRef(`${key}-${hashedUserId.value}`, refSyncedRawValue);
-        } else {
-            return ref(initialValue);
+    watchImmediate(
+        () => hashedUserId.value,
+        () => {
+            if (hashedUserId.value && !hasSynced) {
+                syncRefToLocalStorage(`${key}-${hashedUserId.value}`, refToSync);
+                hasSynced = true;
+            }
         }
-    });
+    );
 
-    const currentValue = customRef((track, trigger) => ({
-        get() {
-            track();
-            return storedRef.value.value;
-        },
-        set(newValue) {
-            storedRef.value.value = newValue;
-            refSyncedRawValue = newValue as T;
-            trigger();
-        },
-    }));
-
-    return currentValue;
+    return refToSync;
 }

From f4e37c9ed073a737ba9e8ad841c0cc017eec5e32 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Thu, 12 Dec 2024 04:09:14 +0100
Subject: [PATCH 17/28] fix workflow creation

---
 client/src/components/Workflow/Editor/Index.vue      |  1 +
 client/src/entry/analysis/modules/WorkflowEditor.vue | 12 +++++-------
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index dec4617e26d4..287d227488e1 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -819,6 +819,7 @@ export default {
                 const { id, name, number_of_steps } = await this.services.createWorkflow(this);
                 const message = `Created new workflow '${name}' with ${number_of_steps} steps.`;
                 this.hasChanges = false;
+                this.$emit("skipNextReload");
                 await this.routeToWorkflow(id);
                 Toast.success(message);
             } catch (e) {
diff --git a/client/src/entry/analysis/modules/WorkflowEditor.vue b/client/src/entry/analysis/modules/WorkflowEditor.vue
index c3010426c026..b05627cfbdb1 100644
--- a/client/src/entry/analysis/modules/WorkflowEditor.vue
+++ b/client/src/entry/analysis/modules/WorkflowEditor.vue
@@ -7,7 +7,8 @@
         :initial-version="editorConfig.initialVersion"
         :module-sections="editorConfig.moduleSections"
         :workflow-tags="editorConfig.tags"
-        @update:confirmation="$emit('update:confirmation', $event)" />
+        @update:confirmation="$emit('update:confirmation', $event)"
+        @skipNextReload="() => (skipNextReload = true)" />
 </template>
 <script>
 import Editor from "components/Workflow/Editor/Index";
@@ -25,7 +26,7 @@ export default {
             version: null,
             editorConfig: null,
             editorReloadKey: 0,
-            previousHistoryLength: 0,
+            skipNextReload: false,
         };
     },
     watch: {
@@ -40,12 +41,9 @@ export default {
         async getEditorConfig() {
             let reloadEditor = true;
 
-            const noStoredIds = !this.storedWorkflowId && !this.workflowId;
-            const historyNavigatedForwards = window.history.length > this.previousHistoryLength;
-
-            // this will only be the case the first time the route updates from a new workflow
-            if (noStoredIds && historyNavigatedForwards) {
+            if (this.skipNextReload) {
                 reloadEditor = false;
+                this.skipNextReload = false;
             }
 
             this.storedWorkflowId = Query.get("id");

From 5561c4e74b776f22a796745666db00497dd9609c Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 16 Dec 2024 09:50:34 +0000
Subject: [PATCH 18/28] Replace mambaforge Docker image with miniforge3

mambaforge is deprecated upstream, see:

https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/
https://github.com/conda-forge/miniforge-images/blob/b5f19cb22e4c9e3a6524ae714cce8d4933e7765b/ubuntu/mambaforge_deprecation.sh

Suggested in

https://github.com/galaxyproject/galaxy/pull/19293#discussion_r1878522140
---
 lib/galaxy/tool_util/deps/mulled/invfile.lua | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/deps/mulled/invfile.lua b/lib/galaxy/tool_util/deps/mulled/invfile.lua
index 38ddc860cc3b..f7bef84d18b5 100644
--- a/lib/galaxy/tool_util/deps/mulled/invfile.lua
+++ b/lib/galaxy/tool_util/deps/mulled/invfile.lua
@@ -42,7 +42,7 @@ end
 
 local conda_image = VAR.CONDA_IMAGE
 if conda_image == '' then
-    conda_image = 'quay.io/condaforge/mambaforge:latest'
+    conda_image = 'quay.io/condaforge/miniforge3:latest'
 end
 
 local conda_bin = VAR.CONDA_BIN

From faa79047349b897985aef81f1aac3d73d5a2bc1e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 16 Dec 2024 17:47:35 +0100
Subject: [PATCH 19/28] Use correct label to display in ObjectStoreActions

