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Recent Releases of gene-normalizer

gene-normalizer - 0.10.3

What's Changed

  • fix: guard against importerrors for etl dependencies by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/419

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.10.2...0.10.3

- Python
Published by korikuzma 10 months ago

gene-normalizer - 0.10.2

What's Changed

  • chore: remove references to pipenv by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/416
  • chore: add pipfile + uv lock to gitignore by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/417
  • build: bump wags-tails version by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/415

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.10.1...0.10.2

- Python
Published by korikuzma 11 months ago

gene-normalizer - 0.10.1

What's Changed

  • docs: update documentation for CLI changes in #405 by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/411
  • feat: add docker install instructions by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/412
  • build: tighten ga4gh.vrs version to >=2.1.3,<3.0 by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/414
  • style: update ruff and precommit by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/413

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.10.0...0.10.1

- Python
Published by jsstevenson 11 months ago

gene-normalizer - 0.10.0

What's Changed

  • feat!: overhaul CLI by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/405
  • build: bump wags-tails to latest version (v0.3.2) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/408

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.9.0...0.10.0

- Python
Published by korikuzma about 1 year ago

gene-normalizer - 0.9.0

What's Changed

  • style: update ruff by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/392
  • cicd: update precommit + hooks by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/400
  • feat!: Update to include primaryCoding attribute by @jarbesfeld in https://github.com/cancervariants/gene-normalization/pull/406

New Contributors

  • @jarbesfeld made their first contribution in https://github.com/cancervariants/gene-normalization/pull/406

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.8.0...0.9.0

- Python
Published by korikuzma about 1 year ago

gene-normalizer - 0.8.0

What's Changed

  • revert(ci): revert back to using ubuntu-latest in gh action test job by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/398
  • build!: update ga4gh.vrs by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/399

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.7.0...0.8.0

- Python
Published by korikuzma over 1 year ago

gene-normalizer - 0.7.0

What's Changed

  • fix!: use correct representation of Coding object in mappings by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/395
  • fix!: xrefs should have exactMatch for ConceptMapping.relation by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/397

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.6.0...0.7.0

- Python
Published by korikuzma over 1 year ago

gene-normalizer - 0.6.0

What's Changed

  • chore!: rename optional dependency by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/388
  • fix!: ConceptMapping.coding.code should be a CURIE by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/390

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.5.0...0.6.0

- Python
Published by korikuzma over 1 year ago

gene-normalizer - 0.5.0

What's Changed

  • docs: update VRS 2 branch link by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/369
  • build: pin setuptools for 3.12 by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/373
  • build!: require python >=3.11 by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/375
  • chore: add acceptance criteria to issue templates by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/372
  • style: update ruff configs by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/371
  • chore: update gitignore by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/370
  • cicd: update precommit configs by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/374
  • build: use latest wags-tails release by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/376
  • feat!: update models to vrs 2.0.0 community review ballot by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/378
  • docs: clean up autodoc pages and refs by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/382
  • feat!: remove normalized_id and leverage MappableConcept.primaryCode by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/381
  • test: update test data by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/385
  • feat!: use preferred formats for MappableConcept.mappings by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/386
  • refactor: remove unnecessary .lower() call when creating concept mapping by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/387
  • fix!: system should use source homepage by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/389

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.4.1...0.5.0

- Python
Published by korikuzma over 1 year ago

gene-normalizer - 0.4.1

What's Changed

  • cicd: update workflows/templates from template repo by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/364
  • feat: update pre-commit version + add more hooks by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/363
  • cicd: target stale workflow rev by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/365
  • refactor: resolve Pylance warnings by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/366
  • build: pin ga4gh.vrs~=2.0.0a10 by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/367

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.4.0...0.4.1

- Python
Published by korikuzma almost 2 years ago

gene-normalizer - 0.4.0

What's Changed

  • build: require >= Python 3.10 by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/353
  • build!: update ga4gh.vrs version + reduce vrs id checks in tests by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/354
  • style: update ruff to 0.5.0 by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/355
  • feat!: use setuptools-scm, capture version at package root by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/359
  • chore: remove unused configs in pyproject.toml by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/358
  • style: ruff format by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/357
  • refactor: remove unused code by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/360
  • refactor: use DataLicenseAttributes Pydantic model by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/361
  • cicd: update actions + docs workflow from template by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/356
  • fix(docs): rearrange structure + update ci workflow deps by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/362

