v2025.5.0

What's Changed

• feat: add AlphaFold version proxy endpoint by @davereinhart in #547
• feat: Add Gzip middleware to fastapi, and score set search parameter to optionally skip experiment score set URNs and count by @davereinhart in #548
• feat: Score set search result optimization by @jstone-dev in #525
• feat: Enhance docs for mat view refresh methods and commit their transactions by @bencap in #557
• chore: Remove platform specification from python-base image in Dockerfile by @bencap in #559
• feat: Adds column metadata support and a multipart PATCH endpoint to update score sets and variants by @davereinhart in #546
• fixed: variant count endpoint was returning a count including non-distinct variants by @bencap in #573
• chore: Bump Vulnerable Deps by @bencap in #570
• feat: Modify the function of get_score_set_variants_csv to allow downloading multiple data types together. by @EstelleDa in #541
• feat: Refactor Score Ranges to Score Calibrations and Strengthen Their Data Model by @bencap in #545
• feat: output VRS digest with post mapped HGVS strings by @bencap in #577
• feat: Streaming Endpoints for VA-Spec Annotations by @bencap in #574
• chore: Clean and Standardize OpenAPI Documentation by @bencap in #555
• chore: Add comprehensive instruction files for GitHub Copilot and project guidelines by @bencap in #558
• feat: refactor pillar project calibration loader for use against simplified json by @bencap in #578
• feat: Populate and surface post-mapped HGVS expressions and VEP functional consequence, and surface gnomAD AF by @sallybg in #553

New Contributors

• 🚀 @davereinhart made their first contribution in #547

Full Changelog: v205.4.1...v2025.5.0

v2025.4.1

What's Changed

• Additional Brnich Style Calibrations by @bencap in #519
• Allow ranges to contain a standalone baseline score by @bencap in #527

Full Changelog: v2025.4.0...v205.4.1

v2025.4.0

What's Changed

• Disabled the Gene Ontology code requirement for the "phenotypic assay mechanism" experiment attribute.

Full Changelog: v2025.3.1...v2025.4.0

v2025.3.1

What's Changed

• Rename tax_id to code in Taxonomy by @EstelleDa in #500
• ClinVar control query optimization and control response size reduction by @jstone-dev in #506
• Calibration script and ClinVar control refresh script improvements by @jstone-dev in #507
• Controlled keywords - gene ontology by @EstelleDa in #407
• Release 2025.3.1 by @jstone-dev in #508

Full Changelog: v2025.3.0...v2025.3.1

v2025.3.0

What's Changed

• Add associated score set urn in target gene API functions. by @EstelleDa in #462
• Bugfix/estelle/474/target gene identifier search key error by @EstelleDa in #475
• Add local cdot-rest image by @bencap in #453
• Remove user id from mat view refresh job enqueue by @bencap in #457
• Remove \r and \n from uploading sequence files by @EstelleDa in #479
• Score Calibration/Score Range Harmonization and Other Improvements by @bencap in #480
• Endpoints for Resolving Sequence Hashes by @bencap in #478
• Enhance ClinVar variant summary fetching by @bencap in #482
• Enhance df validation by removing quotes from quoted strings and stripping whitespace by @bencap in #477
• Support for gnomAD Joint Frequency Data by @bencap in #460
• Do release 2025.2.2 as release 2025.3.0 by @bencap in #491
• UniProt ID Mapping for Targets with Post Mapped Metadata by @bencap in #485
• Explicit Score Range Boundary Handling by @bencap in #487
• Annotated Variant Export by @bencap in #380
• Submit to ClinGen Allele Registry Before Linked Data Hub by @bencap in #472
• AA-NT mapping by @sallybg in #498
• fixed: Publication wish NULL publication journal causing 500 errors on /journals route by @bencap in #499

Full Changelog: v2025.2.1...v2025.3.0

v2025.2.1

What's Changed

• Enhance Clingen Allele ID lookup with logging and error handling by @bencap in #464
• API endpoint for score set variant scores with mapped coordinates by @jstone-dev in #465

Full Changelog: v2025.2.0...v2025.2.1

v2025.2.0

What's Changed

• Variant Search by @sallybg and @jstone-dev in #388
• Modify the mapped variants' filter condition so that it works correctly. by @EstelleDa in #433
• Support for Base Editor Data by @bencap in #395
• Show the variants that have problem in error message. by @EstelleDa in #420
• ClinGen & ClinVar script enhancements by @jstone-dev in #435
• Modified add_contributor function and add two more related tests. by @EstelleDa in #442
• Add OddsPath Property to ScoreRange Data Model by @bencap in #439
• Bugfix/estelle/61/num score sets and experiments by @EstelleDa in #447
• Support mapper update for multi-target score sets by @sallybg in #436
• Release 2025.2.0 by @bencap in #455

New Contributors

• @sallybg made their first contribution in #436 (🚀)

Full Changelog: v2025.1.2...v2025.2.0

v2025.1.2

What's Changed

• Support for Score Ranges with an Unspecified Classification by @bencap in #414
• Simplify Published Variant MV Indexes by @bencap in #410
• Release 2025.1.2 by @bencap in #415

Full Changelog: v2025.1.1...v2025.1.2

v2025.1.1

What's Changed

• Modify tentivirus to lentivirus in alembic file. by @EstelleDa in #393
• Debug UnicodeDecodeError problem and add a related test. by @EstelleDa in #396
• Additional Statistics Endpoints and Statistics Router Refactor by @bencap in #397
• Fixes #358: Literal 'null' inserted for NULL score ranges. by @bencap in #399
• Materialized View Utilities for SQLAlchemy Models by @bencap in #402
• Additional Statistics Endpoints by @bencap in #404

Full Changelog: v2025.1.0...v2025.1.1

v2025.1.0

What's Changed

• Data collections by @jstone-dev and @sallybg in #374
• Typo in mock_worker_variant_insertion leads to a wrong counts file path. by @EstelleDa in #384
• Remove NA columns from dowloading scores and counts files. by @EstelleDa in #385
• Add a PubMed url test. by @EstelleDa in #387
• Tmp permissions bugfix by @EstelleDa in #366

Full Changelog: v2025.0.0...v2025.1.0