Merge branch 'release_24.1' into dev

client/src/api/index.ts

@@ -211,6 +211,10 @@ export function isHistorySummaryExtended(history: AnyHistory): history is Histor
     return "contents_active" in history && "user_id" in history;
 }
 
+export function isHistoryItem(item: object): item is HistoryItemSummary {
+    return item && "history_content_type" in item;
+}
+
 type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
 
 /** Represents a registered user.**/

client/src/api/schema/schema.ts

@@ -315,7 +315,7 @@ export interface paths {
         post: operations["file_sources__test_new_instance_configuration"];
     };
     "/api/file_source_instances/{user_file_source_id}": {
-        /** Get a list of persisted file source instances defined by the requesting user. */
+        /** Get a persisted user file source instance. */
         get: operations["file_sources__instances_get"];
         /** Update or upgrade user file source instance. */
         put: operations["file_sources__instances_update"];
@@ -1266,7 +1266,7 @@ export interface paths {
         post: operations["object_stores__test_new_instance_configuration"];
     };
     "/api/object_store_instances/{user_object_store_id}": {
-        /** Get a persisted object store instances owned by the requesting user. */
+        /** Get a persisted user object store instance. */
         get: operations["object_stores__instances_get"];
         /** Update or upgrade user object store instance. */
         put: operations["object_stores__instances_update"];
@@ -14966,7 +14966,7 @@ export interface operations {
         };
     };
     file_sources__instances_get: {
-        /** Get a list of persisted file source instances defined by the requesting user. */
+        /** Get a persisted user file source instance. */
         parameters: {
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -20890,7 +20890,7 @@ export interface operations {
         };
     };
     object_stores__instances_get: {
-        /** Get a persisted object store instances owned by the requesting user. */
+        /** Get a persisted user object store instance. */
         parameters: {
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {

client/src/components/ConfigTemplates/InstanceDropdown.vue

@@ -42,7 +42,7 @@ const emit = defineEmits<{
                 :href="routeUpgrade"
                 @keypress="router.push(routeUpgrade)"
                 @click.prevent="router.push(routeUpgrade)">
-                <FontAwesomeIcon icon="arrowUp" />
+                <FontAwesomeIcon :icon="faArrowUp" />
                 <span v-localize>Upgrade</span>
             </button>
             <button

client/src/components/DataDialog/DataDialog.vue

@@ -23,6 +23,7 @@ interface Record {
 interface Props {
     allowUpload?: boolean;
     callback?: (results: Array<Record>) => void;
+    filterOkState?: boolean;
     format?: string;
     library?: boolean;
     modalStatic?: boolean;
@@ -34,6 +35,7 @@ interface Props {
 const props = withDefaults(defineProps<Props>(), {
     allowUpload: true,
     callback: () => {},
+    filterOkState: false,
     format: "download",
     library: true,
     modalStatic: false,
@@ -90,7 +92,11 @@ function formatRows() {
 
 /** Returns the default url i.e. the url of the current history **/
 function getHistoryUrl() {
-    return `${getAppRoot()}api/histories/${props.history}/contents?deleted=false`;
+    let queryString = "&q=deleted&qv=false";
+    if (props.filterOkState) {
+        queryString += "&q=state-eq&qv=ok";
+    }
+    return `${getAppRoot()}api/histories/${props.history}/contents?v=dev${queryString}`;
 }
 
 /** Called when the modal is hidden */

client/src/components/Dataset/DatasetAsImage/DatasetAsImage.vue

@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { computedAsync } from "@vueuse/core";
 import { computed } from "vue";
 
 import { type PathDestination, useDatasetPathDestination } from "@/composables/datasetPathDestination";
@@ -24,13 +25,23 @@ const imageUrl = computed(() => {
 
     return pathDestination.value?.fileLink;
 });
+
+const isImage = computedAsync(async () => {
+    if (!imageUrl.value) {
+        return null;
+    }
+    const res = await fetch(imageUrl.value);
+    const buff = await res.blob();
+    return buff.type.startsWith("image/");
+}, null);
 </script>
 
