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Testbed module #38
Testbed module #38
Commits on Aug 22, 2018
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refactor: move testbed out of orchestrator module
Add functions for retrieving and submitting workflow checker jobs to testbed module (remove from orchestrator module).
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refactor: submit checker jobs as params, not full WES requests
Update functions and logic in the testbed module to prepare and create new workflow checker jobs as test params (JSON), submitted to evaluation queues. Information about how to run the actual workflow and post the WES request will be associated directly with the evaluation queue. See #33
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Commits on Aug 26, 2018
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fix: modify bravado TRS client to use correct api url
Use the bravado loader class to construct a spec dict from the swagger yaml, then load the client from the spec with the proper origin url specified. Loading 'from_url' with a local file doesn't provide an option to specify the origin url and instead uses the relative local path (even with the http client provided).
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fix: modify bravado WES client to use correct api url
Use the bravado loader class to construct a spec dict from the swagger yaml, then load the client from the spec with the proper origin url specified. Loading 'from_url' with a local file doesn't provide an option to specify the origin url and instead uses the relative local path (even with the http client provided).
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Commits on Aug 27, 2018
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fix: add option to specify WES client library
Include argument for named WES client when 'load_wes_client' is called by the wrapper class. Use a global variable to set the current option for client library.
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refactor: update config to match testbed design and language
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fix: update remaining config settings needed to poll services
Fix any calls to retrieve queue configs, and use only TRS or WES ID to initiate respective instances while checking testbed services for connectivity.
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refactor: move TRS/WES bridge functionality to trs2wes module
Add function for retrieving workflow data for a queue from TRS when not provided; need to add steps to convert this info into a valid WES request next.
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test: move all fixtures to pytest config module
Use conftest.py to describe all test fixtures to avoid redundancy (and discrepancies) across modules.
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Commits on Aug 28, 2018
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fix: use consistent terminology (queue_id) for queue config
Stick with unique queue identifiers for keys in the queue config, rather than workflow IDs or handles. Update variable names and accessor steps in assorted modules.
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Commits on Aug 30, 2018
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refactor: fix/debug various modules to work with WES v1.0
Update functions that were either mismatched with the latest WES spec or with the workflow-service wes_client library. Lots of changes made during live testing, not very well tracked. Also add test data and simplify app config (at least for version to be stored in repo).
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Commits on Aug 31, 2018
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refactor: update format of orchestrator logs
Modify run and monitor functions in orchestrator module to increase consistency and reduce modification between levels.
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