Merge branch 'release_24.2' into dev

client/src/components/Help/terms.yml

@@ -145,3 +145,5 @@ galaxy:
       A utility for uploading files to a Galaxy server from the command line. Use ``galaxy-upload`` to upload
       file(s) to a Galaxy server, and ``galaxy-history-search``, a helper utility to find Galaxy histories
       to pass to the ``galaxy-upload`` command.
+    ruleBased: |
+      Galaxy can bulk import lists & tables of URLs into datasets or collections using reproducible rules.

client/src/components/Masthead/Masthead.vue

@@ -191,7 +191,7 @@ onMounted(() => {
                         position: absolute;
                         left: 1.6rem;
                         top: 1.6rem;
-                        font-size: 0.4rem;
+                        font-size: 0.6rem;
                         font-weight: bold;
                     }
                 }

client/src/components/Panels/ToolPanel.test.ts

@@ -6,18 +6,32 @@ import MockAdapter from "axios-mock-adapter";
 import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
+import { ref } from "vue";
 
 import toolsList from "@/components/ToolsView/testData/toolsList.json";
 import toolsListInPanel from "@/components/ToolsView/testData/toolsListInPanel.json";
+import { useUserLocalStorage } from "@/composables/userLocalStorage";
+import { useToolStore } from "@/stores/toolStore";
 
-import viewsList from "./testData/viewsList.json";
+import viewsListJson from "./testData/viewsList.json";
 import { types_to_icons } from "./utilities";
 
 import ToolPanel from "./ToolPanel.vue";
 
+interface ToolPanelView {
+    id: string;
+    model_class: string;
+    name: string;
+    description: string | null;
+    view_type: string;
+    searchable: boolean;
+}
+
 const localVue = getLocalVue();
 
 const TEST_PANELS_URI = "/api/tool_panels";
+const DEFAULT_VIEW_ID = "default";
+const PANEL_VIEW_ERR_MSG = "Error loading panel view";
 
 jest.mock("@/composables/config", () => ({
     useConfig: jest.fn(() => ({
@@ -26,16 +40,59 @@ jest.mock("@/composables/config", () => ({
     })),
 }));
 
+jest.mock("@/composables/userLocalStorage", () => ({
+    useUserLocalStorage: jest.fn(() => ref(DEFAULT_VIEW_ID)),
+}));
+
 describe("ToolPanel", () => {
-    it("test navigation of tool panel views menu", async () => {
+    const viewsList = viewsListJson as Record<string, ToolPanelView>;
+
+    /** Mocks and stores a non-default panel view as the current panel view */
+    function storeNonDefaultView() {
+        // find a view in object viewsList that is not DEFAULT_VIEW_ID
+        const viewKey = Object.keys(viewsList).find((id) => id !== DEFAULT_VIEW_ID);
+        if (!viewKey) {
+            throw new Error("No non-default view found in viewsList");
+        }
+        const view = viewsList[viewKey];
+        if (!view) {
+            throw new Error(`View with key ${viewKey} not found in viewsList`);
+        }
+        // ref and useUserLocalStorage are already imported at the top
+        (useUserLocalStorage as jest.Mock).mockImplementation(() => ref(viewKey));
+        return { viewKey, view };
+    }
+
+    /**
+     * Sets up wrapper for ToolPanel component
+     * @param {String} errorView If provided, we mock an error for this view
+     * @param {Boolean} failDefault If true and error view is provided, we
+     *                              mock an error for the default view as well
+     * @returns wrapper
+     */
+    async function createWrapper(errorView = "", failDefault = false) {
         const axiosMock = new MockAdapter(axios);
         axiosMock
-            .onGet(/\/api\/tool_panels\/.*/)
-            .reply(200, toolsListInPanel)
             .onGet(`/api/tools?in_panel=False`)
             .replyOnce(200, toolsList)
             .onGet(TEST_PANELS_URI)
-            .reply(200, { default_panel_view: "default", views: viewsList });
+            .reply(200, { default_panel_view: DEFAULT_VIEW_ID, views: viewsList });
+
+        if (errorView) {
+            axiosMock.onGet(`/api/tool_panels/${errorView}`).reply(400, { err_msg: PANEL_VIEW_ERR_MSG });
+            if (errorView !== DEFAULT_VIEW_ID && !failDefault) {
+                axiosMock.onGet(`/api/tool_panels/${DEFAULT_VIEW_ID}`).reply(200, toolsListInPanel);
+            } else if (failDefault) {
+                axiosMock.onGet(`/api/tool_panels/${DEFAULT_VIEW_ID}`).reply(400, { err_msg: PANEL_VIEW_ERR_MSG });
+            }
+        } else {
+            // mock response for all panel views
+            axiosMock.onGet(/\/api\/tool_panels\/.*/).reply(200, toolsListInPanel);
+        }
+
+        // setting this because for the default view, we just show "Tools" as the name
+        // even though the backend returns "Full Tool Panel"
+        viewsList[DEFAULT_VIEW_ID]!.name = "Tools";
 
         const pinia = createPinia();
         const wrapper = mount(ToolPanel as object, {
@@ -56,12 +113,17 @@ describe("ToolPanel", () => {
 
         await flushPromises();
 
