Migrate the VEP functional-consequence job (Step 2 of the annotation
infrastructure migration) off MappedVariant onto the deduplicated allele
model.

- New ValidTime vep_allele_consequences table: a single allele-keyed row
  collapses record + link (the consequence is a scalar with no shared
  external entity, unlike gnomAD/ClinVar). One live consequence per allele
  via a partial unique index.
- Job runs over the score set's full allele set (authoritative + RT-derived)
  via get_alleles_for_score_set + the shared grouping primitive; VAS still
  fans only to authoritative variants (the bandaid seam).
- Version-key the refresh on the Ensembl release (/info/software): skip
  alleles already current, abort if the release can't be fetched. Supersede
  is value-keyed, not version-keyed — an unchanged consequence at a new
  release bumps source_version/access_date in place to avoid churning
  history. force bypasses the skip (e.g. after editing VEP_CONSEQUENCES).
- A no-result is treated as a non-answer, never a negative: held
  consequences are not retired on an empty/failed VEP fetch.
- Annotation links stay one-directional to Allele (no reverse back-ref).

Adds lib + job tests covering linkage, RT-derived scope, version skip,
in-place bump, supersede-on-change, no-result handling, and release-fetch
failure.

Step 3 of the #742 external-annotation migration. ClinVar linkage moves
off MappedVariant onto the deduplicated allele model.

- Rename clinical_controls -> clinvar_controls (ORM model + table +
  unique constraint). Internal only: the ClinicalControl* view models,
  the /clinical-controls serving endpoints, and the frozen
  mapped_variants_clinical_controls association are unchanged, since the
  view-model name is both the OpenAPI schema name and the record_type
  discriminator consumed by the UI.
- New clinvar_allele_links ValidTime table + ClinvarAlleleLink model.
  Multi-live: partial unique index (allele_id, clinvar_control_id) WHERE
  valid_to IS NULL, so an allele accumulates one live link per release.
- Refactor refresh_clinvar_controls onto get_alleles_for_score_set +
  group_alleles_for_annotation (payload = CAID, full allele scope). Links
  are get-or-create; a same-version re-resolution to a different control
  supersedes newest-wins (gap-free retire+insert) rather than leaving two
  live links. VAS writes funnel through the _annotate_clinvar choke point,
  fanned only to authoritative_variant_ids and version-scoped.
- Additively capture ClinVar's VariationID: nullable clinvar_variation_id
  column populated forward from the variant_summary TSV (parse degrades to
  None on archival schemas lacking the column). Unserved; the dedicated
  clinvar_variants remodel is deferred to the read-cutover.

Tests rewritten for the allele model, covering the multi-live link writes,
the version-scoped supersede guard, and the authoritative-only VAS fan-out.

Steps 4 & 5 of the #742 migration. Both jobs are redundant under the allele model:
Allele.hgvs_g/c/p are populated by the mapping job, and the reverse-translation
equivalence space (genomic/coding/protein alleles linked per MappingRecord) replaces
the ClinGen PA<->CA translation table.

- Remove populate_hgvs_for_score_set and populate_variant_translations_for_score_set
  from the pipeline DAG (both were leaf nodes — no dependency edges to repair), the
  worker registry (BACKGROUND_FUNCTIONS + STANDALONE_JOB_DEFINITIONS), and the
  external_services package exports.
- Delete the two job modules and the now-orphaned ClinGen HGVS helpers
  (extract_hgvs_from_ca_allele_data / extract_hgvs_from_pa_allele_data), used only by
  the HGVS job.
- Keep lib/variant_translations.py and the variant_translations table/model, marked
  FROZEN (serving-only) — they back old-model serving and are dropped at read-cutover.
- Delete the obsolete job tests and their conftest fixtures.

get_allele_translations(db, allele_id, *, as_of=None) returns an allele's full
cross-layer equivalence set (genomic/coding/protein) by traversing the
MappingRecordAllele link graph: allele -> its live links -> mapping record(s) ->
all co-linked alleles.

The relation is co-membership in a MappingRecord's allele set, not a shared
identifier — ClinGen's CAID spans only the nucleotide layers (the protein allele
carries a distinct PA), so the link graph is the only thing tying all layers
together. This replaces what the retired variant_translations PA<->CA table provided.

Forward-compatible with temporal reads: the same half-open valid-time predicate is
applied at both the anchor and fan-out hops, so passing as_of reconstructs the
equivalence set as of any instant. Defaults to the currently-live set.