---
 .../User/DiskUsage/Visualizations/ObjectStoreActions.vue        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/User/DiskUsage/Visualizations/ObjectStoreActions.vue b/client/src/components/User/DiskUsage/Visualizations/ObjectStoreActions.vue
index 2f28f1fcba8b..55d7a7c70d75 100644
--- a/client/src/components/User/DiskUsage/Visualizations/ObjectStoreActions.vue
+++ b/client/src/components/User/DiskUsage/Visualizations/ObjectStoreActions.vue
@@ -17,7 +17,7 @@ const props = defineProps<Props>();
 
 library.add(faChartBar);
 
-const label = computed(() => props.data.id);
+const label = computed(() => props.data.label);
 const viewDetailsIcon = computed(() => "chart-bar");
 
 const emit = defineEmits<{

From ea3626e3638d6171d399268954f2122741f37265 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 17 Dec 2024 08:18:08 +0100
Subject: [PATCH 20/28] Fix importing shared workflows with deeply nested
 subworkflows

We need to pass the user also to the workflow copy method when copying
subworkflow steps. Adds a few bonus type annotations that made it easier
to debug.

Fixes
https://sentry.galaxyproject.org/share/issue/454be6bbb98b43a1aa504309e1c6bc7b/::

```
NotNullViolation: null value in column "user_id" of relation "stored_workflow" violates not-null constraint
DETAIL:  Failing row contains (296863, 2024-12-16 17:04:34.329066, 2024-12-16 17:04:34.329067, null, null, TreeValGal bed to bigwig, f, f, null, f, null, t).

  File "sqlalchemy/engine/base.py", line 2116, in _exec_insertmany_context
    dialect.do_execute(
  File "sqlalchemy/engine/default.py", line 924, in do_execute
    cursor.execute(statement, parameters)
IntegrityError: (psycopg2.errors.NotNullViolation) null value in column "user_id" of relation "stored_workflow" violates not-null constraint
DETAIL:  Failing row contains (296863, 2024-12-16 17:04:34.329066, 2024-12-16 17:04:34.329067, null, null, TreeValGal bed to bigwig, f, f, null, f, null, t).

[SQL: INSERT INTO stored_workflow (create_time, update_time, user_id, latest_workflow_id, name, deleted, hidden, importable, slug, from_path, published) SELECT p0::TIMESTAMP WITHOUT TIME ZONE, p1::TIMESTAMP WITHOUT TIME ZONE, p2::INTEGER, p3::INTEGER, p4:: ... 1138 characters truncated ... p9, p10, sen_counter) ORDER BY sen_counter RETURNING stored_workflow.id, stored_workflow.id AS id__1]
[parameters: {'from_path__0': None, 'user_id__0': 91803, 'name__0': 'TreeValGalBaseOneHaplotype', 'create_time__0': datetime.datetime(2024, 12, 16, 17, 4, 34, 329062), 'update_time__0': datetime.datetime(2024, 12, 16, 17, 4, 34, 329065), 'deleted__0': False, 'published__0': False, 'importable__0': False, 'latest_workflow_id__0': None, 'hidden...
  File "galaxy/web/framework/middleware/error.py", line 167, in __call__
    app_iter = self.application(environ, sr_checker)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.11/site-packages/paste/httpexceptions.py", line 635, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 176, in __call__
    return self.handle_request(request_id, path_info, environ, start_response)
  File "galaxy/web/framework/base.py", line 271, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/web/framework/decorators.py", line 94, in decorator
    return func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/controllers/workflow.py", line 125, in imp
    self._import_shared_workflow(trans, stored)
  File "galaxy/webapps/base/controller.py", line 1161, in _import_shared_workflow
    session.commit()
  File "sqlalchemy/orm/scoping.py", line 597, in commit
    return self._proxied.commit()
  File "sqlalchemy/orm/session.py", line 2017, in commit
    trans.commit(_to_root=True)
  File "<string>", line 2, in commit
    # Copyright (C) 2005-2024 the SQLAlchemy authors and contributors
  File "sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
  File "sqlalchemy/orm/session.py", line 1302, in commit
    self._prepare_impl()
  File "<string>", line 2, in _prepare_impl
    # Copyright (C) 2005-2024 the SQLAlchemy authors and contributors
  File "sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
  File "sqlalchemy/orm/session.py", line 1277, in _prepare_impl
    self.session.flush()
  File "sqlalchemy/orm/session.py", line 4341, in flush
    self._flush(objects)
  File "sqlalchemy/orm/session.py", line 4476, in _flush
    with util.safe_reraise():
  File "sqlalchemy/util/langhelpers.py", line 146, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "sqlalchemy/orm/session.py", line 4437, in _flush
    flush_context.execute()
  File "sqlalchemy/orm/unitofwork.py", line 466, in execute
    rec.execute(self)
  File "sqlalchemy/orm/unitofwork.py", line 642, in execute
    util.preloaded.orm_persistence.save_obj(
  File "sqlalchemy/orm/persistence.py", line 93, in save_obj
    _emit_insert_statements(
  File "sqlalchemy/orm/persistence.py", line 1143, in _emit_insert_statements
    result = connection.execute(
  File "sqlalchemy/engine/base.py", line 1418, in execute
    return meth(
  File "sqlalchemy/sql/elements.py", line 515, in _execute_on_connection
    return connection._execute_clauseelement(
  File "sqlalchemy/engine/base.py", line 1640, in _execute_clauseelement
    ret = self._execute_context(
  File "sqlalchemy/engine/base.py", line 1844, in _execute_context
    return self._exec_insertmany_context(dialect, context)
  File "sqlalchemy/engine/base.py", line 2124, in _exec_insertmany_context
    self._handle_dbapi_exception(
  File "sqlalchemy/engine/base.py", line 2353, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "sqlalchemy/engine/base.py", line 2116, in _exec_insertmany_context
    dialect.do_execute(
  File "sqlalchemy/engine/default.py", line 924, in do_execute
    cursor.execute(statement, parameters)
```
---
 lib/galaxy/model/__init__.py          | 10 +++++-----
 lib/galaxy/webapps/base/controller.py |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 9843696f0db8..77480d6ffa75 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7616,7 +7616,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
         order_by=lambda: -Workflow.id,
         cascade_backrefs=False,
     )
-    latest_workflow = relationship(
+    latest_workflow: Mapped["Workflow"] = relationship(
         "Workflow",
         post_update=True,
         primaryjoin=(lambda: StoredWorkflow.latest_workflow_id == Workflow.id),
@@ -7722,7 +7722,7 @@ def show_in_tool_panel(self, user_id):
         )
         return bool(sa_session.scalar(stmt))
 
-    def copy_tags_from(self, target_user, source_workflow):
+    def copy_tags_from(self, target_user, source_workflow: "StoredWorkflow"):
         # Override to only copy owner tags.
         for src_swta in source_workflow.owner_tags:
             new_swta = src_swta.copy()
@@ -8238,10 +8238,10 @@ def copy_to(self, copied_step, step_mapping, user=None):
                 copied_step.subworkflow = subworkflow
                 copied_subworkflow = subworkflow
             else:
-                # Can this even happen, building a workflow with a subworkflow you don't own ?
-                copied_subworkflow = subworkflow.copy()
+                # Importing a shared workflow with a subworkflow step
+                copied_subworkflow = subworkflow.copy(user=user)
                 stored_workflow = StoredWorkflow(
-                    user, name=copied_subworkflow.name, workflow=copied_subworkflow, hidden=True
+                    user=user, name=copied_subworkflow.name, workflow=copied_subworkflow, hidden=True
                 )
                 copied_subworkflow.stored_workflow = stored_workflow
                 copied_step.subworkflow = copied_subworkflow
diff --git a/lib/galaxy/webapps/base/controller.py b/lib/galaxy/webapps/base/controller.py
index 83c3ae620560..4f5d85de86d1 100644
--- a/lib/galaxy/webapps/base/controller.py
+++ b/lib/galaxy/webapps/base/controller.py
@@ -1144,7 +1144,7 @@ def get_stored_workflow_steps(self, trans, stored_workflow: model.StoredWorkflow
             except exceptions.ToolMissingException:
                 pass
 
-    def _import_shared_workflow(self, trans, stored):
+    def _import_shared_workflow(self, trans, stored: model.StoredWorkflow):
         """Imports a shared workflow"""
         # Copy workflow.
         imported_stored = model.StoredWorkflow()

From 25db34e925579ea7f53d91854adabd561209c230 Mon Sep 17 00:00:00 2001
From: Matt Pawelczyk <mapk@amazon.com>
Date: Tue, 15 Oct 2024 15:37:43 +0000
Subject: [PATCH 21/28] Account that k8s pods may be uncounted yet.