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.3.2...0.4.0

- Python
Published by korikuzma almost 2 years ago

gene-normalizer - 0.3.2

What's Changed

  • fix: more logging config fixes by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/351

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.3.1...0.3.2

- Python
Published by jsstevenson almost 2 years ago

gene-normalizer - 0.3.1

What's Changed

  • docs: fix link in openapi description by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/345
  • docs: fix stable version badge by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/344
  • fix: correctly configure logging by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/349

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.3.0-dev2...0.3.1

- Python
Published by jsstevenson almost 2 years ago

gene-normalizer - 0.3.0-dev2

What's Changed

  • cicd: use ruff for autoformatting by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/292
  • test: suppress noisy boto logs by default by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/300
  • feat!: use wags-tails for data acquisition by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/303
  • style: update ruff version by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/316
  • docs: add description metadata by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/315
  • docs: incorporate latest template elements by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/322
  • style: pin ruff version from template by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/323
  • cicd: reorganize QC checks by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/324
  • cicd: require priority label on PR by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/325
  • docs: fix api reference link in readme by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/327
  • fix: handle password param in postgres connection by @nickzoic in https://github.com/cancervariants/gene-normalization/pull/333

New Contributors

  • @nickzoic made their first contribution in https://github.com/cancervariants/gene-normalization/pull/333

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.3.0-dev1...0.3.0-dev2

- Python
Published by jsstevenson about 2 years ago

gene-normalizer - 0.3.0-dev1

What's Changed

  • cicd: add Ruff and Black by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/253
  • feat!: merge concepts and source dynamodb tables by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/258
  • feat!: remove search result formatting options by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/261
  • feat!: use vrs 2.0-alpha core gene model in /normalize by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/252
  • feat!: update data acquisition methods by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/262
  • feat: update HGNC license by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/263
  • fix: correct gene info file glob typo by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/265
  • fix: catch ETL module import errors by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/268
  • fix: set responsemodelexclude_none=True in /normalize by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/273
  • cicd: add gh action for closing issue on staging branch by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/276
  • docs: incorporate Alex feedback by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/269
  • test: add basic route tests by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/277
  • build: modernize build configs by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/271
  • refactor: remove unused error handling by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/280
  • cicd: update release.yaml (publish python distribution to pypi) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/284
  • docs: update VRS compliance by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/287
  • build: define build system by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/288
  • build: properly pin pydantic v2 major version by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/290

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.3.0-dev0...0.3.0-dev1

- Python
Published by korikuzma over 2 years ago

gene-normalizer - 0.1.40-dev1

What's Changed

  • fix: catch ETL module import errors by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/249
  • docs: fix documentation link by @Rajdeep1311 in https://github.com/cancervariants/gene-normalization/pull/257
  • fix: correct gene info file glob typo by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/266
  • feat: update HGNC license by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/267
  • cicd: add gh action for closing issue on staging branch by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/275
  • test: add basic route tests by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/278
  • build: modernize build configs by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/279
  • build: update ga4gh.vrsatile.pydantic version by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/281
  • cicd: update release.yaml (publish python distribution to pypi) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/283

New Contributors

  • @Rajdeep1311 made their first contribution in https://github.com/cancervariants/gene-normalization/pull/257

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.1.40-dev0...0.1.40-dev1

- Python
Published by korikuzma over 2 years ago

gene-normalizer - v0.1.40-dev0

What's Changed

  • cicd: add Ruff and Black by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/232
  • refactor: use isinstance instead of type() check by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/243
  • feat!: store source metadata in concepts table by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/233
  • feat!: remove search result formatting options by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/244
  • feat!: update data acquisition methods by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/236
  • docs: incorporate Alex feedback by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/242

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.1.39...v0.1.40-dev0

- Python
Published by jsstevenson over 2 years ago

gene-normalizer - 0.3.0-dev0

What's Changed

  • feat: add getallrecords DB method by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/231
  • build!: use vrs-python for VRS 2.0-alpha models by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/239
  • refactor!: Remove ChromosomeLocation + SequenceLocation classes by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/245

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.2.10...0.3.0-dev0

- Python
Published by korikuzma over 2 years ago

gene-normalizer - v0.1.39

What's Changed

  • feat: add getallrecords DB method by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/230

