BBMRI-cz / fhir-module

A data integration tool for BBMRI-ERIC biobanks.
Apache License 2.0
2 stars 1 forks source link

Attribute to collection #21

Closed SimonKonar closed 1 month ago

SimonKonar commented 1 month ago

Description:

This PR adds an env variable that determines by which attribute the sample should be mapped to corresponding collection, as specified in the type_to_collection_map.json

Checklist:

Make sure you tick all the boxes bellow if they are true or do not apply:

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 84.95575% with 17 lines in your changes missing coverage. Please review.

Project coverage is 90.74%. Comparing base (61b9b5b) to head (95e1799).

Files Patch % Lines
persistence/sample_donor_csv_repository.py 50.00% 6 Missing :warning:
persistence/condition_csv_repository.py 66.66% 5 Missing :warning:
persistence/sample_csv_repository.py 78.94% 4 Missing :warning:
persistence/factories/csv_repository_factory.py 0.00% 1 Missing :warning:
persistence/factories/xml_repository_factory.py 0.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #21 +/- ## ========================================== - Coverage 90.81% 90.74% -0.07% ========================================== Files 63 64 +1 Lines 2319 2399 +80 ========================================== + Hits 2106 2177 +71 - Misses 213 222 +9 ``` | [Flag](https://app.codecov.io/gh/BBMRI-cz/fhir-module/pull/21/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BBMRI-cz) | Coverage Δ | | |---|---|---| | [integration](https://app.codecov.io/gh/BBMRI-cz/fhir-module/pull/21/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BBMRI-cz) | `33.27% <0.00%> (-1.17%)` | :arrow_down: | | [unit](https://app.codecov.io/gh/BBMRI-cz/fhir-module/pull/21/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BBMRI-cz) | `73.04% <84.95%> (+0.54%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BBMRI-cz#carryforward-flags-in-the-pull-request-comment) to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.