From 86ac9ca9562dae2cdc56048f2deb80de4df82f7b Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Thu, 11 Feb 2021 16:00:18 +0100
Subject: [PATCH] first implementation

---
 .../LibraryFolder/LibraryFolder.vue           |   2 +-
 .../LibraryFolderDatasetPermissions.vue       | 148 ++++++++++++++++++
 .../LibraryFolderPermissions.vue              | 127 +++++----------
 .../LibraryPermissionsWarning.vue             |  25 +++
 .../PermissionsInputField.vue                 |  71 ++++++---
 .../LibraryFolderPermissions/services.js      |  23 ++-
 .../LibraryFolderPermissions/utils.js         |   9 ++
 .../LibraryFolder/LibraryFolderRouter.vue     |   9 +-
 client/src/entry/analysis/AnalysisRouter.js   |   1 +
 lib/galaxy/webapps/galaxy/buildapp.py         |   1 +
 10 files changed, 308 insertions(+), 108 deletions(-)
 create mode 100644 client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryFolderDatasetPermissions.vue
 create mode 100644 client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryPermissionsWarning.vue
 create mode 100644 client/src/components/LibraryFolder/LibraryFolderPermissions/utils.js

diff --git a/client/src/components/LibraryFolder/LibraryFolder.vue b/client/src/components/LibraryFolder/LibraryFolder.vue
index 10248d84889..432402730e7 100644
--- a/client/src/components/LibraryFolder/LibraryFolder.vue
+++ b/client/src/components/LibraryFolder/LibraryFolder.vue
@@ -461,7 +461,7 @@ export default {
             else if (element.type === "folder") return `${this.root}library/folders/${element.id}`;
         },
         navigateToPermission(element) {
-            if (element.type === "file") window.location.replace(`${this.createContentLink(element)}/permissions`);
+            if (element.type === "file") this.$router.push({ path: `/permissions/${this.folder_id}/dataset/${element.id}` })
             else if (element.type === "folder") this.$router.push({ path: `/permissions/${element.id}` });
         },
         getMessage(element) {
diff --git a/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryFolderDatasetPermissions.vue b/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryFolderDatasetPermissions.vue
new file mode 100644
index 00000000000..c5abd0db36b
--- /dev/null
+++ b/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryFolderDatasetPermissions.vue
@@ -0,0 +1,148 @@
+<template>
+    <div>
+        <div v-if="dataset">
+            <b-button variant="primary" :to="{ path: `/${this.folder_id}` }">
+                <font-awesome-icon icon="angle-double-left">1</font-awesome-icon>
+            </b-button>
+            <div>
+                <div class="header text-center">{{ dataset.name }}</div>
+            </div>
+        </div>
+        <LibraryPermissionsWarning :is_admin="is_admin" />
+        <hr class="my-4" />
+        <b-container fluid>
+            <h2 class="text-center">Library-related permissions</h2>
+            <PermissionsInputField
+                v-if="modify_item_roles"
+                :id="dataset_id"
+                :permission_type="manage_type"
+                :initial_value="modify_item_roles"
+                title="Roles that can modify the library item"
+                :apiRootUrl="apiRootUrl"
+                alert="User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item."
+                @input="setUserPermissionsPreferences"
+            />
+            <hr class="my-4" />
+            <h2 class="text-center">Dataset-related permissions</h2>
+            <div class="alert alert-warning text-center">
+                Changes made below will affect <strong>every</strong> library item that was created from this dataset
+                and also every history this dataset is part of.
+            </div>
+            <PermissionsInputField
+                v-if="access_dataset_roles"
+                :id="dataset_id"
+                :permission_type="manage_type"
+                :initial_value="access_dataset_roles"
+                :apiRootUrl="apiRootUrl"
+                title="Roles that can access the dataset"
+                alert="User has to have <strong>all these roles</strong> in order to access this dataset.
+                        Users without access permission <strong>cannot</strong> have other permissions on this dataset.
+                        If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>."
