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fix the resolving of genbank and jgi IDs #285

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merged 2 commits into from
Nov 26, 2024

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@CunliangGeng CunliangGeng commented Nov 25, 2024

The unit test tests/unit/genomics/test_podp_antismash_downloader.py (e.g. action output) has failed because the code cannot successfully resolve the RefSeq accessions for GenBank ID or JGI ID any more. This caused by the change of NCBI website.

This PR fixes the issue by requesting latest NCBI REST API to replace the parsing of webpage.

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@CunliangGeng CunliangGeng requested a review from gcroci2 November 25, 2024 15:28
@CunliangGeng CunliangGeng marked this pull request as ready for review November 25, 2024 15:28
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CunliangGeng commented Nov 26, 2024

Merge activity

  • Nov 26, 7:31 AM EST: A user started a stack merge that includes this pull request via Graphite.
  • Nov 26, 7:32 AM EST: Graphite rebased this pull request as part of a merge.
  • Nov 26, 7:33 AM EST: A user merged this pull request with Graphite.

Replace webpage parsing with requesting NCBI REST API v2
@CunliangGeng CunliangGeng force-pushed the fix_resolving_genbank_jgi_ids branch from 254690b to 1528ee8 Compare November 26, 2024 12:31
@CunliangGeng CunliangGeng merged commit 505496e into dev Nov 26, 2024
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@CunliangGeng CunliangGeng deleted the fix_resolving_genbank_jgi_ids branch November 26, 2024 12:33
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Quality Gate Failed Quality Gate failed

Failed conditions
75.0% Coverage on New Code (required ≥ 80%)

See analysis details on SonarQube Cloud

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