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Testbed module #38

Merged
merged 17 commits into from
Aug 31, 2018
Merged

Testbed module #38

merged 17 commits into from
Aug 31, 2018

Commits on Aug 22, 2018

  1. refactor: move testbed out of orchestrator module

    Add functions for retrieving and submitting workflow checker
    jobs to testbed module (remove from orchestrator module).
    jaeddy committed Aug 22, 2018
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  2. 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
    jaeddy committed Aug 22, 2018
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Commits on Aug 26, 2018

  1. 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).
    jaeddy committed Aug 26, 2018
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  2. 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).
    jaeddy committed Aug 26, 2018
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Commits on Aug 27, 2018

  1. 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.
    jaeddy committed Aug 27, 2018
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  2. refactor: update config to match testbed design and language

    Modify the orchestrator config for queues (renamed from 'evals')
    to store basic information needed for the testbed, including
    where workflow files can be retrieved and a list of WES endpoints
    on which to run jobs.
    
    See #33, #34
    jaeddy committed Aug 27, 2018
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  3. 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.
    jaeddy committed Aug 27, 2018
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  4. 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.
    jaeddy committed Aug 27, 2018
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  7. test: move all fixtures to pytest config module

    Use conftest.py to describe all test fixtures to avoid
    redundancy (and discrepancies) across modules.
    jaeddy committed Aug 27, 2018
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Commits on Aug 28, 2018

  1. 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.
    jaeddy committed Aug 28, 2018
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Commits on Aug 30, 2018

  1. 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).
    jaeddy committed Aug 30, 2018
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Commits on Aug 31, 2018

  1. refactor: update format of orchestrator logs

    Modify run and monitor functions in orchestrator module to
    increase consistency and reduce modification between levels.
    jaeddy committed Aug 31, 2018
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  2. update/simplify README

    jaeddy committed Aug 31, 2018
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