+                @input="setUserPermissionsPreferences"
+            />
+            <PermissionsInputField
+                v-if="manage_dataset_roles"
+                :id="dataset_id"
+                :permission_type="manage_type"
+                :initial_value="manage_dataset_roles"
+                :apiRootUrl="apiRootUrl"
+                title="Roles that can manage permissions on the dataset"
+                alert="User with <strong>any</strong> of these roles can manage permissions of this dataset.
+                        If you remove yourself you will lose the ability manage this dataset unless you are an admin."
+                @input="setUserPermissionsPreferences"
+            />
+        </b-container>
+    </div>
+</template>
+
+<script>
+import Vue from "vue";
+import { getAppRoot } from "onload/loadConfig";
+import BootstrapVue from "bootstrap-vue";
+import { Services } from "./services";
+import { Toast } from "ui/toast";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { getGalaxyInstance } from "app";
+import PermissionsInputField from "./PermissionsInputField.vue";
+import { initManageFolderIcons } from "components/LibraryFolder/icons";
+import LibraryPermissionsWarning from "components/LibraryFolder/LibraryFolderPermissions/LibraryPermissionsWarning.vue";
+import { extractRoles } from "./utils";
+
+import "vue-multiselect/dist/vue-multiselect.min.css";
+import VueObserveVisibility from "vue-observe-visibility";
+
+Vue.use(VueObserveVisibility);
+Vue.use(BootstrapVue);
+initManageFolderIcons();
+
+export default {
+    props: {
+        folder_id: {
+            type: String,
+            required: true,
+        },
+        dataset_id: {
+            type: String,
+            required: true,
+        },
+    },
+    components: {
+        PermissionsInputField,
+        LibraryPermissionsWarning,
+        FontAwesomeIcon,
+    },
+    data() {
+        return {
+            permissions: undefined,
+            dataset: undefined,
+            is_admin: undefined,
+            access_dataset_roles: undefined,
+            modify_item_roles: undefined,
+            manage_dataset_roles: undefined,
+            add_type: "add_type",
+            manage_type: "manage_type",
+            modify_type: "modify_type",
+            apiRootUrl: `${getAppRoot()}api/libraries/datasets`,
+        };
+    },
+    created() {
+        const Galaxy = getGalaxyInstance();
+        this.root = getAppRoot();
+        this.services = new Services({ root: this.root });
+        this.is_admin = Galaxy.user.attributes.is_admin;
+        this.services.getDatasetPermissions(this.dataset_id).then((fetched_permissions) => {
+            this.access_dataset_roles = extractRoles(fetched_permissions.access_dataset_roles);
+            this.modify_item_roles = extractRoles(fetched_permissions.modify_item_roles);
+            this.manage_dataset_roles = extractRoles(fetched_permissions.manage_dataset_roles);
+        });
+        this.services.getDataset(this.dataset_id).then((response) => {
+            this.dataset = response;
+        });
+    },
+
+    methods: {
+        getParentLink() {
+            return `${this.root}library/folders/${this.folder_id}`;
+        },
+        setUserPermissionsPreferences(ids, permission_type) {
+            switch (permission_type) {
+                case "manage_type":
+                    this.manage_folder_role_list = ids;
+                    break;
+                case "add_type":
+                    this.add_library_item_role_list = ids;
+                    break;
+                case "modify_type":
+                    this.modify_folder_role_list = ids;
+                    break;
+            }
+        },
+    },
+};
+</script>
+
+<style scoped>
+.header {
+    font-size: 45px;
+}
+</style>
diff --git a/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryFolderPermissions.vue b/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryFolderPermissions.vue
index 982ef7bd18e..8f1340681e2 100644
--- a/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryFolderPermissions.vue
+++ b/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryFolderPermissions.vue
@@ -9,77 +9,44 @@
                     <div class="header text-center">{{ folder.name }}</div>
                 </div>
             </div>
-            <div>
-                <div class="text-center">
-                    <b-alert show variant="warning" v-if="is_admin">
-                        You are logged in as an <strong>administrator</strong> therefore you can manage any folder on
-                        this Galaxy instance. Please make sure you understand the consequences.