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.1.38...v0.1.39

- Python
Published by jsstevenson almost 3 years ago

gene-normalizer - v0.2.10

What's Changed

  • docs: make separate sphinx docs by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/190
  • feat: add DB status check entrypoint by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/196
  • fix: remove duplicate xrefs from merged records by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/197
  • fix: prevent redundant/incorrect AWS confirmation checks by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/198
  • docs: touch up query API documentation by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/199
  • perf: improve PG normalized concept deletion by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/201
  • build: separate dependency groups by use case by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/203
  • fix!: use more precise name for CLI source option by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/205
  • docs: provide readthedocs integration by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/208
  • docs: expand base template and improve descriptions by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/211
  • docs: add more usage details by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/213
  • feat: optionally define dynamo table names via environment variable by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/214
  • test: update test data by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/223
  • ci: use latest pip in sphinx test (metaschema) by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/221
  • doc: preserve arg defaults in docs by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/225
  • chore: add PyPI metadata (metaschema) by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/229
  • feat: provide strand in normalized record (metaschema) by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/228

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.2.9...v0.2.10

- Python
Published by jsstevenson almost 3 years ago

gene-normalizer - v0.1.38

What's Changed

  • ci: use latest pip in sphinx test by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/219
  • fix: preserve arg defaults in docs by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/218
  • test: update test data by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/222
  • feat: provide strand in normalized record by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/226
  • chore: add PyPI metadata by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/224

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.1.37...v0.1.38

- Python
Published by jsstevenson almost 3 years ago

gene-normalizer - v0.1.37

What's Changed

  • fix!: use more precise name for CLI source option by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/204
  • docs: provide readthedocs integration by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/207
  • docs: expand base template and improve descriptions by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/209
  • docs: add more usage details by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/210
  • feat: optionally define dynamo table names via environment variable by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/212

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.1.36...v0.1.37

- Python
Published by jsstevenson almost 3 years ago

gene-normalizer - 0.1.36

What's Changed

  • feat: add DB status check entrypoint by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/191
  • fix: prevent redundant/incorrect AWS confirmation checks by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/193
  • fix: remove duplicate xrefs from merged records by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/194
  • docs: touch up query API documentation by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/192
  • perf: improve PG normalized concept deletion by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/195
  • build: separate dependency groups by use case by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/202

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.1.35...0.1.36

- Python
Published by korikuzma about 3 years ago

gene-normalizer - 0.1.35

What's Changed

VRS 1.3 introduced in this release

  • build: update ga4gh packages to use VRS 1.3 models by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/189

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.1.34...0.1.35

- Python
Published by korikuzma about 3 years ago

gene-normalizer - 0.1.34

What's Changed

  • feat: support PostgreSQL as optional storage backend by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/169
  • docs: make separate sphinx docs by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/182
  • refactor: rename SEQREPODATAPATH --> SEQREPOROOTDIR by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/186

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.1.33...0.1.34

- Python
Published by korikuzma about 3 years ago

gene-normalizer - 0.2.9

What's Changed

  • test: incorporate latest source updates to test cases by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/173
  • refactor: rename SEQREPODATAPATH --> SEQREPOROOTDIR (staging) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/187
  • feat: support PostgreSQL as optional storage backend by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/183

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.2.8...0.2.9

- Python
Published by korikuzma about 3 years ago

gene-normalizer - 0.1.33

What's Changed

  • test: incorporate latest source updates to test cases by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/171
  • build: update ga4gh.vrs version to ~= 0.7.8 by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/180

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/0.1.32...0.1.33

- Python
Published by korikuzma about 3 years ago

gene-normalizer - v0.2.8

What's Changed

  • build: update dev dependencies (staging) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/168

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.2.7...v0.2.8

- Python
Published by korikuzma over 3 years ago

gene-normalizer - 0.1.32

What's Changed

  • build: update dev dependencies by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/167

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.1.31...0.1.32

- Python
Published by korikuzma over 3 years ago

gene-normalizer - v0.2.7

What's Changed

  • remove ebextensions (staging) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/155
  • feat: ensure test and aws env vars are not set at same time (staging) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/159
  • build: update ga4gh versions (staging) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/163

