Comments (5)
Are you sure that control is held until all datasets are completed? Or is it just until scheduling is done? (see response to your message on galaxy-dev)
While it must wait until scheduling is complete (for now), bioblend should not be waiting until all workflow jobs are complete with wait=False.
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I think in this case Galaxy is holding the connection open until it feels scheduling is complete. For 100+ steps, the scheduling took about 2 minutes and I let the connection remain open for another 30 minutes before raising an interrupt.
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Yes. Without wait
the method returns after scheduling, while with wait
it returns after the workflow is complete (i.e., no output dataset is in a "pending" state). The operation is actually blocking in both cases, the only difference being the amount of time it takes to return control to the caller. We should update the docs to clarify this. Thanks for reporting!
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Docs updated as of 3ec511c
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Also @bollig for what it is worth - workflow scheduling taking to long is a known problem and @dannon and I are working on different aspects of fixing that (e.g. https://bitbucket.org/galaxy/galaxy-central/pull-request/453/rfc-workflow-requests-api-only-and-a/diff). There will hopefully be relief with the next version of Galaxy (or if not the following one).
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Related Issues (20)
- Method to cancel a job
- Add type annotations to BioBlend API HOT 2
- Rebuild docs with sphinx-apidoc
- Add an `invoke()` method to the BioBlend.objects `Workflow` class
- Fix unreliable tests
- Add tests for bioblend.toolshed
- 'GalaxyInstance' raises AttributeError when instantiated with email & password combination HOT 2
- Incorrect PyYAML version for bioblend 0.9.0 - 0.16.0 HOT 1
- Getting abosl HOT 1
- Error when trying to get ids of workflow outputs HOT 13
- partial workflow invocation HOT 9
- Drop cloudlaunch support ? HOT 4
- Add support for parameter "all" in get_histories HOT 2
- Tool search in Toolshed: number total results HOT 6
- File name displayed as Pasted Entry for file uploaded using upload_file_contents HOT 2
- Downloading a file from a shared data library HOT 3
- Extend bioblend to support the new notification API HOT 3
- Bioblend reporting workflow as failed while workflow is running or completed successfully. HOT 6
- workflows.refactor_workflows fails on subworkflows HOT 14
- Allow Session Cookies in Requests HOT 1
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