Merge branch 'release_25.0' into release_25.1

Author: mvdbeek

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

@@ -140,6 +140,12 @@
     <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
     <datatype extension="gz" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
+    <datatype extension="las" type="galaxy.datatypes.binary:Binary" mimetype="application/vnd.las" subclass="true" display_in_upload="true" description="The LAS (LASer) format is a file format designed for the interchange and archiving of Lidar point cloud data." description_url="https://www.loc.gov/preservation/digital/formats/fdd/fdd000418.shtml">
+        <infer_from suffix="las" />
+    </datatype>
+    <datatype extension="laz" type="galaxy.datatypes.binary:Binary" mimetype="application/vnd.las" subclass="true" display_in_upload="true" description="LAZ is an open format for lossless compression of LAS." description_url="https://downloads.rapidlasso.de/doc/laszip.pdf">
+        <infer_from suffix="laz" />
+    </datatype>
     <datatype extension="d3_hierarchy" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="true"/>
     <datatype extension="cytoscapejson" type="galaxy.datatypes.text:CytoscapeJson" mimetype="application/json" display_in_upload="true" description="Cytoscape JSON format for network visualization, typically containing 'nodes' and 'edges' in a JSON object." description_url="https://js.cytoscape.org/#notation/elements-json" />
     <datatype extension="freq.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="True" description="A JSON-formatted array of objects containing longitude, latitude, and frequency attributes."/>
@@ -627,6 +633,7 @@
     <datatype extension="iqtree" type="galaxy.datatypes.text:IQTree">
         <infer_from suffix="iqtree" />
     </datatype>
+    <datatype extension="beast.trees" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true" decription="A BEAST specific NEXUS text file containing posterior tree samples generated by BEAST MCMC analyses."/>
     <datatype extension="mldist" type="galaxy.datatypes.mothur:SquareDistanceMatrix"/>
     <!-- Start RGenetics Datatypes -->
     <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>

lib/galaxy/workflow/modules.py

@@ -2034,15 +2034,17 @@ def from_workflow_step(Class, trans, step, **kwds):
 
     # ---- Saving in various forms ------------------------------------------
 
-    def save_to_step(self, step, detached=False):
+    def save_to_step(self, step: WorkflowStep, detached=False):
         super().save_to_step(step, detached=detached)
         step.tool_id = self.tool_id
         if self.tool:
             step.tool_version = self.get_version()
         else:
             step.tool_version = self.tool_version
         if tool_uuid := getattr(self, "tool_uuid", None):
-            step.dynamic_tool = self.trans.app.dynamic_tool_manager.get_tool_by_uuid(tool_uuid)
+            tool = self.trans.app.toolbox.get_tool(tool_uuid=tool_uuid, user=self.trans.user)
+            if tool:
+                step.dynamic_tool_id = tool.dynamic_tool.id
         if not detached:
             for k, v in self.post_job_actions.items():
                 pja = self.__to_pja(k, v, step)

lib/galaxy_test/api/test_workflows.py

@@ -25,8 +25,10 @@
 )
 
 from galaxy.exceptions import error_codes
+from galaxy.tool_util_models import UserToolSource
 from galaxy.util import UNKNOWN
 from galaxy.util.unittest_utils import skip_if_github_down
+from galaxy_test.api.test_tools import TOOL_WITH_SHELL_COMMAND
 from galaxy_test.base import rules_test_data
 from galaxy_test.base.populators import (
     DatasetCollectionPopulator,
@@ -8336,6 +8338,33 @@ def test_cannot_run_workflow_on_immutable_history(self) -> None:
                     history_id=history_id,
                 )
 
+    def test_user_defined_workflow_update(self):
+        with self.dataset_populator.user_tool_execute_permissions():
+            unprivileged_tool = self.dataset_populator.create_unprivileged_tool(
+                UserToolSource(**TOOL_WITH_SHELL_COMMAND)
+            )
+            # Workflow doesn't matter, we're replacing it in the update
+            workflow = self.workflow_populator.load_workflow_from_resource("test_workflow_pause")
+            workflow_id = self.workflow_populator.create_workflow(workflow)
+            update_response = self._update_workflow(
+                workflow_id,
+                {
+                    "steps": {
+                        "0": {
+                            "content_id": "cat_user_defined",
+                            "id": 1,
+                            "input_connections": {"datasets": []},
+                            "name": "Concatenate Files",
+                            "tool_uuid": unprivileged_tool["uuid"],
+                            "type": "tool",
+                        }
+                    },
+                },
+            )
+            assert update_response.status_code == 200, update_response.text
+            workflow = self.workflow_populator.download_workflow(workflow_id)
+            assert workflow["steps"]["0"]["tool_representation"]["class"] == "GalaxyUserTool"
+
     def _invoke_paused_workflow(self, history_id):
         workflow = self.workflow_populator.load_workflow_from_resource("test_workflow_pause")
         workflow_id = self.workflow_populator.create_workflow(workflow)