[23.1] Fix delete collection + elements

client/src/components/History/Content/ContentItem.vue

@@ -63,7 +63,7 @@
                     :state="state"
                     :item-urls="itemUrls"
                     :keyboard-selectable="expandDataset"
-                    @delete="$emit('delete')"
+                    @delete="onDelete"
                     @display="onDisplay"
                     @showCollectionInfo="onShowCollectionInfo"
                     @edit="onEdit"
@@ -234,6 +234,9 @@ export default {
                 this.$router.push(this.itemUrls.display, { title: this.name });
             }
         },
+        onDelete(recursive = false) {
+            this.$emit("delete", this.item, recursive);
+        },
         onDragStart(evt) {
             setDrag(evt, this.item);
         },

client/src/components/History/Content/ContentOptions.vue

@@ -1,5 +1,5 @@
 <template>
-    <span class="align-self-start btn-group">
+    <span class="align-self-start btn-group align-items-baseline">
         <!-- Special case for collections -->
         <b-button
             v-if="isCollection && canShowCollectionDetails"
@@ -43,8 +43,21 @@
             title="Delete"
             size="sm"
             variant="link"
-            @click.stop="$emit('delete')">
-            <icon icon="trash" />
+            @click.stop="onDelete($event)">
+            <icon v-if="isDataset" icon="trash" />
+            <b-dropdown v-else ref="deleteCollectionMenu" size="sm" variant="link" no-caret toggle-class="p-0 m-0">
+                <template v-slot:button-content>
+                    <icon icon="trash" />
+                </template>
+                <b-dropdown-item title="Delete collection Only" @click.prevent.stop="onDeleteItem">
+                    <icon icon="file" />
+                    Collection only
+                </b-dropdown-item>
+                <b-dropdown-item title="Delete collection and elements" @click.prevent.stop="onDeleteItemRecursively">
+                    <icon icon="copy" />
+                    Collection and elements
+                </b-dropdown-item>
+            </b-dropdown>
         </b-button>
         <b-button
             v-if="writable && isHistoryItem && isDeleted"
@@ -130,6 +143,26 @@ export default {
                 this.$emit("display");
             }
         },
+        onDelete() {
+            if (this.isCollection) {
+                this.$refs.deleteCollectionMenu.show();
+            } else {
+                this.onDeleteItem();
+            }
+        },
+        onDeleteItem() {
+            this.$emit("delete");
+        },
+        onDeleteItemRecursively() {
+            const recursive = true;
+            this.$emit("delete", recursive);
+        },
     },
 };
 </script>
+<style lang="css">
+.dropdown-menu .dropdown-item {
+    font-weight: normal;
+}
+</style>
+```

client/src/components/History/Content/GenericItem.vue

@@ -12,7 +12,7 @@
                 :is-dataset="item.history_content_type == 'dataset' || item.element_type == 'hda'"
                 @update:expand-dataset="expandDataset = $event"
                 @view-collection="viewCollection = !viewCollection"
-                @delete="onDelete(item)"
+                @delete="onDelete"
                 @toggleHighlights="onHighlight(item)"
                 @undelete="onUndelete(item)"
                 @unhide="onUnhide(item)" />
@@ -74,8 +74,8 @@ export default {
     },
     methods: {
         ...mapActions(useHistoryStore, ["applyFilters"]),
-        onDelete(item) {
-            deleteContent(item);
+        onDelete(item, recursive = false) {
+            deleteContent(item, { recursive: recursive });
         },
         onUndelete(item) {
             updateContentFields(item, { deleted: false });

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

@@ -127,7 +127,7 @@
                                     @update:expand-dataset="setExpanded(item, $event)"
                                     @update:selected="setSelected(item, $event)"
                                     @view-collection="$emit('view-collection', item, currentOffset)"
-                                    @delete="onDelete(item)"
+                                    @delete="onDelete"
                                     @undelete="onUndelete(item)"
                                     @unhide="onUnhide(item)" />
                             </template>
@@ -357,9 +357,9 @@ export default {
                 this.loading = false;
             }
         },
-        onDelete(item) {
+        onDelete(item, recursive = false) {
             this.setInvisible(item);
-            deleteContent(item);
+            deleteContent(item, { recursive: recursive });
         },
         onHideSelection(selectedItems) {
             selectedItems.forEach((item) => {

lib/galaxy/managers/hdcas.py

@@ -7,6 +7,12 @@
 import logging
 from typing import Dict
 
+from sqlalchemy import (
+    false,
+    func,
+    select,
+)
+
 from galaxy import model
 from galaxy.managers import (
     annotatable,
@@ -103,6 +109,32 @@ def update_attributes(self, content, payload: Dict):
         # pre-requisite checked that attributes are valid
         self.map_datasets(content, fn=lambda item, *args: set_collection_attributes(item, payload.items()))
 
+    def delete(self, item, flush=True, **kwargs):
+        super().delete(item, flush=flush, **kwargs)
+        self.map_datasets(item, fn=self._delete_hda_if_orphaned_and_hidden)
+
+    def _delete_hda_if_orphaned_and_hidden(self, dataset, *parents):
+        if isinstance(dataset, model.HistoryDatasetAssociation):
+            if not dataset.deleted and not dataset.purged and not dataset.visible:
+                if not self._is_hda_used_in_multiple_active_collections(dataset):
+                    super().delete(dataset, flush=False)
+
+    def _is_hda_used_in_multiple_active_collections(self, dataset: model.HistoryDatasetAssociation):
+        stmt = (
+            select(func.count(model.DatasetCollectionElement.id))
+            .join(
+                model.HistoryDatasetCollectionAssociation,
+                model.DatasetCollectionElement.dataset_collection_id
+                == model.HistoryDatasetCollectionAssociation.collection_id,
+            )
+            .where(
+                model.DatasetCollectionElement.hda_id == dataset.id,
+                model.HistoryDatasetCollectionAssociation.deleted == false(),
+            )
+        )
+        usage_count = self.session().execute(stmt).scalar()
+        return usage_count > 1
+
 
 # serializers
 # -----------------------------------------------------------------------------

lib/galaxy_test/api/test_history_contents.py

@@ -1026,6 +1026,73 @@ def test_purging_collection_should_purge_contents(self):
                 if item["history_content_type"] == "dataset":
                     self.dataset_populator.wait_for_purge(history_id=history_id, content_id=item["id"])
 
+    def test_deleting_collection_should_delete_contents_only_if_orphaned(self):
+        with self.dataset_populator.test_history() as history_id:
+            num_expected_collections = 1
+            num_expected_datasets = 2
+            collection_ids = self._create_collection_in_history(history_id, num_expected_collections)
+            original_collection_id = collection_ids[0]
+            # Check datasets are hidden and not deleted
+            history_contents = self._get_history_contents(history_id)
+            datasets = list(filter(lambda item: item["history_content_type"] == "dataset", history_contents))
+            assert len(datasets) == num_expected_datasets
+            for dataset in datasets:
+                assert dataset["deleted"] is False
+                assert dataset["visible"] is False
+
+            # Create a new list collection with the same datasets
+            payload = {
+                "name": "New list with same datasets",
+                "type": "dataset_collection",
+                "collection_type": "list",
+                "copy_elements": False,  # Reference the same datasets
+                "hide_source_items": True,
+                "element_identifiers": [
+                    {"name": "el1", "src": "hda", "id": datasets[0]["id"]},
+                    {"name": "el2", "src": "hda", "id": datasets[1]["id"]},
+                ],
+            }
+            create_response = self._post(f"histories/{history_id}/contents", payload, json=True)
+            self._assert_status_code_is_ok(create_response)
+            new_collection_id = create_response.json()["id"]
+
+            # Delete the original collection
+            payload = {
+                "operation": "delete",
+                "items": [
+                    {
+                        "id": original_collection_id,
+                        "history_content_type": "dataset_collection",
+                    },
+                ],
+            }
+            bulk_operation_result = self._apply_bulk_operation(history_id, payload)
+            self._assert_bulk_success(bulk_operation_result, 1)
+
+            # Check datasets are still not deleted
+            history_contents = self._get_history_contents(history_id)
+            for item in history_contents:
+                if item["history_content_type"] == "dataset":
+                    assert item["deleted"] is False
+
+            # Delete the new collection too
+            payload = {
+                "operation": "delete",
+                "items": [
+                    {
+                        "id": new_collection_id,
+                        "history_content_type": "dataset_collection",
+                    },
+                ],
+            }
+            bulk_operation_result = self._apply_bulk_operation(history_id, payload)
+            self._assert_bulk_success(bulk_operation_result, 1)
+
+            # Check datasets are deleted (and collections too)
+            history_contents = self._get_history_contents(history_id)
+            for item in history_contents:
+                assert item["deleted"] is True
+
     @requires_new_user
     def test_only_owner_can_apply_bulk_operations(self):
         with self.dataset_populator.test_history() as history_id: