Merge branch 'galaxyproject:dev' into irods-objectstore-templates

client/src/api/schema/schema.ts

@@ -8935,6 +8935,8 @@ export interface components {
             error?: string | null;
             /** Success */
             success: boolean;
+            /** Uri */
+            uri?: string | null;
         };
         /**
          * ExportObjectType

client/src/components/Common/models/exportRecordModel.ts

@@ -2,6 +2,7 @@ import { formatDistanceToNow, parseISO } from "date-fns";
 
 import {
     type ExportObjectRequestMetadata,
+    type ExportObjectResultMetadata,
     type ModelStoreFormat,
     type ObjectExportTaskResponse,
     type StoreExportPayload,
@@ -85,12 +86,14 @@ export class ExportRecordModel implements ExportRecord {
     private _data: ObjectExportTaskResponse;
     private _expirationDate?: Date;
     private _requestMetadata?: ExportObjectRequestMetadata;
+    private _resultMetadata?: ExportObjectResultMetadata | null;
     private _exportParameters?: ExportParamsModel;
 
     constructor(data: ObjectExportTaskResponse) {
         this._data = data;
         this._expirationDate = undefined;
         this._requestMetadata = data.export_metadata?.request_data;
+        this._resultMetadata = data.export_metadata?.result_data;
         this._exportParameters = this._requestMetadata?.payload
             ? new ExportParamsModel(this._requestMetadata?.payload)
             : undefined;
@@ -130,7 +133,9 @@ export class ExportRecordModel implements ExportRecord {
 
     get importUri() {
         const payload = this._requestMetadata?.payload;
-        return payload && "target_uri" in payload ? payload.target_uri : undefined;
+        const requestUri = payload && "target_uri" in payload ? payload.target_uri : undefined;
+        const resultUri = this._resultMetadata?.uri;
+        return resultUri || requestUri;
     }
 
     get canReimport() {

client/src/components/Workflow/Editor/Node.test.ts

@@ -42,18 +42,17 @@ describe("Node", () => {
             },
         });
         await flushPromises();
+
         // fa-wrench is the tool icon ...
         expect(wrapper.findAll(".fa-wrench")).toHaveLength(1);
-        const toolLinks = wrapper.findAll("i");
-        expect(toolLinks.length).toBe(3);
         await wrapper.setProps({
             step: { label: "step label", type: "subworkflow", inputs: [], outputs: [], position: { top: 0, left: 0 } },
         });
+
         // fa-sitemap is the subworkflow icon ...
         expect(wrapper.findAll(".fa-sitemap")).toHaveLength(1);
         expect(wrapper.findAll(".fa-wrench")).toHaveLength(0);
-        const subworkflowLinks = wrapper.findAll("i");
-        expect(subworkflowLinks.length).toBe(2);
+
         const workflowTitle = wrapper.find(".node-title");
         expect(workflowTitle.text()).toBe("step label");
     });

client/src/components/Workflow/Editor/Node.vue

@@ -25,7 +25,7 @@
             <b-button-group class="float-right">
                 <LoadingSpan v-if="isLoading" spinner-only />
                 <b-button
-                    v-if="canClone && !readonly"
+                    v-if="!readonly"
                     v-b-tooltip.hover
                     class="node-clone py-0"
                     variant="primary"
@@ -241,7 +241,6 @@ const title = computed(() => props.step.label || props.step.name);
 const idString = computed(() => `wf-node-step-${props.id}`);
 const showRule = computed(() => props.step.inputs?.length > 0 && props.step.outputs?.length > 0);
 const iconClass = computed(() => `icon fa fa-fw ${WorkflowIcons[props.step.type]}`);
-const canClone = computed(() => props.step.type !== "subworkflow"); // Why ?
 const isEnabled = getGalaxyInstance().config.enable_tool_recommendations; // getGalaxyInstance is not reactive
 
 const isActive = computed(() => props.id === props.activeNodeId);

lib/galaxy/datatypes/isa.py

@@ -247,7 +247,8 @@ def groom_dataset_content(self, file_name: str) -> None:
             # perform extraction
             # For some ZIP files CompressedFile::extract() extract the file inside <output_folder>/<file_name> instead of outputing it inside <output_folder>. So we first create a temporary folder, extract inside it, and move content to final destination.
             temp_folder = tempfile.mkdtemp()
-            CompressedFile(file_name).extract(temp_folder)
+            with CompressedFile(file_name) as cf:
+                cf.extract(temp_folder)
             shutil.rmtree(output_path)
             extracted_files = os.listdir(temp_folder)
             logger.debug(" ".join(extracted_files))

