Merge pull request #17225 from jmchilton/page_permissions

Implement a page object accessibility dialog

client/src/api/datasetCollections.ts

@@ -1,4 +1,4 @@
-import { CollectionEntry, DCESummary, HDCADetailed, isHDCA } from "@/api";
+import { CollectionEntry, DCESummary, HDCADetailed, HDCASummary, isHDCA } from "@/api";
 import { fetcher } from "@/api/schema";
 
 const DEFAULT_LIMIT = 50;
@@ -11,7 +11,16 @@ const getCollectionDetails = fetcher.path("/api/dataset_collections/{id}").metho
  */
 export async function fetchCollectionDetails(params: { id: string }): Promise<HDCADetailed> {
     const { data } = await getCollectionDetails({ id: params.id });
-    return data;
+    return data as HDCADetailed;
+}
+
+/**
+ * Fetches the details of a collection.
+ * @param params.id The ID of the collection (HDCA) to fetch.
+ */
+export async function fetchCollectionSummary(params: { id: string }): Promise<HDCASummary> {
+    const { data } = await getCollectionDetails({ id: params.id, view: "collection" });
+    return data as HDCASummary;
 }
 
 const getCollectionContents = fetcher

client/src/api/histories.ts

@@ -12,3 +12,5 @@ export const updateHistoryItemsInBulk = fetcher
     .path("/api/histories/{history_id}/contents/bulk")
     .method("put")
     .create();
+export const sharing = fetcher.path("/api/histories/{history_id}/sharing").method("get").create();
+export const enableLink = fetcher.path("/api/histories/{history_id}/enable_link_access").method("put").create();

client/src/api/jobs.ts

@@ -2,6 +2,8 @@ import { components, fetcher } from "@/api/schema";
 
 export type JobDestinationParams = components["schemas"]["JobDestinationParams"];
 
+export const getJobDetails = fetcher.path("/api/jobs/{job_id}").method("get").create();
+
 export const jobLockStatus = fetcher.path("/api/job_lock").method("get").create();
 export const jobLockUpdate = fetcher.path("/api/job_lock").method("put").create();
 

client/src/api/schema/schema.ts

@@ -13341,8 +13341,10 @@ export interface operations {
         /** Returns detailed information about the given collection. */
         parameters: {
             /** @description The type of collection instance. Either `history` (default) or `library`. */
+            /** @description The view of collection instance to return. */
             query?: {
                 instance_type?: "history" | "library";
+                view?: string;
             };
             /** @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. */
             header?: {
@@ -13357,7 +13359,7 @@ export interface operations {
             /** @description Successful Response */
             200: {
                 content: {
-                    "application/json": components["schemas"]["HDCADetailed"];
+                    "application/json": components["schemas"]["HDCADetailed"] | components["schemas"]["HDCASummary"];
                 };
             };
             /** @description Validation Error */

client/src/api/workflows.ts

@@ -3,3 +3,6 @@ import { fetcher } from "@/api/schema";
 export const workflowsFetcher = fetcher.path("/api/workflows").method("get").create();
 
 export const invocationCountsFetcher = fetcher.path("/api/workflows/{workflow_id}/counts").method("get").create();
+
+export const sharing = fetcher.path("/api/workflows/{workflow_id}/sharing").method("get").create();
+export const enableLink = fetcher.path("/api/workflows/{workflow_id}/enable_link_access").method("put").create();

client/src/components/Markdown/parse.ts

@@ -168,3 +168,48 @@ function namedArgumentRegex(argument: string): RegExp {
 function escapeRegExpReplacement(value: string): string {
     return value.replace(/\$/g, "$$$$");
 }
+
+class ReferencedObjects {
+    jobs: Set<string> = new Set();
+    historyDatasets: Set<string> = new Set();
+    historyDatasetCollections: Set<string> = new Set();
+    workflows: Set<string> = new Set();
+    invocations: Set<string> = new Set();
+}
+
+export function referencedObjects(markdown: string) {
+    const { sections } = splitMarkdown(markdown);
+    const objects = new ReferencedObjects();
+    for (const section of sections) {
+        if (!("args" in section)) {
+            continue;
+        }
+        const args = section.args;
+        if (!args) {
+            continue;
+        }
+        if ("job_id" in args) {
+            addToSetIfHasValue(args.job_id, objects.jobs);
+        }
+        if ("history_dataset_id" in args) {
+            addToSetIfHasValue(args.history_dataset_id, objects.historyDatasets);
+        }
+        if ("history_dataset_collection_id" in args) {
+            addToSetIfHasValue(args.history_dataset_collection_id, objects.historyDatasetCollections);
+        }
+        if ("invocation_id" in args) {
+            addToSetIfHasValue(args.invocation_id, objects.invocations);
+        }
+        if ("workflow_id" in args) {
+            addToSetIfHasValue(args.workflow_id, objects.workflows);
+        }
+        // TODO: implicit collect job ids
+    }
+    return objects;
+}
+
+function addToSetIfHasValue(value: string | undefined, toSet: Set<string>): void {
+    if (value) {
+        toSet.add(value);
+    }
+}

