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refactor!: clean up app #474
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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 |
- Remove unused classification_type method - Update type hints / return types - Remove del_or_dup and use AltType
Might look to see about removing |
- Assumes gene normalizer works correctly. Only checks that gene_context is present if given in the test fixture
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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
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Adding todo's in #163 . Going to merge this into refactor |
- 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)
- 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
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: