Workflow.run() doesn't wait and doesn't return outputs

[innovate-invent]

bioblend/bioblend/galaxy/objects/wrappers.py

Lines 460 to 467 in c1a13cd

	for output_id in res['outputs']:
	if content_infos_dict[output_id].type == 'file':
	outputs.append(out_hist.get_dataset(output_id))
	elif content_infos_dict[output_id].type == 'collection':
	outputs.append(out_hist.get_dataset_collection(output_id))
	if wait:
	self.gi._wait_datasets(outputs, polling_interval=polling_interval,

The api returns an empty 'outputs' dict in the invocation information. This causes this code to immediately exit the loop and produce an empty list.

The code needs to wait for the 'outputs' dict to become populated by Galaxy.

[nsoranzo]

I don't think that's possible with the current implementation of Workflow.run() in BioBlend.objects in case of a non-fixed number of outputs. For that we would need to wrap workflow invocations as objects, probably. See also #171 .

Pull requests welcome!

[innovate-invent]

I am not sure what you mean by 'non-fixed number of outputs'. My workflow creates the same outputs regardless of the input.

#171 doesn't work either as there are race conditions where all jobs are complete but new jobs have yet to be created during an invocation request.