Add consistent support for ldda's, should probably re-consider this u…

…se case

client/src/components/Form/Elements/FormData/FormData.test.js

@@ -153,7 +153,7 @@ describe("FormData", () => {
         expect(wrapper.emitted().input.length).toEqual(1);
         const message = wrapper.findAll(".form-data-entry-label");
         expect(message.length).toBe(1);
-        expect(message.at(0).text()).toBe("1. dceName1");
+        expect(message.at(0).text()).toBe("1. dceName1 (dce)");
         const closeButton = wrapper.find(".alert .close");
         await closeButton.trigger("click");
         expect(wrapper.emitted().input[1][0]).toEqual(null);

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

@@ -191,7 +191,13 @@ const isDCE = computed(() => {
         return false;
     }
 });
-
+const isLDDA = computed(() => {
+    if (props.value && props.value.values.length > 0) {
+        return props.value.values.findIndex((v) => v.src !== SOURCE.LIBRARY_DATASET) === -1;
+    } else {
+        return false;
+    }
+});
 /**
  * Provides placeholder label for select field
  */
@@ -228,7 +234,8 @@ function handleIncoming(incoming: Record<string, unknown>, partial = true) {
                 const newHid = v.hid;
                 const newId = v.id;
                 const newName = v.name ? v.name : newId;
-                const newSrc = v.history_content_type === "dataset_collection" ? SOURCE.COLLECTION : SOURCE.DATASET;
+                const newSrc =
+                    v.src || (v.history_content_type === "dataset_collection" ? SOURCE.COLLECTION : SOURCE.DATASET);
                 const newValue = {
                     id: newId,
                     src: newSrc,
@@ -288,7 +295,9 @@ function matchOption(entry: DataOption) {
  */
 function matchName(entry: DataOption) {
     const option = matchOption(entry);
-    return option?.name || entry.id;
+    const name = option?.name || entry.id;
+    const src = option?.src || "unknown";
+    return `${name} (${src})`;
 }
 
 /**
@@ -310,8 +319,8 @@ function matchValues(entries: Array<DataOption>) {
  */
 function onBrowse() {
     if (currentVariant.value) {
-        const library = currentVariant.value.library;
-        const multiple = currentVariant.value.multiple;
+        const library = !!currentVariant.value.library;
+        const multiple = !!currentVariant.value.multiple;
         getGalaxyInstance().data.dialog(
             (response: Record<string, unknown>) => {
                 handleIncoming(response, false);
@@ -372,6 +381,8 @@ function setValue(val: Array<DataOption> | DataOption | null) {
             let sourceType: string | null = null;
             if (isDCE.value) {
                 sourceType = values[0].hda ? SOURCE.DATASET : SOURCE.COLLECTION;
+            } else if (isLDDA.value) {
+                sourceType = SOURCE.DATASET;
             } else {
                 sourceType = values[0].src;
             }
@@ -383,7 +394,7 @@ function setValue(val: Array<DataOption> | DataOption | null) {
             let batch: string = BATCH.DISABLED;
             if (variantIndex >= 0) {
                 const variantDetails = variant.value[variantIndex];
-                if (isDCE.value && variantDetails && variantDetails.batch) {
+                if ((isLDDA.value || isDCE.value) && variantDetails && variantDetails.batch) {
                     batch = variantDetails.batch;
                 } else {
                     // Switch to another field type if source differs from current field
@@ -414,7 +425,7 @@ onMounted(() => {
     eventBus.$on("waiting", (value: boolean) => {
         waiting.value = value;
     });
-    if (isDCE.value && props.value && props.value.values) {
+    if ((isLDDA.value || isDCE.value) && props.value && props.value.values) {
         setValue(matchValues(props.value.values));
     } else {
         setValue(currentValue.value);
@@ -439,10 +450,10 @@ watch(
         @dragleave.prevent="onDragLeave"
         @dragover.prevent="onDragOver"
         @drop.prevent="onDrop">
-        <b-alert v-if="isDCE" variant="info" dismissible show @dismissed="currentValue = null">
+        <b-alert v-if="isDCE || isLDDA" variant="info" dismissible show @dismissed="$emit('input', null)">
             <span v-localize class="font-weight-bold">Using the following datasets (dismiss to reset):</span>
             <div v-for="(v, vIndex) of props.value.values" :key="vIndex">
-                <span class="form-data-entry-label ml-2">{{ vIndex + 1 }}. {{ matchName(v) || v.id }}</span>
+                <span class="form-data-entry-label ml-2">{{ vIndex + 1 }}. {{ matchName(v) }}</span>
             </div>
         </b-alert>
         <div v-else>

client/src/components/Form/Elements/FormData/variants.ts

@@ -12,7 +12,7 @@ interface VariantInterface {
 export const BATCH = { DISABLED: "disabled", ENABLED: "enabled", LINKED: "linked" };
 
 /** Data source variations */
-export const SOURCE = { DATASET: "hda", COLLECTION: "hdca", COLLECTION_ELEMENT: "dce" };
+export const SOURCE = { DATASET: "hda", COLLECTION: "hdca", COLLECTION_ELEMENT: "dce", LIBRARY_DATASET: "ldda" };
 
 /** List of available data input variations */
 export const VARIANTS: Record<string, Array<VariantInterface>> = {

lib/galaxy/tools/parameters/basic.py

@@ -2137,6 +2137,9 @@ def from_json(self, value, trans, other_values=None):
         elif isinstance(value, (HistoryDatasetAssociation, LibraryDatasetDatasetAssociation)):
             rval.append(value)
         elif isinstance(value, dict) and "src" in value and "id" in value:
+            if value["src"] == "ldda":
+                decoded_id = trans.security.decode_id(value["id"])
+                rval.append(trans.sa_session.query(LibraryDatasetDatasetAssociation).get(decoded_id))
             if value["src"] == "hda":
                 decoded_id = trans.security.decode_id(value["id"])
                 rval.append(trans.sa_session.query(HistoryDatasetAssociation).get(decoded_id))
@@ -2272,7 +2275,7 @@ def to_dict(self, trans, other_values=None):
             # For consistency, should these just always be in the dict?
             d["min"] = self.min
             d["max"] = self.max
-        d["options"] = {"dce": [], "hda": [], "hdca": []}
+        d["options"] = {"dce": [], "ldda": [], "hda": [], "hdca": []}
         d["tag"] = self.tag
 
         # return dictionary without options if context is unavailable
@@ -2311,11 +2314,27 @@ def append_dce(dce):
                 }
             )
 
+        def append_ldda(ldda):
+            d["options"]["ldda"].append(
+                {
+                    "id": trans.security.encode_id(ldda.id),
+                    "name": ldda.name,
+                    "src": "ldda",
+                    "tags": [],
+                    "keep": True,
+                }
+            )
+
         # append DCE
         if isinstance(other_values.get(self.name), DatasetCollectionElement):
             dce = other_values[self.name]
             append_dce(dce)
 
+        # append LDDA
+        if isinstance(other_values.get(self.name), LibraryDatasetDatasetAssociation):
+            ldda = other_values[self.name]
+            append_ldda(ldda)
+
         # add datasets
         hda_list = util.listify(other_values.get(self.name))
         # Prefetch all at once, big list of visible, non-deleted datasets.
@@ -2337,6 +2356,8 @@ def append_dce(dce):
                 append(d["options"]["hda"], hda, f"({hda_state}) {hda.name}", "hda", True)
             elif isinstance(hda, DatasetCollectionElement):
                 append_dce(hda)
+            elif isinstance(hda, LibraryDatasetDatasetAssociation):
+                append_ldda(hda)
 
         # add dataset collections
         dataset_collection_matcher = dataset_matcher_factory.dataset_collection_matcher(dataset_matcher)

lib/galaxy_test/selenium/test_tool_form.py

@@ -243,7 +243,7 @@ def test_rerun_dataset_collection_element(self):
         self.hda_click_primary_action_button(1, "rerun")
         self.sleep_for(self.wait_types.UX_RENDER)
         entry_label = self.components.tool_form.parameter_data_entry_label(parameter="input1").wait_for_visible()
-        assert entry_label.text == "1. test0"
+        assert entry_label.text == "1. test0 (dce)"
         self.tool_form_execute()
         self.components.history_panel.collection_view.back_to_history.wait_for_and_click()
         self.history_panel_wait_for_hid_ok(9)