Page object permissions summary...

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

@@ -4,3 +4,6 @@ export const historiesFetcher = fetcher.path("/api/histories").method("get").cre
 export const archivedHistoriesFetcher = fetcher.path("/api/histories/archived").method("get").create();
 export const undeleteHistory = fetcher.path("/api/histories/deleted/{history_id}/undelete").method("post").create();
 export const purgeHistory = fetcher.path("/api/histories/{history_id}").method("delete").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/workflows.ts

@@ -0,0 +1,4 @@
+import { fetcher } from "@/api/schema";
+
+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

@@ -77,3 +77,48 @@ export function getArgs(content: string) {
         content: content,
     };
 }
+
+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, toSet: Set<string>): void {
+    if (value) {
+        toSet.add(value);
+    }
+}

client/src/components/PageEditor/ObjectPermissions.vue

@@ -0,0 +1,305 @@
+<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 permissionInputs = response.data.permission_inputs;
+                    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>