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refactor!: clean up app #474

Merged
merged 120 commits into from
Aug 7, 2023
Merged

refactor!: clean up app #474

merged 120 commits into from
Aug 7, 2023

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korikuzma
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@korikuzma korikuzma commented Jul 27, 2023 •
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Close #162, #332, #429, #119, #428, #189, #309, #414, #475, #427

@jsstevenson I'm realllly sorry for making this large of a PR. I'm going to open now. There's some places (validators/translators) where I want to use shared methods for DRY principle. However, I'm going to open up now since it's so large and look at doing this while you review.

Notes:

  • Mainly focused on cleanup related to to_vrs and normalize endpoints. Did not really look at gnomad_vcf_to_protein or copy_number_variation modules
  • Remove to canonical variation (no longer support)
  • Combined tests for tokenizers/classifiers/validators/translators into one module
  • Removed amino_acids.csv (accidentally left in)
  • Names changes
    • Coding DNA → cDNA
    • Polypeptide truncation → Protein Stop Gain
    • Silent Mutation → Reference Agree
    • Uncertain/Range → Ambiguous
    • HGVSDupDelModeEnum → HGVSDupDelModeOption
  • Validators no longer do any kind of translations to VRS representations. Translators will do this work
  • Classifier only returns exact matches and only returns a single classification rather than a list
  • Use regex patterns (in variation/regex.py) rather than multiple if/else conditions
  • Remove unused code
  • Create variation schemas for supported variation types. Uses consistent field naming
  • Cleaning up instance variables in classes
  • Only run fully justified allele normalization on VRS Alleles. Do not run on VRS Copy Number
  • Pulled tokenize, classify, validate, translate outside of subdirectories (variation/tokenizers, variation/classifiers, variation/validators, variation/translators) and moved to app root
  • baseline_copies is required in /hgvs_to_copy_number_count
  • cool-seq-tool update
    • Removes file path params from QueryHandler, can set these via environment variables
    • QueryHandler accepts only uta_db_url as param and removes uta_db_pwd
  • new dependencies for linting
    • ruff (replaced flake8)
    • black

@korikuzma
refactor: update TokenType + remove protein termination classifier
b17d52c
@korikuzma
refactor: Remove TokenMatchType (not necessary)
008b632
@korikuzma
forgot to remove additional match_type
c2a47bb
@korikuzma
refactor: clean up handling unknown tokens
111d104
@korikuzma
refactor: Rename GeneMatchToken to GeneToken
cc79fd1
@korikuzma
refactor: create AltType str enum
5cd918d
@korikuzma
refactor: update TokenType type
095c9e9
@korikuzma
refactor: remove LookupType enum (not used)
b79410c
@korikuzma
wip: add work for tokenizers
67ab56a
@korikuzma
wip: storing progress
944d6db
@korikuzma
wip: store progress for delins
a4c2bf7
@korikuzma
wip: store progress for cdna insertion
8b76419
@korikuzma
wip: store progress for ref agree
7857767
@korikuzma
wip: minor cleanup of validators
6778521
@korikuzma
wip: store progress for protein stop gain
d567c5a
@korikuzma
wip: store initial work for genomic dup
59e7942
@korikuzma
wip: store progress for genomic ambiguous dups
4dd8043
@korikuzma
wip: progress for genomic del
b652db8
@korikuzma
wip: remove canonical variation work
d2cf750
@korikuzma
wip: fix classifiers
d909427
@korikuzma
wip: handle if mane none in translators
80dd57c
@korikuzma
wip: tmp stop running gh actions
1b39114
@korikuzma
wip: more progress for normalize
8dd9d92
@korikuzma
wip: store more progress
df8e845
@korikuzma
wip: add genomic del ambiguous
450981e
@korikuzma
iMerge branch 'main' into issue-332-kori-merge-main
8310cdf
@korikuzma
wip: fix tokenizers
8512eea
@korikuzma
wip: clean up classifier tests
6ee5110
@korikuzma
wip: rename coding dna --> cdna
666ab23
@korikuzma
wip: storing progress for dup1
f194615
@korikuzma
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@jsstevenson Thanks for all your feedback so far! So happy to get another set of eyes to find things I've missed

@korikuzma
pr review changes
1bb95ae 
- Remove unused classification_type method
- Update type hints / return types
- Remove del_or_dup and use AltType
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korikuzma commented Aug 1, 2023 •
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Might look to see about removing AltType and seeing if we can use an existing field in the models. Also think I may remove CoordinateType and just use MoleculeContext. Although I think molecule context is being removed once we move to 2.0-alpha (at least I don't see it in the schema yet).

