Merge remote-tracking branch 'upstream/release_23.0' into dev

client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.js

@@ -3,6 +3,15 @@ import { shallowMount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
 import Vuex from "vuex";
 import invocationData from "../Workflow/test/json/invocation.json";
+import { useConfig } from "composables/config";
+
+jest.mock("composables/config");
+useConfig.mockReturnValue({
+    config: {
+        enable_celery_tasks: true,
+    },
+    isLoaded: true,
+});
 
 const invocationJobsSummaryById = {
     id: "d9833097445452b0",

client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue

@@ -17,7 +17,7 @@
         <!-- <b-tab title="Workflow Overview">
             <p>TODO: Insert readonly version of workflow editor here</p>
         </b-tab> -->
-        <b-tab title="Export">
+        <b-tab v-if="canExecuteTasks" title="Export">
             <div v-if="invocationAndJobTerminal">
                 <workflow-invocation-export-options :invocation-id="invocation.id" />
             </div>
@@ -39,6 +39,7 @@ import WorkflowInvocationExportOptions from "./WorkflowInvocationExportOptions.v
 import JOB_STATES_MODEL from "utils/job-states-model";
 import mixin from "components/JobStates/mixin";
 import { mapGetters, mapActions } from "vuex";
+import { useConfig } from "composables/config";
 
 export default {
     components: {
@@ -59,6 +60,13 @@ export default {
             default: null,
         },
     },
+    setup() {
+        const { config, isLoaded: isConfigLoaded } = useConfig();
+        return {
+            config,
+            isConfigLoaded,
+        };
+    },
     data() {
         return {
             stepStatesInterval: null,
@@ -94,6 +102,9 @@ export default {
             const jobsSummary = this.getInvocationJobsSummaryById(this.invocationId);
             return !jobsSummary ? null : new JOB_STATES_MODEL.JobStatesSummary(jobsSummary);
         },
+        canExecuteTasks() {
+            return this.isConfigLoaded && this.config.enable_celery_tasks;
+        },
     },
     created: function () {
         this.pollStepStatesUntilTerminal();

lib/galaxy/dependencies/pinned-requirements.txt

@@ -61,7 +61,7 @@ ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12"
 email-validator==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
-fastapi==0.89.1 ; python_version >= "3.7" and python_version < "3.12"
+fastapi==0.91.0 ; python_version >= "3.7" and python_version < "3.12"
 flupy==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
 frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
 fs==2.4.16 ; python_version >= "3.7" and python_version < "3.12"
@@ -170,7 +170,7 @@ sqlalchemy==1.4.46 ; python_version >= "3.7" and python_version < "3.12"
 sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.12"
 sqlparse==0.4.3 ; python_version >= "3.7" and python_version < "3.12"
 starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
-starlette==0.22.0 ; python_version >= "3.7" and python_version < "3.12"
+starlette==0.24.0 ; python_version >= "3.7" and python_version < "3.12"
 supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12"
 svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
 tempita==0.5.2 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/tool_util/deps/docker_util.py

@@ -198,6 +198,11 @@ def parse_port_text(port_text):
     >>> slurm_ports[8888]['host']
     '0.0.0.0'
     >>> ports = parse_port_text("5432/tcp -> :::5432")
+    >>> len(ports)
+    0
+    >>> ports_new = parse_port_text("5432/tcp -> [::]:5432")
+    >>> len(ports_new)
+    0
     """
     ports = None
     if port_text is not None:
@@ -207,7 +212,7 @@ def parse_port_text(port_text):
                 raise Exception(f"Cannot parse host and port from line [{line}]")
             tool, host = line.split(" -> ", 1)
             hostname, port = host.rsplit(":", 1)
-            if hostname == "::":
+            if hostname in ["::", "[::]"]:
                 # Skip unspecified IPv6 address, which is also specified as 0:0:0:0 in another line.
                 # This is brittle of course, but so is parsing the container ports like this.
                 continue

test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py

@@ -15,6 +15,7 @@ from galaxy.app_unittest_utils.galaxy_mock import MockApp
 from galaxy.webapps.base.api import add_request_id_middleware
 
 app = FastAPI()
+add_request_id_middleware(app)
 GX_APP = None
 
 
@@ -95,7 +96,6 @@ def assert_scoped_session_is_thread_local(gx_app):
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_single_request():
-    add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
         response = await client.get("/")
         assert response.status_code == 200
@@ -106,7 +106,6 @@ async def test_request_scoped_sa_session_single_request():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_exception():
-    add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
         with pytest.raises(UnexpectedException):
             await client.get("/internal_server_error")
@@ -116,7 +115,6 @@ async def test_request_scoped_sa_session_exception():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_sync():
-    add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
         awaitables = (client.get("/sync_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
@@ -131,7 +129,6 @@ async def test_request_scoped_sa_session_concurrent_requests_sync():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_async():
-    add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
         awaitables = (client.get("/async_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
@@ -146,7 +143,6 @@ async def test_request_scoped_sa_session_concurrent_requests_async():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_and_background_thread():
-    add_request_id_middleware(app)
     loop = asyncio.get_running_loop()
     target = functools.partial(assert_scoped_session_is_thread_local, GX_APP)
     with concurrent.futures.ThreadPoolExecutor() as pool: