Add support for custom metadata validation & custom BioSample packages#228

Merged

jessicarowell merged 20 commits intodevfrom add-bs-pkgs-support-ick4

Dec 18, 2024

+1,204-1,573

Commits on Nov 21, 2024

updates to add custom fields to Attributes in BioSample submission.xml file

Jessica Rowell
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Jessica Rowell
committed
some corrections to metadata validation to get the custom fields to add correctly

Jessica Rowell
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Jessica Rowell
committed
ignore the test fields in case they are accidentally submitte as custom fields

Jessica Rowell
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Jessica Rowell
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change sex to host_sex and age to host_age in metadata_template.xlsx

Jessica Rowell
authored and
Jessica Rowell
committed

Commits on Dec 4, 2024

fixing custom metadata functionality

Jessica Rowell
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Jessica Rowell
committed
Remove extraneous Unnamed column after import

Jessica Rowell
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Jessica Rowell
committed

Commits on Dec 6, 2024

Rewrite the custom fields script to correct field name changes

Jessica Rowell
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Jessica Rowell
committed
Fix code to skip submissions where reqd files not provided

Jessica Rowell
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Jessica Rowell
committed
correction to update_submission main.nf to match new optional params

Jessica Rowell
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Jessica Rowell
committed
ignore JSON keys that are not used and fix error file write location

Jessica Rowell
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Jessica Rowell
committed

Commits on Dec 9, 2024

don't print org_id if not provided

Jessica Rowell
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Jessica Rowell
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Update README to add section for custom metadata and update JSON

Jessica Rowell
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Jessica Rowell
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move example submission config file to conf/ folder and remove bin/config_files

Jessica Rowell
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Jessica Rowell
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add example templates for One Health Enterics BioSample package

Jessica Rowell
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Jessica Rowell
committed

Commits on Dec 16, 2024

add better handling for JSON Vs. Excel file discrepancies

Jessica Rowell
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Jessica Rowell
committed

Commits on Dec 17, 2024

add error handling for empty input metadata spreadsheets

Jessica Rowell
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Jessica Rowell
committed
correction to code that checks metadata file custom fields against the JSON

Jessica Rowell
authored and
Jessica Rowell
committed

Commits on Dec 18, 2024

Merge branch 'dev' into add-bs-pkgs-support-ick4

Jessica Rowell
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Jessica Rowell
committed
Check for duplicate columns, read_excel automatically makes them unique with .1, .2, etc

Jessica Rowell
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Jessica Rowell
committed
Add better error logging for the connect function which sometimnes errors out during update_submission

Jessica Rowell
authored and
Jessica Rowell
committed