-                    </b-alert>
-                    <b-alert show variant="warning" v-else>
-                        You can assign any number of roles to any of the following permission types. However please read
-                        carefully the implications of such actions.
-                    </b-alert>
-                </div>
-            </div>
+            <LibraryPermissionsWarning :is_admin="is_admin" />
             <hr class="my-4" />
             <b-container fluid>
                 <div class="dataset_table">
-                    <h2>Folder permissions</h2>
-                    <h4>
-                        Roles that can manage permissions on this folder
-                    </h4>
-                    <b-row>
-                        <b-col>
-                            <PermissionsInputField
-                                v-if="manage_folder_role_list"
-                                :folder_id="folder_id"
-                                :permission_type="manage_type"
-                                :initial_value="manage_folder_role_list"
-                                @input="setUserPermissionsPreferences"
-                        /></b-col>
-                        <b-col>
-                            <b-alert show variant="info">
-                                User with <strong>any</strong> of these roles can manage permissions on this folder.
-                            </b-alert>
-                        </b-col>
-                    </b-row>
-                    <h4>
-                        Roles that can add items to this folder
-                    </h4>
-                    <b-row>
-                        <b-col>
-                            <PermissionsInputField
-                                v-if="add_library_item_role_list"
-                                :folder_id="folder_id"
-                                :permission_type="add_type"
-                                :initial_value="add_library_item_role_list"
-                                @input="setUserPermissionsPreferences"
-                        /></b-col>
-                        <b-col>
-                            <b-alert class="p-3" show variant="info">
-                                User with <strong>any</strong> of these roles can add items to this folder (folders and
-                                datasets).
-                            </b-alert>
-                        </b-col>
-                    </b-row>
-                    <h4>
-                        Roles that can modify this folder
-                    </h4>
-                    <b-row>
-                        <b-col>
-                            <PermissionsInputField
-                                v-if="modify_folder_role_list"
-                                :folder_id="folder_id"
-                                :permission_type="modify_type"
-                                :initial_value="modify_folder_role_list"
-                                @input="setUserPermissionsPreferences"
-                        /></b-col>
-                        <b-col>
-                            <b-alert show variant="info">
-                                User with <strong>any</strong> of these roles can modify this folder (name, etc.).
-                            </b-alert></b-col
-                        >
-                    </b-row>
+                    <h2 class="text-center">Folder permissions</h2>
+                    <PermissionsInputField
+                        v-if="manage_folder_role_list"
+                        :id="folder_id"
+                        :permission_type="manage_type"
+                        :initial_value="manage_folder_role_list"
+                        :apiRootUrl="apiRootUrl"
+                        alert="User with <strong>any</strong> of these roles can manage permissions on this folder."
+                        title="Roles that can manage permissions on this folder"
+                        @input="setUserPermissionsPreferences"
+                    />
+
+                    <PermissionsInputField
+                        v-if="add_library_item_role_list"
+                        :id="folder_id"
+                        :permission_type="add_type"
+                        :initial_value="add_library_item_role_list"
+                        :apiRootUrl="apiRootUrl"
+                        title="Roles that can add items to this folder"
+                        alert="User with <strong>any</strong> of these roles can add items to this folder (folders and
+                                datasets)."
+                        @input="setUserPermissionsPreferences"
+                    />
+
+                    <PermissionsInputField
+                        v-if="modify_folder_role_list"
+                        :id="folder_id"
+                        :permission_type="modify_type"
+                        :initial_value="modify_folder_role_list"
+                        :apiRootUrl="apiRootUrl"
+                        title="Roles that can modify this folder"
+                        alert="User with <strong>any</strong> of these roles can modify this folder (name, etc.)."
