Skip to content

Conversation

@bencap
Copy link
Collaborator

@bencap bencap commented Dec 13, 2025

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_name field, and refactors how gene annotation metadata is structured and accessed to support VariantEffect/dcd_mapping2#67.

Database and Model Updates:

  • Added a new nullable column mapped_hgnc_name to the target_genes table via Alembic migration and updated the TargetGene ORM model to include this field. [1] [2]
  • Updated the SavedTargetGene view model to expose the new mapped_hgnc_name attribute.

Mapping and Data Handling Refactor:

  • Refactored the mapping logic in map_variants_for_score_set to extract HGNC gene information from the new gene_info structure in mapping results, storing the symbol in mapped_hgnc_name and the selection method in post_mapped_metadata.
  • Updated the VRSMap type definitions to introduce GeneInfo and TargetAnnotation structures, and to use these in mapping results for clarity and future extensibility.

Testing and Constants Updates:

  • Refactored mapping test scaffolds and constants to use the new gene_info and layers structure, ensuring test data matches the refactored mapping result format. [1] [2] [3] [4]
  • Minor test setup improvements, including import cleanup and enabling test environment mode for the email validator. [1] [2] [3]

@bencap bencap force-pushed the feature/bencap/derived-gene-name-from-mapped-output branch from 4154ced to 5d8dcc2 Compare December 15, 2025 18:38
@bencap bencap requested review from jstone-dev and sallybg December 15, 2025 21:54
@bencap bencap marked this pull request as ready for review December 15, 2025 21:54
Base automatically changed from feature/bencap/593/ensure-dcd-mapping-platform-is-amd64 to release-2025.5.1 December 18, 2025 00:49
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Determine Mapped Target HGNC Name During Mapping

2 participants