Merge pull request #14816 from assuntad23/6493/feature/undelete-workflows

6493/feature/undelete workflows

client/src/components/Common/Tags.vue

@@ -1,5 +1,5 @@
 <template>
-    <StatelessTags :value="tags" @input="onInput" @tag-click="onTagClick" />
+    <StatelessTags :value="tags" :disabled="disabled" @input="onInput" @tag-click="onTagClick" />
 </template>
 <script>
 import StatelessTags from "components/Tags/StatelessTags";
@@ -14,6 +14,10 @@ export default {
         tags: {
             type: Array,
         },
+        disabled: {
+            type: Boolean,
+            default: false,
+        },
     },
     methods: {
         onInput(tags) {

client/src/components/Workflow/WorkflowDropdown.test.js

@@ -93,7 +93,6 @@ describe("WorkflowDropdown.vue", () => {
 
     describe("workflow clicking workflow deletion", () => {
         let axiosMock;
-        let confirmRequest;
 
         async function mountAndDelete() {
             const workflow = {
@@ -109,33 +108,30 @@ describe("WorkflowDropdown.vue", () => {
 
         beforeEach(async () => {
             axiosMock = new MockAdapter(axios);
-            confirmRequest = true;
-            global.confirm = jest.fn(() => confirmRequest);
             axiosMock.onDelete("/api/workflows/workflowid123").reply(202, "deleted...");
+            axiosMock.onPost("/api/workflows/workflowid123/undelete").reply(204, "restored...");
         });
 
         afterEach(() => {
             axiosMock.restore();
         });
 
-        it("should confirm with localized deletion message", async () => {
-            await mountAndDelete();
-            expect(global.confirm).toHaveBeenCalledWith(expect.toBeLocalized());
-        });
-
-        it("should fire deletion API request upon confirmation", async () => {
+        it("should fire deletion API request upon remove action", async () => {
             await mountAndDelete();
             const emitted = wrapper.emitted();
             expect(emitted["onRemove"][0][0]).toEqual("workflowid123");
             expect(emitted["onSuccess"][0][0]).toEqual("deleted...");
         });
 
-        it("should not fire deletion API request if not confirmed", async () => {
-            confirmRequest = false;
+        it("should restore previously deleted workflows", async () => {
             await mountAndDelete();
             const emitted = wrapper.emitted();
-            expect(emitted["onRemove"]).toBeFalsy();
-            expect(emitted["onSuccess"]).toBeFalsy();
+            expect(emitted["onRemove"][0][0]).toEqual("workflowid123");
+            expect(emitted["onSuccess"][0][0]).toEqual("deleted...");
+            await wrapper.vm.onRestore();
+            await flushPromises();
+            expect(emitted["onRestore"][0][0]).toEqual("workflowid123");
+            expect(emitted["onSuccess"][1][0]).toEqual("restored...");
         });
     });
 });

client/src/components/Workflow/WorkflowDropdown.vue

@@ -23,57 +23,61 @@
         <p v-if="workflow.description" class="workflow-dropdown-description">{{ workflow.description }}</p>
         <div class="dropdown-menu" aria-labelledby="workflow-dropdown">
             <a
-                v-if="!readOnly"
+                v-if="!readOnly && !isDeleted"
                 class="dropdown-item"
                 @keypress="$router.push(urlEdit)"
                 @click.prevent="$router.push(urlEdit)">
                 <span class="fa fa-edit fa-fw mr-1" />
                 <span v-localize>Edit</span>
             </a>
-            <a class="dropdown-item" href="#" @click.prevent="onCopy">
+            <a v-if="!isDeleted" class="dropdown-item" href="#" @click.prevent="onCopy">
                 <span class="fa fa-copy fa-fw mr-1" />
                 <span v-localize>Copy</span>
             </a>
             <a
-                v-if="!readOnly"
+                v-if="!readOnly && !isDeleted"
                 class="dropdown-item"
                 @keypress="$router.push(urlInvocations)"
                 @click.prevent="$router.push(urlInvocations)">
                 <span class="fa fa-list fa-fw mr-1" />
                 <span v-localize>Invocations</span>
             </a>
-            <a class="dropdown-item" :href="urlDownload">
+            <a v-if="!isDeleted" class="dropdown-item" :href="urlDownload">
                 <span class="fa fa-download fa-fw mr-1" />
                 <span v-localize>Download</span>
             </a>
-            <a v-if="!readOnly" class="dropdown-item" href="#" @click.prevent="onRename">
+            <a v-if="!readOnly && !isDeleted" class="dropdown-item" href="#" @click.prevent="onRename">
                 <span class="fa fa-signature fa-fw mr-1" />
                 <span v-localize>Rename</span>
             </a>
             <a
-                v-if="!readOnly"
+                v-if="!readOnly && !isDeleted"
                 class="dropdown-item"
                 @keypress="$router.push(urlShare)"
                 @click.prevent="$router.push(urlShare)">
                 <span class="fa fa-share-alt fa-fw mr-1" />
                 <span v-localize>Share</span>
             </a>
-            <a v-if="!readOnly" class="dropdown-item" :href="urlExport">
+            <a v-if="!readOnly && !isDeleted" class="dropdown-item" :href="urlExport">
                 <span class="fa fa-file-export fa-fw mr-1" />
                 <span v-localize>Export</span>
             </a>
-            <a class="dropdown-item" :href="urlView">
+            <a v-if="!isDeleted" class="dropdown-item" :href="urlView">
                 <span class="fa fa-eye fa-fw mr-1" />
                 <span v-localize>View</span>
             </a>
-            <a v-if="sourceLabel" class="dropdown-item" :href="sourceUrl">
+            <a v-if="sourceLabel && !isDeleted" class="dropdown-item" :href="sourceUrl">
                 <span class="fa fa-globe fa-fw mr-1" />
                 <span v-localize>{{ sourceLabel }}</span>
             </a>
-            <a v-if="!readOnly" class="dropdown-item" href="#" @click.prevent="onDelete">
+            <a v-if="!readOnly && !isDeleted" class="dropdown-item" href="#" @click.prevent="onDelete">
                 <span class="fa fa-trash fa-fw mr-1" />
                 <span v-localize>Delete</span>
             </a>
+            <a v-if="isDeleted" class="dropdown-item" href="#" @click.prevent="onRestore">
+                <span class="fa fa-trash fa-fw mr-1" />
+                <span v-localize>Restore</span>
+            </a>
         </div>
     </div>
 </template>
@@ -121,6 +125,9 @@ export default {
         readOnly() {
             return !!this.workflow.shared;
         },
+        isDeleted() {
+            return this.workflow.deleted;
+        },
         sourceUrl() {
             if (this.workflow.source_metadata?.url) {
                 return this.workflow.source_metadata.url;
@@ -175,19 +182,15 @@ export default {
         },
         onDelete: function () {
             const id = this.workflow.id;
-            const name = this.workflow.name;
-            const confirmationMessage = this.l(`Are you sure you want to delete workflow '${name}'?`);
-            if (window.confirm(confirmationMessage)) {
-                this.services
-                    .deleteWorkflow(id)
-                    .then((message) => {
-                        this.$emit("onRemove", id);
-                        this.$emit("onSuccess", message);
-                    })
-                    .catch((error) => {
-                        this.$emit("onError", error);
-                    });
-            }
+            this.services
+                .deleteWorkflow(id)
+                .then((message) => {
+                    this.$emit("onRemove", id);
+                    this.$emit("onSuccess", message);
+                })
+                .catch((error) => {
+                    this.$emit("onError", error);
+                });
         },
         onRename: function () {
             const id = this.workflow.id;
@@ -206,6 +209,18 @@ export default {
                     });
             }
         },
+        onRestore: function () {
+            const id = this.workflow.id;
+            this.services
+                .undeleteWorkflow(id)
+                .then((message) => {
+                    this.$emit("onRestore", id);
+                    this.$emit("onSuccess", message);
+                })
+                .catch((error) => {
+                    this.$emit("onError", error);
+                });
+        },
     },
 };
 </script>

