@jsstevenson sorry (again) 😅 . Need to pull in changes for metaschema branch that is needed for plenary work. I'm going to open now since it's large, but going to look through once more to make sure I didn't accidentally pull in things from prod that we didn't want and that we included everything.
Notes:
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)
Close #162, #332, #429, #119, #428, #189, #309, #414, #475, #427
@jsstevenson sorry (again) 😅 . Need to pull in changes for metaschema branch that is needed for plenary work. I'm going to open now since it's large, but going to look through once more to make sure I didn't accidentally pull in things from prod that we didn't want and that we included everything.
Notes: