Add new Upload Modal Dialog

client/src/components/DataDialog/DataDialog.vue

@@ -1,11 +1,14 @@
 <script setup lang="ts">
 import { faUpload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BBadge } from "bootstrap-vue";
 import { onMounted, type Ref, ref, watch } from "vue";
 import Vue from "vue";
 
+import type { DataOption } from "@/components/Form/Elements/FormData/types";
 import type { SelectionItem } from "@/components/SelectionDialog/selectionTypes";
 import { useGlobalUploadModal } from "@/composables/globalUploadModal";
+import { useUploadMethodModal } from "@/composables/upload/useUploadMethodModal";
 import { useUrlTracker } from "@/composables/urlTracker";
 import { getAppRoot } from "@/onload/loadConfig";
 import { errorMessageAsString } from "@/utils/simple-error";
@@ -20,14 +23,16 @@ type Record = SelectionItem;
 
 interface Props {
     allowUpload?: boolean;
-    callback?: (results: Array<Record>) => void;
+    callback?: (results: Record[] | DataOption[]) => void;
     filterOkState?: boolean;
     filterByTypeIds?: string[];
     format?: string;
     library?: boolean;
     multiple?: boolean;
     title?: string;
     history: string;
+    /** Optional formats to constrain the upload modal */
+    uploadModalFormats?: string[];
 }
 
 const props = withDefaults(defineProps<Props>(), {
@@ -39,6 +44,7 @@ const props = withDefaults(defineProps<Props>(), {
     library: true,
     multiple: false,
     title: "",
+    uploadModalFormats: undefined,
 });
 
 const emit = defineEmits<{
@@ -48,6 +54,7 @@ const emit = defineEmits<{
 }>();
 
 const { openGlobalUploadModal } = useGlobalUploadModal();
+const { openUploadModal } = useUploadMethodModal();
 
 const errorMessage = ref("");
 const filter = ref("");
@@ -125,7 +132,7 @@ function onClick(record: Record) {
 function onOk() {
     const results = model.finalize();
     modalShow.value = false;
-    props.callback(results);
+    props.callback?.(results);
     emit("onOk", results);
 }
 
@@ -135,7 +142,7 @@ function onOpen(record: Record) {
 }
 
 /** Called when user decides to upload new data */
-function onUpload() {
+function onLegacyUpload() {
     const propsData = {
         multiple: props.multiple,
         format: props.format,
@@ -148,6 +155,21 @@ function onUpload() {
     emit("onUpload");
 }
 
+async function onBetaUpload() {
+    const result = await openUploadModal({
+        formats: props.uploadModalFormats,
+        multiple: props.multiple,
+        hideTips: true,
+    });
+    modalShow.value = false;
+    if (!result.cancelled) {
+        const uploadedOptions = result.toDataOptions();
+        props.callback?.(uploadedOptions);
+        emit("onOk", uploadedOptions);
+    }
+    emit("onUpload");
+}
+
 /** Performs server request to retrieve data records **/
 function load(url?: string) {
     if (url) {
@@ -207,10 +229,14 @@ watch(
         @onOpen="onOpen"
         @onUndo="load()">
         <template v-slot:buttons>
-            <GButton v-if="allowUpload" size="small" @click="onUpload">
+            <GButton v-if="allowUpload" size="small" class="mr-1" @click="onLegacyUpload">
                 <FontAwesomeIcon :icon="faUpload" />
                 Upload
             </GButton>
+            <GButton v-if="allowUpload" size="small" title="Try our new upload experience" @click="onBetaUpload">
+                <FontAwesomeIcon :icon="faUpload" />
+                <span v-localize>New upload<BBadge variant="warning" class="ml-1">Beta</BBadge></span>
+            </GButton>
         </template>
     </SelectionDialog>
 </template>

client/src/components/FilesDialog/utilities.ts

@@ -25,3 +25,10 @@ export function fileSourcePluginToItem(plugin: BrowsableFilesSourcePlugin): Sele
     };
     return result;
 }
+
+/**
+ * Normalize SelectionDialog's Model.finalize() return value (single item or array) into an array.
+ */
+export function selectionToArray(selection: SelectionItem | SelectionItem[]): SelectionItem[] {
+    return Array.isArray(selection) ? selection : selection ? [selection] : [];
+}

client/src/components/Form/Elements/FormData/FormData.vue

@@ -28,7 +28,7 @@ import { type EventData, useEventStore } from "@/stores/eventStore";
 import { orList } from "@/utils/strings";
 
 import type { DataOption, ExtendedCollectionType } from "./types";
-import { containsDataOption } from "./types";
+import { containsDataOption, isDataOption } from "./types";
 import { BATCH, SOURCE, VARIANTS } from "./variants";
 
 import FormSelection from "../FormSelection.vue";
@@ -38,13 +38,25 @@ import FormDataWorkflowRunTabs from "./FormDataWorkflowRunTabs.vue";
 import FormSelect from "@/components/Form/Elements/FormSelect.vue";
 import HelpText from "@/components/Help/HelpText.vue";
 
