Fix conditional database operation tool step skipping (06a43944) · Commits · NDIP / Galaxy

lib/galaxy/tools/actions/model_operations.py

+16 −2

Original line number	Diff line number	Diff line
		@@ -39,6 +39,7 @@ class ModelOperationToolAction(DefaultToolAction):
		execution_cache=None,
		collection_info=None,
		job_callback=None,
		skip=False,
		**kwargs,
		):
		incoming = incoming or {}
		@@ -93,11 +94,15 @@ class ModelOperationToolAction(DefaultToolAction):
		history=history,
		tags=preserved_tags,
		hdca_tags=preserved_hdca_tags,
		skip=skip,
		)
		self._record_inputs(trans, tool, job, incoming, inp_data, inp_dataset_collections)
		self._record_outputs(job, out_data, output_collections)
		if job_callback:
		job_callback(job)
		if skip:
		job.state = job.states.SKIPPED
		else:
		job.state = job.states.OK
		trans.sa_session.add(job)

		@@ -108,7 +113,7 @@ class ModelOperationToolAction(DefaultToolAction):
		return job, out_data, history

		def _produce_outputs(
		self, trans: "ProvidesUserContext", tool, out_data, output_collections, incoming, history, tags, hdca_tags
		self, trans: "ProvidesUserContext", tool, out_data, output_collections, incoming, history, tags, hdca_tags, skip
		):
		tag_handler = trans.tag_handler
		tool.produce_outputs(
		@@ -128,4 +133,13 @@ class ModelOperationToolAction(DefaultToolAction):
		value.visible = False
		mapped_over_elements[name].hda = value

		# We probably need to mark all outputs as skipped, not just the outputs of whatever the database op tools do ?
		# This is probably not exactly right, but it might also work in most cases
		if skip:
		for output_collection in output_collections.out_collections.values():
		output_collection.mark_as_populated()
		for hdca in output_collections.out_collection_instances.values():
		hdca.visible = False
		# Would we also need to replace the datasets with skipped datasets?

		trans.sa_session.add_all(out_data.values())