Use new layers/gene info format in mapped target metadata #611
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This pull request introduces support for storing and handling mapped HGNC gene names in the target gene model and related data structures. It updates the database schema, models, mapping logic, and test scaffolding to include a new
mapped_hgnc_namefield, and refactors how gene annotation metadata is structured and accessed to support VariantEffect/dcd_mapping2#67.Database and Model Updates:
mapped_hgnc_nameto thetarget_genestable via Alembic migration and updated theTargetGeneORM model to include this field. [1] [2]SavedTargetGeneview model to expose the newmapped_hgnc_nameattribute.Mapping and Data Handling Refactor:
map_variants_for_score_setto extract HGNC gene information from the newgene_infostructure in mapping results, storing the symbol inmapped_hgnc_nameand the selection method inpost_mapped_metadata.VRSMaptype definitions to introduceGeneInfoandTargetAnnotationstructures, and to use these in mapping results for clarity and future extensibility.Testing and Constants Updates:
gene_infoandlayersstructure, ensuring test data matches the refactored mapping result format. [1] [2] [3] [4]