Merge branch 'release_23.2' into release-titles

client/src/components/Page/PageList.test.js

@@ -5,6 +5,7 @@ import MockAdapter from "axios-mock-adapter";
 import { formatDistanceToNow, parseISO } from "date-fns";
 import flushPromises from "flush-promises";
 import { PiniaVuePlugin } from "pinia";
+import { useUserStore } from "stores/userStore";
 import { getLocalVue, wait } from "tests/jest/helpers";
 
 import PageList from "./PageList.vue";
@@ -98,16 +99,29 @@ describe("PgeList.vue", () => {
     const mockPublishedPageData = [publishedPage];
     const mockTwoPageData = [privatePage, pageA];
 
-    function mountPersonalGrid() {
+    function mountGrid(propsData) {
+        const pinia = createTestingPinia();
+        const userStore = useUserStore();
+        userStore.currentUser = { username: "jimmyPage", tags_used: [] };
+
         wrapper = mount(PageList, {
-            propsData: propsDataPersonalGrid,
+            propsData,
             localVue,
+            pinia,
             stubs: {
                 icon: { template: "<div></div>" },
             },
         });
     }
 
+    function mountPersonalGrid() {
+        mountGrid(propsDataPersonalGrid);
+    }
+
+    function mountPublishedGrid() {
+        mountGrid(propsDataPublishedGrid);
+    }
+
     describe(" with empty page list", () => {
         beforeEach(async () => {
             axiosMock.onAny().reply(200, [], { total_matches: "0" });
@@ -145,14 +159,7 @@ describe("PgeList.vue", () => {
             jest.spyOn(PageList.methods, "decorateData").mockImplementation((page) => {
                 page.shared = false;
             });
-            wrapper = mount(PageList, {
-                propsData: propsDataPersonalGrid,
-                localVue,
-                pinia: createTestingPinia(),
-                stubs: {
-                    icon: { template: "<div></div>" },
-                },
-            });
+            mountPersonalGrid();
             await flushPromises();
         });
 
@@ -215,14 +222,7 @@ describe("PgeList.vue", () => {
             jest.spyOn(PageList.methods, "decorateData").mockImplementation((page) => {
                 page.shared = true;
             });
-            wrapper = mount(PageList, {
-                propsData: propsDataPersonalGrid,
-                localVue,
-                pinia: createTestingPinia(),
-                stubs: {
-                    icon: { template: "<div></div>" },
-                },
-            });
+            mountPersonalGrid();
             await flushPromises();
         });
         it("updates filter when published icon is clicked", async () => {
@@ -257,14 +257,7 @@ describe("PgeList.vue", () => {
             jest.spyOn(PageList.methods, "decorateData").mockImplementation((page) => {
                 page.shared = false;
             });
-            wrapper = mount(PageList, {
-                propsData: propsDataPublishedGrid,
-                localVue,
-                pinia: createTestingPinia(),
-                stubs: {
-                    icon: { template: "<div></div>" },
-                },
-            });
+            mountPublishedGrid();
             await flushPromises();
         });
 
@@ -301,14 +294,7 @@ describe("PgeList.vue", () => {
             jest.spyOn(PageList.methods, "decorateData").mockImplementation((page) => {
                 page.shared = false;
             });
-            wrapper = mount(PageList, {
-                propsData: propsDataPublishedGrid,
-                localVue,
-                pinia: createTestingPinia(),
-                stubs: {
-                    icon: { template: "<div></div>" },
-                },
-            });
+            mountPublishedGrid();
             await flushPromises();
         });
 

client/src/components/Page/PageList.vue

@@ -50,7 +50,7 @@
                     clickable
                     :value="row.item.tags"
                     :index="row.index"
-                    :disabled="published"
+                    :disabled="published || !currentUserOwnsItem(row.item)"
                     @input="(tags) => onTags(tags, row.index)"
                     @tag-click="(tag) => applyFilter('tag', tag, true)" />
             </template>
@@ -100,11 +100,13 @@ import StatelessTags from "components/TagsMultiselect/StatelessTags";
 import UtcDate from "components/UtcDate";
 import paginationMixin from "components/Workflow/paginationMixin";
 import { getAppRoot } from "onload/loadConfig";
+import { storeToRefs } from "pinia";
 import Filtering, { contains, equals, expandNameTag, toBool } from "utils/filtering";
 import _l from "utils/localization";
 import { useRouter } from "vue-router/composables";
 
 import { updateTags } from "@/api/tags";
+import { useUserStore } from "@/stores/userStore";
 import { absPath } from "@/utils/redirect";
 
 import PageDropdown from "./PageDropdown";
@@ -224,8 +226,10 @@ export default {
     },
     setup() {
         const router = useRouter();
+        const { currentUser } = storeToRefs(useUserStore());
         return {
             router,
+            currentUser,
         };
     },
     data() {
@@ -304,6 +308,9 @@ export default {
         shareLink: function (item) {
             this.router.push(`sharing?id=${item.id}`);
         },
+        currentUserOwnsItem: function (item) {
+            return item.username === this.currentUser.username;
+        },
         decorateData(page) {
             const Galaxy = getGalaxyInstance();
             page.shared = page.username !== Galaxy.user.attributes.username;

doc/source/releases/23.2.rst

@@ -14,6 +14,9 @@ Enhancements
 
 .. feature
 
+* Initial release notes  for 23.2
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 17259`_
 * Make form repeat blocks reorderable
   (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
   `Pull Request 14892`_
@@ -135,6 +138,9 @@ Enhancements
   `Pull Request 16345`_
 .. enhancement_tag_jobs
 