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

diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
index 56fef20a0ecb..9b75870005d2 100644
--- a/lib/galaxy/jobs/runners/kubernetes.py
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -736,7 +736,10 @@ def check_watched_item(self, job_state):
             # as probably this means that the k8s API server hasn't
             # had time to fill in the object status since the
             # job was created only too recently.
-            if len(job.obj["status"]) == 0:
+            # It is possible that k8s didn't account for the status of the pods
+            # and they are in the uncountedTerminatedPods status. In this
+            # case we also need to wait a moment
+            if len(job.obj["status"]) == 0 or 'uncountedTerminatedPods' in job.obj["status"]:
                 return job_state
             if "succeeded" in job.obj["status"]:
                 succeeded = job.obj["status"]["succeeded"]

From cbeedf371c0e63c394433b1f91a2e984c883d991 Mon Sep 17 00:00:00 2001
From: Matt Pawelczyk <mapk@amazon.com>
Date: Tue, 15 Oct 2024 17:00:23 +0000
Subject: [PATCH 22/28] Fix linting

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

diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
index 9b75870005d2..9a358c107acd 100644
--- a/lib/galaxy/jobs/runners/kubernetes.py
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -739,7 +739,7 @@ def check_watched_item(self, job_state):
             # It is possible that k8s didn't account for the status of the pods
             # and they are in the uncountedTerminatedPods status. In this
             # case we also need to wait a moment
-            if len(job.obj["status"]) == 0 or 'uncountedTerminatedPods' in job.obj["status"]:
+            if len(job.obj["status"]) == 0 or "uncountedTerminatedPods" in job.obj["status"]:
                 return job_state
             if "succeeded" in job.obj["status"]:
                 succeeded = job.obj["status"]["succeeded"]

From c311092aad316805872670999538cada60f551f5 Mon Sep 17 00:00:00 2001
From: Matt Pawelczyk <125464188+mapk-amazon@users.noreply.github.com>
Date: Wed, 16 Oct 2024 20:33:45 +0200
Subject: [PATCH 23/28] Update lib/galaxy/jobs/runners/kubernetes.py

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 lib/galaxy/jobs/runners/kubernetes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
index 9a358c107acd..be3d4239ff79 100644
--- a/lib/galaxy/jobs/runners/kubernetes.py
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -739,7 +739,7 @@ def check_watched_item(self, job_state):
             # It is possible that k8s didn't account for the status of the pods
             # and they are in the uncountedTerminatedPods status. In this
             # case we also need to wait a moment
-            if len(job.obj["status"]) == 0 or "uncountedTerminatedPods" in job.obj["status"]:
+            if len(job.obj["status"]) == 0 or in job.obj["status"].get("uncountedTerminatedPods"):
                 return job_state
             if "succeeded" in job.obj["status"]:
                 succeeded = job.obj["status"]["succeeded"]

From df1bb9a53632402ccd14a041657068c568cd3883 Mon Sep 17 00:00:00 2001
From: Matt Pawelczyk <125464188+mapk-amazon@users.noreply.github.com>
Date: Wed, 16 Oct 2024 21:02:27 +0200
Subject: [PATCH 24/28] Update lib/galaxy/jobs/runners/kubernetes.py

Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
---
 lib/galaxy/jobs/runners/kubernetes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
index be3d4239ff79..68bbddc81ebb 100644
--- a/lib/galaxy/jobs/runners/kubernetes.py
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -739,7 +739,7 @@ def check_watched_item(self, job_state):
             # It is possible that k8s didn't account for the status of the pods
             # and they are in the uncountedTerminatedPods status. In this
             # case we also need to wait a moment
-            if len(job.obj["status"]) == 0 or in job.obj["status"].get("uncountedTerminatedPods"):
+            if len(job.obj["status"]) == 0 or job.obj["status"].get("uncountedTerminatedPods"):
                 return job_state
             if "succeeded" in job.obj["status"]:
                 succeeded = job.obj["status"]["succeeded"]

From 53944010fd38365de759215e65eb4cc86d52b7d9 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 16 Dec 2024 00:04:30 +0000
Subject: [PATCH 25/28] Use ``resource_path()`` to access
 datatypes_conf.xml.sample as a package resource

This required other changes included here as well:

1) Extend `parse_xml()` to accept a `Traversable` (i.e. the output of
   `resource_path()`.

