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…nheritance - Added mapping of HGNC gene symbols into VariationDescriptor.gene_context - Added zygosity → GA4GH GENO allelicState mapping - Added inheritance parsing (stored in Genotype dataclass, reserved for future use) - Updated DefaultMapper._add_genotype_interpretations to use new Genotype.to_variation_descriptor(), ensuring expressions + VRS JSON description + allelicState + geneContext are emitted in phenopackets - Preserved previous behavior for phenotype/disease/measurement/biosample
…or construction
- Replaced `except Exception:` with explicit attribute checks (`hasattr`, `getattr`)
to comply with Ruff BLE001 and avoid masking unrelated runtime errors.
- In `to_variation_descriptor`:
- Guarded `molecule_context` assignment with `hasattr` instead of try/except.
- Guarded stable ID assignment with `if g_expr` check.
- In `_add_hgvs_expression`:
- Use `getattr(type(expr), "HGVS", None)` instead of try/except.
- In `_attempt_pyphetools_normalize`:
- Removed redundant try/except; explicitly return `None` until a stable
pyphetools API exists.
… for VariationDescriptor construction - Replaced `except Exception:` blocks with explicit `hasattr` / `getattr` checks to comply with Ruff BLE001 and avoid masking unrelated errors. - In `Genotype.to_variation_descriptor`: - Guarded `gene_context` and `allelic_state` assignments with explicit checks. - Rewrote allele JSON description building without try/except. - Added molecule_context assignment only when supported. - Generated stable IDs using an explicit guard instead of catching failures. - In `_add_hgvs_expression`, probed for `HGVS` enum explicitly instead of relying on try/except. - In `_attempt_pyphetools_normalize`, removed no-op try/except; return `None` until a stable API emerges. - In `__main__.py`, replaced CopyFrom fallback try/except with feature detection (`getattr` + callable check).
- Introduced `vv_lookup.py` module to query VariantValidator’s REST API for transcript and gene cross-references. - Provides `get_gene_xrefs_vv()` helper to return HGNC ID, Ensembl gene ID, and RefSeq transcripts for a given HGNC gene symbol. - Handles API rate limits (1 request/sec) and provides robust error handling via custom `VVLookupError`. - Designed to integrate with Genotype → VariationDescriptor pipeline as an optional enrichment step when P6_ENRICH_GENE_XREFS is enabled.
… retries
- New module `vv_lookup.py` to enrich gene_context with HGNC/Ensembl IDs and
canonical transcript accessions using VariantValidator.
- Prefer v2 `gene2transcripts_v2` endpoint; fallback to v1 when needed.
- Normalize variable VV payloads into a compact dict:
{hgnc_id, ensembl_gene_id, refseq_transcripts, ensembl_transcripts}.
- Add small retry/backoff and a custom VVLookupError for clean failure handling.
- Thorough docstrings and comments explaining the high-level P6 flow.
… enrichment - Clear sectioned comments/docstrings describing P6’s high-level flow. - Narrow overly broad exception handlers to satisfy linting and improve safety. - Optional enrichment via `vv_lookup.get_gene_xrefs_vv` behind P6_ENRICH_GENE_XREFS. - Keep P6_SKIP_VV escape hatch; maintain robust local fallback descriptor path. - Ensure normalized g. expression and allelic_state are always present.
… satisfy C901 - Extract _should_skip_vv, _try_build_descriptor_via_vv, _enrich_descriptor_common, and _maybe_enrich_gene_xrefs helpers. - Try to keep exact behavior and error handling; just reduce branching in the main method.
… docstrings. Ruff check and format as well
Add the Variant field using VariationDescriptor, implement the VariantValidator lookup from PyPheTools, and lint/refactor some code
Latest transformation of Tony's Excel genotype/phenotype records into Phenopackets
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Pull latest changes into main