Hide deleted items

guerler · guerler · commit 2c8a1dd6e043 · 2026-03-28T15:47:23.000+03:00
diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
@@ -13368,6 +13368,8 @@ export interface components {
         GraphNode: {
             /** Collection Type */
             collection_type?: string | null;
+            /** Deleted */
+            deleted?: boolean | null;
             /** Extension */
             extension?: string | null;
             /** Hid */
@@ -13387,6 +13389,8 @@ export interface components {
              * @enum {string}
              */
             type: "dataset" | "collection" | "tool_request";
+            /** Visible */
+            visible?: boolean | null;
         };
         /**
          * GroupCreatePayload
@@ -34947,6 +34951,8 @@ export interface operations {
                 depth?: number;
                 /** @description Maximum number of nodes returned. Must be 1-2000. */
                 limit?: number;
+                /** @description Include deleted datasets and collections in the graph. */
+                include_deleted?: boolean;
             };
             header?: {
                 /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
diff --git a/client/src/components/Graph/GraphNode.vue b/client/src/components/Graph/GraphNode.vue
@@ -32,9 +32,7 @@ const iconSpin = computed(() => Boolean(props.node.data?.stateSpin));
         :class="[node.cssClass, { 'node-highlight': selected }]"
         :style="nodeStyle"
         @click.stop="emit('select', node.id)">
-        <div
-            class="graph-node-header card-header unselectable py-1 px-2"
-            :data-state="node.data?.state ?? undefined">
+        <div class="graph-node-header card-header unselectable py-1 px-2" :data-state="node.data?.state ?? undefined">
             <FontAwesomeIcon :icon="node.icon" class="graph-node-icon mr-1" :spin="iconSpin" />
             <span class="graph-node-label" :title="node.label">{{ node.label }}</span>
             <span v-if="hasPorts && node.badge" class="badge badge-light ml-auto">{{ node.badge }}</span>
diff --git a/client/src/components/History/Graph/HistoryGraphView.vue b/client/src/components/History/Graph/HistoryGraphView.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { faBezierCurve, faProjectDiagram } from "@fortawesome/free-solid-svg-icons";
+import { faBezierCurve, faProjectDiagram, faTrash } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton, BButtonGroup } from "bootstrap-vue";
 import { computed, ref, toRef } from "vue";
@@ -28,8 +28,16 @@ const { seed, seedLoading, noLineage } = useHistoryGraphSeed(toRef(props, "histo
 const direction = ref("both");
 const depth = ref(20);
 const limit = ref(500);
+const includeDeleted = ref(false);
 
-const { graphData, loading, error } = useHistoryGraphData(toRef(props, "historyId"), seed, direction, depth, limit);
+const { graphData, loading, error } = useHistoryGraphData(
+    toRef(props, "historyId"),
+    seed,
+    direction,
+    depth,
+    limit,
+    includeDeleted,
+);
 
 // Layout
 const edgeStyle = ref<EdgeStyle>("orthogonal");
@@ -80,6 +88,15 @@ const isTruncated = computed(() => graphData.value?.truncated?.capped === true);
                         <FontAwesomeIcon :icon="faBezierCurve" />
                     </BButton>
                 </BButtonGroup>
+                <BButtonGroup size="sm" class="ml-2">
+                    <BButton
+                        :pressed="includeDeleted"
+                        variant="outline-primary"
+                        title="Show deleted items"
+                        @click="includeDeleted = !includeDeleted">
+                        <FontAwesomeIcon :icon="faTrash" />
+                    </BButton>
+                </BButtonGroup>
             </div>
             <GraphView :layout="layout" :focus-node-id="seed" :edge-style="edgeStyle" @node-selected="onNodeSelected" />
             <GraphDetails :node="selectedNode" :details="selectedDetails" />
diff --git a/client/src/components/History/Graph/useHistoryGraphData.ts b/client/src/components/History/Graph/useHistoryGraphData.ts
@@ -17,6 +17,7 @@ export function useHistoryGraphData(
     direction: Ref<string>,
     depth: Ref<number>,
     limit: Ref<number>,
+    includeDeleted: Ref<boolean>,
 ) {
     const graphData = ref<HistoryGraphResponse | null>(null);
     const loading = ref(false);
@@ -40,6 +41,7 @@ export function useHistoryGraphData(
                         direction: direction.value as "backward" | "forward" | "both",
                         depth: depth.value,
                         limit: limit.value,
+                        include_deleted: includeDeleted.value,
                     },
                 },
             });
@@ -58,7 +60,9 @@ export function useHistoryGraphData(
         }
     }
 
