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Update ClinVar script to import somatic classifications + patch db schema 115 #1117

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merged 24 commits into from
Feb 4, 2025

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dglemos
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@dglemos dglemos commented Aug 19, 2024

Ticket: https://www.ebi.ac.uk/panda/jira/browse/ENSVAR-5941

  • add db schema patches: patch_114_115_a.sql and patch_114_115_b.sql
  • add new clinvar attrib types to attrib_entries.sql (new attrib types were inserted in the production db on 2024-10-31)
  • update clinvar import
  • update clinvar post process
  • update API
  • add tests

This update should be merged before Ensembl/ensembl-vep#1794

@dglemos dglemos added the e115 label Aug 19, 2024
@dglemos dglemos changed the title Update ClinVar script to import somatic classifications Update ClinVar script to import somatic classifications + patch db schema Sep 3, 2024
@dglemos dglemos changed the title Update ClinVar script to import somatic classifications + patch db schema Update ClinVar script to import somatic classifications + patch db schema 115 Sep 3, 2024
@dglemos dglemos marked this pull request as ready for review October 31, 2024 16:32
@dglemos dglemos requested a review from nakib103 October 31, 2024 16:33
@nakib103 nakib103 self-assigned this Nov 4, 2024
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LGTM!~ Thanks @dglemos for the updates.

@jamie-m-a jamie-m-a requested a review from nakib103 February 4, 2025 09:17
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The logic seems sound, we have reviewed this in meetings as well and Sarah has had oversight of the changes. Ok to merge.

@jamie-m-a jamie-m-a merged commit a273161 into Ensembl:main Feb 4, 2025
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3 participants