+                        @input="setUserPermissionsPreferences"
+                    />
                     <button
                         data-toggle="tooltip"
                         data-placement="top"
@@ -106,12 +73,11 @@ import { Toast } from "ui/toast";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { getGalaxyInstance } from "app";
 import PermissionsInputField from "./PermissionsInputField.vue";
+import LibraryPermissionsWarning from "components/LibraryFolder/LibraryFolderPermissions/LibraryPermissionsWarning.vue";
+import { extractRoles } from "./utils";
+
 import { initManageFolderIcons } from "components/LibraryFolder/icons";
 
-import "vue-multiselect/dist/vue-multiselect.min.css";
-import VueObserveVisibility from "vue-observe-visibility";
-
-Vue.use(VueObserveVisibility);
 Vue.use(BootstrapVue);
 initManageFolderIcons();
 
@@ -124,6 +90,7 @@ export default {
     },
     components: {
         PermissionsInputField,
+        LibraryPermissionsWarning,
         FontAwesomeIcon,
     },
     data() {
@@ -137,6 +104,7 @@ export default {
             add_type: "add_type",
             manage_type: "manage_type",
             modify_type: "modify_type",
+            apiRootUrl: `${getAppRoot()}api/folders`,
         };
     },
     created() {
@@ -145,9 +113,9 @@ export default {
         this.services = new Services({ root: this.root });
         this.is_admin = Galaxy.user.attributes.is_admin;
         this.services.getFolderPermissions(this.folder_id).then((fetched_permissions) => {
-            this.add_library_item_role_list = this._serializeRoles(fetched_permissions.add_library_item_role_list);
-            this.manage_folder_role_list = this._serializeRoles(fetched_permissions.manage_folder_role_list);
-            this.modify_folder_role_list = this._serializeRoles(fetched_permissions.modify_folder_role_list);
+            this.add_library_item_role_list = extractRoles(fetched_permissions.add_library_item_role_list);
+            this.manage_folder_role_list = extractRoles(fetched_permissions.manage_folder_role_list);
+            this.modify_folder_role_list = extractRoles(fetched_permissions.modify_folder_role_list);
         });
         this.services.getFolder(this.folder_id).then((response) => {
             this.folder = response;
@@ -187,15 +155,6 @@ export default {
                 }
             );
         },
-
-        _serializeRoles: function (role_list) {
-            const selected_roles = [];
-            role_list.forEach((item) => {
-                selected_roles.push({ name: item[0], id: item[1] });
-            });
-
-            return selected_roles;
-        },
     },
 };
 </script>
diff --git a/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryPermissionsWarning.vue b/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryPermissionsWarning.vue
new file mode 100644
index 00000000000..1eb6b871ad3
--- /dev/null
+++ b/client/src/components/LibraryFolder/LibraryFolderPermissions/LibraryPermissionsWarning.vue
@@ -0,0 +1,25 @@
+<template>
+    <div>
+        <div class="text-center">
+            <b-alert show variant="warning" v-if="is_admin">
+                You are logged in as an <strong>administrator</strong> therefore you can manage any folder on
+                this Galaxy instance. Please make sure you understand the consequences.
+            </b-alert>
+            <b-alert show variant="warning" v-else>
+                You can assign any number of roles to any of the following permission types. However please read
+                carefully the implications of such actions.