lib/galaxy/dependencies/dev-requirements.txt

@@ -20,8 +20,8 @@ backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine !=
 backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
 black==24.8.0 ; python_full_version < '3.9'
 black==24.10.0 ; python_full_version >= '3.9'
-boto3==1.35.93
-botocore==1.35.93
+boto3==1.36.1
+botocore==1.36.1
 build==1.2.2.post1
 cachecontrol==0.14.2
 certifi==2024.12.14
@@ -93,7 +93,8 @@ mdurl==0.1.2
 mirakuru==2.5.2 ; python_full_version < '3.9'
 mirakuru==2.5.3 ; python_full_version >= '3.9'
 mistune==3.0.2
-more-itertools==10.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
+more-itertools==10.5.0 ; python_full_version < '3.9' and platform_machine != 'ppc64le' and platform_machine != 's390x'
+more-itertools==10.6.0 ; python_full_version >= '3.9' and platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.0
 multidict==6.1.0
 mypy-extensions==1.0.0
@@ -124,7 +125,7 @@ prettytable==3.12.0 ; python_full_version >= '3.9'
 propcache==0.2.0 ; python_full_version < '3.9'
 propcache==0.2.1 ; python_full_version >= '3.9'
 psutil==6.1.1 ; sys_platform != 'cygwin'
-psycopg==3.2.3
+psycopg==3.2.4
 pycparser==2.22
 pyee==12.0.0
 pygithub==2.5.0
@@ -161,19 +162,20 @@ rdflib==7.0.0 ; python_full_version >= '3.8.1' and python_full_version < '3.9'
 rdflib==7.1.2 ; python_full_version >= '3.9'
 readme-renderer==43.0 ; python_full_version < '3.9'
 readme-renderer==44.0 ; python_full_version >= '3.9'
-referencing==0.35.1 ; python_full_version >= '3.9'
+referencing==0.35.1 ; python_version < '0'
+referencing==0.36.1 ; python_full_version >= '3.9'
 requests==2.32.3
 requests-toolbelt==1.0.0
-responses==0.25.5
+responses==0.25.6
 rfc3986==2.0.0
 rich==13.9.4
 rpds-py==0.20.1 ; python_version < '0'
 rpds-py==0.22.3 ; python_full_version >= '3.9'
 ruamel-yaml==0.18.10
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.9' and platform_python_implementation == 'CPython'
 ruamel-yaml-clib==0.2.12 ; python_full_version >= '3.9' and python_full_version < '3.13' and platform_python_implementation == 'CPython'
-rucio-clients==36.0.0.post2 ; python_full_version >= '3.9'
-s3transfer==0.10.4
+rucio-clients==36.1.0 ; python_full_version >= '3.9'
+s3transfer==0.11.1
 schema-salad==8.7.20241010092723 ; python_full_version < '3.9'
 schema-salad==8.8.20241206093842 ; python_full_version >= '3.9'
 scipy==1.10.1 ; python_full_version < '3.9'
@@ -228,7 +230,7 @@ wcwidth==0.2.13
 websocket-client==1.8.0
 werkzeug==3.0.6 ; python_full_version < '3.9'
 werkzeug==3.1.3 ; python_full_version >= '3.9'
-wrapt==1.17.1
+wrapt==1.17.2
 wsproto==1.2.0
 yarl==1.15.2 ; python_full_version < '3.9'
 yarl==1.18.3 ; python_full_version >= '3.9'

