Merge pull request #20826 from nsoranzo/fixes_from_cwl

Small improvements for running CWL tools

Author: mvdbeek

lib/galaxy/webapps/galaxy/api/tools.py

@@ -361,7 +361,9 @@ def index(self, trans: GalaxyWebTransaction, **kwds):
         except exceptions.MessageException:
             raise
         except Exception:
-            raise exceptions.InternalServerError("Error: Could not convert toolbox to dictionary")
+            msg = "Error: Could not convert toolbox to dictionary"
+            log.exception(msg)
+            raise exceptions.InternalServerError(msg)
 
     @expose_api_anonymous_and_sessionless
     def panel_views(self, trans: GalaxyWebTransaction, **kwds):

lib/galaxy_test/base/populators.py

@@ -2808,12 +2808,10 @@ def _run_cwl_tool_job(
 
         if os.path.exists(tool_id):
             raw_tool_id = os.path.basename(tool_id)
-            index = self.dataset_populator._get("tools", data=dict(in_panel=False))
-            index.raise_for_status()
-            tools = index.json()
-            # In panels by default, so flatten out sections...
-            tool_ids = [itemgetter("id")(_) for _ in tools]
-            if raw_tool_id in tool_ids:
+            get_response = self.dataset_populator._get("tools", data=dict(tool_id=raw_tool_id))
+            get_response.raise_for_status()
+            tool_versions: list[str] = get_response.json()
+            if tool_versions:
                 galaxy_tool_id = raw_tool_id
             else:
                 dynamic_tool = self.dataset_populator.create_tool_from_path(tool_id)