Open the file before passing it to `etree.parse()`, since lxml's
implementation probably doesn't support a `Traversable`. This also
simplifies the exception handling, since the workaround for the missing
`errno` in the `OSError` exception is not needed any more.

------

2) Fix Galaxy startup when the ``data_manager_config_file`` config option
   is set to an empty value

When does this happen?
----------------------

planemo (which we use in the converters tests) set this option to an
empty value when not testing data managers:

https://github.com/galaxyproject/planemo/blob/master/planemo/galaxy/config.py#L452

This empty config value was resolved to the `path_resolves_to` directory
for this option.
With the change in 1) above, this results in the following traceback at
Galaxy startup:

```
Traceback (most recent call last):
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 68, in app_pair
    app = galaxy.app.UniverseApplication(global_conf=global_conf, is_webapp=True, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/app.py", line 777, in __init__
    self.data_managers = self._register_singleton(DataManagers)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/di.py", line 27, in _register_singleton
    instance = self[dep_type]
               ~~~~^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 381, in __getitem__
    return self.resolve(dep)
           ^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 265, in resolve
    return self._reflection_build_with_err_handling(dep_type, suppress_error)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 392, in _reflection_build_with_err_handling
    return self._reflection_build(dep_type)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 408, in _reflection_build
    return dep_type(**sub_deps)  # type: ignore
           ^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/tools/data_manager/manager.py", line 44, in __init__
    self.load_from_xml(filename)
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/tools/data_manager/manager.py", line 58, in load_from_xml
    tree = util.parse_xml(xml_filename)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/util/__init__.py", line 360, in parse_xml
    with source.open("rb") as f:
         ^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/pathlib.py", line 1013, in open
    return io.open(self, mode, buffering, encoding, errors, newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IsADirectoryError: [Errno 21] Is a directory: '/tmp/tmps2qq5htq'
```

Why is this a problem now?
--------------------------

Before this commit, `util.parse_xml()` was raising a `XMLSyntaxError`
exception if passed a directory, but now it raises an `IsADirectoryError`,
which is a subclass of `OSError` with errno 21.

As a consequence, when `load_from_xml()` in
lib/galaxy/tools/data_manager/manager.py
calls `util.parse_xml()` passing a directory, the resulting exception
is now re-raised in the `except OSError as e:` branch instead of
just being logged, which is actually good since this is a
misconfiguration.

Solutions
--------

- Do not resolve an empty/None path to the `path_resolves_to` directory.
- Do not check empty/None paths against root
- Adjst unit tests accordingly
- Raise an OSError if the `job_config_file` config option is set to null
  (previously this would be resolved to a directory, also raising an
  OSError when trying to open that as a file).

N.B.: This will also need to be fixed in Planemo by not setting the
`data_manager_config_file` option when not needed.
---
 lib/galaxy/config/__init__.py             |  8 +++++---
 lib/galaxy/jobs/__init__.py               |  2 ++
 lib/galaxy/tool_util/linters/datatypes.py |  7 +++++--
 lib/galaxy/util/__init__.py               | 25 +++++++++++++++--------
 test/unit/config/test_path_graph.py       |  6 +++---
 test/unit/config/test_path_resolves_to.py |  8 ++++----
 6 files changed, 36 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index d253b3d0d9b6..909df2ba1483 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -511,10 +511,10 @@ def resolve(key):
             if not parent:  # base case: nothing else needs resolving
                 return path
             parent_path = resolve(parent)  # recursively resolve parent path
-            if path is not None:
+            if path:
                 path = os.path.join(parent_path, path)  # resolve path
             else:
-                path = parent_path  # or use parent path
+                log.warning("Trying to resolve path for the '%s' option but it's empty/None", key)
 
             setattr(self, key, path)  # update property
             _cache[key] = path  # cache it!
@@ -538,7 +538,7 @@ def resolve(key):
             if self.is_set(key) and self.paths_to_check_against_root and key in self.paths_to_check_against_root:
                 self._check_against_root(key)
 
