Merge pull request galaxyproject#18022 from davelopez/add_zenodo_inte…

…gration

Add Zenodo integration

client/src/api/remoteFiles.ts

@@ -7,6 +7,7 @@ import { fetcher } from "@/api/schema/fetcher";
  * - `source` - allows to select a source plugin root and doesn't list its contents
  */
 export type FileSourceBrowsingMode = "file" | "directory" | "source";
+export type FilesSourcePlugin = components["schemas"]["FilesSourcePlugin"];
 export type BrowsableFilesSourcePlugin = components["schemas"]["BrowsableFilesSourcePlugin"];
 export type RemoteFile = components["schemas"]["RemoteFile"];
 export type RemoteDirectory = components["schemas"]["RemoteDirectory"];

client/src/components/Common/ExportRDMForm.test.ts

@@ -2,7 +2,7 @@ import { getLocalVue } from "@tests/jest/helpers";
 import { mount, Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 
-import { CreatedEntry } from "@/api/remoteFiles";
+import { type BrowsableFilesSourcePlugin, CreatedEntry } from "@/api/remoteFiles";
 import { mockFetcher } from "@/api/schema/__mocks__";
 
 import ExportRDMForm from "./ExportRDMForm.vue";
@@ -25,11 +25,13 @@ const FAKE_ENTRY: CreatedEntry = {
     external_link: "http://example.com",
 };
 
-async function initWrapper() {
+async function initWrapper(fileSource?: BrowsableFilesSourcePlugin) {
     mockFetcher.path("/api/remote_files").method("post").mock({ data: FAKE_ENTRY });
 
-    const wrapper = mount(ExportRDMForm, {
-        propsData: {},
+    const wrapper = mount(ExportRDMForm as object, {
+        propsData: {
+            fileSource,
+        },
         localVue,
     });
     await flushPromises();
@@ -100,8 +102,53 @@ describe("ExportRDMForm", () => {
         });
     });
 
-    async function selectExportChoice(choice: string) {
-        const exportChoice = wrapper.find(`#radio-${choice}`);
+    describe("Pre-select specific File Source", () => {
+        beforeEach(async () => {
+            const specificFileSource: BrowsableFilesSourcePlugin = {
+                id: "test-file-source",
+                label: "Test File Source",
+                doc: "Test File Source Description",
+                uri_root: "gxfiles://test-file-source",
+                writable: true,
+                browsable: true,
+                type: "rdm",
+            };
+            wrapper = await initWrapper(specificFileSource);
+        });
+
+        it("enables the create new record button only by setting the record name", async () => {
+            await selectExportChoice("new", "test-file-source");
+            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeTruthy();
+
+            await setRecordNameInput(FAKE_RECORD_NAME);
+
+            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeFalsy();
+        });
+
+        it("displays the export to this record button when the create new record button is clicked", async () => {
+            await selectExportChoice("new", "test-file-source");
+            expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeFalsy();
+
+            await setRecordNameInput(FAKE_RECORD_NAME);
+            await clickCreateNewRecordButton();
+
+            expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeTruthy();
+        });
+
+        it("emits an export event when the export to new record button is clicked", async () => {
+            await selectExportChoice("new", "test-file-source");
+            await setFileNameInput("test file name");
+            await setRecordNameInput(FAKE_RECORD_NAME);
+            await clickCreateNewRecordButton();
+
+            await wrapper.find(EXPORT_TO_NEW_RECORD_BTN).trigger("click");
+            expect(wrapper.emitted("export")).toBeTruthy();
+        });
+    });
+
+    async function selectExportChoice(choice: string, fileSourceId?: string) {
+        const suffix = fileSourceId ? `${fileSourceId}` : "any";
+        const exportChoice = wrapper.find(`#radio-${choice}-${suffix}`);
         await exportChoice.setChecked(true);
     }
 

client/src/components/Common/ExportRDMForm.vue

@@ -2,11 +2,18 @@
 import { BButton, BCard, BFormGroup, BFormInput, BFormRadio, BFormRadioGroup } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import { CreatedEntry, createRemoteEntry, FilterFileSourcesOptions } from "@/api/remoteFiles";
+import {
+    BrowsableFilesSourcePlugin,
+    CreatedEntry,
+    createRemoteEntry,
+    FilterFileSourcesOptions,
+} from "@/api/remoteFiles";
 import { useToast } from "@/composables/toast";
 import localize from "@/utils/localization";
 import { errorMessageAsString } from "@/utils/simple-error";
 
+import { fileSourcePluginToItem } from "../FilesDialog/utilities";
+
 import ExternalLink from "@/components/ExternalLink.vue";
 import FilesInput from "@/components/FilesDialog/FilesInput.vue";
 