+type HistoryOrCollectionItem = HistoryItemSummary | DCESummary;
+
+/**
+ * These are raw API items that need to be converted to DataOption format.
+ */
+type SingleOrMultipleHistoryItems = HistoryOrCollectionItem | HistoryOrCollectionItem[];
+
+/**
+ * Response types from the data dialog callback.
+ * DataOption[] is returned by the beta upload path for fresh uploads.
+ * SingleOrMultipleHistoryItems (HistoryItemSummary and DCESummary) are returned for dataset/collection selection.
+ */
+type DialogResponse = DataOption[] | SingleOrMultipleHistoryItems;
+
 type SelectOption = {
     label: string;
     value: DataOption | null;
 };
 
-type HistoryOrCollectionItem = HistoryItemSummary | DCESummary;
-
 const props = withDefaults(
     defineProps<{
         loading?: boolean;
@@ -225,6 +237,10 @@ const formattedOptions = computed(() => {
                 // check if option (with same id) is already in result, if yes replace it with keepOption
                 const existingOptionIndex = result.findIndex((v) => v.value?.id === option.value?.id);
                 if (existingOptionIndex >= 0) {
+                    const existingOption = result[existingOptionIndex];
+                    if (existingOption?.value && shouldPreferCanonicalOption(existingOption.value, option.value)) {
+                        return;
+                    }
                     result[existingOptionIndex] = option;
                 } else {
                     result.unshift(option);
@@ -351,8 +367,16 @@ function getSourceType(val: DataOption) {
     }
 }
 
-/** Add values from drag/drop or data dialog sources */
-function handleIncoming(incoming: Record<string, unknown> | Record<string, unknown>[], partial = true) {
+/**
+ * Handle incoming data from sources that require validation and transformation.
+ * This includes drag-drop operations and data dialog selections.
+ * Validates datatype compatibility, source type compatibility, and converts to DataOption format.
+ *
+ * @param incoming - The incoming data objects to process
+ * @param partial - If true, merge with existing selection; if false, replace selection
+ * @returns true if processing succeeded, false otherwise
+ */
+function handleIncoming(incoming: SingleOrMultipleHistoryItems, partial = true) {
     if (incoming) {
         const values = Array.isArray(incoming) ? incoming : [incoming];
 
@@ -478,6 +502,81 @@ function toDataOption(item: HistoryOrCollectionItem): DataOption | null {
     return newValue;
 }
 
+/**
+ * Normalize an uploaded option by finding matching options in existing props.
+ * Returns the canonical option if found, otherwise returns the uploaded option.
+ */
+function normalizeOption(option: DataOption): DataOption {
+    const keepKey = `${option.id}_${option.src}`;
+    const existingOptions = props.options?.[option.src];
+    const foundOption = existingOptions?.find((existing) => existing.id === option.id);
+
+    if (foundOption) {
+        return foundOption;
+    }
+
+    // Cache new option in keepOptions if not already present
+    if (!isInKeepOptions(keepKey, option)) {
+        keepOptions[keepKey] = {
+            label: `${option.hid || "Selected"}: ${option.name}`,
+            value: option,
+        };
+        keepOptionsUpdate.value++;
+    }
+
+    return option;
+}
+
+/**
+ * Normalize an array of uploaded options, preferring existing matches.
+ */
+function normalizeUploadedOptions(options: DataOption[]): DataOption[] {
+    return options.map(normalizeOption);
+}
+
+/**
+ * Update currentValue based on the current variant configuration.
+ * For multiple dataset fields, merges new options. Otherwise, selects the first option.
+ */
+function updateCurrentValue(options: DataOption[]): void {
+    const config = currentVariant.value;
+
+    if (config?.src === SOURCE.DATASET && config.multiple) {
+        // Merge new options into existing selection, avoiding duplicates
+        const merged = currentValue.value ? [...currentValue.value] : [];
+        for (const option of options) {
+            if (!containsDataOption(merged, option)) {
+                merged.push(option);
+            }
+        }
+        currentValue.value = merged;
+    } else {
+        // Single selection: use first option
+        currentValue.value = [options[0]!];
+    }
+}
+
+/**
+ * Handle data options freshly uploaded through the upload dialog.
+ * Normalizes options against existing props and updates the current selection.
+ */
+function handleUploadedDataOptions(uploadedOptions: DataOption[]): void {
+    if (!uploadedOptions?.length) {
+        return;
+    }
+
+    const normalized = normalizeUploadedOptions(uploadedOptions);
+    updateCurrentValue(normalized);
+}
+
+function isUnavailableName(name: string | undefined): boolean {
+    return Boolean(name && name.toLowerCase().startsWith("(unavailable)"));
+}
+
+function shouldPreferCanonicalOption(canonical: DataOption, keep: DataOption): boolean {
+    return (isUnavailableName(keep.name) && !isUnavailableName(canonical.name)) || (!keep.hid && !!canonical.hid);
+}
+
 /**
  * Check if the new value is already in the keepOptions.
  * This doesn't only check if the value is already stored by the `keepKey`, but also if the new value
@@ -495,23 +594,35 @@ function isInKeepOptions(keepKey: string, newValue: DataOption): boolean {
 }
 