-    def _check_against_root(self, key):
+    def _check_against_root(self, key: str):
         def get_path(current_path, initial_path):
             # if path does not exist and was set as relative:
             if not self._path_exists(current_path) and not os.path.isabs(initial_path):
@@ -557,6 +557,8 @@ def get_path(current_path, initial_path):
             return current_path
 
         current_value = getattr(self, key)  # resolved path or list of resolved paths
+        if not current_value:
+            return
         if isinstance(current_value, list):
             initial_paths = listify(self._raw_config[key], do_strip=True)  # initial unresolved paths
             updated_paths = []
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 3e9a306e4116..f55562de63b0 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -384,6 +384,8 @@ def __init__(self, app: MinimalManagerApp):
                             f" release of Galaxy. Please convert to YAML at {self.app.config.job_config_file} or"
                             f" explicitly set `job_config_file` to {job_config_file} to remove this message"
                         )
+                if not job_config_file:
+                    raise OSError()
                 if ".xml" in job_config_file:
                     tree = load(job_config_file)
                     job_config_dict = self.__parse_job_conf_xml(tree)
diff --git a/lib/galaxy/tool_util/linters/datatypes.py b/lib/galaxy/tool_util/linters/datatypes.py
index 534868ed01ec..f05ae5c7ab23 100644
--- a/lib/galaxy/tool_util/linters/datatypes.py
+++ b/lib/galaxy/tool_util/linters/datatypes.py
@@ -2,6 +2,7 @@
 from typing import (
     Set,
     TYPE_CHECKING,
+    Union,
 )
 
 # from galaxy import config
@@ -10,15 +11,17 @@
     listify,
     parse_xml,
 )
+from galaxy.util.resources import resource_path
 
 if TYPE_CHECKING:
     from galaxy.tool_util.lint import LintContext
     from galaxy.tool_util.parser import ToolSource
+    from galaxy.util.resources import Traversable
 
-DATATYPES_CONF = os.path.join(os.path.dirname(__file__), "datatypes_conf.xml.sample")
+DATATYPES_CONF = resource_path(__package__, "datatypes_conf.xml.sample")
 
 
-def _parse_datatypes(datatype_conf_path: str) -> Set[str]:
+def _parse_datatypes(datatype_conf_path: Union[str, "Traversable"]) -> Set[str]:
     datatypes = set()
     tree = parse_xml(datatype_conf_path)
     root = tree.getroot()
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index d2c8617c08bd..797ba6f4428c 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -45,6 +45,7 @@
     Optional,
     overload,
     Tuple,
+    TYPE_CHECKING,
     TypeVar,
     Union,
 )
@@ -75,6 +76,7 @@
 LXML_AVAILABLE = True
 try:
     from lxml import etree
+    from lxml.etree import DocumentInvalid
 
     # lxml.etree.Element is a function that returns a new instance of the
     # lxml.etree._Element class. This class doesn't have a proper __init__()
@@ -123,6 +125,10 @@ def XML(text: Union[str, bytes]) -> Element:
         XML,
     )
 
+    class DocumentInvalid(Exception):  # type: ignore[no-redef]
+        pass
+
+
 from . import requests
 from .custom_logging import get_logger
 from .inflection import Inflector
@@ -142,6 +148,9 @@ def shlex_join(split_command):
         return " ".join(map(shlex.quote, split_command))
 
 
+if TYPE_CHECKING:
+    from galaxy.util.resources import Traversable
+
 inflector = Inflector()
 
 log = get_logger(__name__)
@@ -333,7 +342,10 @@ def unique_id(KEY_SIZE=128):
 
 
 def parse_xml(
-    fname: StrPath, strip_whitespace=True, remove_comments=True, schemafname: Union[StrPath, None] = None
+    fname: Union[StrPath, "Traversable"],
+    strip_whitespace: bool = True,
+    remove_comments: bool = True,
+    schemafname: Union[StrPath, None] = None,
 ) -> ElementTree:
     """Returns a parsed xml tree"""
     parser = None
@@ -348,8 +360,10 @@ def parse_xml(
             schema_root = etree.XML(schema_file.read())
             schema = etree.XMLSchema(schema_root)
 
