BBMRI-cz / fhir-module

A data integration tool for BBMRI-ERIC biobanks.
Apache License 2.0
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Multiple diagnoses for one sample #20

Closed SimonKonar closed 2 months ago

SimonKonar commented 2 months ago

Negotiator pull request:

Description:

This PR adds functionality to add multiple diagnoses for one sample. It also allows to update already existing samples located in the Blaze storage. sample will be updated if any of the attribute changes.

Checklist:

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

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 69.43231% with 70 lines in your changes missing coverage. Please review.

Project coverage is 33.30%. Comparing base (cc04c40) to head (a676fae). Report is 29 commits behind head on main.

:exclamation: Current head a676fae differs from pull request most recent head 732c1e6

Please upload reports for the commit 732c1e6 to get more accurate results.

Files Patch % Lines
...est/unit/persistence/test_sample_xml_repository.py 0.00% 22 Missing :warning:
test/unit/model/test_sample.py 0.00% 17 Missing :warning:
model/sample.py 84.78% 7 Missing :warning:
persistence/sample_csv_repository.py 0.00% 7 Missing :warning:
...est/unit/persistence/test_sample_csv_repository.py 0.00% 7 Missing :warning:
service/blaze_service.py 93.24% 5 Missing :warning:
persistence/sample_xml_repository.py 0.00% 3 Missing :warning:
test/integration/test_blaze.py 96.87% 1 Missing :warning:
util/sample_util.py 95.23% 1 Missing :warning:

:exclamation: There is a different number of reports uploaded between BASE (cc04c40) and HEAD (a676fae). Click for more details.

HEAD has 10 uploads less than BASE | Flag | BASE (cc04c40) | HEAD (a676fae) | |------|------|------| |integration|11|1|
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #20 +/- ## =========================================== - Coverage 90.16% 33.30% -56.87% =========================================== Files 47 62 +15 Lines 1495 2270 +775 =========================================== - Hits 1348 756 -592 - Misses 147 1514 +1367 ``` | [Flag](https://app.codecov.io/gh/BBMRI-cz/fhir-module/pull/20/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/20/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BBMRI-cz) | `33.30% <69.43%> (-4.23%)` | :arrow_down: | | [unit](https://app.codecov.io/gh/BBMRI-cz/fhir-module/pull/20/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BBMRI-cz) | `?` | | 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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