Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MetaWorkflow Handler and MetaWorkflow Run Handler: Pipeline Automation #11

Open
wants to merge 43 commits into
base: master
Choose a base branch
from

Commits on Sep 28, 2022

  1. Configuration menu
    Copy the full SHA
    15615cd View commit details
    Browse the repository at this point in the history

Commits on Oct 24, 2022

  1. Configuration menu
    Copy the full SHA
    165a612 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    ad1cbec View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    469804d View commit details
    Browse the repository at this point in the history
  4. Creation of helper functions that may eventually be added to dcic utils.

    Some are specific to the structure of CGAP portal schemas, but tried to
    generalize as much as possible. Also includes partial draft of dependency
    validation via topological sort.
    vstevensf committed Oct 24, 2022
    Configuration menu
    Copy the full SHA
    6cccc8e View commit details
    Browse the repository at this point in the history
  5. Configuration menu
    Copy the full SHA
    f62fabd View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    4d50191 View commit details
    Browse the repository at this point in the history

Commits on Oct 26, 2022

  1. Configuration menu
    Copy the full SHA
    81c826d View commit details
    Browse the repository at this point in the history

Commits on Nov 1, 2022

  1. Configuration menu
    Copy the full SHA
    32a576f View commit details
    Browse the repository at this point in the history

Commits on Nov 3, 2022

  1. Configuration menu
    Copy the full SHA
    fa02b5b View commit details
    Browse the repository at this point in the history
  2. Modified some tests, removed a few extraneous. Still need to finish t…

    …ests for topological sort.
    vstevensf committed Nov 3, 2022
    Configuration menu
    Copy the full SHA
    3e9348d View commit details
    Browse the repository at this point in the history

Commits on Nov 4, 2022

  1. Refactored the utils functions for topological sort into its own file.

    Resulted in edits within test files, including creation of a new
    test file for topological sort, and changes in imports for
    magma/metawfl_handler.py.
    vstevensf committed Nov 4, 2022
    Configuration menu
    Copy the full SHA
    dcb737e View commit details
    Browse the repository at this point in the history

Commits on Nov 9, 2022

  1. Added some pytests for topological sort.

    Changes included additions of different directed graph global vars
    for testing -- tests for the topological sort on their way.
    Also removed function for creating "forward dependencies" --
    this version of topological sort works with "backward dependencies".
    vstevensf committed Nov 9, 2022
    Configuration menu
    Copy the full SHA
    6bf3809 View commit details
    Browse the repository at this point in the history

Commits on Nov 17, 2022

  1. Completed first draft of completed topological sort tests.

    Addressed some prior comments. Future planned changes include
    creating a class for the topological sort function to decrease
    the number of command line arguments that are common among
    several functions.
    vstevensf committed Nov 17, 2022
    Configuration menu
    Copy the full SHA
    0ddf3d1 View commit details
    Browse the repository at this point in the history
  2. Small changes to utils -- mainly variable naming.

    Also addressed some prior comments on draft.
    vstevensf committed Nov 17, 2022
    Configuration menu
    Copy the full SHA
    c2231c2 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    5752c83 View commit details
    Browse the repository at this point in the history

Commits on Nov 23, 2022

  1. Configuration menu
    Copy the full SHA
    dae1229 View commit details
    Browse the repository at this point in the history

Commits on Nov 28, 2022

  1. Configuration menu
    Copy the full SHA
    8795286 View commit details
    Browse the repository at this point in the history

Commits on Jan 11, 2023

  1. Configuration menu
    Copy the full SHA
    ffefa6a View commit details
    Browse the repository at this point in the history

Commits on Jan 13, 2023

  1. Finished ValidatedDictionary class

    Changes included merging some former magma utils fxns
    into this class, and removing extraneous utils fxns.
    Also includes new test file for this class.
    vstevensf committed Jan 13, 2023
    Configuration menu
    Copy the full SHA
    5fd8916 View commit details
    Browse the repository at this point in the history

Commits on Jan 20, 2023

  1. Refactored Topological Sort with TopologicalSorter from dcicutils.

    Also wrote a draft of pytests
    vstevensf committed Jan 20, 2023
    Configuration menu
    Copy the full SHA
    2d16ab0 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    c6a0e7f View commit details
    Browse the repository at this point in the history

Commits on Feb 6, 2023

  1. Further edits to basic handler classes

    includes addition of custom Exception classes
    vstevensf committed Feb 6, 2023
    Configuration menu
    Copy the full SHA
    6cb41ac View commit details
    Browse the repository at this point in the history

Commits on Feb 16, 2023

  1. Configuration menu
    Copy the full SHA
    993361d View commit details
    Browse the repository at this point in the history

Commits on Apr 21, 2023

  1. Check in

    vstevensf committed Apr 21, 2023
    Configuration menu
    Copy the full SHA
    6321fbf View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    f4a47ba View commit details
    Browse the repository at this point in the history

Commits on Apr 24, 2023

  1. More updates the mwfr handler creation

    dbmi authored and dbmi committed Apr 24, 2023
    Configuration menu
    Copy the full SHA
    ae249bb View commit details
    Browse the repository at this point in the history

Commits on May 3, 2023

  1. Configuration menu
    Copy the full SHA
    58add81 View commit details
    Browse the repository at this point in the history

Commits on May 5, 2023

  1. Configuration menu
    Copy the full SHA
    e411ceb View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    dcbbec0 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    2db5bff View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    c1d2a0b View commit details
    Browse the repository at this point in the history

Commits on May 8, 2023

  1. Configuration menu
    Copy the full SHA
    3c54a4c View commit details
    Browse the repository at this point in the history
  2. Added docstrings to MWF handler files and tests, and added to magma c…

    …onstants. Got rid of duplication_flag.
    vstevensf committed May 8, 2023
    Configuration menu
    Copy the full SHA
    111a0c5 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    ffdabb6 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    d5deff5 View commit details
    Browse the repository at this point in the history

Commits on May 10, 2023

  1. Configuration menu
    Copy the full SHA
    4908f1b View commit details
    Browse the repository at this point in the history

Commits on May 16, 2023

  1. Configuration menu
    Copy the full SHA
    c684121 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    503cd00 View commit details
    Browse the repository at this point in the history

Commits on Jun 1, 2023

  1. Configuration menu
    Copy the full SHA
    93c1715 View commit details
    Browse the repository at this point in the history
  2. renamed test file

    vstevensf committed Jun 1, 2023
    Configuration menu
    Copy the full SHA
    82c8d55 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    1d5e77b View commit details
    Browse the repository at this point in the history

Commits on Jun 24, 2023

  1. Draft of checkstatus tests

    vstevensf committed Jun 24, 2023
    Configuration menu
    Copy the full SHA
    4f17490 View commit details
    Browse the repository at this point in the history