imrpove ro-crate with eli's review (c6267d69) · Commits · NDIP / Galaxy

lib/galaxy/model/store/ro_crate_utils.py

+3 −3

Original line number	Diff line number	Diff line
		@@ -311,6 +311,7 @@ class WorkflowRunCrateProfileBuilder:
		"position": position[0],
		"name": step.tool_id,
		"description": step_description,
		"workExample": f"#{step.tool_id}"
		},
		)
		)
		@@ -359,13 +360,12 @@ class WorkflowRunCrateProfileBuilder:
		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
		},
		)
		)
		@@ -375,7 +375,7 @@ class WorkflowRunCrateProfileBuilder:

		# 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":

+1 −2

Original line number	Diff line number	Diff line
		@@ -516,7 +516,7 @@ 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()
		@@ -524,7 +524,6 @@ def validate_tools(ro_crate: ROCrate):
		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)