 <template>
     <div>
         <div v-if="imageUrl" class="w-100 p-2">
             <b-card nobody body-class="p-1">
                 <b-img :src="imageUrl" fluid />
+                <span v-if="!isImage" class="text-danger">This dataset does not appear to be an image.</span>
             </b-card>
         </div>
         <div v-else>

client/src/components/History/CurrentHistory/HistoryPanel.vue

@@ -3,7 +3,7 @@ import { BAlert } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, onMounted, type Ref, ref, set as VueSet, unref, watch } from "vue";
 
-import { type HistoryItemSummary, type HistorySummaryExtended, userOwnsHistory } from "@/api";
+import { type HistoryItemSummary, type HistorySummaryExtended, isHistoryItem, userOwnsHistory } from "@/api";
 import { copyDataset } from "@/api/datasets";
 import ExpandedItems from "@/components/History/Content/ExpandedItems";
 import SelectedItems from "@/components/History/Content/SelectedItems";
@@ -225,28 +225,11 @@ function dragSameHistory() {
 
 function getDragData() {
     const eventStore = useEventStore();
-    const multiple = eventStore.multipleDragData;
-    let data: HistoryItemSummary[] | undefined;
-    let historyId: string | undefined;
-    try {
-        if (multiple) {
-            const dragData = eventStore.getDragData() as Record<string, HistoryItemSummary>;
-            // set historyId to the first history_id in the multiple drag data
-            const firstItem = Object.values(dragData)[0];
-            if (firstItem) {
-                historyId = firstItem.history_id;
-            }
-            data = Object.values(dragData);
-        } else {
-            data = [eventStore.getDragData() as HistoryItemSummary];
-            if (data[0]) {
-                historyId = data[0].history_id;
-            }
-        }
-    } catch (error) {
-        // this was not a valid object for this dropzone, ignore
-    }
-    return { data, sameHistory: historyId === props.history.id, multiple };
+    const dragItems = eventStore.getDragItems();
+    // Filter out any non-history items
+    const historyItems = dragItems?.filter((item: any) => isHistoryItem(item)) as HistoryItemSummary[];
+    const historyId = historyItems?.[0]?.history_id;
+    return { data: historyItems, sameHistory: historyId === props.history.id, multiple: historyItems?.length > 1 };
 }
 
 function getHighlight(item: HistoryItemSummary) {

client/src/components/History/Multiple/MultipleViewList.vue

@@ -6,7 +6,7 @@ import { computed, type Ref, ref } from "vue";
 //@ts-ignore missing typedefs
 import VirtualList from "vue-virtual-scroll-list";
 
-import { HistoryItemSummary } from "@/api";
+import { HistoryItemSummary, isHistoryItem } from "@/api";
 import { copyDataset } from "@/api/datasets";
 import { useAnimationFrameResizeObserver } from "@/composables/sensors/animationFrameResizeObserver";
 import { useAnimationFrameScroll } from "@/composables/sensors/animationFrameScroll";
@@ -75,37 +75,21 @@ async function onDrop(evt: any) {
     }
     processingDrop.value = true;
     showDropZone.value = false;
-    let data: HistoryItemSummary[] | undefined;
-    let originalHistoryId: string | undefined;
-    const multiple = eventStore.multipleDragData;
-    try {
-        if (multiple) {
-            const dragData = eventStore.getDragData() as Record<string, HistoryItemSummary>;
-            // set originalHistoryId to the first history_id in the multiple drag data
-            const firstItem = Object.values(dragData)[0];
-            if (firstItem) {
-                originalHistoryId = firstItem.history_id;
-            }
-            data = Object.values(dragData);
-        } else {
-            data = [eventStore.getDragData() as HistoryItemSummary];
-            if (data[0]) {
-                originalHistoryId = data[0].history_id;
-            }
-        }
-    } catch (error) {
-        // this was not a valid object for this dropzone, ignore
-    }
+    const dragItems = eventStore.getDragItems();
+    // Filter out any non-history items
+    const historyItems = dragItems?.filter((item: any) => isHistoryItem(item)) as HistoryItemSummary[];
+    const multiple = historyItems.length > 1;
+    const originalHistoryId = historyItems?.[0]?.history_id;
 