-    watch([historyId, seed, direction, depth, limit], () => fetchGraph(), { immediate: true });
+    watch([historyId, seed, direction, depth, limit, includeDeleted], () => fetchGraph(), {
+        immediate: true,
+    });
 
     return { graphData, loading, error };
 }
diff --git a/lib/galaxy/managers/history_graph.py b/lib/galaxy/managers/history_graph.py
@@ -69,6 +69,7 @@ def __init__(
         depth: int,
         limit: int,
         toolbox=None,
+        include_deleted: bool = False,
     ):
         self.sa_session = sa_session
         self.security = security
@@ -78,6 +79,7 @@ def __init__(
         self.depth = depth
         self.limit = limit
         self.toolbox = toolbox
+        self.include_deleted = include_deleted
 
         # Global visited set: (node_type, db_id) — prevents re-expansion and preserves BFS depth semantics
         self.visited: set[tuple[str, int]] = set()
@@ -221,6 +223,8 @@ def _fetch_dataset_node(self, db_id: int) -> tuple[Optional[GraphNode], bool]:
                 HistoryDatasetAssociation._state,
                 Dataset.state.label("dataset_state"),
                 HistoryDatasetAssociation.extension,
+                HistoryDatasetAssociation.deleted,
+                HistoryDatasetAssociation.visible,
             )
             .join(Dataset, HistoryDatasetAssociation.dataset_id == Dataset.id)
             .where(HistoryDatasetAssociation.id == db_id)
@@ -238,8 +242,10 @@ def _fetch_dataset_node(self, db_id: int) -> tuple[Optional[GraphNode], bool]:
                 )
             )
             return None, True
+        if not self._should_include(row.deleted, row.visible):
+            return None, False
         state = row._state if row._state else row.dataset_state
-        return GraphNode(id=encoded, type="dataset", name=row.name, hid=row.hid, state=state, extension=row.extension), False
+        return GraphNode(id=encoded, type="dataset", name=row.name, hid=row.hid, state=state, extension=row.extension, deleted=row.deleted, visible=row.visible), False
 
     def _fetch_collection_node(self, db_id: int) -> tuple[Optional[GraphNode], bool]:
         stmt = (
@@ -248,6 +254,8 @@ def _fetch_collection_node(self, db_id: int) -> tuple[Optional[GraphNode], bool]
                 HistoryDatasetCollectionAssociation.history_id,
                 HistoryDatasetCollectionAssociation.name,
                 HistoryDatasetCollectionAssociation.hid,
+                HistoryDatasetCollectionAssociation.deleted,
+                HistoryDatasetCollectionAssociation.visible,
                 DatasetCollection.collection_type,
                 DatasetCollection.populated_state,
             )
@@ -267,8 +275,10 @@ def _fetch_collection_node(self, db_id: int) -> tuple[Optional[GraphNode], bool]
                 )
             )
             return None, True
+        if not self._should_include(row.deleted, row.visible):
+            return None, False
         state = row.populated_state
-        return GraphNode(id=encoded, type="collection", name=row.name, hid=row.hid, state=state, collection_type=row.collection_type), False
+        return GraphNode(id=encoded, type="collection", name=row.name, hid=row.hid, state=state, collection_type=row.collection_type, deleted=row.deleted, visible=row.visible), False
 
     def _fetch_tool_request_node(self, db_id: int) -> tuple[Optional[GraphNode], bool]:
         # Get tool_request and tool_id from first associated job
@@ -309,6 +319,8 @@ def _fetch_dataset_nodes_batch(self, db_ids: list[int]) -> list[GraphNode]:
                     HistoryDatasetAssociation._state,
                     Dataset.state.label("dataset_state"),
                     HistoryDatasetAssociation.extension,
+                    HistoryDatasetAssociation.deleted,
+                    HistoryDatasetAssociation.visible,
                 )
                 .join(Dataset, HistoryDatasetAssociation.dataset_id == Dataset.id)
                 .where(HistoryDatasetAssociation.id.in_(chunk))
@@ -325,9 +337,11 @@ def _fetch_dataset_nodes_batch(self, db_ids: list[int]) -> list[GraphNode]:
                             history_id=self.security.encode_id(row.history_id) if row.history_id else None,
                         )
                     )
+                elif not self._should_include(row.deleted, row.visible):
+                    pass  # Filtered out — not admitted
                 else:
                     state = row._state if row._state else row.dataset_state
-                    nodes.append(GraphNode(id=encoded, type="dataset", name=row.name, hid=row.hid, state=state, extension=row.extension))
+                    nodes.append(GraphNode(id=encoded, type="dataset", name=row.name, hid=row.hid, state=state, extension=row.extension, deleted=row.deleted, visible=row.visible))
             for missing_id in set(chunk) - found:
                 self._add_external_ref(
                     ExternalRef(id=self._encode_node_id("dataset", missing_id), type="dataset")
@@ -343,6 +357,8 @@ def _fetch_collection_nodes_batch(self, db_ids: list[int]) -> list[GraphNode]:
                     HistoryDatasetCollectionAssociation.history_id,
                     HistoryDatasetCollectionAssociation.name,
                     HistoryDatasetCollectionAssociation.hid,
+                    HistoryDatasetCollectionAssociation.deleted,
+                    HistoryDatasetCollectionAssociation.visible,
                     DatasetCollection.collection_type,
                     DatasetCollection.populated_state,
                 )
@@ -361,9 +377,11 @@ def _fetch_collection_nodes_batch(self, db_ids: list[int]) -> list[GraphNode]:
                             history_id=self.security.encode_id(row.history_id) if row.history_id else None,
                         )
                     )
+                elif not self._should_include(row.deleted, row.visible):
+                    pass
                 else:
                     state = row.populated_state
-                    nodes.append(GraphNode(id=encoded, type="collection", name=row.name, hid=row.hid, state=state, collection_type=row.collection_type))
+                    nodes.append(GraphNode(id=encoded, type="collection", name=row.name, hid=row.hid, state=state, collection_type=row.collection_type, deleted=row.deleted, visible=row.visible))
             for missing_id in set(chunk) - found:
                 self._add_external_ref(
                     ExternalRef(id=self._encode_node_id("collection", missing_id), type="collection")
@@ -493,10 +511,21 @@ def _expand_level(
         self.external_refs = self.external_refs[:external_before]
 