+        return { wrapper };
+    }
+
+    it("test navigation of tool panel views menu", async () => {
+        const { wrapper } = await createWrapper();
         // there is a panel view selector initially collapsed
         expect(wrapper.find(".panel-view-selector").exists()).toBe(true);
         expect(wrapper.find(".dropdown-menu.show").exists()).toBe(false);
 
         // Test: starts up with a default panel view, click to open menu
-        expect(wrapper.find("#toolbox-heading").text()).toBe("Tools");
+        expect(wrapper.find("#toolbox-heading").text()).toBe(viewsList[DEFAULT_VIEW_ID]!.name);
         await wrapper.find("#toolbox-heading").trigger("click");
         await flushPromises();
 
@@ -76,7 +138,7 @@ describe("ToolPanel", () => {
         for (const [key, value] of Object.entries(viewsList)) {
             // find dropdown item
             const currItem = dropdownMenu.find(`[data-panel-id='${key}']`);
-            if (key !== "default") {
+            if (key !== DEFAULT_VIEW_ID) {
                 // Test: check if the panel view has appropriate description
                 const description = currItem.attributes().title || null;
                 expect(description).toBe(value.description);
@@ -93,12 +155,50 @@ describe("ToolPanel", () => {
                 expect(panelViewIcon.classes()).toContain(
                     `fa-${types_to_icons[value.view_type as keyof typeof types_to_icons]}`
                 );
-                expect(wrapper.find("#toolbox-heading").text()).toBe(value.name);
+                expect(wrapper.find("#toolbox-heading").text()).toBe(value!.name);
             } else {
                 // Test: check if the default panel view is already selected, and no icon
                 expect(currItem.find(".fa-check").exists()).toBe(true);
                 expect(wrapper.find("[data-description='panel view header icon']").exists()).toBe(false);
             }
         }
     });
+
+    it("initializes non default current panel view correctly", async () => {
+        const { viewKey, view } = storeNonDefaultView();
+
+        const { wrapper } = await createWrapper();
+
+        // starts up with a non default panel view
+        expect(wrapper.find("#toolbox-heading").text()).toBe(view!.name);
+        const toolStore = useToolStore();
+        expect(toolStore.currentPanelView).toBe(viewKey);
+    });
+
+    it("changes panel to default if current panel view throws error", async () => {
+        const { viewKey, view } = storeNonDefaultView();
+
+        const { wrapper } = await createWrapper(viewKey);
+
+        // does not initialize non default panel view, and changes to default
+        expect(wrapper.find("#toolbox-heading").text()).not.toBe(view!.name);
+        expect(wrapper.find("#toolbox-heading").text()).toBe(viewsList[DEFAULT_VIEW_ID]!.name);
+        const toolStore = useToolStore();
+        expect(toolStore.currentPanelView).toBe(DEFAULT_VIEW_ID);
+
+        // toolbox loaded
+        expect(wrapper.find('[data-description="panel toolbox"]').exists()).toBe(true);
+    });
+
+    it("simply shows error if even default panel view throws error", async () => {
+        const { viewKey } = storeNonDefaultView();
+
+        const { wrapper } = await createWrapper(viewKey, true);
+
+        // toolbox not loaded
+        expect(wrapper.find('[data-description="panel toolbox"]').exists()).toBe(false);
+
+        // error message shown
+        expect(wrapper.find('[data-description="tool panel error message"]').text()).toBe(PANEL_VIEW_ERR_MSG);
+    });
 });

client/src/components/Panels/ToolPanel.vue

@@ -2,10 +2,11 @@
 import { faCaretDown } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { storeToRefs } from "pinia";
-import { computed, onMounted, ref, watch } from "vue";
+import { computed, ref, watch } from "vue";
 
 import { useToolStore } from "@/stores/toolStore";
 import localize from "@/utils/localization";
+import { errorMessageAsString, rethrowSimple } from "@/utils/simple-error";
 
 import { types_to_icons } from "./utilities";
 
