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refactor!: rearrange app architecture #196

Merged
merged 8 commits into from
Oct 12, 2023
Merged

refactor!: rearrange app architecture #196

merged 8 commits into from
Oct 12, 2023

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korikuzma
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Close #192, #194 . I think we can remove the vrs-2.0-alpha branch and just bump to 0.3.x

Notes:

  • Remove gene-normalizer dependency
  • Rearranges app architecture
    • handlers
      • SeqRepoAccess
        • get_fasta_file is now a method
    • mappers
      • AlignmentMapper
      • MANETranscript
      • ExonGenomicCoordsMapper
        • These methods were originally in CoolSeqTool
    • data_sources
      • MANETranscriptMappings
      • TranscriptMappings
      • UTADatabase

@korikuzma korikuzma added priority:medium Medium priority technical debt A feature/requirement implemented in a sub-optimal way & must be re-written. Contrast to "cleanup" labels Oct 6, 2023
@korikuzma korikuzma self-assigned this Oct 6, 2023
@korikuzma korikuzma requested review from jsstevenson and removed request for jsstevenson October 8, 2023 19:21
@korikuzma korikuzma mentioned this pull request Oct 9, 2023
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@jsstevenson jsstevenson mentioned this pull request Oct 10, 2023
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This was referenced Oct 11, 2023
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@jsstevenson
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I'll re-review once all of the child branches are merged in to double-check, but as of right now, I think this looks good 👍

@korikuzma
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I'll re-review once all of the child branches are merged in to double-check, but as of right now, I think this looks good 👍

@jsstevenson I was planning on merging this one first for commit history. I can re-request review on each PR when base is updated?

@korikuzma korikuzma merged commit 1424f1b into main Oct 12, 2023
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@korikuzma korikuzma deleted the issue-192 branch October 12, 2023 16:13
This was referenced Oct 13, 2023
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@jsstevenson jsstevenson jsstevenson approved these changes

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priority:medium Medium priority technical debt A feature/requirement implemented in a sub-optimal way & must be re-written. Contrast to "cleanup"
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Successfully merging this pull request may close these issues.

Rearrange resource classes architecture
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@korikuzma @jsstevenson