-    if (data && originalHistoryId) {
+    if (historyItems && originalHistoryId) {
         await historyStore.createNewHistory();
         const currentHistoryId = historyStore.currentHistoryId;
 
         let datasetCount = 0;
         let collectionCount = 0;
         if (currentHistoryId) {
             // iterate over the data array and copy each item to the new history
-            for (const item of data) {
+            for (const item of historyItems) {
                 const dataSource = item.history_content_type === "dataset" ? "hda" : "hdca";
                 await copyDataset(item.id, currentHistoryId, item.history_content_type, dataSource)
                     .then(() => {

client/src/components/Panels/VisualizationPanel.vue

@@ -93,9 +93,10 @@ onMounted(() => {
             <BAlert v-else v-localize variant="info" show> No matching visualization found. </BAlert>
         </div>
         <DataDialog
-            v-if="showDataDialog"
+            v-if="currentHistoryId && showDataDialog"
             format=""
             :history="currentHistoryId"
+            :filter-ok-state="true"
             @onOk="createVisualization"
             @onCancel="showDataDialog = false" />
     </ActivityPanel>

client/src/entry/analysis/App.vue

@@ -167,7 +167,9 @@ export default {
             this.$router.confirmation = this.confirmation;
         },
         currentHistory() {
-            this.Galaxy.currHistoryPanel.syncCurrentHistoryModel(this.currentHistory);
+            if (!this.embedded) {
+                this.Galaxy.currHistoryPanel.syncCurrentHistoryModel(this.currentHistory);
+            }
         },
     },
     mounted() {

client/src/stores/eventStore.ts

@@ -22,6 +22,13 @@ export const useEventStore = defineStore("eventStore", () => {
         return dragData.value;
     }
 
+    function getDragItems(): EventData[] {
+        if (!dragData.value) {
+            return [];
+        }
+        return multipleDragData.value ? (Object.values(dragData.value) as EventData[]) : [dragData.value];
+    }
+
     function setDragData(data: EventData, multiple = false) {
         dragData.value = data;
         multipleDragData.value = multiple;
@@ -32,6 +39,7 @@ export const useEventStore = defineStore("eventStore", () => {
         multipleDragData,
         clearDragData,
         getDragData,
+        getDragItems,
         setDragData,
     };
 });

client/src/utils/mountVueComponent.js

@@ -4,7 +4,7 @@
 
 import BootstrapVue from "bootstrap-vue";
 import { iconPlugin, localizationPlugin, vueRxShortcutPlugin } from "components/plugins";
-import { createPinia, PiniaVuePlugin } from "pinia";
+import { getActivePinia, PiniaVuePlugin } from "pinia";
 import Vue from "vue";
 
 // Load Pinia
@@ -22,18 +22,17 @@ Vue.use(vueRxShortcutPlugin);
 // font-awesome svg icon registration/loading
 Vue.use(iconPlugin);
 
-// Create Pinia
-const pinia = createPinia();
-
 export const mountVueComponent = (ComponentDefinition) => {
     const component = Vue.extend(ComponentDefinition);
+    const pinia = getActivePinia();
     return (propsData, el) => new component({ propsData, el, pinia });
 };
 
 export const replaceChildrenWithComponent = (el, ComponentDefinition, propsData = {}) => {
     const container = document.createElement("div");
     el.replaceChildren(container);
     const component = Vue.extend(ComponentDefinition);
+    const pinia = getActivePinia();
     const mountFn = (propsData, el) => new component({ propsData, el, pinia });
     return mountFn(propsData, container);
 };

client/src/utils/setDrag.ts

@@ -1,9 +1,9 @@
 /**
  * Helper to configure datatransfer for drag & drop operations
  */
-import { useEventStore } from "@/stores/eventStore";
+import { type EventData, useEventStore } from "@/stores/eventStore";
 
