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the value zero is not stored correctly in certain phenotype uploads #5329

Merged
merged 21 commits into from
Feb 19, 2025
Merged

the value zero is not stored correctly in certain phenotype uploads #5329

merged 21 commits into from
Feb 19, 2025

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lukasmueller
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Description

fixes #5328

Checklist

  • Refactoring only
  • Documentation only
  • Fixture update only
  • Bug fix
    • The relevant issue has been closed.
    • Further work is required.
  • New feature
    • Relevant tests have been created and run.
    • Data was added to the fixture
      • Data was added via a patch in /t/data/fixture/patches/.
    • User-Facing Change
      • The user manual in /docs has been updated.
    • Any new Perl has been documented using perldoc.
    • Any new JavaScript has been documented using JSDoc.
    • Any new legacy JavaScript has been moved from /js to /js/source/legacy.

@lukasmueller lukasmueller added Priority: Critical Issue/PR requires immediate resolution. Type: Bug Issue describes a bug. and removed Priority: Critical Issue/PR requires immediate resolution. Type: Bug Issue describes a bug. labels Feb 15, 2025
@lukasmueller lukasmueller requested a review from nmenda February 15, 2025 03:55
@dwaring87
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It looks like these changes are properly storing 0s, but the upload is no longer skipping blank values.

If a trial already had stored trait values and a new upload file has blank values for those traits, it now seems to remove those values instead of keeping them unchanged (even when the option to remove them is not checked)

@dwaring87
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Here is a script that can be used to find any 0s in recently uploaded files so they can be re-uploaded and stored properly
extract_pheno_zeros.pl

@lukasmueller
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We should have a test for this!

lukasmueller and others added 15 commits February 17, 2025 15:31
@lukasmueller
process store only when cvterm_row is defined.
9aa0891
@lukasmueller
remove fieldbook image file references.
3965dcf
@lukasmueller
output more diagnostic info.
4b793b1
@lukasmueller
bring back some tests that were commented out previously.
d7570aa
@lukasmueller
delete metadata associated images before deleting md_metadata.
e27ff45
@lukasmueller
print error if available.
3736abe
@lukasmueller
fix a linting issue (return undef)
e64aa62
@lukasmueller
do not delete nd_experiment entries when deleting phenotypes.
e84bf4d
@dwaring87
StorePhenotypes: fix spacing
a6851f6
@dwaring87
Project: restore deletion of nd_experiment entries when deleting phen…
c86164f 
…otypes
@dwaring87
Store Phenotypes: fix query looking up phenotype and experiment ids f…
7583091 
…rom stocks and traits
@dwaring87
StorePhenotypes: use temp table for finding phenotypes to delete
4803f51
@dwaring87
Delete ND Experiments: check for no ids to delete
2aba632
@dwaring87
StorePhenotypes: fix typo in table name
d7f1564
@dwaring87
StorePhenotypes: use temp table for saved nd_experiment_ids when dele…
7773686 
…ting phenotypes
@lukasmueller lukasmueller requested a review from isaak February 19, 2025 15:46
@lukasmueller lukasmueller merged commit 20c98e7 into master Feb 19, 2025
4 checks passed
@lukasmueller lukasmueller deleted the topic/fix_missing_0s_in_csv_parsing branch February 19, 2025 18:42
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Reviewers

@nmenda nmenda nmenda approved these changes

@dwaring87 dwaring87 dwaring87 approved these changes

@isaak isaak Awaiting requested review from isaak

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zero is not stored in the database in certain phenotype uploads
3 participants
@lukasmueller @dwaring87 @nmenda