lib/galaxy/dependencies/pinned-lint-requirements.txt

@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.9.1
+ruff==0.9.2

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,7 +2,7 @@
 #    uv export --frozen --no-hashes --no-dev
 a2wsgi==1.10.8
 adal==1.2.7
-aiobotocore==2.17.0
+aiobotocore==2.18.0
 aiodataloader==0.4.0
 aiofiles==24.1.0
 aiohappyeyeballs==2.4.4
@@ -37,7 +37,7 @@ bleach==6.1.0 ; python_full_version < '3.9'
 bleach==6.2.0 ; python_full_version >= '3.9'
 boltons==24.1.0
 boto==2.49.0
-botocore==1.35.93
+botocore==1.36.1
 bx-python==0.13.0
 cachecontrol==0.14.2
 celery==5.4.0
@@ -112,15 +112,15 @@ jsonschema-specifications==2023.12.1 ; python_full_version < '3.9'
 jsonschema-specifications==2024.10.1 ; python_full_version >= '3.9'
 kombu==5.4.2
 lagom==2.7.5
-legacy-cgi==2.6.1 ; python_full_version >= '3.13'
+legacy-cgi==2.6.2 ; python_full_version >= '3.13'
 lxml==5.3.0
 mako==1.3.8
 markdown==3.7
 markdown-it-py==3.0.0
 markupsafe==2.1.5 ; python_full_version < '3.9'
 markupsafe==3.0.2 ; python_full_version >= '3.9'
 mdurl==0.1.2
-mercurial==6.9
+mercurial==6.9.1
 mistune==3.0.2
 mrcfile==1.5.3
 msal==1.31.1
@@ -182,7 +182,8 @@ pyzmq==26.2.0
 rdflib==6.3.2 ; python_full_version < '3.8.1'
 rdflib==7.0.0 ; python_full_version >= '3.8.1' and python_full_version < '3.9'
 rdflib==7.1.2 ; python_full_version >= '3.9'
-referencing==0.35.1
+referencing==0.35.1 ; python_full_version < '3.9'
+referencing==0.36.1 ; python_full_version >= '3.9'
 refgenconf==0.12.2
 regex==2024.11.6
 repoze-lru==0.7
@@ -245,7 +246,7 @@ wcwidth==0.2.13
 webencodings==0.5.1
 webob==1.8.9
 whoosh==2.7.4
-wrapt==1.17.1
+wrapt==1.17.2
 yacman==0.9.3
 yarl==1.15.2 ; python_full_version < '3.9'
 yarl==1.18.3 ; python_full_version >= '3.9'

lib/galaxy/dependencies/pinned-typecheck-requirements.txt

@@ -1,13 +1,13 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.35.97
-botocore-stubs==1.35.97
+boto3-stubs==1.36.2
+botocore-stubs==1.36.2
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==44.0.0
 lxml-stubs==0.5.1
 mypy==1.14.1
-mypy-boto3-s3==1.35.93
+mypy-boto3-s3==1.36.0
 mypy-extensions==1.0.0
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
 pydantic==2.10.5
@@ -27,7 +27,7 @@ types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20241230
 types-requests==2.31.0.6 ; python_full_version < '3.10'
 types-requests==2.32.0.20241016 ; python_full_version >= '3.10'
-types-s3transfer==0.10.4
+types-s3transfer==0.11.1
 types-setuptools==75.8.0.20250110
 types-six==1.17.0.20241205
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'

lib/galaxy/files/sources/__init__.py

@@ -220,7 +220,7 @@ def write_from(
         native_path: str,
         user_context: "OptionalUserContext" = None,
         opts: Optional[FilesSourceOptions] = None,
-    ):
+    ) -> str:
         """Write file at native path to target_path (relative to uri root).
 
         :param target_path: url of the target file to write to within the filesource. e.g. `gxfiles://myftp1/myfile.txt`
@@ -231,6 +231,9 @@ def write_from(
         :type user_context: _type_, optional
         :param opts: A set of options to exercise additional control over the write_from method. Filesource specific, defaults to None
         :type opts: Optional[FilesSourceOptions], optional
+        :return: Actual url of the written file, fixed by the service backing the FileSource. May differ from the target
+            path.
+        :rtype: str
         """
 
     @abc.abstractmethod
@@ -511,10 +514,10 @@ def write_from(
         native_path: str,
         user_context: "OptionalUserContext" = None,
         opts: Optional[FilesSourceOptions] = None,
-    ):
+    ) -> str:
         self._ensure_writeable()
         self._check_user_access(user_context)
-        self._write_from(target_path, native_path, user_context=user_context, opts=opts)
+        return self._write_from(target_path, native_path, user_context=user_context, opts=opts) or target_path
 
     @abc.abstractmethod
     def _write_from(
@@ -523,7 +526,7 @@ def _write_from(
         native_path: str,
         user_context: "OptionalUserContext" = None,
         opts: Optional[FilesSourceOptions] = None,
-    ):
+    ) -> Optional[str]:
         pass
 
     def realize_to(