From b7e0ddd55831574d9e9991a319f814569af69a6a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 20 Dec 2023 12:15:50 -0500
Subject: [PATCH] Page object permissions summary...

---
 client/src/api/datasetCollections.ts          |   2 +-
 client/src/api/histories.ts                   |   3 +
 client/src/api/workflows.ts                   |   4 +
 client/src/components/Markdown/parse.ts       |  45 +++
 .../PageEditor/ObjectPermissions.vue          | 267 ++++++++++++++++++
 .../PageEditor/ObjectPermissionsModal.vue     |  15 +
 .../PageEditor/PageEditorMarkdown.vue         |  22 +-
 .../PageEditor/PermissionObjectType.vue       |  31 ++
 .../PageEditor/SharingIndicator.vue           |  60 ++++
 .../webapps/galaxy/api/dataset_collections.py |  11 +-
 .../galaxy/services/dataset_collections.py    |   6 +-
 11 files changed, 459 insertions(+), 7 deletions(-)
 create mode 100644 client/src/api/workflows.ts
 create mode 100644 client/src/components/PageEditor/ObjectPermissions.vue
 create mode 100644 client/src/components/PageEditor/ObjectPermissionsModal.vue
 create mode 100644 client/src/components/PageEditor/PermissionObjectType.vue
 create mode 100644 client/src/components/PageEditor/SharingIndicator.vue

diff --git a/client/src/api/datasetCollections.ts b/client/src/api/datasetCollections.ts
index cb09d46c66b5..47b17ea2baa3 100644
--- a/client/src/api/datasetCollections.ts
+++ b/client/src/api/datasetCollections.ts
@@ -11,7 +11,7 @@ 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;
 }
 
 const getCollectionContents = fetcher
diff --git a/client/src/api/histories.ts b/client/src/api/histories.ts
index 65ad7e2d6b1d..9d3788a9505d 100644
--- a/client/src/api/histories.ts
+++ b/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();
diff --git a/client/src/api/workflows.ts b/client/src/api/workflows.ts
new file mode 100644
index 000000000000..ae5a054a6584
--- /dev/null
+++ b/client/src/api/workflows.ts
@@ -0,0 +1,4 @@
+import { fetcher } from "@/api/schema";
+
+export const sharing = fetcher.path("/api/workflows/{id}/sharing").method("get").create();
+export const enableLink = fetcher.path("/api/workflows/{id}/enable_link_access").method("put").create();
diff --git a/client/src/components/Markdown/parse.ts b/client/src/components/Markdown/parse.ts
index 900bbd3135db..3eb11ae54f89 100644
--- a/client/src/components/Markdown/parse.ts
+++ b/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);
+    }
+}
diff --git a/client/src/components/PageEditor/ObjectPermissions.vue b/client/src/components/PageEditor/ObjectPermissions.vue
new file mode 100644
index 000000000000..9e8aa15464ea
--- /dev/null
+++ b/client/src/components/PageEditor/ObjectPermissions.vue
@@ -0,0 +1,267 @@
+<script setup lang="ts">
+import axios from "axios";
+import Vue, { computed, Ref, ref, watch } from "vue";
+
+import { enableLink, sharing } from "@/api/histories";
+import { enableLink as enableLinkWorkflow, sharing as sharingWorkflow } from "@/api/workflows";
+import { referencedObjects } from "@/components/Markdown/parse";
+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 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();
+
+interface ObjectPermissionsProps {
+    markdownContent: string;
+}
+
+const props = defineProps<ObjectPermissionsProps>();
+
+const referencedJobIds = ref<string[]>([]);
+const referencedHistoryDatasetIds = ref<string[]>([]);
+const referencedHistoryDatasetCollectionIds = ref<string[]>([]);
+const referencedWorkflowIds = ref<string[]>([]);
+const referencedInvocationIds = ref<string[]>([]);
+
+// We mostly defer to history permissions for all these objects. Track them...