+            </b-alert>
+        </div>
+    </div>
+</template>
+
+<script>
+    export default {
+        props: {
+            is_admin: {
+                type: Boolean,
+                required: true,
+            },
+        },
+    }
+</script>
\ No newline at end of file
diff --git a/client/src/components/LibraryFolder/LibraryFolderPermissions/PermissionsInputField.vue b/client/src/components/LibraryFolder/LibraryFolderPermissions/PermissionsInputField.vue
index 3a889956ebc..f2dcfa8a9ff 100644
--- a/client/src/components/LibraryFolder/LibraryFolderPermissions/PermissionsInputField.vue
+++ b/client/src/components/LibraryFolder/LibraryFolderPermissions/PermissionsInputField.vue
@@ -1,33 +1,56 @@
 <template>
-    <div v-if="options && value">
-        <multiselect
-            v-model="value"
-            :options="fetched_options"
-            :clear-on-select="true"
-            :preserve-search="true"
-            :multiple="true"
-            label="name"
-            track-by="id"
-            @input="valueChanged"
-            @search-change="searchChanged"
-            :internal-search="false"
-        >
-            <template slot="afterList">
-                <div v-observe-visibility="reachedEndOfList" v-if="hasMorePages">
-                    <span class="spinner fa fa-spinner fa-spin fa-1x" />
+    <div>
+        <h4>
+            {{ title }}
+        </h4>
+        <b-row>
+            <b-col>
+                <div v-if="options && value">
+                    <multiselect
+                        v-model="value"
+                        :options="fetched_options"
+                        :clear-on-select="true"
+                        :preserve-search="true"
+                        :multiple="true"
+                        label="name"
+                        track-by="id"
+                        @input="valueChanged"
+                        @search-change="searchChanged"
+                        :internal-search="false"
+                    >
+                        <template slot="afterList">
+                            <div v-observe-visibility="reachedEndOfList" v-if="hasMorePages">
+                                <span class="spinner fa fa-spinner fa-spin fa-1x" />
+                            </div>
+                        </template>
+                    </multiselect>
                 </div>
-            </template>
-        </multiselect>
+            </b-col>
+            <b-col>
+                <b-alert show variant="info">
+                    <div v-html="alert" />
+                </b-alert>
+            </b-col>
+        </b-row>
     </div>
 </template>
 
 <script>
+import Vue from "vue";
+
+import VueObserveVisibility from "vue-observe-visibility";
 import Multiselect from "vue-multiselect";
 import { Services } from "./services";
+import "vue-multiselect/dist/vue-multiselect.min.css";
 
+Vue.use(VueObserveVisibility);
 export default {
     props: {
-        folder_id: {
+        id: {
+            type: String,
+            required: true,
+        },
+        title: {
             type: String,
             required: true,
         },
@@ -39,6 +62,14 @@ export default {
             type: Array,
             required: true,
         },
+        apiRootUrl: {
+            type: String,
+            required: true,
+        },
+        alert: {
+            type: String,
+            required: true,
+        },
     },
     components: {
         Multiselect,
@@ -70,7 +101,7 @@ export default {
     methods: {
         getSelectOptions(searchChanged = false) {
             this.services
-                .getSelectOptions(this.folder_id, true, this.page, this.page_limit, this.searchValue)
+                .getSelectOptions(this.apiRootUrl, this.id, true, this.page, this.page_limit, this.searchValue)
                 .then((response) => {
                     this.options = response;
                     if (searchChanged) this.fetched_options = this.options.roles;
diff --git a/client/src/components/LibraryFolder/LibraryFolderPermissions/services.js b/client/src/components/LibraryFolder/LibraryFolderPermissions/services.js
index a7781482066..478c6cd4db7 100644
--- a/client/src/components/LibraryFolder/LibraryFolderPermissions/services.js
+++ b/client/src/components/LibraryFolder/LibraryFolderPermissions/services.js
@@ -16,6 +16,24 @@ export class Services {
             rethrowSimple(e);
         }
     }
+    async getDatasetPermissions(id) {
+        const url = `${this.root}api/libraries/datasets/${id}/permissions?scope=current`;
+        try {
+            const response = await axios.get(url);