@@ -37,17 +38,20 @@ const { currentPanelView, defaultPanelView, isPanelPopulated, loading, panel, pa
 const loadingView = ref<string | undefined>(undefined);
 const query = ref("");
 const showAdvanced = ref(false);
+const errorMessage = ref<string | undefined>(undefined);
 
-onMounted(async () => {
+initializeToolPanel();
+async function initializeToolPanel() {
     try {
         await toolStore.fetchPanelViews();
         await initializeTools();
     } catch (error) {
         console.error(error);
+        errorMessage.value = errorMessageAsString(error);
     } finally {
         arePanelsFetched.value = true;
     }
-});
+}
 
 watch(
     () => currentPanelView.value,
@@ -118,6 +122,8 @@ async function initializeTools() {
         await toolStore.initCurrentPanelView(defaultPanelView.value);
     } catch (error: any) {
         console.error("ToolPanel - Intialize error:", error);
+        errorMessage.value = errorMessageAsString(error);
+        rethrowSimple(error);
     }
 }
 
@@ -206,6 +212,11 @@ watch(
             @onInsertModule="onInsertModule"
             @onInsertWorkflow="onInsertWorkflow"
             @onInsertWorkflowSteps="onInsertWorkflowSteps" />
+        <div v-else-if="errorMessage" data-description="tool panel error message">
+            <b-alert class="m-2" variant="danger" show>
+                {{ errorMessage }}
+            </b-alert>
+        </div>
         <div v-else>
             <b-badge class="alert-info w-100">
                 <LoadingSpan message="Loading Toolbox" />

client/src/components/Upload/UploadModal.vue

@@ -1,5 +1,5 @@
 <script setup>
-import { BModal } from "bootstrap-vue";
+import { BCarousel, BCarouselSlide, BModal } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { ref, watch } from "vue";
 
@@ -13,7 +13,7 @@ import ExternalLink from "../ExternalLink.vue";
 import HelpText from "../Help/HelpText.vue";
 import UploadContainer from "./UploadContainer.vue";
 
-const { currentUser } = storeToRefs(useUserStore());
+const { currentUser, hasSeenUploadHelp } = storeToRefs(useUserStore());
 const { currentHistoryId, currentHistory } = useUserHistories(currentUser);
 
 const { config, isConfigLoaded } = useConfig();
@@ -65,7 +65,14 @@ async function open(overrideOptions) {
 
 watch(
     () => showModal.value,
-    (modalShown) => setIframeEvents(["galaxy_main"], modalShown)
+    (modalShown) => {
+        setIframeEvents(["galaxy_main"], modalShown);
+
+        // once the modal closes the first time a user sees help, we never show it again
+        if (!modalShown && !hasSeenUploadHelp.value) {
+            hasSeenUploadHelp.value = true;
+        }
+    }
 );
 
 defineExpose({
@@ -91,12 +98,33 @@ defineExpose({
                         to <b>{{ currentHistory.name }}</b>
                     </span>
                 </h2>
-                <span>
-                    <ExternalLink href="https://galaxy-upload.readthedocs.io/en/latest/"> Click here </ExternalLink>
-                    to check out the
-                    <HelpText uri="galaxy.upload.galaxyUploadUtil" text="galaxy-upload" />
-                    util!
-                </span>
+
+                <BCarousel v-if="!hasSeenUploadHelp" :interval="4000" no-touch>
+                    <BCarouselSlide>
+                        <template v-slot:img>
+                            <span class="text-nowrap float-right">
+                                <ExternalLink href="https://galaxy-upload.readthedocs.io/en/latest/">
+                                    Click here
+                                </ExternalLink>
+                                to check out the
+                                <HelpText uri="galaxy.upload.galaxyUploadUtil" text="galaxy-upload" />
+                                util!
+                            </span>
+                        </template>
+                    </BCarouselSlide>
+                    <BCarouselSlide>
+                        <template v-slot:img>
+                            <span class="text-nowrap float-right">
+                                More info on <HelpText uri="galaxy.upload.ruleBased" text="Rule-based" /> uploads
+                                <ExternalLink
+                                    href="https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/upload-rules/tutorial.html">
+                                    here
+                                </ExternalLink>
+                                .
+                            </span>
+                        </template>
+                    </BCarouselSlide>
+                </BCarousel>
             </div>
         </template>
         <UploadContainer

client/src/composables/persistentRef.ts

@@ -32,7 +32,7 @@ export function syncRefToLocalStorage<T>(key: string, refToSync: Ref<T>) {
         window.localStorage.setItem(key, stringified);
     };
 
-    if (stored) {
+    if (stored !== null) {
         try {
             refToSync.value = parse(stored, typeof refToSync.value as "string" | "number" | "boolean" | "object");
         } catch (e) {