8000 SEAB-7184: Generate DOI for workflow with existent-but-empty author name by svonworl · Pull Request #6120 · dockstore/dockstore · GitHub
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SEAB-7184: Generate DOI for workflow with existent-but-empty author name #6120

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Merged
merged 2 commits into from
Jun 10, 2025
Merged

SEAB-7184: Generate DOI for workflow with existent-but-empty author name #6120

merged 2 commits into from
Jun 10, 2025

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svonworl
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@svonworl svonworl commented Jun 6, 2025 •
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Description
This PR makes a couple of changes to the webservice's DOI-related code:

  1. Changes the DOI creation code to filter out (not use) empty author names, which cause the following Zenodo error:
io.swagger.zenodo.client.ApiException: 
{
    "status": 400,
    "message": "A validation error occurred.",
    "errors": [
        {
            "field": "metadata.creators.0.person_or_org.family_name",
            "messages": [
                "Family name cannot be blank."
            ]
        }
    ]
}
  1. Ignores archived workflows in the query that determines the workflows that are eligible for an automatic DOI. This change doesn't relate to the "empty name" problem, I piggybacked it here to save some time.

Note that although I am a not a fan of the 8-space continuation indent style, I used it in this PR, so as to maintain consistency with the adjacent code.

Review Instructions
After this change is deployed to prod and the retroactive auto DOI creation script has been run, confirm that an automatic DOI was generated for https://dockstore.org/workflows/github.com/aryeelab/topology-tools/preprocess_microc, which contains author: '' in its wdl metadata.

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-7184

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@svonworl svonworl self-assigned this Jun 6, 2025
@svonworl svonworl requested review from denis-yuen and kathy-t June 6, 2025 23:10
@svonworl svonworl changed the title SEAB-7184: Generate doi for workflow with empty author SEAB-7184: Generate doi for workflow with existent-but-empty author name Jun 6, 2025
@svonworl svonworl changed the title SEAB-7184: Generate doi for workflow with existent-but-empty author name SEAB-7184: Generate DOI for workflow with existent-but-empty author name Jun 6, 2025
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Note that although I am a not a fan of the 8-space continuation indent style, I used it in this PR, so as to maintain consistency with the adjacent code.

I actually don't mind a separate PR/commit to reformat things. I find github's blame interface pretty powerful

denis-yuen
denis-yuen approved these changes Jun 9, 2025
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(re-ran build, looks unrelated gpg issue?)

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sonarqubecloud bot commented Jun 9, 2025

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

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codecov bot commented Jun 9, 2025 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 74.18%. Comparing base (eaf6245) to head (897a2ae).

Additional details and impacted files 
@@                 Coverage Diff                 @@
##             hotfix/1.17.1    #6120      +/-   ##
===================================================
- Coverage            74.22%   74.18%   -0.05%     
+ Complexity            5663     5660       -3     
===================================================
  Files                  389      389              
  Lines                20329    20331       +2     
  Branches              2100     2100              
===================================================
- Hits                 15090    15083       -7     
- Misses                4237     4245       +8     
- Partials              1002     1003       +1
Flag Coverage Δ
bitbuckettests 25.93% <0.00%> (-0.01%) ⬇️
hoverflytests 27.63% <100.00%> (+<0.01%) ⬆️
integrationtests 56.08% <0.00%> (-0.01%) ⬇️
languageparsingtests 10.82% <0.00%> (-0.01%) ⬇️
localstacktests 21.34% <0.00%> (-0.01%) ⬇️
regressionintegrationtests ?
toolintegrationtests 29.90% <0.00%> (-0.01%) ⬇️
unit-tests_and_non-confidential-tests 26.32% <100.00%> (+<0.01%) ⬆️
workflowintegrationtests 37.36% <0.00%> (-0.01%) ⬇️

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@svonworl svonworl merged commit 250dd06 into hotfix/1.17.1 Jun 10, 2025
23 of 24 checks passed
@svonworl svonworl deleted the feature/seab-7184/generate-doi-for-workflow-with-empty-author branch June 10, 2025 05:33
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@kathy-t kathy-t kathy-t approved these changes

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