client/src/components/Workflow/WorkflowList.vue

@@ -33,24 +33,37 @@
                     @onRemove="onRemove"
                     @onUpdate="onUpdate"
                     @onSuccess="onSuccess"
-                    @onError="onError" />
+                    @onError="onError"
+                    @onRestore="onRestore" />
             </template>
             <template v-slot:cell(tags)="row">
-                <Tags :index="row.index" :tags="row.item.tags" @input="onTags" @tag-click="onTagClick" />
+                <Tags
+                    :index="row.index"
+                    :tags="row.item.tags"
+                    :disabled="row.item.deleted"
+                    @input="onTags"
+                    @tag-click="onTagClick" />
             </template>
             <template v-slot:cell(published)="row">
-                <SharingIndicators :object="row.item" @filter="(filter) => appendFilter(filter)" />
+                <SharingIndicators
+                    v-if="!row.item.deleted"
+                    :object="row.item"
+                    @filter="(filter) => appendFilter(filter)" />
+                <div v-else>&#8212;</div>
             </template>
             <template v-slot:cell(show_in_tool_panel)="row">
                 <WorkflowBookmark
+                    v-if="!row.item.deleted"
                     :checked="row.item.show_in_tool_panel"
                     @bookmark="(checked) => bookmarkWorkflow(row.item.id, checked)" />
+                <div v-else>&#8212;</div>
             </template>
             <template v-slot:cell(update_time)="data">
                 <UtcDate :date="data.value" mode="elapsed" />
             </template>
             <template v-slot:cell(execute)="row">
-                <WorkflowRunButton :id="row.item.id" :root="root" />
+                <WorkflowRunButton v-if="!row.item.deleted" :id="row.item.id" :root="root" />
+                <div v-else>&#8212;</div>
             </template>
         </b-table>
         <b-pagination
@@ -78,30 +91,49 @@ import WorkflowRunButton from "./WorkflowRunButton.vue";
 import SharingIndicators from "components/Indices/SharingIndicators";
 
 const helpHtml = `<div>
-<p>This textbox box can be used to filter the workflows displayed.
+    <p>This input can be used to filter the workflows displayed.</p>
 
-<p>Text entered here will be searched against workflow names and tags. Additionally, advanced
-filtering tags can be used to refine the search more precisely. Tags are of the form
-<code>&lt;tag_name&gt;:&lt;tag_value&gt;</code> or <code>&lt;tag_name&gt;:'&lt;tag_value&gt;'</code>.
-For instance to search just for RNAseq in the workflow name, <code>name:rnsseq</code> can be used.
-Notice by default the search is not case-sensitive.
+    <p>
+        Text entered here will be searched against workflow names and workflow
+        tags. Additionally, advanced filtering tags can be used to refine the
+        search more precisely. Filtering tags are of the form
+        <code>&lt;tag_name&gt;:&lt;tag_value&gt;</code> or
+        <code>&lt;tag_name&gt;:'&lt;tag_value&gt;'</code>. For instance to
+        search just for RNAseq in the workflow name,
+        <code>name:rnsseq</code> can be used. Notice by default the search is
+        not case-sensitive. If the quoted version of tag is used, the search is
+        case sensitive and only full matches will be returned. So
+        <code>name:'RNAseq'</code> would show only workflows named exactly
+        <code>RNAseq</code>.
+    </p>
 
