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Enable use of RefGetStore for sequence and alias data - #626

Draft

theferrit32 wants to merge 40 commits into

ga4gh:v3from

theferrit32:kf/dataproxy-backend-refactor

Draft

Enable use of RefGetStore for sequence and alias data#626
theferrit32 wants to merge 40 commits into
ga4gh:v3from
theferrit32:kf/dataproxy-backend-refactor

Commits on Feb 12, 2026
- refactor: split DataProxy into provider-agnostic interface and SeqRepo backend
  theferrit32
  committed
  c1719c8
Commits on Feb 13, 2026
- feat: add CompositeDataProxy and RefgetSequenceDataProxy (gtars backend)
  
  theferrit32
  and
  claude
  committed
  c487dc1
Commits on Feb 25, 2026
- Add lru_cache to sequence lengths and aliases
  theferrit32
  committed
  6076fce
Commits on Apr 13, 2026
- feat(misc/refgetstore): loader + verify scripts for custom refgetstore archive
  
  theferrit32
  and
  claude
  committed
  6dd55bb
Commits on Apr 14, 2026
- feat(dataproxy): refget-backed alias proxy + seqrepo equivalence harness
  
  theferrit32
  and
  claude
  committed
  93e5409
- Merge branch 'main' into kf/dataproxy-backend-refactor
  theferrit32
  committed
  503e698
Commits on Apr 15, 2026
Commits on Apr 16, 2026
- feat(misc/refgetstore): add Ensembl r113 cdna/ncrna/pep + seqrepo comparison
  
  theferrit32
  and
  claude
  committed
  e49f9fa
- investigate Ensembl digest mismatches: root cause is * normalization
  
  theferrit32
  and
  claude
  committed
  fb9ffee
Commits on Aug 31, 2026
- feat(dataproxy_refget): support remote refget stores over HTTP(S)
  theferrit32
  committed
  ba44477
Commits on Sep 1, 2026
- perf(dataproxy): faster accession resolution and configurable cache sizes
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  committed
  1e9430f
Commits on Sep 23, 2026
Commits on Sep 24, 2026
- cleanup: trim location bounds validation
  theferrit32
  committed
  6c81988
- cleanup: inline single-use bounds helpers
  theferrit32
  committed
  3fb4abc
- cleanup: validate bounds against the refget accession
  theferrit32
  committed
  0c6ea81
- cleanup: address review of location bounds validation
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  committed
  4b3684f
Commits on Oct 1, 2026
- cleanup: name both input and refget ids in bounds errors
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  committed
  e3790a4
- cleanup: use dict test cases to match existing parametrize style
  theferrit32
  committed
  31ba35e
Commits on Oct 6, 2026
- revert: drop _from_vrs fix from location bounds branch
  theferrit32
  committed
  dd353c8
Commits on Oct 9, 2026
Commits on Oct 20, 2026
Commits on Oct 26, 2026
- Merge branch 'main' into kf/location-bounds
  theferrit32
  authored
  96666fe
- cleanup: trim start-after-end docstrings, comments and error message
  theferrit32
  committed
  d6f5059
Commits on Oct 27, 2026
- Enforce sequence coordinate bounds (#663)
  theferrit32
  authored
  a9cc68c
- Merge branch 'main' into kf/dataproxy-backend-refactor
  theferrit32
  committed
  95523cc
- fix: resolve accessions on remote refget stores
  theferrit32
  committed
  b82b79f
Commits on Oct 28, 2026
- merge: migrate `main` into `v3`
  theferrit32
  committed
  1859491
- Merge branch 'kf/merge-main-into-v3' into kf/dataproxy-backend-refactor
  theferrit32
  committed
  8ce6d70

Commits

Commits on Feb 12, 2026

Commits on Feb 13, 2026

Commits on Feb 25, 2026

Commits on Apr 13, 2026

Commits on Apr 14, 2026

Commits on Apr 15, 2026

Commits on Apr 16, 2026

Commits on Aug 31, 2026

Commits on Sep 1, 2026

Commits on Sep 23, 2026

Commits on Sep 24, 2026

Commits on Oct 1, 2026

Commits on Oct 6, 2026

Commits on Oct 9, 2026

Commits on Oct 20, 2026

Commits on Oct 26, 2026

Commits on Oct 27, 2026

Commits on Oct 28, 2026