Mint pre-mapped VRS for accession-target variants

[bencap]

Summary

Mint a pre-mapped VRS allele for each accession-target variant inside validate_genomic_variant, reusing the variant object and CDOT provider it already has.

Problem

Transcript accessions (NM_/ENST) have 5' UTRs, so c.197 is not position 197 of the fetched transcript sequence. Positions have to go through a coordinate-aware mapper before SPDI conversion. Non-accession targets (#868) don't have this problem.

Proposed behavior

• Reuse variant_obj after hgvs.validator.Validator(hdp=cdot_rest()) validates it. Don't parse or validate it again.
• Project it to a sequence-relative position with hgvs.variantmapper.VariantMapper or AssemblyMapper, built on hdp=cdot_rest(). Don't use ga4gh.vrs's AlleleTranslator, which is hardwired to the public UTA server.
• Fetch the sequence with cdot_rest().get_seq(TargetAccession.accession), memoized per (target, accession).
• Pass the position and sequence through the Mint pre-mapped VRS for non-accession-target variants #868 pipeline unchanged: SPDI → _from_spdi → normalize_and_identify over a LiteralSequenceDataProxy.
• Set allele.expressions to the original HGVS string.
• Call site: in validate_genomic_variant, after validator.validate(...) succeeds. Keep minting failures (CDOT unavailable, accession not found, projection failure) out of the validity return. They must never raise ValidationError.

Acceptance criteria

• First, in a dev environment with cdot-rest, confirm that a transcript with a non-trivial 5' UTR projects to a sequence position that differs from its c. number.
• For such an accession, the digest uses the offset-adjusted position.
• CDOT fetches each (target, accession) at most once per validation pass.
• CDOT failures (network, timeout, accession not found) and projection failures (such as an intronic variant with no resolvable sequence) raise different typed exceptions. That lets Attach minted pre-mapped VRS to created Variant rows and record the outcome #870 record them under different AnnotationFailureCategory values, and the existing EXTERNAL_API_ERROR and EXTERNAL_REFERENCE_NOT_FOUND are enough.
• Corpus cross-check: accession variants that have a MappedVariant.pre_mapped and a clean alignment (no near_gap/at_mismatched_locus) produce matching digests. A mismatch on a flagged variant is expected.

Implementation notes

• cdot_rest() (data_providers/services.py) is the internal service that validate_hgvs_genomic_column already calls.
• Variant.hgvs_nt/hgvs_pro store bare edits without the accession, even for accession targets. dcd-mapping's _map_accession adds TargetAccession.accession itself.