client/src/components/PageEditor/ObjectPermissions.vue

@@ -0,0 +1,311 @@
+<script setup lang="ts">
+import axios from "axios";
+import Vue, { computed, Ref, ref, watch } from "vue";
+
+import { fetchCollectionSummary } from "@/api/datasetCollections";
+import { enableLink, sharing } from "@/api/histories";
+import { fetchInvocationDetails } from "@/api/invocations";
+import { getJobDetails } from "@/api/jobs";
+import { enableLink as enableLinkWorkflow, sharing as sharingWorkflow } from "@/api/workflows";
+import { useToast } from "@/composables/toast";
+import { useDatasetStore } from "@/stores/datasetStore";
+import { useHistoryStore } from "@/stores/historyStore";
+import { useWorkflowStore } from "@/stores/workflowStore";
+import _l from "@/utils/localization";
+import { withPrefix } from "@/utils/redirect";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import {
+    initializeObjectReferences,
+    initializeObjectToHistoryRefs,
+    updateReferences,
+} from "./object-permission-composables";
+
+import PermissionObjectType from "./PermissionObjectType.vue";
+import SharingIndicator from "./SharingIndicator.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+const { getHistoryNameById, loadHistoryById } = useHistoryStore();
+const { getStoredWorkflowNameByInstanceId, fetchWorkflowForInstanceId } = useWorkflowStore();
+const { getDataset, fetchDataset } = useDatasetStore();
+
+const toast = useToast();
+
+interface ObjectPermissionsProps {
+    markdownContent: string;
+}
+
+const props = defineProps<ObjectPermissionsProps>();
+
+const referencedObjects = initializeObjectReferences();
+const {
+    referencedJobIds,
+    referencedHistoryDatasetIds,
+    referencedHistoryDatasetCollectionIds,
+    referencedWorkflowIds,
+    referencedInvocationIds,
+} = referencedObjects;
+
+// We mostly defer to history permissions for various objects. Track them and merge
+// into histories IDs.
+const { jobsToHistories, invocationsToHistories, historyDatasetCollectionsToHistories, historyIds } =
+    initializeObjectToHistoryRefs(referencedObjects);
+
+type ErrorString = string;
+type AccessibleState = Boolean | null | ErrorString;
+type AccessibleMapRef = Ref<{ [key: string]: AccessibleState }>;
+const historyAccessible: AccessibleMapRef = ref({});
+const workflowAccessible: AccessibleMapRef = ref({});
+const historyDatasetAccessible: AccessibleMapRef = ref({});
+
+function catchErrorToToast(title: string, prolog: string) {
+    function handleError(e: Error) {
+        toast.error(`${prolog} Reason: ${errorMessageAsString(e)}.`, title);
+    }
+    return handleError;
+}
+
+watch(referencedJobIds, async () => {
+    referencedJobIds.value.forEach((jobId) => {
+        if (jobId in jobsToHistories.value) {
+            return;
+        }
+        const handleError = catchErrorToToast(
+            "Failed to job information",
+            "Some referenced objects may not be listed."
+        );
+        getJobDetails({ job_id: jobId })
+            .then(({ data }) => {
+                if ("history_id" in data) {
+                    const historyId = data.history_id;
+                    Vue.set(jobsToHistories.value, jobId, historyId);
+                }
+            })
+            .catch(handleError);
+    });
+});
+
+watch(referencedInvocationIds, async () => {
+    referencedInvocationIds.value.forEach((invocationId) => {
+        if (invocationId in invocationsToHistories.value) {
+            return;
+        }
+        const handleError = catchErrorToToast(
+            "Failed to fetch workflow information",
+            "Some referenced objects may not be listed."
+        );
+        fetchInvocationDetails({ id: invocationId })
+            .then(({ data }) => {
+                if ("history_id" in data) {
+                    const historyId = data.history_id;
+                    Vue.set(invocationsToHistories.value, invocationId, historyId);
+                }
+            })
+            .catch(handleError);
+    });
+});
+
+watch(referencedHistoryDatasetCollectionIds, async () => {
+    referencedHistoryDatasetCollectionIds.value.forEach((historyDatasetCollectionId) => {
+        if (historyDatasetCollectionId in historyDatasetCollectionsToHistories.value) {
+            return;
+        }
+        const handleError = catchErrorToToast(
+            "Failed to fetch collection information",
+            "Some referenced objects may not be listed."
+        );
+        fetchCollectionSummary({ id: historyDatasetCollectionId })
+            .then((data) => {
+                const historyId = data.history_id;
+                Vue.set(historyDatasetCollectionsToHistories.value, historyDatasetCollectionId, historyId);
+            })
+            .catch(handleError);
+    });
+});
+
+interface ItemInterface {
+    id: string;
+    accessible: Boolean | null;
+    name: string;
+    type: string;
+}
+
+const histories = computed<ItemInterface[]>(() => {
+    return historyIds.value.map((historyId: string) => {
+        return {
+            id: historyId,
+            type: "history",
+            name: getHistoryNameById(historyId),
+            accessible: historyAccessible.value[historyId],
+        } as ItemInterface;
+    });
+});
+
+const workflows = computed<ItemInterface[]>(() => {
+    return referencedWorkflowIds.value.map((workflowId: string) => {
+        return {
+            id: workflowId,
+            type: "workflow",
+            name: getStoredWorkflowNameByInstanceId(workflowId),
+            accessible: workflowAccessible.value[workflowId],
+        } as ItemInterface;
+    });
+});
+
+const datasets = computed<ItemInterface[]>(() => {
+    return referencedHistoryDatasetIds.value.map((historyDatasetId: string) => {
+        return {
+            id: historyDatasetId,
+            type: "historyDataset",
+            name: getDataset(historyDatasetId)?.name || "Fetching dataset name...",
+            accessible: historyDatasetAccessible.value[historyDatasetId],
+        } as ItemInterface;
+    });
+});
+
+const loading = ref(false);
+
+const SHARING_FIELD = { key: "accessible", label: _l("Accessible"), sortable: false, thStyle: { width: "10%" } };
+const NAME_FIELD = { key: "name", label: _l("Name"), sortable: true };
+const TYPE_FIELD = { key: "type", label: _l("Type"), sortable: true, thStyle: { width: "10%" } };
+
+const tableFields = [SHARING_FIELD, TYPE_FIELD, NAME_FIELD];
+
+watch(
+    props,
+    () => {
+        updateReferences(referencedObjects, props.markdownContent);
+        initWorkflowData();
+        initHistoryDatasetData();
+    },
+    { immediate: true }
+);
+
+watch(historyIds, () => {
+    for (const historyId of historyIds.value) {
+        loadHistoryById(historyId);
+        if (historyId && !(historyId in historyAccessible.value)) {
+            Vue.set(historyAccessible.value, historyId, null);
+            sharing({ history_id: historyId })
+                .then((response) => {
+                    const accessible = response.data.importable;
+                    Vue.set(historyAccessible.value, historyId, accessible);
+                })
+                .catch((e) => {
+                    const errorMessage = errorMessageAsString(e);
+                    const title = "Failed to fetch history metadata.";
+                    toast.error(errorMessage, title);
+                    Vue.set(historyAccessible.value, historyId, `${title} Reason: ${errorMessage}.`);
+                });
+        }
+    }
+});
+
+function initWorkflowData() {
+    for (const workflowId of referencedWorkflowIds.value) {
+        fetchWorkflowForInstanceId(workflowId);
+        if (workflowId && !(workflowId in workflowAccessible.value)) {
+            Vue.set(workflowAccessible.value, workflowId, null);
+            sharingWorkflow({ workflow_id: workflowId })
+                .then((response) => {
+                    const accessible = response.data.importable;
+                    Vue.set(workflowAccessible.value, workflowId, accessible);
+                })
+                .catch((e) => {
+                    const errorMessage = errorMessageAsString(e);
+                    const title = "Failed to fetch workflow metadata.";