@@ -17,13 +24,19 @@ interface Props {
     clearInputAfterExport?: boolean;
     defaultRecordName?: string;
     defaultFilename?: string;
+    /**
+     * If undefined, the user will need to select a repository to export to,
+     * otherwise this file source will be pre-selected.
+     */
+    fileSource?: BrowsableFilesSourcePlugin;
 }
 
 const props = withDefaults(defineProps<Props>(), {
     what: "archive",
     clearInputAfterExport: false,
     defaultRecordName: "",
     defaultFilename: "",
+    fileSource: undefined,
 });
 
 const emit = defineEmits<{
@@ -35,7 +48,7 @@ type ExportChoice = "existing" | "new";
 const includeOnlyRDMCompatible: FilterFileSourcesOptions = { include: ["rdm"] };
 
 const recordUri = ref<string>("");
-const sourceUri = ref<string>("");
+const sourceUri = ref<string>(props.fileSource?.uri_root ?? "");
 const fileName = ref<string>(props.defaultFilename);
 const exportChoice = ref<ExportChoice>("new");
 const recordName = ref<string>(props.defaultRecordName);
@@ -53,6 +66,9 @@ const recordNameDescription = computed(() => localize("Give the new record a nam
 const namePlaceholder = computed(() => localize("File name"));
 const recordNamePlaceholder = computed(() => localize("Record name"));
 
+const uniqueSourceId = computed(() => props.fileSource?.id ?? "any");
+const fileSourceAsItem = computed(() => (props.fileSource ? fileSourcePluginToItem(props.fileSource) : undefined));
+
 function doExport() {
     emit("export", recordUri.value, fileName.value);
 
@@ -72,7 +88,7 @@ async function doCreateRecord() {
 
 function clearInputs() {
     recordUri.value = "";
-    sourceUri.value = "";
+    sourceUri.value = props.fileSource?.uri_root ?? "";
     fileName.value = "";
     newEntry.value = undefined;
 }
@@ -84,10 +100,17 @@ function clearInputs() {
             <BFormInput id="file-name-input" v-model="fileName" :placeholder="namePlaceholder" required />
         </BFormGroup>
 
+        <p>
+            Your {{ what }} needs to be uploaded to an existing <i>draft</i> record. You will need to create a
+            <b>new record</b> or select an existing <b>draft record</b> and then export your {{ what }} to it.
+        </p>
+
         <BFormRadioGroup v-model="exportChoice" class="export-radio-group">
-            <BFormRadio id="radio-new" v-localize name="exportChoice" value="new"> Export to new record </BFormRadio>
+            <BFormRadio :id="`radio-new-${uniqueSourceId}`" v-localize name="exportChoice" value="new">
+                Export to new record
+            </BFormRadio>
 
-            <BFormRadio id="radio-existing" v-localize name="exportChoice" value="existing">
+            <BFormRadio :id="`radio-existing-${uniqueSourceId}`" v-localize name="exportChoice" value="existing">
                 Export to existing draft record
             </BFormRadio>
         </BFormRadioGroup>
@@ -123,6 +146,7 @@ function clearInputs() {
             </div>
             <div v-else>
                 <BFormGroup
+                    v-if="!props.fileSource"
                     id="fieldset-record-new"
                     label-for="source-selector"
                     :description="repositoryRecordDescription"
@@ -172,7 +196,8 @@ function clearInputs() {
                     v-model="recordUri"
                     mode="directory"
                     :require-writable="true"
-                    :filter-options="includeOnlyRDMCompatible" />
+                    :filter-options="fileSource ? undefined : includeOnlyRDMCompatible"
+                    :selected-item="fileSourceAsItem" />
             </BFormGroup>
 
             <BButton

client/src/components/FilesDialog/FilesDialog.vue

@@ -3,15 +3,14 @@ import { BAlert } from "bootstrap-vue";
 import Vue, { computed, onMounted, ref } from "vue";
 
 import {
-    BrowsableFilesSourcePlugin,
     browseRemoteFiles,
     FileSourceBrowsingMode,
     FilterFileSourcesOptions,
     getFileSources,
     RemoteEntry,
 } from "@/api/remoteFiles";
 import { UrlTracker } from "@/components/DataDialog/utilities";
-import { isSubPath } from "@/components/FilesDialog/utilities";
+import { fileSourcePluginToItem, isSubPath } from "@/components/FilesDialog/utilities";
 import { SELECTION_STATES, type SelectionItem } from "@/components/SelectionDialog/selectionTypes";
 import { useConfig } from "@/composables/config";
 import { errorMessageAsString } from "@/utils/simple-error";
@@ -33,6 +32,8 @@ interface FilesDialogProps {
     multiple?: boolean;
     /** Whether to show only writable sources */
     requireWritable?: boolean;
+    /** Optional selected item to start browsing from */
+    selectedItem?: SelectionItem;
 }
 
 const props = withDefaults(defineProps<FilesDialogProps>(), {
@@ -42,6 +43,7 @@ const props = withDefaults(defineProps<FilesDialogProps>(), {
     mode: "file",
     multiple: false,
     requireWritable: false,
+    selectedItem: undefined,
 });
 
 const { config, isConfigLoaded } = useConfig();
@@ -233,7 +235,7 @@ function load(record?: SelectionItem) {
             .then((results) => {
                 const convertedItems = results
                     .filter((item) => !props.requireWritable || item.writable)
-                    .map(fileSourcePluginToRecord);
+                    .map(fileSourcePluginToItem);
                 items.value = convertedItems;
                 formatRows();
                 optionsShow.value = true;
@@ -290,17 +292,6 @@ function entryToRecord(entry: RemoteEntry): SelectionItem {
     return result;
 }
 
-function fileSourcePluginToRecord(plugin: BrowsableFilesSourcePlugin): SelectionItem {
-    const result = {
-        id: plugin.id,
-        label: plugin.label,
-        details: plugin.doc,
-        isLeaf: false,
-        url: plugin.uri_root,
-    };
-    return result;
-}
-
 /** select all files in current folder**/
 function onSelectAll() {
     if (!currentDirectory.value) {
@@ -343,7 +334,7 @@ function onOk() {
 }
 
 onMounted(() => {
-    load();
+    load(props.selectedItem);
 });
 </script>
 

client/src/components/FilesDialog/FilesInput.vue

@@ -5,11 +5,14 @@ import { computed } from "vue";
 import { FileSourceBrowsingMode, FilterFileSourcesOptions } from "@/api/remoteFiles";
 import { filesDialog } from "@/utils/data";
 
+import { SelectionItem } from "../SelectionDialog/selectionTypes";
+
 interface Props {
     value: string;
     mode?: FileSourceBrowsingMode;
     requireWritable?: boolean;
     filterOptions?: FilterFileSourcesOptions;
+    selectedItem?: SelectionItem;
 }
 
 interface SelectableFile {
@@ -20,6 +23,7 @@ const props = withDefaults(defineProps<Props>(), {
     mode: "file",
     requireWritable: false,
     filterOptions: undefined,
+    selectedItem: undefined,
 });
 
 const emit = defineEmits<{
@@ -40,6 +44,7 @@ const selectFile = () => {
         mode: props.mode,
         requireWritable: props.requireWritable,
         filterOptions: props.filterOptions,
+        selectedItem: props.selectedItem,
     };
     filesDialog((selected: SelectableFile) => {
         currentValue.value = selected?.url;

client/src/components/FilesDialog/utilities.ts

@@ -1,3 +1,7 @@
+import type { BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
+
+import type { SelectionItem } from "../SelectionDialog/selectionTypes";
+
 export const isSubPath = (originPath: string, destinationPath: string) => {
     return subPathCondition(ensureTrailingSlash(originPath), ensureTrailingSlash(destinationPath));
 };
@@ -9,3 +13,14 @@ function ensureTrailingSlash(path: string) {
 function subPathCondition(originPath: string, destinationPath: string) {
     return originPath !== destinationPath && destinationPath.startsWith(originPath);
 }
+
+export function fileSourcePluginToItem(plugin: BrowsableFilesSourcePlugin): SelectionItem {
+    const result = {
+        id: plugin.id,
+        label: plugin.label,
+        details: plugin.doc,
+        isLeaf: false,
+        url: plugin.uri_root,
+    };
+    return result;
+}

client/src/components/History/Export/HistoryExport.test.ts

@@ -6,7 +6,7 @@ import { setActivePinia } from "pinia";
 
 import type { HistorySummary } from "@/api";
 import { fetchHistoryExportRecords } from "@/api/histories.export";
-import type { components } from "@/api/schema";
+import type { FilesSourcePlugin } from "@/api/remoteFiles";
 import { mockFetcher } from "@/api/schema/__mocks__";
 import {
     EXPIRED_STS_DOWNLOAD_RECORD,
@@ -32,8 +32,7 @@ const FAKE_HISTORY = {
 
 const REMOTE_FILES_API_ENDPOINT = new RegExp("/api/remote_files/plugins");
 
-type FilesSourcePluginList = components["schemas"]["FilesSourcePlugin"][];
-const REMOTE_FILES_API_RESPONSE: FilesSourcePluginList = [
+const REMOTE_FILES_API_RESPONSE: FilesSourcePlugin[] = [
     {
         id: "test-posix-source",
         type: "posix",
@@ -57,7 +56,7 @@ async function mountHistoryExport() {
         (_history_id: string) => FAKE_HISTORY as HistorySummary
     );
 
-    const wrapper = shallowMount(HistoryExport, {
+    const wrapper = shallowMount(HistoryExport as object, {
         propsData: { historyId: FAKE_HISTORY_ID },
         localVue,
         pinia,
@@ -121,4 +120,22 @@ describe("HistoryExport.vue", () => {
         expect(wrapper.find("#direct-download-tab").exists()).toBe(true);
         expect(wrapper.find("#file-source-tab").exists()).toBe(false);
     });
+
+    it("should display the ZENODO tab if the Zenodo plugin is available", async () => {
+        const zenodoPlugin: FilesSourcePlugin = {
+            id: "zenodo",
+            type: "rdm",
+            label: "Zenodo",
+            doc: "For testing",
+            writable: true,
+            browsable: true,
+        };
+        mockFetcher
+            .path(REMOTE_FILES_API_ENDPOINT)
+            .method("get")
+            .mock({ data: [zenodoPlugin] });
+        const wrapper = await mountHistoryExport();
+
+        expect(wrapper.find("#zenodo-file-source-tab").exists()).toBe(true);
+    });
 });