+            return response.data;
+        } catch (e) {
+            rethrowSimple(e);
+        }
+    }
+    async getDataset(id) {
+        const url = `${this.root}api/libraries/datasets/${id}`;
+        try {
+            const response = await axios.get(url);
+            return response.data;
+        } catch (e) {
+            rethrowSimple(e);
+        }
+    }
     async getFolder(id) {
         const url = `${this.root}api/folders/${id}`;
         try {
@@ -25,9 +43,9 @@ export class Services {
             rethrowSimple(e);
         }
     }
-    async getSelectOptions(id, is_library_access, page, page_limit, searchQuery) {
+    async getSelectOptions(apiRootUrl, id, is_library_access, page, page_limit, searchQuery) {
         searchQuery = searchQuery ? `&q=${searchQuery}` : "";
-        const url = `${this.root}api/folders/${id}/permissions?scope=available&is_library_access=${is_library_access}&page_limit=${page_limit}&page=${page}${searchQuery}`;
+        const url = `${apiRootUrl}/${id}/permissions?scope=available&is_library_access=${is_library_access}&page_limit=${page_limit}&page=${page}${searchQuery}`;
         try {
             const response = await axios.get(url);
             return response.data;
@@ -35,6 +53,7 @@ export class Services {
             rethrowSimple(e);
         }
     }
+
     async setPermissions(id, add_ids, manage_ids, modify_ids, onSuccess, onError) {
         var formData = new FormData();
         formData.append(
diff --git a/client/src/components/LibraryFolder/LibraryFolderPermissions/utils.js b/client/src/components/LibraryFolder/LibraryFolderPermissions/utils.js
new file mode 100644
index 00000000000..692c1db1b51
--- /dev/null
+++ b/client/src/components/LibraryFolder/LibraryFolderPermissions/utils.js
@@ -0,0 +1,9 @@
+// legacy code
+export function extractRoles(role_list) {
+    const selected_roles = [];
+    role_list.forEach((item) => {
+        selected_roles.push({ name: item[0], id: item[1] });
+    });
+
+    return selected_roles;
+}
diff --git a/client/src/components/LibraryFolder/LibraryFolderRouter.vue b/client/src/components/LibraryFolder/LibraryFolderRouter.vue
index 7de34fcdf67..f3bd91063a2 100644
--- a/client/src/components/LibraryFolder/LibraryFolderRouter.vue
+++ b/client/src/components/LibraryFolder/LibraryFolderRouter.vue
@@ -2,8 +2,9 @@
 import { getAppRoot } from "onload/loadConfig";
 import Vue from "vue";
 import VueRouter from "vue-router";
-import LibraryFolderPermissions from "./LibraryFolderPermissions/LibraryFolderPermissions.vue";
+import LibraryFolderPermissions from "components/LibraryFolder/LibraryFolderPermissions/LibraryFolderPermissions.vue";
 import LibraryFolder from "components/LibraryFolder/LibraryFolder.vue";
+import LibraryFolderDatasetPermissions from "components/LibraryFolder/LibraryFolderPermissions/LibraryFolderDatasetPermissions.vue";
 
 Vue.use(VueRouter);
 
@@ -23,6 +24,12 @@ export default new VueRouter({
             component: LibraryFolderPermissions,
             props: true,
         },
+        {
+            path: "/permissions/:folder_id/dataset/:dataset_id",
+            name: "LibraryFolder",
+            component: LibraryFolderDatasetPermissions,
+            props: true,
+        },
     ],
 });
 </script>
diff --git a/client/src/entry/analysis/AnalysisRouter.js b/client/src/entry/analysis/AnalysisRouter.js
index f38c044cdef..21e7e4430e0 100644
--- a/client/src/entry/analysis/AnalysisRouter.js
+++ b/client/src/entry/analysis/AnalysisRouter.js
@@ -101,6 +101,7 @@ export const getAnalysisRouter = (Galaxy) => {
             "(/)interactivetool_entry_points(/)list": "show_interactivetool_list",
             "(/)library/folders(/)(:folder_id)": "show_library_folder",
             "(/)library/folders/permissions(/)(:folder_id)": "show_library_folder",
+            "(/)library/folders/permissions(/)(:folder_id)(/)dataset(/)(:dataset_id)": "show_library_folder",
         },
 
         require_login: ["show_user", "show_user_form", "show_workflows", "show_cloud_auth", "show_external_ids"],
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 6c63ce4e672..e57818d9b45 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -193,6 +193,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     webapp.add_client_route('/interactivetool_entry_points/list')
     webapp.add_client_route('/library/folders/{folder_id}')
     webapp.add_client_route('/library/folders/permissions/{folder_id}')
+    webapp.add_client_route('/library/folders/permissions/{folder_id}/dataset/{dataset_id}')
 
     # ==== Done
     # Indicate that all configuration settings have been provided