…bulary

Introduces the AnnotationEvent log: a single append-only event table whose
subjects are Variant and Allele, selected by annotation_type via a polymorphic
CHECK. "Current" is derived (DISTINCT ON … id DESC), never stored. Adds the
shared Disposition (present/absent/not_applicable/failed) and EventReason
vocabulary, the v_current_annotation_events view, and the supporting migrations.

group_alleles_for_annotation now returns one job-specific payload per allele
instead of an AlleleAnnotationGroup. Drops the authoritative_variant_ids bandaid
seam (and is_authoritative from ScoreSetAlleleRow): annotation is an allele-level
fact, and with the AnnotationEvent log the per-variant status fan-out goes away.

AnnotationStatusManager now writes AnnotationEvent rows via record_event and
derives current status from the event log instead of maintaining per-variant
status rows. Resolves subjects through VARIANT_SUBJECT_TYPES/ALLELE_SUBJECT_TYPES
and the Disposition vocabulary.

link_gnomad_variants_to_alleles now returns a GnomadLinkVerdict per touched allele
(CREATED/UNCHANGED) as the single source of truth for per-allele status; the job
derives annotation events directly from the verdict map rather than re-querying
link state. Alleles absent from the map are read as 'gnomAD had no record'.

VEP resolution now returns a VepResolution (consequences vs errored) so a genuine
empty is distinguished from an unknown, and linking returns a VepLinkVerdict per
allele (CREATED/UNCHANGED). The job derives annotation events from these outcomes
instead of re-querying consequence state; errored HGVS are retried, not recorded
as negatives.

The ClinGen allele-registration and LDH-submission jobs now record AnnotationEvents
via record_event, using the shared EventReason vocabulary (created/preexisting/
reconfirmed/submitted, and the CAR-specific failure and reconfirmation-skipped
reasons) in place of per-variant status updates.

The ClinVar job records AnnotationEvents via record_event, distinguishing
superseded/no_record/no_caid/multi_variant_caid cases through the shared
EventReason vocabulary. Clarifies the ClinicalControl comments to mark the
row-level vs variation-level link identifiers.

The mapping job records AnnotationEvents via record_event, deriving disposition
and reason from the typed MappingOutcome (mapped / intronic /
no_protein_consequence / failed) rather than writing per-variant status rows.

The reverse-translation job records AnnotationEvents via record_event, using the
RT-specific EventReason cases (translated / no_coding_transcript /
no_assay_level_hgvs / translation_failed / translation_error /
transcript_unresolved) to distinguish informative negatives from failures.

Adds the pipeline_tracking script for querying pipeline progress from the
AnnotationEvent log, and updates the variant_annotations script to read/write
through the event model.

An allele with an existing CAID always matched the preexisting branch first, so
force_reregister never re-submitted it. Existing-CAID alleles now route to pending
whenever force_reregister is set.

Split the resolution exception handling: an HTTPError (VEP rejecting a batch, e.g.
a 400 for protein HGVS it cannot parse) now routes the batch to Variant Recoder,
which may still resolve it via genomic recoding. Only transport/network errors
(RequestException) are marked errored and held for retry — fixing the case where
recoverable inputs were wrongly recorded as unknown.

normalize_and_identify/_rle_to_lse assume an inlined SequenceReference and integer coordinates, but the VRS models type location.sequenceReference and location.start/rle.length as unions (iriReference/Range/None). Add narrowing assertions documenting that contract — restoring a green `mypy src/` (a required CI job) and turning the unreachable bad-input case into a clear AssertionError instead of a deeper AttributeError. Adds guard tests.

The newest-wins ClinvarAlleleLink supersede stamped valid_to/valid_from with a tz-naive datetime.now() into timestamptz columns, skewing the valid-time axis against every other job's func.now()-stamped rows. Use supersede_with so retire and insert share one DB timestamp. Test now asserts the boundary is timezone-aware.

Every other FK on annotation_event was indexed except score_set_id. Add it (model __table_args__ + migration) to back the ON DELETE SET NULL cascade on score-set deletion and score-set-scoped audit queries.

Revision a1b2c3d4e5f6 creates alleles/mapping_records/mapping_record_alleles — there is no allele-closure table anywhere (equivalence is a runtime query). Rename the file so it stops misleading readers; the revision id is unchanged.

Re-add cases dropped in the manager rewrite: None/empty reads, no-op flush, auto-flush-before-read for both query methods, a FAILED-disposition round-trip through the manager, and per-subject current-status isolation.

…ents

split_cis_phased_hgvs raised ValueError on bracketed input lacking an accession; it now degrades to a single-element list. join_cis_phased_hgvs emits components in coordinate order so CSV exports are deterministic regardless of VRS member ordering (the block digest is order-independent).