Merge branch 'release_25.0' into release_25.1

Author: mvdbeek

client/src/components/Dataset/DatasetView.vue

@@ -8,6 +8,7 @@ import { usePersistentToggle } from "@/composables/persistentToggle";
 import { useDatasetStore } from "@/stores/datasetStore";
 import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
 import { useDatatypeStore } from "@/stores/datatypeStore";
+import { withPrefix } from "@/utils/redirect";
 import { bytesToString } from "@/utils/utils";
 
 import DatasetError from "../DatasetInformation/DatasetError.vue";
@@ -56,6 +57,7 @@ const showError = computed(
 const isAutoDownloadType = computed(
     () => dataset.value && datatypeStore.isDatatypeAutoDownload(dataset.value.file_ext),
 );
+const downloadUrl = computed(() => withPrefix(`/datasets/${props.datasetId}/display`));
 const preferredVisualization = computed(
     () => dataset.value && datatypeStore.getPreferredVisualization(dataset.value.file_ext),
 );
@@ -195,7 +197,7 @@ watch(
                     <h4>Download Required</h4>
                     <p>This file type ({{ dataset.file_ext }}) will download automatically when accessed directly.</p>
                     <p>File size: <strong v-html="bytesToString(dataset.file_size || 0, false)" /></p>
-                    <a :href="`/datasets/${datasetId}/display`" class="btn btn-primary mt-2" download>
+                    <a :href="downloadUrl" class="btn btn-primary mt-2" download>
                         <FontAwesomeIcon :icon="faFileAlt" class="mr-1" /> Download File
                     </a>
                 </div>
@@ -222,7 +224,7 @@ watch(
                     <h4>Download Required</h4>
                     <p>This file type ({{ dataset.file_ext }}) will download automatically when accessed directly.</p>
                     <p>File size: <strong v-html="bytesToString(dataset.file_size || 0, false)" /></p>
-                    <a :href="`/datasets/${datasetId}/display`" class="btn btn-primary mt-2" download>
+                    <a :href="downloadUrl" class="btn btn-primary mt-2" download>
                         <FontAwesomeIcon :icon="faFileAlt" class="mr-1" /> Download File
                     </a>
                 </div>

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -599,6 +599,7 @@
     <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi." display_in_upload="true"/>
     <datatype extension="vg" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" description="Genomic variation graphs." display_in_upload="true"/>
     <datatype extension="xg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs with vg index." display_in_upload="true"/>
+    <datatype extension="gam" type="galaxy.datatypes.binary:Binary" subclass="true" description="Binary file storing sequencing read alignments to genome variation graphs, used by the VG toolkit." display_in_upload="true" description_url="https://github.com/vgteam/vg/wiki/File-Formats#gam-graph-alignment--map-vgs-bam"/>
     <datatype extension="protobuf2" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data." display_in_upload="true"/>
     <datatype extension="protobuf3" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data." display_in_upload="true"/>
     <datatype extension="onnx" type="galaxy.datatypes.binary:Binary" subclass="true" description="ONNX (Open neural network exchange) is data format for storing and sharing machine learning and deep learning models." display_in_upload="true">

lib/galaxy/managers/landing.py

@@ -4,7 +4,10 @@
 )
 from uuid import uuid4
 
-from pydantic import UUID4
+from pydantic import (
+    UUID4,
+    ValidationError,
+)
 from sqlalchemy import select
 
 from galaxy.exceptions import (
@@ -38,6 +41,7 @@
     LandingRequestInternalToolState,
     LandingRequestToolState,
 )
+from galaxy.tool_util_models.parameters import DataOrCollectionRequestAdapter
 from galaxy.util import safe_str_cmp
 from .context import ProvidesUserContext
 from .tools import (
@@ -107,11 +111,25 @@ def create_workflow_landing_request(self, payload: CreateWorkflowLandingRequestP
             model.workflow_source = payload.workflow_id
         model.uuid = uuid4()
         model.client_secret = payload.client_secret
-        model.request_state = payload.request_state
+        model.request_state = self.validate_workflow_request_state(payload.request_state)
         model.public = payload.public
         self._save(model)
         return self._workflow_response(model)
 
+    def validate_workflow_request_state(self, request_state: Optional[dict]) -> Optional[dict]:
+        # This would ideally be run in the context of a workflow input definition
+        if isinstance(request_state, dict):
+            for key, value in request_state.items():
+                if isinstance(value, dict):
+                    try:
+                        # persist values after model validators and aliases have been applied
+                        request_state[key] = DataOrCollectionRequestAdapter.validate_python(value).model_dump(
+                            by_alias=True, exclude_unset=True, mode="json"
+                        )
+                    except ValidationError:
+                        pass
+        return request_state
+
     def claim_tool_landing_request(
         self, trans: ProvidesUserContext, uuid: UUID4, claim: Optional[ClaimLandingPayload]
     ) -> ToolLandingRequest:

lib/galaxy/tool_util/parser/yaml.py

@@ -403,7 +403,10 @@ def parse_input_type(self):
             return "param"
 
     def parse_extensions(self):
-        return [ext.strip().lower() for ext in self.input_dict.get("extensions", ["data"])]
+        extensions = self.input_dict.get("extensions")
+        if not extensions:
+            extensions = self.get("format", "data").split(",")
+        return [ext.strip().lower() for ext in extensions]
 
     def parse_nested_inputs_source(self):
         assert self.parse_input_type() == "repeat"

lib/galaxy_test/api/test_landing.py

@@ -232,6 +232,14 @@ def test_create_private_workflow_landing_anonymous_user(self):
         _cannot_claim_request(self.dataset_populator, response)
         _cannot_use_request(self.dataset_populator, response)
 
+    @skip_without_tool("cat1")
+    def test_workflow_landing_uniform_response(self):
+        request = _get_simple_landing_payload(self.workflow_populator, public=True)
+        response = self.dataset_populator.create_workflow_landing(request)
+        landing_request = self.dataset_populator.use_workflow_landing_raw(response.uuid)
+        # Make sure url is turned into location
+        assert landing_request["request_state"]["WorkflowInput1"]["location"]
+
     def test_landing_claim_preserves_source_metadata(self):
         request = CreateWorkflowLandingRequestPayload(
             workflow_id="https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.12",

lib/galaxy_test/api/test_workflows.py

@@ -831,6 +831,33 @@ def test_workflow_download_instance(self):
             assert initial_instance_download["workflow_id"] == first_instance_id
             assert initial_instance_download["name"] == original_name
 
+    def test_workflow_run_input_extension_restriction_applied(self):
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+inputs:
+  tabular_input:
+    type: data
+    format:
+     - tabular
+steps:
+  first_cat:
+    tool_id: cat1
+    in:
+      input1: tabular_input
+"""
+        )
+        with self.dataset_populator.test_history() as history_id:
+            # Upload a txt file that should NOT be available for the tabular input
+            self.dataset_populator.new_dataset(history_id, content="hello world", file_type="txt", wait=True)
+
+            # Download workflow in run style to get the form with available datasets
+            run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
+            tabular_input_step = run_workflow["steps"][0]
+            input_options = tabular_input_step["inputs"][0]
+            assert input_options["extensions"] == ["tabular"]
+            assert not input_options["options"]["hda"]
+
     def test_update(self):
         original_workflow = self.workflow_populator.load_workflow(name="test_import")
         uuids = {}

lib/galaxy_test/base/populators.py

@@ -952,6 +952,12 @@ def use_tool_landing(self, uuid: UUID4) -> ToolLandingRequest:
         api_asserts.assert_status_code_is(landing_reponse, 200)
         return ToolLandingRequest.model_validate(landing_reponse.json())
 
+    def use_workflow_landing_raw(self, uuid: UUID4):
+        url = f"workflow_landings/{uuid}"
+        landing_reponse = self._get(url, {"client_secret": "foobar"})
+        api_asserts.assert_status_code_is(landing_reponse, 200)
+        return landing_reponse.json()
+
     def create_tool_from_path(self, tool_path: str) -> dict[str, Any]:
         tool_directory = os.path.dirname(os.path.abspath(tool_path))
         payload = dict(