Merge pull request #17818 from martenson/noexpand-private

[24.0] do not expand datasets that are known to be inaccessible

client/openapi_to_schema.mjs

@@ -7,11 +7,15 @@ const inputFilePath = process.argv[2];
 const localPath = new URL(inputFilePath, import.meta.url);
 openapiTS(localPath, {
     transform(schemaObject, metadata) {
-        if (
-            "const" in schemaObject &&
-            (typeof schemaObject.const === "string" || schemaObject.const instanceof String)
-        ) {
-            return `"${schemaObject.const}"`;
+        if ("const" in schemaObject) {
+            const constType = typeof schemaObject.const;
+            switch (constType) {
+                case "number":
+                case "boolean":
+                    return `${schemaObject.const}`;
+                default:
+                    return `"${schemaObject.const}"`;
+            }
         }
     },
 }).then((output) => console.log(output));

client/src/api/index.ts

@@ -89,6 +89,11 @@ export type DatasetSummary = components["schemas"]["HDASummary"];
  */
 export type DatasetDetails = components["schemas"]["HDADetailed"];
 
+/**
+ * Represents a HistoryDatasetAssociation that is inaccessible to the user.
+ */
+export type HDAInaccessible = components["schemas"]["HDAInaccessible"];
+
 /**
  * Contains storage (object store, quota, etc..) details for a dataset.
  */
@@ -97,7 +102,7 @@ export type DatasetStorageDetails = components["schemas"]["DatasetStorageDetails
 /**
  * Represents a HistoryDatasetAssociation with either summary or detailed information.
  */
-export type DatasetEntry = DatasetSummary | DatasetDetails;
+export type DatasetEntry = DatasetSummary | DatasetDetails | HDAInaccessible;
 
 /**
  * Contains summary information about a DCE (DatasetCollectionElement).
@@ -183,6 +188,10 @@ export function hasDetails(entry: DatasetEntry): entry is DatasetDetails {
     return "peek" in entry;
 }
 
+export function isInaccessible(entry: DatasetEntry): entry is HDAInaccessible {
+    return "accessible" in entry && !entry.accessible;
+}
+
 /**
  * Contains dataset metadata information.
  */

client/src/api/schema/schema.ts

@@ -5998,11 +5998,94 @@ export interface components {
              */
             visible: boolean;
         };
+        /**
+         * HDAInaccessible
+         * @description History Dataset Association information when the user can not access it.
+         */
+        HDAInaccessible: {
+            /**
+             * Accessible
+             * @constant
+             */
+            accessible: false;
+            /** Copied From Ldda Id */
+            copied_from_ldda_id?: string | null;
+            /**
+             * Create Time
+             * @description The time and date this item was created.
+             */
+            create_time: string | null;
+            /**
+             * Deleted
+             * @description Whether this item is marked as deleted.
+             */
+            deleted: boolean;
+            /**
+             * HID
+             * @description The index position of this item in the History.
+             */
+            hid: number;
+            /**
+             * History Content Type
+             * @description This is always `dataset` for datasets.
+             * @constant
+             */
+            history_content_type: "dataset";
+            /**
+             * History ID
+             * @example 0123456789ABCDEF
+             */
+            history_id: string;
+            /**
+             * Id
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Name
+             * @description The name of the item.
+             */
+            name: string | null;
+            /**
+             * State
+             * @description The current state of this dataset.
+             */
+            state: components["schemas"]["DatasetState"];
+            tags: components["schemas"]["TagCollection"];
+            /**
+             * Type
+             * @description The type of this item.
+             */
+            type: string;
+            /**
+             * Type - ID
+             * @description The type and the encoded ID of this item. Used for caching.
+             */
+            type_id?: string | null;
+            /**
+             * Update Time
+             * @description The last time and date this item was updated.
+             */
+            update_time: string | null;
+            /**
+             * URL
+             * @deprecated
+             * @description The relative URL to access this item.
+             */
+            url: string;
+            /**
+             * Visible
+             * @description Whether this item is visible or hidden to the user by default.
+             */
+            visible: boolean;
+        };
         /**
          * HDAObject
          * @description History Dataset Association Object
          */
         HDAObject: {
+            /** Accessible */
+            accessible?: boolean | null;
             /** Copied From Ldda Id */
             copied_from_ldda_id?: string | null;
             /**
@@ -6925,6 +7008,7 @@ export interface components {
             | components["schemas"]["HDACustom"]
             | components["schemas"]["HDADetailed"]
             | components["schemas"]["HDASummary"]
+            | components["schemas"]["HDAInaccessible"]
             | components["schemas"]["HDCADetailed"]
             | components["schemas"]["HDCASummary"]
         )[];
@@ -6941,6 +7025,7 @@ export interface components {
                 | components["schemas"]["HDACustom"]
                 | components["schemas"]["HDADetailed"]
                 | components["schemas"]["HDASummary"]
+                | components["schemas"]["HDAInaccessible"]
                 | components["schemas"]["HDCADetailed"]
                 | components["schemas"]["HDCASummary"]
             )[];
@@ -13533,6 +13618,7 @@ export interface operations {
                         | components["schemas"]["HDACustom"]
                         | components["schemas"]["HDADetailed"]
                         | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
                         | components["schemas"]["HDCADetailed"]
                         | components["schemas"]["HDCASummary"]
                     )[];
@@ -13713,7 +13799,8 @@ export interface operations {
                     "application/json":
                         | components["schemas"]["HDACustom"]
                         | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"];
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"];
                 };
             };
             /** @description Validation Error */
@@ -16465,12 +16552,14 @@ export interface operations {
                         | components["schemas"]["HDACustom"]
                         | components["schemas"]["HDADetailed"]
                         | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
                         | components["schemas"]["HDCADetailed"]
                         | components["schemas"]["HDCASummary"]
                         | (
                               | components["schemas"]["HDACustom"]
                               | components["schemas"]["HDADetailed"]
                               | components["schemas"]["HDASummary"]
+                              | components["schemas"]["HDAInaccessible"]
                               | components["schemas"]["HDCADetailed"]
                               | components["schemas"]["HDCASummary"]
                           )[];
@@ -17054,6 +17143,7 @@ export interface operations {
                         | components["schemas"]["HDACustom"]
                         | components["schemas"]["HDADetailed"]
                         | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
                         | components["schemas"]["HDCADetailed"]
                         | components["schemas"]["HDCASummary"];
                 };
@@ -17105,6 +17195,7 @@ export interface operations {
                         | components["schemas"]["HDACustom"]
                         | components["schemas"]["HDADetailed"]
                         | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
                         | components["schemas"]["HDCADetailed"]
                         | components["schemas"]["HDCASummary"];
                 };
@@ -17337,12 +17428,14 @@ export interface operations {
                         | components["schemas"]["HDACustom"]
                         | components["schemas"]["HDADetailed"]
                         | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
                         | components["schemas"]["HDCADetailed"]
                         | components["schemas"]["HDCASummary"]
                         | (
                               | components["schemas"]["HDACustom"]
                               | components["schemas"]["HDADetailed"]
                               | components["schemas"]["HDASummary"]
+                              | components["schemas"]["HDAInaccessible"]
                               | components["schemas"]["HDCADetailed"]
                               | components["schemas"]["HDCASummary"]
                           )[];
@@ -17393,6 +17486,7 @@ export interface operations {
                         | components["schemas"]["HDACustom"]
                         | components["schemas"]["HDADetailed"]
                         | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
                         | components["schemas"]["HDCADetailed"]
                         | components["schemas"]["HDCASummary"];
                 };
@@ -17443,6 +17537,7 @@ export interface operations {
                         | components["schemas"]["HDACustom"]
                         | components["schemas"]["HDADetailed"]
                         | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
                         | components["schemas"]["HDCADetailed"]
                         | components["schemas"]["HDCASummary"];
                 };
@@ -17674,6 +17769,7 @@ export interface operations {
                         | components["schemas"]["HDACustom"]
                         | components["schemas"]["HDADetailed"]
                         | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
                         | components["schemas"]["HDCADetailed"]
                         | components["schemas"]["HDCASummary"]
                     )[];

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

@@ -91,7 +91,9 @@ const contentId = computed(() => {
 
 const contentCls = computed(() => {
     const status = contentState.value && contentState.value.status;
-    if (props.selected) {
+    if (props.item.accessible === false) {
+        return "alert-inaccessible";
+    } else if (props.selected) {
         return "alert-info";
     } else if (!status) {
         return `alert-success`;
@@ -99,7 +101,6 @@ const contentCls = computed(() => {
         return `alert-${status}`;
     }
 });
-
 const contentState = computed(() => {
     return STATES[state.value] && STATES[state.value];
 });
@@ -116,6 +117,9 @@ const state = computed<keyof StateMap>(() => {
     if (props.isPlaceholder) {
         return "placeholder";
     }
+    if (props.item.accessible === false) {
+        return "inaccessible";
+    }
     if (props.item.populated_state === "failed") {
         return "failed_populated_state";
     }
@@ -135,7 +139,13 @@ const state = computed<keyof StateMap>(() => {
 });
 
 const dataState = computed(() => {
-    return state.value === "new_populated_state" ? "new" : state.value;
+    if (props.item.accessible === false) {
+        return "inaccessible";
+    } else if (state.value === "new_populated_state") {
+        return "new";
+    } else {
+        return state.value;
+    }
 });
 
 const tags = computed(() => {
@@ -334,7 +344,7 @@ function unexpandedClick(event: Event) {
         :data-state="dataState"
         tabindex="0"
         role="button"
-        draggable
+        :draggable="props.item.accessible === false ? false : true"
         @dragstart="onDragStart"
         @dragend="onDragEnd"
         @keydown="onKeyDown">
@@ -428,8 +438,9 @@ function unexpandedClick(event: Event) {
         </span>
         <!-- collections are not expandable, so we only need the DatasetDetails component here -->
         <BCollapse :visible="expandDataset" class="px-2 pb-2">
+            <div v-if="item.accessible === false">You are not allowed to access this dataset</div>
             <DatasetDetails
-                v-if="expandDataset && item.id"
+                v-else-if="expandDataset && item.id"
                 :id="item.id"
                 :writable="writable"
                 :show-highlight="(isHistoryItem && filterable) || addHighlightBtn"

client/src/components/History/Content/Dataset/DatasetDetails.vue

@@ -2,6 +2,7 @@
 import { BLink } from "bootstrap-vue";
 import { computed } from "vue";
 
+import { hasDetails } from "@/api";
 import { STATES } from "@/components/History/Content/model/states";
 import { useDatasetStore } from "@/stores/datasetStore";
 
@@ -26,6 +27,7 @@ const props = withDefaults(defineProps<Props>(), {
 
 const emit = defineEmits<{
     (e: "toggleHighlights"): void;
+    (e: "edit"): void;
 }>();
 
 const result = computed(() => datasetStore.getDataset(props.id));
@@ -40,7 +42,7 @@ function toggleHighlights() {
 
 <template>
     <div>
-        <div v-if="result && !isLoading" class="dataset">
+        <div v-if="result && !isLoading && hasDetails(result)" class="dataset">
             <div class="details not-loading">
                 <div class="summary">
                     <div v-if="stateText" class="mb-1">{{ stateText }}</div>

client/src/components/History/Content/model/states.ts

@@ -2,7 +2,13 @@ import type { components } from "@/api/schema";
 
 type DatasetState = components["schemas"]["DatasetState"];
 // The 'failed' state is for the collection job state summary, not a dataset state.
-type State = DatasetState | "failed" | "placeholder" | "failed_populated_state" | "new_populated_state";
+type State =
+    | DatasetState
+    | "failed"
+    | "placeholder"
+    | "failed_populated_state"
+    | "new_populated_state"
+    | "inaccessible";
 
 interface StateRepresentation {
     status: "success" | "warning" | "info" | "danger" | "secondary";
@@ -120,6 +126,12 @@ export const STATES: StateMap = {
         icon: "clock",
         nonDb: true,
     },
+    inaccessible: {
+        status: "warning",
+        text: "User not allowed to access this dataset.",
+        icon: "lock",
+        nonDb: true,
+    },
 } as const satisfies StateMap;
 
 /** We want to display a single state for a dataset collection whose elements may have mixed states.

client/src/components/History/CurrentCollection/CollectionPanel.vue

@@ -76,7 +76,7 @@ function updateDsc(collection: any, fields: Object | undefined) {
 }
 
 function getItemKey(item: DCESummary) {
-    return item.id;
+    return `${item.element_type}-${item.id}`;
 }
 
 function onScroll(newOffset: number) {

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

@@ -45,7 +45,7 @@ const emit = defineEmits(["update:filter-text", "reloadContents"]);
 
 const router = useRouter();
 const { config } = useConfig();
-const { currentUser } = storeToRefs(useUserStore());
+const { currentUser, isAnonymous } = storeToRefs(useUserStore());
 const { historySize, numItemsActive, numItemsDeleted, numItemsHidden } = useHistoryContentStats(
     toRef(props, "history")
 );
@@ -146,7 +146,7 @@ onMounted(() => {
 
         <BButtonGroup v-if="currentUser">
             <BButton
-                v-if="config && config.object_store_allows_id_selection"
+                v-if="config && config.object_store_allows_id_selection && !isAnonymous"
                 :id="`history-storage-${history.id}`"
                 title="Manage Preferred History Storage"
                 variant="link"
@@ -157,7 +157,7 @@ onMounted(() => {
             </BButton>
 
             <PreferredStorePopover
-                v-if="config && config.object_store_allows_id_selection"
+                v-if="config && config.object_store_allows_id_selection && !isAnonymous"
                 :history-id="history.id"
                 :history-preferred-object-store-id="historyPreferredObjectStoreId"
                 :user="currentUser">

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

@@ -425,7 +425,7 @@ function updateFilterValue(filterKey: string, newValue: any) {
 }
 
 function getItemKey(item: HistoryItem) {
-    return item.type_id;
+    return itemUniqueKey(item);
 }
 
 function itemUniqueKey(item: HistoryItem) {

client/src/stores/collectionElementsStore.test.ts

@@ -150,6 +150,7 @@ function mockElement(collectionId: string, i: number): DCESummary {
             hda_ldda: "hda",
             history_id: "1",
             tags: [],
+            accessible: true,
         },
     };
 }

client/src/stores/datasetStore.ts

@@ -1,7 +1,7 @@
 import { defineStore } from "pinia";
 import { computed, set } from "vue";
 
-import type { DatasetDetails, DatasetEntry, HistoryContentItemBase } from "@/api";
+import { type DatasetDetails, type DatasetEntry, type HistoryContentItemBase, isInaccessible } from "@/api";
 import { fetchDataset } from "@/api/datasets";
 import { ApiResponse } from "@/api/schema";
 import { useKeyedCache } from "@/composables/keyedCache";
@@ -17,6 +17,9 @@ export const useDatasetStore = defineStore("datasetStore", () => {
             if (!dataset) {
                 return true;
             }
+            if (isInaccessible(dataset)) {
+                return false;
+            }
             const isNotDetailed = !("peek" in dataset);
             return isNotDetailed;
         };

client/src/style/scss/base.scss

@@ -203,6 +203,7 @@ $galaxy-state-border: (
     "deleted": darken($state-default-border, 30%),
     "hidden": $state-default-border,
     "setting_metadata": $state-warning-border,
+    "inaccessible": darken($state-default-border, 10%),
 );
 
 $galaxy-state-bg: (
@@ -216,6 +217,7 @@ $galaxy-state-bg: (
     "deleted": darken($state-default-bg, 30%),
     "hidden": $state-default-bg,
     "setting_metadata": $state-warning-bg,
+    "inaccessible": darken($state-default-bg, 10%),
 );
 
 @each $state in map-keys($galaxy-state-border) {

lib/galaxy/schema/schema.py

@@ -695,7 +695,7 @@ class HDASummary(HDACommon):
 class HDAInaccessible(HDACommon):
     """History Dataset Association information when the user can not access it."""
 
-    accessible: bool = AccessibleField
+    accessible: Literal[False]
     state: DatasetStateField
 
 
@@ -946,6 +946,7 @@ class HDAObject(Model, WithModelClass):
     history_id: HistoryID
     tags: List[str]
     copied_from_ldda_id: Optional[EncodedDatabaseIdField] = None
+    accessible: Optional[bool] = None
     model_config = ConfigDict(extra="allow")
 
 
@@ -3278,7 +3279,7 @@ class HDACustom(HDADetailed):
     model_config = ConfigDict(extra="allow")
 
 
-AnyHDA = Union[HDACustom, HDADetailed, HDASummary]
+AnyHDA = Union[HDACustom, HDADetailed, HDASummary, HDAInaccessible]
 AnyHDCA = Union[HDCADetailed, HDCASummary]
 AnyHistoryContentItem = Annotated[
     Union[

lib/galaxy/webapps/galaxy/services/dataset_collections.py

@@ -24,6 +24,7 @@ from galaxy.managers.collections_util import (
     dictify_element_reference,
 )
 from galaxy.managers.context import ProvidesHistoryContext
+from galaxy.managers.hdas import HDAManager
 from galaxy.managers.hdcas import HDCAManager
 from galaxy.managers.histories import HistoryManager
 from galaxy.model import DatasetCollectionElement
@@ -94,12 +95,14 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
         self,
         security: IdEncodingHelper,
         history_manager: HistoryManager,
+        hda_manager: HDAManager,
         hdca_manager: HDCAManager,
         collection_manager: DatasetCollectionManager,
         datatypes_registry: Registry,
     ):
         super().__init__(security)
         self.history_manager = history_manager
+        self.hda_manager = hda_manager
         self.hdca_manager = hdca_manager
         self.collection_manager = collection_manager
         self.datatypes_registry = datatypes_registry
@@ -270,6 +273,8 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
                     hdca_id=self.encode_id(hdca.id),
                     parent_id=self.encode_id(result["object"]["id"]),
                 )
+            else:
+                result["object"]["accessible"] = self.hda_manager.is_accessible(dsc_element.element_object, trans.user)
             return result
 
         rval = [serialize_element(el) for el in contents]