+const jobsToHistories: Ref<{ [key: string]: string }> = ref({});
+const invocationsToHistories: Ref<{ [key: string]: string }> = ref({});
+const historyDatasetCollectionsToHistories: Ref<{ [key: string]: string }> = ref({});
+
+const historyAccessible: Ref<{ [key: string]: Boolean | null }> = ref({});
+const workflowAccessible: Ref<{ [key: string]: Boolean | null }> = ref({});
+const historyDatasetAccessible: Ref<{ [key: string]: Boolean | null }> = ref({});
+
+watch(referencedJobIds, async () => {
+    referencedJobIds.value.forEach((jobId) => {
+        if (jobId in jobsToHistories.value) {
+            return;
+        }
+        axios.get(withPrefix(`/api/jobs/${jobId}`)).then((response) => {
+            const historyId = response.data.history_id;
+            Vue.set(jobsToHistories.value, jobId, historyId);
+        });
+    });
+});
+
+watch(referencedInvocationIds, async () => {
+    referencedInvocationIds.value.forEach((invocationId) => {
+        if (invocationId in invocationsToHistories.value) {
+            return;
+        }
+        axios.get(withPrefix(`/api/invocations/${invocationId}`)).then((response) => {
+            const historyId = response.data.history_id;
+            console.log(`${invocationId} => ${historyId}`);
+            Vue.set(invocationsToHistories.value, invocationId, historyId);
+        });
+    });
+});
+
+watch(referencedHistoryDatasetCollectionIds, async () => {
+    referencedHistoryDatasetCollectionIds.value.forEach((historyDatasetCollectionId) => {
+        if (historyDatasetCollectionId in historyDatasetCollectionsToHistories.value) {
+            return;
+        }
+        axios.get(withPrefix(`/api/invocations/${historyDatasetCollectionId}`)).then((response) => {
+            const historyId = response.data.history_id;
+            console.log(`${historyDatasetCollectionId} => ${historyId}`);
+            Vue.set(historyDatasetCollectionsToHistories.value, historyDatasetCollectionId, historyId);
+        });
+    });
+});
+
+const historyIds = computed<string[]>(() => {
+    // be sure to reference all refs required for full computation
+    const jobIds = referencedJobIds.value;
+    const jobMapping = jobsToHistories.value;
+
+    const invocationIds = referencedInvocationIds.value;
+    const invocationMapping = invocationsToHistories.value;
+
+    const collectionIds = 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;
+});
+
+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,
+    () => {
+        const objects = referencedObjects(props.markdownContent);
+        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());
+
+        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);
+            });
+        }
+    }
+});
+
+function initWorkflowData() {
+    for (const workflowId of referencedWorkflowIds.value) {
+        console.log(`workflow id is ${workflowId}`);
+        fetchWorkflowForInstanceId(workflowId);
+        if (workflowId && !(workflowId in workflowAccessible.value)) {
+            Vue.set(workflowAccessible.value, workflowId, null);
+            sharingWorkflow({ id: workflowId }).then((response) => {
+                const accessible = response.data.importable;
+                Vue.set(workflowAccessible.value, workflowId, accessible);
+            });
+        }
+    }
+}
+
+function initHistoryDatasetData() {
+    for (const historyDatasetId of referencedHistoryDatasetIds.value) {
+        fetchDataset({ id: historyDatasetId });
+        if (historyDatasetId && !(historyDatasetId in historyDatasetAccessible.value)) {
+            axios.get(withPrefix(`/dataset/get_edit?dataset_id=${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);
+            });
+        }
+    }
+}
+
+const tableItems = computed<ItemInterface[]>(() => {
+    return [...histories.value, ...workflows.value, ...datasets.value];
+});
+
+function makeAccessible(item: ItemInterface) {
+    if (item.type == "history") {
+        enableLink({ history_id: item.id }).then((response) => {
+            Vue.set(historyAccessible.value, item.id, true);
+        });
+    } else if (item.type == "workflow") {
+        enableLinkWorkflow({ id: item.id }).then((response) => {
+            Vue.set(workflowAccessible.value, item.id, true);
+        });
+    } else if (item.type == "historyDataset") {
+        const data = {
+            dataset_id: item.id,
+            action: "remove_restrictions",
+        };
+        axios.put(withPrefix(`/api/datasets/${item.id}/permissions`), data).then((response) => {
+            console.log(response);
+            Vue.set(historyDatasetAccessible.value, item.id, true);
+        });
+    }
+}
