[ORCA-175] Add CsvUpdater and update_csv command
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✅ Linked to Story ORCA-175 · As an output, return the input manifest but with dcqc_status column for ease of use |
BWMac
changed the title
CsvUpdater and update_csv command
Codecov Report
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## main #39 +/- ##
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Coverage 100.00% 100.00%
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Files 22 23 +1
Lines 1090 1143 +53
Branches 126 189 +63
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+ Hits 1090 1143 +53
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thomasyu888
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bwmac/orca-175/update_input_with_status
thomasyu888
reviewed
Jun 13, 2023
thomasyu888
reviewed
Jun 13, 2023
thomasyu888
reviewed
Jun 13, 2023
thomasyu888
reviewed
Jun 13, 2023
thomasyu888
approved these changes
Jun 13, 2023
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🔥 @BWMac Nice work! I'm going to pre-approve, but please add the missing test case for when there is no status.
thomasyu888
reviewed
Jun 13, 2023
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This PR follows on from #38 and implements a
CsvUpdaterclass (and needed tests) which will be used to update the input CSV file for the DCQC run with a new column indicating theSuiteStatusfor each file following processing. It also adds a new CLI commandupdate_csvwhich will apply this new class to make the needed changes. The logic for updating CSV files is agnostic to single/multi-target QC runs, and uses the file URL as an ID to evaluate all suites generated against each individual target file. Necessary example filesinput.csv,output.csv, andsuites.jsonare also added totests/data.suite_abc.pyis also updated to include aget_statusmethod for accessing theSuiteStatusfrom outside of the class.edit: I am marking this as ready for review after successfully testing these changes in
nf-dcqc.