+                    toast.error(errorMessage, title);
+                    Vue.set(workflowAccessible.value, workflowId, `${title} Reason: ${errorMessage}.`);
+                });
+        }
+    }
+}
+
+function initHistoryDatasetData() {
+    for (const historyDatasetId of referencedHistoryDatasetIds.value) {
+        fetchDataset({ id: historyDatasetId });
+        if (historyDatasetId && !(historyDatasetId in historyDatasetAccessible.value)) {
+            axios
+                .get(withPrefix(`/dataset/get_edit?dataset_id=${historyDatasetId}`))
+                .then((response) => {
+                    const permissionDisable = response.data.permission_disable;
+                    const permissionInputs = response.data.permission_inputs;
+                    if (permissionDisable) {
+                        const errorStr = `Cannot modify permissions of this dataset. Reason: ${permissionInputs[0].label}`;
+                        Vue.set(historyDatasetAccessible.value, historyDatasetId, errorStr);
+                        return;
+                    }
+                    const accessPermissionInput = permissionInputs[1];
+                    if (accessPermissionInput.name != "DATASET_ACCESS") {
+                        throw Error("Galaxy Bug");
+                    }
+                    const accessible = (accessPermissionInput.value || []).length == 0;
+                    Vue.set(historyDatasetAccessible.value, historyDatasetId, accessible);
+                })
+                .catch((e) => {
+                    const errorMessage = errorMessageAsString(e);
+                    const title = "Failed to fetch dataset metadata.";
+                    toast.error(errorMessage, title);
+                    Vue.set(historyDatasetAccessible.value, historyDatasetId, `${title} Reason: ${errorMessage}.`);
+                });
+        }
+    }
+}
+
+const tableItems = computed<ItemInterface[]>(() => {
+    return [...histories.value, ...workflows.value, ...datasets.value];
+});
+
+function makeAccessible(item: ItemInterface) {
+    let promise;
+    let accessibleMap: AccessibleMapRef;
+    if (item.type == "history") {
+        promise = enableLink({ history_id: item.id });
+        accessibleMap = historyAccessible;
+    } else if (item.type == "workflow") {
+        promise = enableLinkWorkflow({ workflow_id: item.id });
+        accessibleMap = workflowAccessible;
+    } else if (item.type == "historyDataset") {
+        const data = {
+            dataset_id: item.id,
+            action: "remove_restrictions",
+        };
+        promise = axios.put(withPrefix(`/api/datasets/${item.id}/permissions`), data);
+        accessibleMap = historyDatasetAccessible;
+    }
+    if (!promise) {
+        console.log("Serious client programming error - unknown object type encountered.");
+        return;
+    }
+    promise
+        .then(() => Vue.set(accessibleMap.value, item.id, true))
+        .catch((e) => {
+            const errorMessage = errorMessageAsString(e);
+            const title = "Failed update object accessibility.";
+            toast.error(errorMessage, title);
+            Vue.set(accessibleMap.value, item.id, `${title} Reason: ${errorMessage}.`);
+        });
+}
+</script>
+
+<template>
+    <div>
+        <b-table :items="tableItems" :fields="tableFields">
+            <template v-slot:empty>
+                <LoadingSpan v-if="loading" message="Loading objects" />
+                <b-alert v-else variant="info" show>
+                    <div>No objects found in referenced Galaxy markdown content.</div>
+                </b-alert>
+            </template>
+            <template v-slot:cell(name)="row">
+                {{ row.item.name }}
+            </template>
+            <template v-slot:cell(accessible)="row">
+                <SharingIndicator :accessible="row.item.accessible" @makeAccessible="makeAccessible(row.item)" />
+            </template>
+            <template v-slot:cell(type)="row">
+                <PermissionObjectType :type="row.item.type" />
+            </template>
+        </b-table>
+    </div>
+</template>

client/src/components/PageEditor/ObjectPermissionsModal.vue

@@ -0,0 +1,15 @@
+<script setup lang="ts">
+import ObjectPermissions from "./ObjectPermissions.vue";
+
+interface ObjectPermissionsProps {
+    markdownContent: string;
+}
+
+defineProps<ObjectPermissionsProps>();
+</script>
+
+<template>
+    <b-modal v-bind="$attrs" title="Page Object Permissions" title-tag="h2" ok-only v-on="$listeners">
+        <ObjectPermissions :markdown-content="markdownContent" />
+    </b-modal>
+</template>

client/src/components/PageEditor/PageEditorMarkdown.vue

@@ -6,6 +6,20 @@
         mode="page"
         @onUpdate="onUpdate">
         <template v-slot:buttons>
+            <ObjectPermissionsModal
+                id="object-permissions-modal"
+                v-model="showPermissions"
+                :markdown-content="markdownText" />
+            <b-button
+                id="permissions-button"
+                v-b-tooltip.hover.bottom
+                v-b-modal:object-permissions-modal
+                title="Permissions"
+                variant="link"
+                role="button"
+                @click="showPermissions = true">
+                <FontAwesomeIcon icon="users" />
+            </b-button>
             <b-button
                 id="save-button"
                 v-b-tooltip.hover.bottom
@@ -30,7 +44,7 @@
 
 <script>
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faEye, faSave } from "@fortawesome/free-solid-svg-icons";
+import { faEye, faSave, faUsers } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import BootstrapVue from "bootstrap-vue";
 import MarkdownEditor from "components/Markdown/MarkdownEditor";
@@ -39,14 +53,17 @@ import Vue from "vue";
 
 import { save } from "./util";
 
+import ObjectPermissionsModal from "./ObjectPermissionsModal.vue";
+
 Vue.use(BootstrapVue);
 
-library.add(faEye, faSave);
+library.add(faEye, faSave, faUsers);
 
 export default {
     components: {
         MarkdownEditor,
         FontAwesomeIcon,
+        ObjectPermissionsModal,
     },
     props: {
         pageId: {
@@ -73,6 +90,7 @@ export default {
     data: function () {
         return {
             markdownText: this.content,
+            showPermissions: false,
         };
     },
     methods: {

client/src/components/PageEditor/PermissionObjectType.vue

@@ -0,0 +1,31 @@
+<script setup lang="ts">
+import { computed } from "vue";
+
+interface PermissionObjectTypeProps {
+    type: "history" | "historyDataset" | "workflow";
+}
+
+const props = defineProps<PermissionObjectTypeProps>();
+
+const typeTitle = computed(() => {
+    if (props.type == "history") {
+        return "History";
+    } else if (props.type == "historyDataset") {
+        return "Dataset";
+    } else {
+        return "Workflow";
+    }
+});
+</script>
+
+<template>
+    <span class="object-type">
+        {{ typeTitle }}
+    </span>
+</template>
+
+<style scoped>
+.object-type {
+    text-decoration: underline;
+}
+</style>

client/src/components/PageEditor/SharingIndicator.vue

@@ -0,0 +1,70 @@
+<script setup lang="ts">
+import { ref, watch } from "vue";
+
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+interface SharingIndicatorProps {
+    accessible: Boolean | String | null;
+}
+
+const emit = defineEmits<{
+    (e: "makeAccessible"): void;
+}>();
+
+const props = defineProps<SharingIndicatorProps>();
+
+const makingAccessible = ref(false);
+
+function makeAccessible() {
+    makingAccessible.value = true;
+    emit("makeAccessible");
+}
+
+watch(props, () => {
+    makingAccessible.value = false;
+});
+</script>
+<template>
+    <div>
+        <LoadingSpan v-if="accessible == null || makingAccessible" spinner-only> </LoadingSpan>
+        <div v-else-if="typeof accessible == 'string'">
+            <Icon
+                :title="accessible"
+                icon="exclamation-triangle"
+                class="make-page-object-accessible-sharing-error-icon" />
+        </div>
+        <BFormCheckbox
+            v-else
+            switch
+            :checked="accessible"
+            class="make-page-object-accessible"
+            :disabled="accessible"
+            @change="
+                (event) => {
+                    makeAccessible(event);
+                }
+            ">
+        </BFormCheckbox>
+    </div>
+</template>
+
+<style lang="scss">
+/* scoped doesn't seem to work to prefixing with a class name */
+@import "theme/blue.scss";
+
+.make-page-object-accessible-sharing-error-icon {
+    color: $brand-danger;
+}
+
+.make-page-object-accessible .custom-control-label::after {
+    background-color: white;
+}
+
+.make-page-object-accessible .custom-control-label::before {
+    background-color: lighten($brand-warning, 15%) !important;
+}
+
+.make-page-object-accessible .custom-control-input[disabled] ~ .custom-control-label::before {
+    background-color: lighten($brand-success, 15%) !important;
+}
+</style>

client/src/components/PageEditor/object-permission-composables.test.js

@@ -0,0 +1,81 @@
+import { set } from "vue";
+
+import {
+    initializeObjectReferences,
+    initializeObjectToHistoryRefs,
+    updateReferences,
+} from "./object-permission-composables";
+
+describe("object-permission-composables", () => {
+    it("should initialize and update refs in a markdown document", () => {
+        const refs = initializeObjectReferences();
+        expect(refs.referencedJobIds.value.length).toBe(0);
+
+        updateReferences(refs, "some content\n```galaxy\njob_metrics(job_id=THISFAKEID)\n```\nfoo bar\n");
+        expect(refs.referencedJobIds.value.length).toBe(1);
+        expect(refs.referencedJobIds.value[0]).toBe("THISFAKEID");
+    });
+
+    describe("initializeObjectToHistoryRefs", () => {
+        function init() {
+            const refs = initializeObjectReferences();
+            const historyMaps = initializeObjectToHistoryRefs(refs);
+            return { refs, historyMaps };
+        }
+
+        describe("historyIds computed", () => {
+            it("should merge in referenced job histories once they've been cached", async () => {
+                const { refs, historyMaps } = init();
+                refs.referencedJobIds.value = ["THISFAKEID"];
+                expect(historyMaps.historyIds.value.length).toBe(0);
+                set(historyMaps.jobsToHistories.value, "THISFAKEID", "THATFAKEID");
+                expect(historyMaps.historyIds.value.length).toBe(1);
+                expect(historyMaps.historyIds.value[0]).toBe("THATFAKEID");
+            });
+
+            it("should merge in referenced invocation histories once they've been cached", async () => {
+                const { refs, historyMaps } = init();
+                refs.referencedInvocationIds.value = ["THISFAKEID"];
+                expect(historyMaps.historyIds.value.length).toBe(0);
+                set(historyMaps.invocationsToHistories.value, "THISFAKEID", "THATFAKEID");
+                expect(historyMaps.historyIds.value.length).toBe(1);
+                expect(historyMaps.historyIds.value[0]).toBe("THATFAKEID");
+            });
+
+            it("should merge in referenced collections once they've been cached", async () => {
+                const { refs, historyMaps } = init();
+                refs.referencedHistoryDatasetCollectionIds.value = ["THISFAKEID"];
+                expect(historyMaps.historyIds.value.length).toBe(0);
+                set(historyMaps.historyDatasetCollectionsToHistories.value, "THISFAKEID", "THATFAKEID");
+                expect(historyMaps.historyIds.value.length).toBe(1);
+                expect(historyMaps.historyIds.value[0]).toBe("THATFAKEID");
+            });
+
+            it("should merge in referenced objects across sources once they've been cached", async () => {
+                const { refs, historyMaps } = init();
+                refs.referencedJobIds.value = ["THISFAKEJOBID"];
+                refs.referencedInvocationIds.value = ["THISFAKEINVOCATIONID"];
+                refs.referencedHistoryDatasetCollectionIds.value = ["THISFAKECOLLECTIONID"];
+                set(historyMaps.jobsToHistories.value, "THISFAKEJOBID", "HISTORYID1");
+                set(historyMaps.invocationsToHistories.value, "THISFAKEINVOCATIONID", "HISTORYID2");
+                set(historyMaps.historyDatasetCollectionsToHistories.value, "THISFAKECOLLECTIONID", "HISTORYID3");
+                expect(historyMaps.historyIds.value.length).toBe(3);
+                expect(historyMaps.historyIds.value).toContain("HISTORYID1");
+                expect(historyMaps.historyIds.value).toContain("HISTORYID2");
+                expect(historyMaps.historyIds.value).toContain("HISTORYID3");
+            });
+
+            it("should merge in referenced objects across sources once they've been cached and de-duplicate", async () => {
+                const { refs, historyMaps } = init();
+                refs.referencedJobIds.value = ["THISFAKEJOBID"];
+                refs.referencedInvocationIds.value = ["THISFAKEINVOCATIONID"];
+                refs.referencedHistoryDatasetCollectionIds.value = ["THISFAKECOLLECTIONID"];
+                set(historyMaps.jobsToHistories.value, "THISFAKEJOBID", "THATFAKEID");
+                set(historyMaps.invocationsToHistories.value, "THISFAKEINVOCATIONID", "THATFAKEID");
+                set(historyMaps.historyDatasetCollectionsToHistories.value, "THISFAKECOLLECTIONID", "THATFAKEID");
+                expect(historyMaps.historyIds.value.length).toBe(1);
+                expect(historyMaps.historyIds.value[0]).toBe("THATFAKEID");
+            });
+        });
+    });
+});

client/src/components/PageEditor/object-permission-composables.ts

@@ -0,0 +1,89 @@
+import { computed, Ref, ref } from "vue";
+
+import { referencedObjects } from "@/components/Markdown/parse";
+
+interface ObjectVueRefs {
+    referencedJobIds: Ref<string[]>;
+    referencedHistoryDatasetIds: Ref<string[]>;
+    referencedHistoryDatasetCollectionIds: Ref<string[]>;
+    referencedWorkflowIds: Ref<string[]>;
+    referencedInvocationIds: Ref<string[]>;
+}
+
+export function initializeObjectReferences(): ObjectVueRefs {
+    const referencedJobIds = ref<string[]>([]);
+    const referencedHistoryDatasetIds = ref<string[]>([]);
+    const referencedHistoryDatasetCollectionIds = ref<string[]>([]);
+    const referencedWorkflowIds = ref<string[]>([]);
+    const referencedInvocationIds = ref<string[]>([]);
+    return {
+        referencedJobIds,
+        referencedHistoryDatasetIds,
+        referencedHistoryDatasetCollectionIds,
+        referencedWorkflowIds,
+        referencedInvocationIds,
+    };
+}
+
+export function updateReferences(objectsRefs: ObjectVueRefs, markdown: string) {
+    const {
+        referencedJobIds,
+        referencedHistoryDatasetIds,
+        referencedHistoryDatasetCollectionIds,
+        referencedWorkflowIds,
+        referencedInvocationIds,
+    } = objectsRefs;
+
+    const objects = referencedObjects(markdown);
+
+    referencedJobIds.value = Array.from(objects.jobs.values());
+    referencedHistoryDatasetIds.value = Array.from(objects.historyDatasets.values());
+    referencedHistoryDatasetCollectionIds.value = Array.from(objects.historyDatasetCollections.values());
+    referencedWorkflowIds.value = Array.from(objects.workflows.values());
+    referencedInvocationIds.value = Array.from(objects.invocations.values());
+}
+
+export function initializeObjectToHistoryRefs(referenceObjects: ObjectVueRefs) {
+    const jobsToHistories: Ref<{ [key: string]: string }> = ref({});
+    const invocationsToHistories: Ref<{ [key: string]: string }> = ref({});
+    const historyDatasetCollectionsToHistories: Ref<{ [key: string]: string }> = ref({});
+
+    const historyIds = computed<string[]>(() => {
+        // be sure to reference all refs required for full computation
+        const jobIds = referenceObjects.referencedJobIds.value;
+        const jobMapping = jobsToHistories.value;
+
+        const invocationIds = referenceObjects.referencedInvocationIds.value;
+        const invocationMapping = invocationsToHistories.value;
+
+        const collectionIds = referenceObjects.referencedHistoryDatasetCollectionIds.value;
+        const collectionMapping = historyDatasetCollectionsToHistories.value;
+
+        const theHistories = new Set();
+
+        for (const jobId of jobIds) {
+            if (jobId in jobMapping) {
+                theHistories.add(jobMapping[jobId]);
+            }
+        }
+        for (const invocationId of invocationIds) {
+            if (invocationId in invocationMapping) {
+                theHistories.add(invocationMapping[invocationId]);
+            }
+        }
+        for (const historyDatasetCollectionId of collectionIds) {
+            if (historyDatasetCollectionId in collectionMapping) {
+                theHistories.add(collectionMapping[historyDatasetCollectionId]);
+            }
+        }
+        const historyIds = Array.from(theHistories.values()) as string[];
+        return historyIds;
+    });
+
+    return {
+        jobsToHistories,
+        invocationsToHistories,
+        historyDatasetCollectionsToHistories,
+        historyIds,
+    };
+}

lib/galaxy/webapps/galaxy/api/dataset_collections.py

@@ -11,6 +11,7 @@ from typing_extensions import Annotated
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.schema.fields import DecodedDatabaseIdField
 from galaxy.schema.schema import (
+    AnyHDCA,
     CreateNewCollectionPayload,
     DatasetCollectionInstanceType,
     DCESummary,
@@ -43,6 +44,11 @@ InstanceTypeQueryParam: DatasetCollectionInstanceType = Query(
     description="The type of collection instance. Either `history` (default) or `library`.",
 )
 
+ViewTypeQueryParam: str = Query(
+    default="element",
+    description="The view of collection instance to return.",
+)
+
 
 @router.cbv
 class FastAPIDatasetCollections:
@@ -104,8 +110,9 @@ class FastAPIDatasetCollections:
         id: HistoryHDCAIDPathParam,
         trans: ProvidesHistoryContext = DependsOnTrans,
         instance_type: DatasetCollectionInstanceType = InstanceTypeQueryParam,
-    ) -> HDCADetailed:
-        return self.service.show(trans, id, instance_type)
+        view: str = ViewTypeQueryParam,
+    ) -> AnyHDCA:
+        return self.service.show(trans, id, instance_type, view=view)
 
     @router.get(
         "/api/dataset_collections/{hdca_id}/contents/{parent_id}",

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

@@ -32,6 +32,7 @@ from galaxy.schema.fields import (
     ModelClassField,
 )
 from galaxy.schema.schema import (
+    AnyHDCA,
     CreateNewCollectionPayload,
     DatasetCollectionInstanceType,
     DCESummary,
@@ -184,7 +185,8 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
         trans: ProvidesHistoryContext,
         id: DecodedDatabaseIdField,
         instance_type: DatasetCollectionInstanceType = "history",
-    ) -> HDCADetailed:
+        view: str = "element",
+    ) -> AnyHDCA:
         """
         Returns information about a particular dataset collection.
         """
@@ -203,7 +205,7 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
             security=trans.security,
             url_builder=trans.url_builder,
             parent=parent,
-            view="element",
+            view=view,
         )
         return rval