         # Build admitted keys from materialized nodes only. External refs and
-        # filtered nodes (e.g., __DATA_FETCH__) are terminal — they must not
-        # appear in the next frontier.
+        # filtered nodes (e.g., __DATA_FETCH__, deleted, hidden) are terminal —
+        # they must not appear in the next frontier.
         admitted_keys = [encoded_to_key[n.id] for n in new_nodes if n.id in encoded_to_key]
 
+        # Remove edges that reference filtered-out nodes (deleted/hidden items
+        # that were discovered but not admitted). An edge is valid if both its
+        # source and target exist as either: previously admitted nodes, newly
+        # admitted nodes, external refs, or frontier nodes from this expansion.
+        valid_ids: set[str] = {n.id for n in self.nodes}  # previously admitted
+        valid_ids.update(n.id for n in new_nodes)  # newly admitted
+        valid_ids.update(r.id for r in new_external)  # external refs
+        # Also include frontier nodes (they were admitted in a previous level)
+        valid_ids.update(self._encode_node_id(t, d) for t, d in frontier)
+        new_edges = [e for e in new_edges if e.source in valid_ids and e.target in valid_ids]
+
         return new_nodes, admitted_keys, new_edges, new_external
 
     # ── Edge discovery queries ──
@@ -763,6 +792,19 @@ def _find_outputs_for_trs(self, tr_ids: list[int]) -> list[tuple[str, int, str,
                 results.append(("collection", row3.dataset_collection_id, tr_enc, c_enc, "collection_output"))
         return results
 
+    # ── Visibility filtering ──
+
+    def _should_include(self, deleted: bool, visible: bool) -> bool:
+        """Check if a dataset/collection should be included based on deleted/visible flags.
+
+        Hidden items are always included in the graph because intermediate
+        tool outputs are commonly hidden in Galaxy — they are essential
+        lineage nodes. Only deleted items are filtered by default.
+        """
+        if deleted and not self.include_deleted:
+            return False
+        return True
+
     # ── Tool name resolution ──
 
     def _resolve_tool_names(self):
diff --git a/lib/galaxy/schema/history_graph.py b/lib/galaxy/schema/history_graph.py
@@ -17,6 +17,8 @@ class GraphNode(BaseModel):
     state: Optional[str] = None
     extension: Optional[str] = None
     collection_type: Optional[str] = None
+    deleted: Optional[bool] = None
+    visible: Optional[bool] = None
     tool_id: Optional[str] = None
     tool_name: Optional[str] = None
 
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -363,9 +363,13 @@ def graph(
             ge=1,
             le=2000,
         ),
+        include_deleted: bool = Query(
+            default=False,
+            description="Include deleted datasets and collections in the graph.",
+        ),
         trans: ProvidesHistoryContext = DependsOnTrans,
     ) -> HistoryGraphResponse:
-        return self.service.graph(trans, history_id, seed=seed, direction=direction, depth=depth, limit=limit)
+        return self.service.graph(trans, history_id, seed=seed, direction=direction, depth=depth, limit=limit, include_deleted=include_deleted)
 
     @router.post(
         "/api/histories/{history_id}/prepare_store_download",
diff --git a/lib/galaxy/webapps/galaxy/services/histories.py b/lib/galaxy/webapps/galaxy/services/histories.py
@@ -380,6 +380,7 @@ def graph(
         direction: str,
         depth: int,
         limit: int,
+        include_deleted: bool = False,
     ):
         from galaxy.managers.history_graph import HistoryGraphBuilder
 
@@ -394,6 +395,7 @@ def graph(
             depth=depth,
             limit=limit,
             toolbox=toolbox,
+            include_deleted=include_deleted,
         )
         return builder.build()
 