 /**
- * Open file dialog
+ * Callback handler for the data dialog.
+ * Routes responses to appropriate handlers based on their type.
+ *
+ * @param response - The response from the data dialog
+ */
+function onDataDialogResponse(response: DialogResponse): void {
+    // The data dialog's beta upload path returns DataOption[] directly
+    if (isDataOptionArray(response)) {
+        handleUploadedDataOptions(response);
+        return;
+    }
+    // Handle responses that require validation and transformation
+    handleIncoming(response, false);
+}
+
+/**
+ * Open file dialog for data selection or upload.
  */
 function onBrowse() {
     if (currentVariant.value) {
         const library = !!currentVariant.value.library;
         const multiple = !!currentVariant.value.multiple;
-        getGalaxyInstance().data.dialog(
-            (response: Record<string, unknown>) => {
-                handleIncoming(response, false);
-            },
-            {
-                allowUpload: true,
-                format: null,
-                library,
-                multiple,
-            },
-        );
+        const options = {
+            allowUpload: true,
+            format: null,
+            library,
+            multiple,
+        };
+        getGalaxyInstance().data.dialog(onDataDialogResponse, options);
     }
 }
 
@@ -716,6 +827,10 @@ function isHistoryOrCollectionItem(item: EventData): item is HistoryOrCollection
     return isHistoryItem(item) || isDCE(item);
 }
 
+function isDataOptionArray(value: unknown): value is DataOption[] {
+    return Array.isArray(value) && value.every((item) => isDataOption(item as object));
+}
+
 /**
  * Helper function to handle collection type changes safely
  */
@@ -792,7 +907,10 @@ function onDragLeave(evt: DragEvent) {
 
 function onDrop(e: DragEvent) {
     if (dragData.value.length) {
-        if (handleIncoming(dragData.value, dragData.value.length === 1)) {
+        // Filter to only valid history/collection items
+        const filteredItems = dragData.value.filter(isHistoryOrCollectionItem) as HistoryOrCollectionItem[];
+        const partial = filteredItems.length === 1;
+        if (handleIncoming(filteredItems, partial)) {
             currentHighlighting.value = "success";
             if (props.workflowRun) {
                 workflowTab.value = "view";
@@ -895,10 +1013,13 @@ const noOptionsWarningMessage = computed(() => {
                 :collection-types="props.collectionTypes"
                 :current-source="currentSource || undefined"
                 :is-populated="currentValue && currentValue.length > 0"
+                :extensions="props.extensions"
+                :multiple="Boolean(currentVariant?.multiple)"
                 show-field-options
                 :show-view-create-options="props.workflowRun && !usingSimpleSelect"
                 :workflow-tab.sync="workflowTab"
                 @create-collection-type="handleCollectionTypeChange"
+                @uploaded-data="handleUploadedDataOptions"
                 @on-browse="onBrowse"
                 @set-current-field="(value) => (currentField = value)" />
 
@@ -946,9 +1067,12 @@ const noOptionsWarningMessage = computed(() => {
                 :collection-types="props.collectionTypes"
                 :current-source="currentSource || undefined"
                 :is-populated="currentValue && currentValue.length > 0"
+                :extensions="props.extensions"
+                :multiple="Boolean(currentVariant?.multiple)"
                 show-view-create-options
                 :workflow-tab.sync="workflowTab"
-                @create-collection-type="handleCollectionTypeChange" />
+                @create-collection-type="handleCollectionTypeChange"
+                @uploaded-data="handleUploadedDataOptions" />
         </div>
 
         <FormDataExtensions