TRON-Bioinformatics / covigator

CoVigator - Monitoring SARS-CoV-2 mutations
MIT License
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ENA api update #128

Closed johausmann closed 11 months ago

johausmann commented 1 year ago

With this merge request we adapt the accessor module to the ENA API changes. With the update a new field "tax_id" was introduced, which is returned in the payload of a request and thus led to a crash. For simplicity we remove the field to not change the database model. We also added the option to optionally skip the check of the host tax id, since this information is not always given.

codecov[bot] commented 12 months ago

Codecov Report

Patch coverage: 97.56% and project coverage change: +0.15% :tada:

Comparison is base (4e5ed2c) 85.61% compared to head (efecc9f) 85.77%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #128 +/- ## =========================================== + Coverage 85.61% 85.77% +0.15% =========================================== Files 48 48 Lines 4964 4991 +27 =========================================== + Hits 4250 4281 +31 + Misses 714 710 -4 ``` | [Files Changed](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics) | Coverage Δ | | |---|---|---| | [covigator/accessor/ena\_accessor.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2FjY2Vzc29yL2VuYV9hY2Nlc3Nvci5weQ==) | `88.66% <94.73%> (+2.95%)` | :arrow_up: | | [covigator/accessor/abstract\_accessor.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2FjY2Vzc29yL2Fic3RyYWN0X2FjY2Vzc29yLnB5) | `100.00% <100.00%> (+2.85%)` | :arrow_up: | | [covigator/tests/unit\_tests/faked\_objects.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL3Rlc3RzL3VuaXRfdGVzdHMvZmFrZWRfb2JqZWN0cy5weQ==) | `87.27% <100.00%> (ø)` | | | [covigator/tests/unit\_tests/test\_ena\_accessor.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL3Rlc3RzL3VuaXRfdGVzdHMvdGVzdF9lbmFfYWNjZXNzb3IucHk=) | `100.00% <100.00%> (ø)` | |

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