Refactor #503
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Refactor #503
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- 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
Was not looking at outer coords, but now we are
Forgot to catch the case where there are no valid results. Fixes so that translations is defined
- Was using `translations` when it should have been using `preferred_translations`
…507) - Creates an enum for vrs sequence location accession status - Fix getting priority translation result in `_get_priority_translation_result` when there are multiple translation results for a given ac status
Close #450 , #458 , #465 , #444 Notes: - feat: add parsed to copy number change endpoint (#453) - fix!: /parsed_to_cn_var should accept number, definite range, and indefinite range (#455) - feat: add do_liftover param in parsed to copy number endpoints (#459) - refactor!: parsed to copy number should accept request body (#460) - fix: Copy Number Count copies should be Number or Indef/Def Range (#468) - fix: allow comparator to be set in start/end values (#469)
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All of these commits have been reviewed. I think we're in a good place to make a release. Going to rebase and merge. |
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I'm probably just planning to rebase these rather than squash+merge/merge