+    source = Path(fname) if isinstance(fname, (str, os.PathLike)) else fname
     try:
-        tree = cast(ElementTree, etree.parse(str(fname), parser=parser))
+        with source.open("rb") as f:
+            tree = cast(ElementTree, etree.parse(f, parser=parser))
         root = tree.getroot()
         if strip_whitespace:
             for elem in root.iter("*"):
@@ -359,15 +373,10 @@ def parse_xml(
                     elem.tail = elem.tail.strip()
         if schema:
             schema.assertValid(tree)
-    except OSError as e:
-        if e.errno is None and not os.path.exists(fname):  # type: ignore[unreachable]
-            # lxml doesn't set errno
-            e.errno = errno.ENOENT  # type: ignore[unreachable]
-        raise
     except etree.ParseError:
         log.exception("Error parsing file %s", fname)
         raise
-    except etree.DocumentInvalid:
+    except DocumentInvalid:
         log.exception("Validation of file %s failed", fname)
         raise
     return tree
diff --git a/test/unit/config/test_path_graph.py b/test/unit/config/test_path_graph.py
index 02f33787081f..77afe7333c55 100644
--- a/test/unit/config/test_path_graph.py
+++ b/test/unit/config/test_path_graph.py
@@ -142,7 +142,7 @@ def test_resolves_to_invalid_type(monkeypatch):
 
 
 def test_resolves_with_empty_component(monkeypatch):
-    # A path can be None (root path is never None; may be asigned elsewhere)
+    # A path can be None (root path is never None; may be assigned elsewhere)
     mock_schema = {
         "path0": {
             "type": "str",
@@ -155,7 +155,7 @@ def test_resolves_with_empty_component(monkeypatch):
         "path2": {
             "type": "str",
             "default": "value2",
-            "path_resolves_to": "path1",
+            "path_resolves_to": "path0",
         },
     }
     monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(mock_schema))
@@ -163,5 +163,5 @@ def test_resolves_with_empty_component(monkeypatch):
 
     config = BaseAppConfiguration()
     assert config.path0 == "value0"
-    assert config.path1 == "value0"
+    assert config.path1 is None
     assert config.path2 == "value0/value2"
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index 97953b3d0787..d7e7dd0918d6 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -132,21 +132,21 @@ def test_kwargs_relative_path_old_prefix_for_other_option(mock_init):
 
 def test_kwargs_relative_path_old_prefix_empty_after_strip(mock_init):
     # Expect: use value from kwargs, strip old prefix, then resolve
-    new_path1 = "old-config"
+    new_path1 = "old-config/foo"
     config = BaseAppConfiguration(path1=new_path1)
 
-    assert config.path1 == "my-config/"  # stripped of old prefix, then resolved
+    assert config.path1 == "my-config/foo"  # stripped of old prefix, then resolved
     assert config.path2 == "my-data/my-data-files"  # stripped of old prefix, then resolved
     assert config.path3 == "my-other-files"  # no change
 
 
 def test_kwargs_set_to_null(mock_init):
-    # Expected: allow overriding with null, then resolve
+    # Expected: allow overriding with null
     # This is not a common scenario, but it does happen: one example is
     # `job_config` set to `None` when testing
     config = BaseAppConfiguration(path1=None)
 
-    assert config.path1 == "my-config"  # resolved
+    assert config.path1 is None
     assert config.path2 == "my-data/my-data-files"  # resolved
     assert config.path3 == "my-other-files"  # no change
 

From 2406c879f24f289da0a2f8dfbbb27eea36931911 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 18 Dec 2024 14:54:26 +0100
Subject: [PATCH 26/28] Make user a required argument

---
 lib/galaxy/model/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 77480d6ffa75..38aac43223e2 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7895,7 +7895,7 @@ def top_level_stored_workflow(self):
         """
         return self.top_level_workflow.stored_workflow
 
-    def copy(self, user=None):
+    def copy(self, user: User):
         """Copy a workflow for a new StoredWorkflow object.
 
         Pass user if user-specific information needed.
@@ -8206,7 +8206,7 @@ def workflow_output_for(self, output_name):
                 break
         return target_output
 
-    def copy_to(self, copied_step, step_mapping, user=None):
+    def copy_to(self, copied_step: "WorkflowStep", step_mapping: Dict[int, "WorkflowStep"], user: User):
         copied_step.order_index = self.order_index
         copied_step.type = self.type
         copied_step.tool_id = self.tool_id

From 173f17073618f7f8700a80e1cef49f4bc4715771 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 18 Dec 2024 18:33:45 +0100
Subject: [PATCH 27/28] Fix reactive reference for selection change warning
 dismissal