-export function setDrag(evt: DragEvent, data = null, multiple = false) {
+export function setDrag(evt: DragEvent, data?: EventData, multiple = false) {
     const eventStore = useEventStore();
     if (data) {
         evt.dataTransfer?.setData("text", JSON.stringify([data]));

config/plugins/webhooks/demo/tour_generator/tour_generator.js

@@ -13,7 +13,8 @@ window.TourGenerator = Backbone.View.extend({
         $("#execute").attr("tour_id", "execute");
         Toastr.info("Tour generation might take some time.");
         $.getJSON(
-            `${Galaxy.root}api/webhooks/tour_generator/data/`, {
+            `${Galaxy.root}api/webhooks/tour_generator/data/`,
+            {
                 tool_id: toolId,
                 tool_version: toolVersion,
             },
@@ -31,7 +32,7 @@ window.TourGenerator = Backbone.View.extend({
             }
         );
     },
-    _getData: function(obj, attempts = 20, delay = 1000) {
+    _getData: function (obj, attempts = 20, delay = 1000) {
         let datasets = [];
         _.each(obj.data.hids, (hid) => {
             Galaxy.currHistoryPanel.collection.each((dataset) => {
@@ -49,8 +50,8 @@ window.TourGenerator = Backbone.View.extend({
             console.error("Some of the test datasets cannot be found in the history.");
         }
     },
-    _generateTour: function (data) {
-        const tour = window.bundleEntries.runTour("auto.generated", data);
+    _generateTour: async function (data) {
+        const tour = await window.bundleEntries.runTour("auto.generated", data);
         // Force ending the tour when pressing the Execute button
         $("#execute").on("mousedown", () => {
             if (tour) {

lib/galaxy/config/sample/galaxy.yml.sample

@@ -1283,7 +1283,7 @@ galaxy:
   # defaults to "GLOBAL" if not set or the
   # `geographical_server_location_code` value is invalid or unsupported.
   # To see a full list of supported locations, visit
-  # https://galaxyproject.org/admin/carbon_emissions
+  # https://docs.galaxyproject.org/en/master/admin/carbon_emissions.html
   #geographical_server_location_code: GLOBAL
 
   # The estimated power usage effectiveness of the data centre housing

lib/galaxy/files/templates/examples/testing_multi_version_with_secrets.yml

@@ -0,0 +1,34 @@
+# a template with multiple versions that could be coherent for unit/integration
+# testing upgrading object stores templates
+- id: secure_disk
+  version: 0
+  name: Secure Disk
+  description: Secure Disk Bound to You
+  secrets:
+    sec1:
+      help: This is my test secret.
+  configuration:
+    type: posix
+    root: '/data/secure/{{ user.username }}/{{ secrets.sec1 }}/aftersec'
+- id: secure_disk
+  version: 1
+  name: Secure Disk
+  description: Secure Disk Bound to You
+  secrets:
+    sec1:
+      help: This is my test secret.
+    sec2:
+      help: This is my test secret 2.
+  configuration:
+    type: posix
+    root: '/data/secure/{{ user.username }}/{{ secrets.sec1 }}/{{ secrets.sec2 }}'
+- id: secure_disk
+  version: 2
+  name: Secure Disk
+  description: Secure Disk Bound to You
+  secrets:
+    sec2:
+      help: This is my test secret 2.
+  configuration:
+    type: posix
+    root: '/data/secure/{{ user.username }}/newbar/{{ secrets.sec2 }}'