This was referenced Aug 1, 2023
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@jsstevenson jsstevenson self-requested a review August 2, 2023 13:30
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@korikuzma astounding work! I think I'm caught up through f422b4d, so I'll just do an approve now in the interest of keeping this moving

@korikuzma korikuzma changed the base branch from main to refactor August 2, 2023 13:47
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Need to make this change, otherwise RSE default won't work as expected. Should add a test for dup > 100 bps
Screenshot 2023-08-06 at 5 51 40 PM

@korikuzma korikuzma mentioned this pull request Aug 7, 2023
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Adding todo's in #163 . Going to merge this into refactor

@korikuzma korikuzma merged commit 77d3ef3 into refactor Aug 7, 2023
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@korikuzma korikuzma deleted the issue-332-kori branch August 7, 2023 20:30
@korikuzma korikuzma mentioned this pull request Aug 21, 2023
Merged
korikuzma added a commit that referenced this pull request Aug 25, 2023
@korikuzma
refactor!: clean up app (metaschema) (#494)
043285a 
- Refactor app (#474)
  - Mainly focused on cleanup related to to_vrs and normalize endpoints. Did not really look at gnomad_vcf_to_protein or copy_number_variation modules
  - Remove to canonical variation (no longer support)
  - Combined tests for tokenizers/classifiers/validators/translators into one module
  - Removed amino_acids.csv (accidentally left in)
  - Names changes
    - Coding DNA → cDNA
    - Polypeptide truncation → Protein Stop Gain
    - Silent Mutation → Reference Agree
    - Uncertain/Range → Ambiguous
    - HGVSDupDelModeEnum → HGVSDupDelModeOption
  - Validators no longer do any kind of translations to VRS representations. Translators will do this work
  - Classifier only returns exact matches and only returns a single classification rather than a list
  - Use regex patterns (in variation/regex.py) rather than multiple if/else conditions
  - Remove unused code
  - Create variation schemas for supported variation types. Uses consistent field naming
  - Cleaning up instance variables in classes
  - Only run fully justified allele normalization on VRS Alleles. Do not run on VRS Copy Number
  - Pulled tokenize, classify, validate, translate outside of subdirectories (variation/tokenizers, variation/classifiers, variation/validators, variation/translators) and moved to app root 
  - baseline_copies is required in /hgvs_to_copy_number_count
  - cool-seq-tool update
      - Removes file path params from QueryHandler, can set these via environment variables
      - QueryHandler accepts only uta_db_url as param and removes uta_db_pwd
   - new dependencies for linting
    - ruff (replaced flake8)
    - black 
- Add more support for gnomad vcf expressions in normalize (#479, #489)
- Remove pyliftover from deps (covered by cool-seq-tool) (#480) 
- Fix default mode for hgvs dup del mode wrt rse (#482)
- Fix default HGVS dup del mode - dels should be allele w lse (#484)
- Use cool-seq-tool AnnotationLayer and rm CoordinateType (#485)
- Remove structural type from varaition descriptor (#487)
@korikuzma korikuzma mentioned this pull request Aug 25, 2023
Closed
korikuzma added a commit that referenced this pull request Sep 22, 2023
@korikuzma
refactor!: clean up app (#474)
6156419 
- Mainly focused on cleanup related to to_vrs and normalize endpoints. Did not really look at gnomad_vcf_to_protein or copy_number_variation modules
- Remove to canonical variation (no longer support)
- Combined tests for tokenizers/classifiers/validators/translators into one module
- Removed amino_acids.csv (accidentally left in)
- Names changes
  - Coding DNA → cDNA
  - Polypeptide truncation → Protein Stop Gain
  - Silent Mutation → Reference Agree
  - Uncertain/Range → Ambiguous
  - HGVSDupDelModeEnum → HGVSDupDelModeOption
- Validators no longer do any kind of translations to VRS representations. Translators will do this work
- Classifier only returns exact matches and only returns a single classification rather than a list
- Use regex patterns (in variation/regex.py) rather than multiple if/else conditions
- Remove unused code
- Create variation schemas for supported variation types. Uses consistent field naming
- Cleaning up instance variables in classes
- Only run fully justified allele normalization on VRS Alleles. Do not run on VRS Copy Number
- Pulled tokenize, classify, validate, translate outside of subdirectories (variation/tokenizers, variation/classifiers, variation/validators, variation/translators) and moved to app root 
- baseline_copies is required in /hgvs_to_copy_number_count
- cool-seq-tool update
    - Removes file path params from QueryHandler, can set these via environment variables
    - QueryHandler accepts only uta_db_url as param and removes uta_db_pwd
- new dependencies for linting
  - ruff (replaced flake8)
  - black
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priority:high High priority technical debt A feature/requirement implemented in a sub-optimal way & must be re-written. Contrast to "cleanup"
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