Merge branch 'release_23.1' into dev

client/src/components/Form/Elements/FormSelect.test.js

@@ -66,6 +66,7 @@ describe("FormSelect", () => {
 
     it("multiple values", async () => {
         const wrapper = createTarget({
+            optional: true,
             multiple: true,
             optional: true,
             options: defaultOptions,

client/src/components/History/HistoryView.test.js

@@ -13,13 +13,14 @@ import HistoryView from "./HistoryView";
 const localVue = getLocalVue();
 jest.mock("stores/services/history.services");
 
-function create_history(historyId, userId, purged = false) {
+function create_history(historyId, userId, purged = false, archived = false) {
     const historyName = `${userId}'s History ${historyId}`;
     return {
         model_class: "History",
         id: historyId,
         name: historyName,
         purged: purged,
+        archived: archived,
         count: 10,
         annotation: "This is a history",
         tags: ["tag_1", "tag_2"],
@@ -164,13 +165,43 @@ describe("History center panel View", () => {
         const wrapper = await createWrapper(localVue, "user_1", history);
         expect(wrapper.vm.history).toEqual(history);
 
-        // switch/import buttons: purged they don't exist
+        // history purged, not switchable and not importable
         const switchButton = wrapper.find("[data-description='switch to history button']");
         const importButton = wrapper.find("[data-description='import history button']");
-        expect(switchButton.exists()).toBe(false);
+        expect(switchButton.attributes("disabled")).toBeTruthy();
         expect(importButton.exists()).toBe(false);
 
         // instead we have an alert
         expect(wrapper.find("[data-description='history state info']").text()).toBe("This history has been purged.");
     });
+
+    it("should not display archived message and should be importable when user is not owner and history is archived", async () => {
+        const history = create_history("history_2", "user_2", false, true);
+        const wrapper = await createWrapper(localVue, "user_1", history);
+        expect(wrapper.vm.history).toEqual(history);
+
+        const switchButton = wrapper.find("[data-description='switch to history button']");
+        const importButton = wrapper.find("[data-description='import history button']");
+        expect(switchButton.exists()).toBe(false);
+        expect(importButton.exists()).toBe(true);
+        expect(importButton.attributes("disabled")).toBeFalsy();
+
+        expectCorrectLayout(wrapper);
+        expect(wrapper.find("[data-description='history state info']").exists()).toBe(false);
+    });
+
+    it("should display archived message and should not be importable when user is owner and history is archived", async () => {
+        const history = create_history("history_2", "user_1", false, true);
+        const wrapper = await createWrapper(localVue, "user_1", history);
+        expect(wrapper.vm.history).toEqual(history);
+
+        const switchButton = wrapper.find("[data-description='switch to history button']");
+        const importButton = wrapper.find("[data-description='import history button']");
+        expect(switchButton.exists()).toBe(true);
+        expect(switchButton.attributes("disabled")).toBeTruthy();
+        expect(importButton.exists()).toBe(false);
+
+        expectCorrectLayout(wrapper);
+        expect(wrapper.find("[data-description='history state info']").text()).toBe("This history has been archived.");
+    });
 });

client/src/components/History/HistoryView.vue

@@ -3,19 +3,19 @@
         <b-alert v-if="showHistoryStateInfo" variant="info" show data-description="history state info">
             {{ historyStateInfoMessage }}
         </b-alert>
-        <div v-else class="flex-row flex-grow-0 pb-3">
+        <div class="flex-row flex-grow-0 pb-3">
             <b-button
                 v-if="userOwnsHistory"
                 size="sm"
                 variant="outline-info"
-                title="Switch to this history"
+                :title="setAsCurrentTitle"
                 :disabled="isSetAsCurrentDisabled"
                 data-description="switch to history button"
                 @click="setCurrentHistory(history.id)">
                 Switch to this history
             </b-button>
             <b-button
-                v-else
+                v-if="canImportHistory"
                 v-b-modal:copy-history-modal
                 size="sm"
                 variant="outline-info"
@@ -77,25 +77,46 @@ export default {
         userOwnsHistory() {
             return this.currentUser.id == this.history.user_id;
         },
+        isCurrentHistory() {
+            return this.currentHistory?.id == this.history?.id;
+        },
         isSetAsCurrentDisabled() {
-            return this.currentHistory?.id == this.history?.id || this.history.archived || this.history.purged;
+            return this.isCurrentHistory || this.history.archived || this.history.purged;
+        },
+        setAsCurrentTitle() {
+            if (this.isCurrentHistory) {
+                return "This history is already your current history.";
+            }
+            if (this.history.archived) {
+                return "This history has been archived and cannot be set as your current history. Unarchive it first.";
+            }
+            if (this.history.purged) {
+                return "This history has been purged and cannot be set as your current history.";
+            }
+            return "Switch to this history";
         },
         canEditHistory() {
             return this.userOwnsHistory && !this.history.archived && !this.history.purged;
         },
+        showHistoryArchived() {
+            return this.history.archived && this.userOwnsHistory;
+        },
         showHistoryStateInfo() {
-            return this.history.archived || this.history.purged;
+            return this.showHistoryArchived || this.history.purged;
         },
         historyStateInfoMessage() {
-            if (this.history.archived && this.history.purged) {
+            if (this.showHistoryArchived && this.history.purged) {
                 return "This history has been archived and purged.";
-            } else if (this.history.archived) {
+            } else if (this.showHistoryArchived) {
                 return "This history has been archived.";
             } else if (this.history.purged) {
                 return "This history has been purged.";
             }
             return "";
         },
+        canImportHistory() {
+            return !this.userOwnsHistory && !this.history.purged;
+        },
     },
     created() {
         this.loadHistoryById(this.id);

client/src/components/History/Modals/CopyModal.vue

@@ -62,7 +62,7 @@ export default {
         };
     },
     computed: {
-        ...mapState(useUserStore, ["isAnonymous"]),
+        ...mapState(useUserStore, ["currentUser", "isAnonymous"]),
         title() {
             return `Copying History: ${this.history.name}`;
         },
@@ -72,9 +72,12 @@ export default {
         saveVariant() {
             return this.loading ? "info" : this.formValid ? "primary" : "secondary";
         },
+        userOwnsHistory() {
+            return this.currentUser.id == this.history.user_id;
+        },
         newNameValid() {
-            if (this.name == this.history.name) {
-                return null;
+            if (this.userOwnsHistory && this.name == this.history.name) {
+                return false;
             }
             return this.name.length > 0;
         },

client/src/components/WorkflowInvocationState/InvocationMessage.vue

@@ -149,6 +149,9 @@ const infoString = computed(() => {
             invocationMessage.workflow_step_id + 1
         } is a conditional step and the result of the when expression is not a boolean type.`;
     } else if (reason === "unexpected_failure") {
+        if (invocationMessage.details) {
+            return `${failFragment} an unexpected failure occurred: '${invocationMessage.details}'`;
+        }
         return `${failFragment} an unexpected failure occurred.`;
     } else if (reason === "workflow_output_not_found") {
         return `Defined workflow output '${invocationMessage.output_name}' was not found in step ${

doc/source/conf.versioning.py

@@ -47,7 +47,7 @@ for _tag in reversed(tags):
         if Version(_ver) >= MIN_DOC_VERSION:
             simpleversioning_versions.append({"id": f"release_{_ver}", "name": _ver})
 
-if re.fullmatch(r"release_\d{2}\.\d{2}", TARGET_GIT_BRANCH):
+if re.fullmatch(r"release_\d{2}\.\d{1,2}", TARGET_GIT_BRANCH):
     if _stable:
         # The current stable release will go here but fail the next conditional, avoiding either banner.
         if TARGET_GIT_BRANCH != f"release_{_stable}":

lib/galaxy/job_execution/actions/post.py

@@ -498,7 +498,7 @@ class RemoveTagDatasetAction(TagDatasetAction):
 
     @classmethod
     def _execute(cls, tag_handler, user, output, tags):
-        tag_handler.remove_tags_from_list(user, output, tags)
+        tag_handler.remove_tags_from_list(user, output, tags, flush=False)
 
 
 class ActionBox:

lib/galaxy/tool_util/toolbox/base.py

@@ -95,7 +95,8 @@ class ToolBoxRegistryImpl(ToolBoxRegistry):
         self.__toolbox = toolbox
 
     def has_tool(self, tool_id: str) -> bool:
-        return tool_id in self.__toolbox._tools_by_id
+        toolbox = self.__toolbox
+        return tool_id in toolbox._tools_by_id or tool_id in toolbox._tools_by_old_id
 
     def get_tool(self, tool_id: str):
         return self.__toolbox.get_tool(tool_id)
@@ -161,6 +162,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         # so each will be present once in the above dictionary. The following
         # dictionary can instead hold multiple tools with different versions.
         self._tool_versions_by_id = {}
+        self._tools_by_old_id = {}
         self._workflows_by_id = {}
         # Cache for tool's to_dict calls specific to toolbox. Invalidates on toolbox reload.
         self._tool_to_dict_cache = {}
@@ -718,9 +720,8 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                         rval.append(lineage_tool)
             if not rval:
                 # still no tool, do a deeper search and try to match by old ids
-                for tool in self._tools_by_id.values():
-                    if tool.old_id == tool_id:
-                        rval.append(tool)
+                if tool_id in self._tools_by_old_id:
+                    rval.extend(self._tools_by_old_id[tool_id])
                 if get_all_versions and tool_id in self._tool_versions_by_id:
                     for tool in self._tool_versions_by_id[tool_id].values():
                         if tool not in rval:
@@ -1160,6 +1161,10 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 self._tools_by_id[tool_id] = tool
         else:
             self._tools_by_id[tool_id] = tool
+        old_id = tool.old_id
+        if old_id not in self._tools_by_old_id:
+            self._tools_by_old_id[old_id] = []
+        self._tools_by_old_id[old_id].append(tool)
 
     def package_tool(self, trans, tool_id):
         """
@@ -1219,6 +1224,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         else:
             tool = self._tools_by_id[tool_id]
             del self._tools_by_id[tool_id]
+            self._tools_by_old_id[tool.old_id].remove(tool)
             tool_cache = getattr(self.app, "tool_cache", None)
             if tool_cache:
                 tool_cache.expire_tool(tool_id)

test/integration/panel_views_1/custom_6.yml

@@ -2,7 +2,7 @@ name: Custom Panel in a New Section
 type: generic
 items:
 - type: section
-  name: My Completely New Sectin
+  name: My Completely New Section
   items:
   - type: label
     text: The Start

test/integration/test_repository_operations.py

@@ -125,9 +125,7 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC
         assert tool["version"] == "0.0.2"
         self.uninstall_repository(REPO.owner, REPO.name, REPO.changeset)
         response = self.get_tool(assert_ok=False)
-        assert (
-            "err_msg" in response
-        ), f"Expected an error message after tool install but response was {response.content}"
+        assert "err_msg" in response, f"Expected an error message after tool install but response was {response}"
         assert response["err_msg"]
         assert self.get_installed_repository_for(REPO.owner, REPO.name, REPO.changeset) is None