---
 .../CurrentHistory/HistoryOperations/SelectionChangeWarning.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionChangeWarning.vue b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionChangeWarning.vue
index cfb3c17149bb..3f1d7c8a468f 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionChangeWarning.vue
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionChangeWarning.vue
@@ -31,7 +31,7 @@ function onDoNotShowAgain() {
 watch(
     () => props.querySelectionBreak,
     () => {
-        dismissCountDown.value = showSelectionQueryBreakWarning ? dismissSecs.value : 0;
+        dismissCountDown.value = showSelectionQueryBreakWarning.value ? dismissSecs.value : 0;
     }
 );
 </script>

From c67ffe8c764ef29d5025dd00319bf68ba2ea9895 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 16 Dec 2024 15:02:48 +0000
Subject: [PATCH 28/28] Fix test_singularity_container_test test

(which started failing since ubuntu-latest was moved to 24.04)
by upgrading apptainer to >=1.3.3 to include
https://github.com/apptainer/apptainer/pull/2262 .

Fix:

```
>       assert "samtools:1.0--1" in results["passed"], results
E       AssertionError:
E       {'failed': [{'commands': ['python -c "import pyBigWig; assert(pyBigWig.numpy '
E                                 '== 1); assert(pyBigWig.remote == 1)"'],
E                    'container': 'pybigwig:0.3.22--py36h54a71a5_0',
E                    'errors': [{'command': 'python -c "import pyBigWig; '
E                                           'assert(pyBigWig.numpy == 1); '
E                                           'assert(pyBigWig.remote == 1)"',
E                                'output': '\x1b[91mERROR  : Could not write info to '
E                                          'setgroups: Permission denied\n'
E                                          '\x1b[0m\x1b[91mERROR  : Error while '
E                                          'waiting event for user namespace mappings: '
E                                          'no event received\n'
E                                          '\x1b[0m'},
E                               {'import': 'pyBigWig',
E                                'output': '\x1b[91mERROR  : Could not write info to '
E                                          'setgroups: Permission denied\n'
E                                          '\x1b[0m\x1b[91mERROR  : Error while '
E                                          'waiting event for user namespace mappings: '
E                                          'no event received\n'
E                                          '\x1b[0m'}],
E                    'import_lang': 'python -c',
E                    'imports': ['pyBigWig']},
E                   {'commands': ['samtools view --help 2>&1 | grep Notes > /dev/null'],
E                    'container': 'samtools:1.0--1',
E                    'errors': [{'command': 'samtools view --help 2>&1 | grep Notes > '
E                                           '/dev/null',
E                                'output': '\x1b[91mERROR  : Could not write info to '
E                                          'setgroups: Permission denied\n'
E                                          '\x1b[0m\x1b[91mERROR  : Error while '
E                                          'waiting event for user namespace mappings: '
E                                          'no event received\n'
E                                          '\x1b[0m'}],
E                    'import_lang': 'python -c'}],
E        'notest': ['yasm:1.3.0--0'],
E        'passed': []}
E       assert 'samtools:1.0--1' in []
```

Also:
- Improve assertion messages to facilitate debugging
---
 .github/workflows/mulled.yaml                               | 2 ++
 pytest.ini                                                  | 2 +-
 .../mulled/test_mulled_update_singularity_containers.py     | 6 +++---
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
index 4d33cc3febd7..6d36a454d807 100644
--- a/.github/workflows/mulled.yaml
+++ b/.github/workflows/mulled.yaml
@@ -44,6 +44,8 @@ jobs:
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-mulled
       - name: Install Apptainer's singularity
         uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.6  # https://github.com/eWaterCycle/setup-apptainer/pull/68
       - name: Install tox
         run: pip install tox
       - name: Run tests
diff --git a/pytest.ini b/pytest.ini
index 7c1d40306310..e2e406ef82ba 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,5 +1,5 @@
 [pytest]
-addopts = --doctest-continue-on-failure --verbosity=1
+addopts = --doctest-continue-on-failure --verbosity=1 --showlocals
 asyncio_mode = auto
 log_level = DEBUG
 # Install pytest-memray and set memray to true here to enable memory profiling of tests
diff --git a/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py b/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
index 728757b52f31..9ec4e47b44f8 100644
--- a/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
+++ b/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
@@ -46,6 +46,6 @@ def test_singularity_container_test(tmp_path) -> None:
         "singularity",
         tmp_path,
     )
-    assert "samtools:1.0--1" in results["passed"]
-    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"]
-    assert "yasm:1.3.0--0" in results["notest"]
+    assert "samtools:1.0--1" in results["passed"], results
+    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"], results
+    assert "yasm:1.3.0--0" in results["notest"], results