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Update existing cohort parser with warning flag #616

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merged 15 commits into from
Nov 20, 2023

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michael-harper
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Closes #614

Added warning flag to log missing data when parsing manifests as opposed to raising a ValueError. Also added test case that fails when a ValueError is raised and the warning flag is set to True.

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@vivbak vivbak left a comment

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Could you resolve the linting and test failures first? Also did you do a test-run of this change?

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codecov-commenter commented Nov 19, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (c05b11e) 70.56% compared to head (74b9031) 70.64%.
Report is 1 commits behind head on dev.

Additional details and impacted files
@@            Coverage Diff             @@
##              dev     #616      +/-   ##
==========================================
+ Coverage   70.56%   70.64%   +0.07%     
==========================================
  Files         116      116              
  Lines        9316     9337      +21     
==========================================
+ Hits         6574     6596      +22     
+ Misses       2742     2741       -1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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Awesome job! Just a few nits.

@@ -1,12 +1,12 @@
{
"name": "metamist",
"version": "6.3.0",
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Did you intend to bump version here?

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@michael-harper michael-harper Nov 20, 2023

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I did not, should it be 6.3.0?

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michael-harper and others added 7 commits November 20, 2023 15:19
…as well as length of read_filenames. Also changed removed /venv in .gitignore file - probably best for a separate PR
Co-authored-by: Vivian Bakiris <79084890+vivbak@users.noreply.github.com>
Co-authored-by: Vivian Bakiris <79084890+vivbak@users.noreply.github.com>
…th-skip-flag' into update-existing-cohort-parser-with-skip-flag
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Great job! We need a release for this to work. I'll action now.

@vivbak vivbak merged commit 4422f3e into dev Nov 20, 2023
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@vivbak vivbak deleted the update-existing-cohort-parser-with-skip-flag branch November 20, 2023 07:28
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Successfully merging this pull request may close these issues.

Introduce a Warning Flag for Missing Fastq Files in parse_existing_cohort.py
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