BBMRI-cz / fhir-module

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

Support for loading data from csv files #12

Closed SimonKonar closed 7 months ago

SimonKonar commented 7 months ago

Negotiator pull request:

Description:

Added support for reading data from Csv files in persistence. The goal is to have more supported formats to extract data from.

Checklist:

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

codecov[bot] commented 7 months ago

Codecov Report

Attention: 82 lines in your changes are missing coverage. Please review.

Comparison is base (5a1bfce) 93.59% compared to head (125ad1c) 90.08%.

Files Patch % Lines
persistence/factories/csv_repository_factory.py 0.00% 19 Missing :warning:
persistence/factories/xml_repository_factory.py 0.00% 19 Missing :warning:
persistence/factories/factory_util.py 0.00% 13 Missing :warning:
main.py 0.00% 9 Missing :warning:
model/gender.py 40.00% 6 Missing :warning:
persistence/factories/repository_factory.py 77.77% 4 Missing :warning:
persistence/sample_donor_csv_repository.py 92.85% 3 Missing :warning:
util/config.py 66.66% 3 Missing :warning:
exception/wrong_records_file_type_exception.py 0.00% 2 Missing :warning:
persistence/condition_csv_repository.py 97.50% 1 Missing :warning:
... and 3 more
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #12 +/- ## ========================================== - Coverage 93.59% 90.08% -3.52% ========================================== Files 34 47 +13 Lines 1108 1482 +374 ========================================== + Hits 1037 1335 +298 - Misses 71 147 +76 ``` | [Flag](https://app.codecov.io/gh/BBMRI-cz/fhir-module/pull/12/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/12/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BBMRI-cz) | `36.97% <6.03%> (-10.50%)` | :arrow_down: | | [unit](https://app.codecov.io/gh/BBMRI-cz/fhir-module/pull/12/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BBMRI-cz) | `71.86% <74.27%> (+1.28%)` | :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.

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