-If the quoted version of tag is used, the search is not case sensitive and only full matches will be
-returned. So <code>name:'RNAseq'</code> would show only workflows named exactly <code>RNAseq</code>.
-
-<p>The available tags are:
-<dl>
-    <dt><code>name</code></dt>
-    <dd>This filters only against the workflow name.</dd>
-    <dt><code>tag</code></dt>
-    <dd>This filters only against the workflow tag. You may also just click on a tag in your list of workflows to filter on that tag using this directly.</dd>
-    <dt><code>is:published</code></dt>
-    <dd>This filters the workflows such that only published workflows are shown. You may also just click on the "published" icon of a workflow in your list to filter on this directly.</dd>
-    <dt><code>is:shared</code></dt>
-    <dd>This filters the workflows such that only workflows shared from another user directly with you are are shown. You may also just click on the "shared with me" icon of a workflow in your list to filter on this directly.</dd>
-</dl>
-</div>
-`;
+    <p>The available filtering tags are:</p>
+    <dl>
+        <dt><code>name</code></dt>
+        <dd>
+            Shows workflows with given sequence of characters in their names.
+        </dd>
+        <dt><code>tag</code></dt>
+        <dd>
+            Shows workflows with the given workflow tag. You may also just click
+            on a tag in your list of workflows to filter on that tag directly.
+        </dd>
+        <dt><code>is:published</code></dt>
+        <dd>
+            Shows published workflows. You may also just click on the
+            "published" icon of a workflow in your list to filter on this
+            directly.
+        </dd>
+        <dt><code>is:shared</code></dt>
+        <dd>
+            Shows workflows shared by another user directly with you. You may
+            also just click on the "shared with me" icon of a workflow in your
+            list to filter on this directly.
+        </dd>
+        <dt><code>is:deleted</code></dt>
+        <dd>Shows deleted workflows.</dd>
+    </dl>
+</div>`;
 
 export default {
     components: {
@@ -234,6 +266,9 @@ export default {
         onUpdate: function (id, data) {
             this.refresh();
         },
+        onRestore: function (id) {
+            this.refresh();
+        },
     },
 };
 </script>

client/src/components/Workflow/services.js

@@ -37,6 +37,16 @@ export class Services {
         }
     }
 
+    async undeleteWorkflow(id) {
+        const url = safePath(`/api/workflows/${id}/undelete`);
+        try {
+            const response = await axios.post(url);
+            return response.data;
+        } catch (e) {
+            rethrowSimple(e);
+        }
+    }
+
     async updateWorkflow(id, data) {
         const url = safePath(`/api/workflows/${id}`);
         try {

lib/galaxy/managers/workflows.py

@@ -166,7 +166,6 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
         query = query.options(latest_workflow_load)
         query = query.filter(or_(*filters))
         query = query.filter(model.StoredWorkflow.table.c.hidden == (true() if show_hidden else false()))
-        query = query.filter(model.StoredWorkflow.table.c.deleted == (true() if show_deleted else false()))
         if payload.search:
             search_query = payload.search
             parsed_search = parse_filters_structured(search_query, INDEX_SEARCH_FILTERS)
@@ -194,6 +193,9 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
                     elif key == "is":
                         if q == "published":
                             query = query.filter(model.StoredWorkflow.published == true())
+                        elif q == "deleted":
+                            query = query.filter(model.StoredWorkflow.deleted == true())
+                            show_deleted = true
                         elif q == "shared_with_me":
                             if not show_shared:
                                 message = "Can only use tag is:shared_with_me if show_shared parameter also true."
@@ -213,6 +215,7 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
                             term,
                         )
                     )
+        query = query.filter(model.StoredWorkflow.table.c.deleted == (true() if show_deleted else false()))
         if include_total_count:
             total_matches = query.count()
         else:

lib/galaxy_test/selenium/test_workflow_management.py

@@ -158,7 +158,6 @@ class TestWorkflowManagement(SeleniumTestCase, TestsGalaxyPagers, UsesWorkflowAs
         self.workflow_index_rename("fordelete")
         self._assert_showing_n_workflows(1)
         self.workflow_index_click_option("Delete")
-        self.accept_alert()
         self._assert_showing_n_workflows(0)
 
         self.workflow_index_open()