+* Enable job resubmissions in k8s runner
+  (thanks to `@pcm32 <https://github.com/pcm32>`__).
+  `Pull Request 15238`_
 * Towards SQLAlchemy 2.0 (upgrades to SQLAlchemy Core usage)
   (thanks to `@jdavcs <https://github.com/jdavcs>`__).
   `Pull Request 16264`_
@@ -154,6 +160,9 @@ Enhancements
   `Pull Request 17178`_
 .. enhancement
 
+* Improve embed performance
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 17326`_
 * Add parameter name to validation errors
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 15440`_
@@ -554,6 +563,9 @@ Fixes
   `Pull Request 17233`_
 .. bug_tag_tools
 
+* Add back 1.1.0 version of Filtering1 tool
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 16883`_
 * Add missing requirements to perl tools
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 16763`_
@@ -571,6 +583,9 @@ Fixes
   `Pull Request 17036`_
 .. bug_tag_workflows
 
+* Fix ``to_cwl`` for nested collections
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 17276`_
 * Fix workflow output display without label
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 16749`_
@@ -629,6 +644,12 @@ Fixes
   `Pull Request 17104`_
 .. bug_tag_jobs
 
+* Rollback invalidated transaction
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 17280`_
+* Rollback invalidated transaction: catch them earlier
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 17312`_
 * Ensure Job belongs to current SQLAlchemy session
   (thanks to `@jdavcs <https://github.com/jdavcs>`__).
   `Pull Request 16647`_
@@ -666,6 +687,30 @@ Fixes
   `Pull Request 17055`_
 .. bug
 
+* Remove duplicates when copying sections for tool panel view
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 17117`_
+* Tagging component performance improvements
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 17253`_
+* Always copy datasets in collection builder modals
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 17268`_
+* Install newer celery on python 3.8+
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 17309`_
+* Backport Rollback invalidated transaction: catch them earlier
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 17315`_
+* Discard SQLAlchemy session after task completion
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 17317`_
+* Scope session for job  runner monitor loop
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 17319`_
+* Fix subworkflow edit button
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 17330`_
 * Disable verbose parso logging in db_shell.py
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 16410`_

doc/source/releases/23.2_announce_user.rst

@@ -172,6 +172,9 @@ Builtin Tool Updates
 ===========================================================
 
 .. tools
+* Add back 1.1.0 version of Filtering1 tool
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 16883`_
 * Update cellxgene interactive tool to 1.1.1
   (thanks to `@pcm32 <https://github.com/pcm32>`__).
   `Pull Request 15313`_

doc/source/releases/23.2_prs.rst

@@ -1,5 +1,21 @@
 
 .. github_links
+.. _Pull Request 15238: https://github.com/galaxyproject/galaxy/pull/15238
+.. _Pull Request 16883: https://github.com/galaxyproject/galaxy/pull/16883
+.. _Pull Request 17117: https://github.com/galaxyproject/galaxy/pull/17117
+.. _Pull Request 17253: https://github.com/galaxyproject/galaxy/pull/17253
+.. _Pull Request 17259: https://github.com/galaxyproject/galaxy/pull/17259
+.. _Pull Request 17268: https://github.com/galaxyproject/galaxy/pull/17268
+.. _Pull Request 17276: https://github.com/galaxyproject/galaxy/pull/17276
+.. _Pull Request 17280: https://github.com/galaxyproject/galaxy/pull/17280
+.. _Pull Request 17309: https://github.com/galaxyproject/galaxy/pull/17309
+.. _Pull Request 17312: https://github.com/galaxyproject/galaxy/pull/17312
+.. _Pull Request 17315: https://github.com/galaxyproject/galaxy/pull/17315
+.. _Pull Request 17317: https://github.com/galaxyproject/galaxy/pull/17317
+.. _Pull Request 17319: https://github.com/galaxyproject/galaxy/pull/17319
+.. _Pull Request 17323: https://github.com/galaxyproject/galaxy/pull/17323
+.. _Pull Request 17326: https://github.com/galaxyproject/galaxy/pull/17326
+.. _Pull Request 17330: https://github.com/galaxyproject/galaxy/pull/17330
 .. _Pull Request 14892: https://github.com/galaxyproject/galaxy/pull/14892
 .. _Pull Request 14955: https://github.com/galaxyproject/galaxy/pull/14955
 .. _Pull Request 15000: https://github.com/galaxyproject/galaxy/pull/15000

doc/source/releases/24.0_announce.rst

@@ -2,7 +2,7 @@
 :orphan:
 
 ===========================================================
-24.0 Galaxy Release
+24.0 Galaxy Release (Early 2024)
 ===========================================================
 
 

lib/galaxy/dependencies/pinned-requirements.txt

@@ -92,6 +92,7 @@ idna==3.5 ; python_version >= "3.7" and python_version < "3.12"
 importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.12"
 importlib-resources==5.12.0 ; python_version >= "3.7" and python_version < "3.12"
 isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.12"
+isal==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
 isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.12"
 jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12"
 jmespath==1.0.1 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/model/store/__init__.py

@@ -2753,7 +2753,7 @@ def _finalize(self) -> None:
             out_file = out_file_name[: -len(".zip")]
         else:
             out_file = out_file_name
-        rval = shutil.make_archive(out_file, "zip", self.export_directory)
+        rval = shutil.make_archive(out_file, "fastzip", self.export_directory)
         if not self.file_source_uri:
             shutil.move(rval, self.out_file)
         else: