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@hjarrell hjarrell commented May 27, 2021

What does this change do? Please be clear and concise.

Instead of skipping the parents of ambiguous children this allows them to be created.

Why was this change made? Including an issue number is sufficient. Otherwise, briefly explain the benefit of the change.

M3C-267

Verification

List the steps needed to make sure this thing works. Be precise.

  1. See the issue comments on JIRA for how to restore the backups
  2. Modify the config.yml to point to your local databases
  3. Run the prefill step from the README
  4. You can optionally comment these lines to reduce the time it takes to run the next step:

    m3c-tools/m3c/triples.py

    Lines 812 to 814 in 5420081

    pubs = get_publications(sup_cur, people)
    pubs_triples = make_publications(cfg.namespace, pubs)
    print_to_file(pubs_triples, pubs_file)
  5. Run the generate step
  6. Ensure that the process finishes.

I have attached a diff of the output triple files to the JIRA issue for you to see.

Affirmations

All of these should have a check by them. Any exception requires an explanation.

  • I matched the style of the existing code.
  • I added and updated any relevant documentation (inline, README, CHANGELOG, and such).
  • I used Python's type hinting.
  • I ran the automated tests and ensured they ALL passed.
  • I ran the linter and ensured my changes have not introduced ANY warnings or errors.
  • I have made an effort to minimize code changes and have not included any cruft (preference files, *.pyc files, old comments, print-debugging, unused variables).
  • I have made an effort maintain a clear commit history (haven't merged other branches or rebased improperly).
  • I have written the code myself or have given credit where credit is due.

Instead of skipping the parents of ambiguous children this allows them to be created.
@hjarrell hjarrell requested a review from s-emerson May 27, 2021 18:34
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...Let me fix the unit test

@pbchase pbchase self-requested a review July 13, 2021 15:18
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M3C RESOURCES FOR TESTING THE CODE

Forge wiki: https://ctsit-forge.ctsi.ufl.edu/projects/m3c/wiki/Wiki
(contains info on M3C servers, metab_admin, the locations of code repositories, how to complete a web release, and how to run the various services like the monthly data import, the Flask server, and the ExpressJS server)

M3C People Portal EPIC on JIRA: https://jira.ctsi.ufl.edu/browse/M3C-270
(contains links to other people portal-related JIRA tasks)

JIRA task "Report fix for ambiguous hierarchy to metab workbench": https://jira.ctsi.ufl.edu/browse/M3C-266
(contains a detailed explanation of the issue that this pull request addresses)

JIRA task "Modify m3c-tools prefill to create institutions in ambiguous hierarchies": https://jira.ctsi.ufl.edu/browse/M3C-267
(contains the information about the pull request and comments on how to restore the local database backups during testing)

@pbchase pbchase requested a review from ChemiKyle July 28, 2021 14:10
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pbchase commented Jul 28, 2021

@s-emerson, @melimore86 who should be invited to a session to develop testing tools this PR and PRs like it? @ChemiKyle will lead.

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4 participants