imrpove ro-crate with eli's review

galaxyproject · Dec 23, 2024 · f1b404d · f1b404d
1 parent e66652e
commit f1b404d
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/lib/galaxy/model/store/ro_crate_utils.py b/lib/galaxy/model/store/ro_crate_utils.py
@@ -309,6 +309,7 @@ def _add_steps_recursive(self, steps, crate: ROCrate, step_entities, position):
                             "position": position[0],
                             "name": step.tool_id,
                             "description": step_description,
+                            "workExample": f"#{step.tool_id}"
                         },
                     )
                 )
@@ -357,13 +358,12 @@ def _add_tools_recursive(self, steps, crate: ROCrate, tool_entities):
                     tool_entity = crate.add(
                         ContextEntity(
                             crate,
-                            tool_id,
+                            f"#{tool_id}",  # Prepend # to tool_id
                             properties={
                                 "@type": "SoftwareApplication",
                                 "name": tool_name,
                                 "version": tool_version,
                                 "description": tool_description,
-                                "url": "https://toolshed.g2.bx.psu.edu",  # URL if relevant
                             },
                         )
                     )
@@ -373,7 +373,7 @@ def _add_tools_recursive(self, steps, crate: ROCrate, tool_entities):
 
                 # Append the tool entity to the workflow (instrument) and store it in the list
                 tool_entities.append(tool_entity)
-                crate.mainEntity.append_to("instrument", tool_entity)
+                crate.mainEntity.append_to("hasPart", tool_entity)
 
             # Handle subworkflows recursively
             elif step.type == "subworkflow":

diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py
@@ -518,15 +518,14 @@ def validate_tools(ro_crate: ROCrate):
     """
     Validate that tools (SoftwareApplication) are correctly added.
     """
-    tools = ro_crate.mainEntity.get("instrument")
+    tools = ro_crate.mainEntity.get("hasPart")
     assert tools, "No tools found in the RO-Crate"
 
     tool_ids = set()
     for tool in tools:
         assert tool["@type"] == "SoftwareApplication"
         assert "name" in tool
         assert "version" in tool
-        assert "url" in tool
         assert "description" in tool or tool["description"] is None
         assert tool.id not in tool_ids, "Duplicate tool found"
         tool_ids.add(tool.id)