+</script>
+
+<template>
+    <div>
+        <b-table :items="tableItems" :fields="tableFields">
+            <template v-slot:empty>
+                <LoadingSpan v-if="loading" message="Loading objects" />
+                <b-alert v-else variant="info" show>
+                    <div>No objects found in referenced Galaxy markdown content.</div>
+                </b-alert>
+            </template>
+            <template v-slot:cell(name)="row">
+                {{ row.item.name }}
+            </template>
+            <template v-slot:cell(accessible)="row">
+                <SharingIndicator :accessible="row.item.accessible" @makeAccessible="makeAccessible(row.item)" />
+            </template>
+            <template v-slot:cell(type)="row">
+                <PermissionObjectType :type="row.item.type" />
+            </template>
+        </b-table>
+    </div>
+</template>
diff --git a/client/src/components/PageEditor/ObjectPermissionsModal.vue b/client/src/components/PageEditor/ObjectPermissionsModal.vue
new file mode 100644
index 000000000000..cb250f1884e6
--- /dev/null
+++ b/client/src/components/PageEditor/ObjectPermissionsModal.vue
@@ -0,0 +1,15 @@
+<script setup lang="ts">
+import ObjectPermissions from "./ObjectPermissions.vue";
+
+interface ObjectPermissionsProps {
+    markdownContent: string;
+}
+
+defineProps<ObjectPermissionsProps>();
+</script>
+
+<template>
+    <b-modal v-bind="$attrs" title="Page Object Permissions" title-tag="h2" ok-only v-on="$listeners">
+        <ObjectPermissions :markdown-content="markdownContent" />
+    </b-modal>
+</template>
diff --git a/client/src/components/PageEditor/PageEditorMarkdown.vue b/client/src/components/PageEditor/PageEditorMarkdown.vue
index 7ef80fe89225..e422a3c8855d 100644
--- a/client/src/components/PageEditor/PageEditorMarkdown.vue
+++ b/client/src/components/PageEditor/PageEditorMarkdown.vue
@@ -1,6 +1,20 @@
 <template>
     <MarkdownEditor :title="title" :markdown-text="markdownText" :markdown-config="contentData" @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
@@ -25,7 +39,7 @@
 
 <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";
@@ -34,14 +48,17 @@ 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: {
@@ -68,6 +85,7 @@ export default {
     data: function () {
         return {
             markdownText: this.content,
+            showPermissions: false,
         };
     },
     methods: {
diff --git a/client/src/components/PageEditor/PermissionObjectType.vue b/client/src/components/PageEditor/PermissionObjectType.vue
new file mode 100644
index 000000000000..01976e5b582d
--- /dev/null
+++ b/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>
diff --git a/client/src/components/PageEditor/SharingIndicator.vue b/client/src/components/PageEditor/SharingIndicator.vue
new file mode 100644
index 000000000000..f43dfc1ae639
--- /dev/null
+++ b/client/src/components/PageEditor/SharingIndicator.vue
@@ -0,0 +1,60 @@
+<script setup lang="ts">
+import { ref, watch } from "vue";
+
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+interface SharingIndicatorProps {
+    accessible: Boolean | 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>
+        <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 .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>
diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
index 0e8d64fcf88b..5ef027c3978c 100644
--- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
@@ -11,6 +11,7 @@
 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 @@
     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 @@ def show(
         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}",
diff --git a/lib/galaxy/webapps/galaxy/services/dataset_collections.py b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
index 53b14d18d209..cc70c757eb73 100644
--- a/lib/galaxy/webapps/galaxy/services/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
@@ -32,6 +32,7 @@
     ModelClassField,
 )
 from galaxy.schema.schema import (
+    AnyHDCA,
     CreateNewCollectionPayload,
     DatasetCollectionInstanceType,
     DCESummary,
@@ -184,7 +185,8 @@ def show(
         trans: ProvidesHistoryContext,
         id: DecodedDatabaseIdField,
         instance_type: DatasetCollectionInstanceType = "history",
-    ) -> HDCADetailed:
+        view: str = "element",
+    ) -> AnyHDCA:
         """
         Returns information about a particular dataset collection.
         """
@@ -203,7 +205,7 @@ def show(
             security=trans.security,
             url_builder=trans.url_builder,
             parent=parent,
-            view="element",
+            view=view,
         )
         return rval