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.2.6...v0.2.7

- Python
Published by korikuzma over 3 years ago

gene-normalizer - v0.1.31

What's Changed

  • remove ebextensions (main) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/154
  • feat: ensure test and aws env vars are not set at same time (main) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/160
  • build: do not pin exact version for ga4gh.vrsatile.pydantic by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/162
  • build: unpin exact version of ga4gh.vrs (main) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/164

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.1.30...v0.1.31

- Python
Published by korikuzma over 3 years ago

gene-normalizer - v0.1.30

What's Changed

  • fix: return all locations in response (#126, #152) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/153

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.1.29...v0.1.30

- Python
Published by korikuzma over 3 years ago

gene-normalizer - v0.1.29

What's Changed

  • fix: move SOURCE_CLASS to cli (main branch) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/149
  • refactor!: remove elastic beanstalk work on main branch by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/151

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.1.28...v0.1.29

- Python
Published by korikuzma over 3 years ago

gene-normalizer - v0.2.6

What's Changed

  • refactor!: remove elastic beanstalk work by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/150

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.2.5...v0.2.6

- Python
Published by korikuzma over 3 years ago

gene-normalizer - v0.2.5

What's Changed

  • ci: resolve action version warnings by @jsstevenson in https://github.com/cancervariants/gene-normalization/pull/139
  • build: separate out etl (dev) dependencies on staging by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/143
  • refactor: how vrs chromosome/sequence locations are stored in dynamodb (staging) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/145
  • fix: move SOURCE_CLASS to cli (staging branch) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/148

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.2.3...v0.2.5

- Python
Published by korikuzma over 3 years ago

gene-normalizer - v0.1.28

What's Changed

  • build: separate out etl (dev) dependencies on main by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/142
  • refactor: how vrs chromosome/sequence locations are stored in dynamodb by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/144

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.1.27...v0.1.28

- Python
Published by korikuzma over 3 years ago

gene-normalizer - v0.2.3

What's Changed

  • feat: return all source locations in normalize response (#126) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/138

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.2.2...v0.2.3

- Python
Published by korikuzma over 3 years ago

gene-normalizer - v0.2.2

What's Changed

  • refactor: update ga4gh vrsatile pydantic (gene_id --> gene) by @korikuzma in https://github.com/cancervariants/gene-normalization/pull/137

Full Changelog: https://github.com/cancervariants/gene-normalization/compare/v0.2.1...v0.2.2

- Python
Published by korikuzma over 3 years ago

gene-normalizer -

  • refactor: allow for nonprod tables to be used when EBENVTYPE is set

- Python
Published by korikuzma almost 4 years ago

gene-normalizer -

  • fix: catch KeyErrors in seqrepo
  • refactor: update models + fix seqrepo key error
  • refactor: add condition for using nonprod db

- Python
Published by korikuzma almost 4 years ago

gene-normalizer -

  • Add /normalize_unmerged
  • Use correct SourceName value type in unmerged normalized records
  • Create Zenodo record

- Python
Published by korikuzma about 4 years ago

gene-normalizer -

  • Remove elastic beanstalk dependencies
  • Allow SEQREPODATAPATH to be set by environment variable
  • Extract biotype / gene type from sources
  • Use latest source data

- Python
Published by korikuzma about 4 years ago

gene-normalizer -

  • Set useenumvalues in pydantic class configs
    • response_datetime is a str in ServiceMeta

- Python
Published by korikuzma about 4 years ago

gene-normalizer -

  • Add url to openapi contact info
  • Return all results in search rather than the highest match

- Python
Published by korikuzma over 4 years ago

gene-normalizer -

  • Unpin ga4gh.vrs and ga4gh.vrsatile.pyantic versions + update

- Python
Published by korikuzma over 4 years ago

gene-normalizer -

  • Update package requirements
  • Set SEQREPODATAPATH value to /usr/local/share/seqrepo/latset

- Python
Published by korikuzma over 4 years ago

gene-normalizer -

  • PROJECTROOT --> APPROOT
  • Use gene_id rather than gene value object in gene descriptor
  • normalize method always returns NormalizeService object

- Python
Published by korikuzma over 4 years ago

gene-normalizer -

  • Use python 3.8
  • Return Pydantic service classes in search and normalize methods

- Python
Published by korikuzma over 4 years ago

gene-normalizer -

  • Update schema examples
  • Fix bug where operations opened at the same time

- Python
Published by korikuzma over 4 years ago

gene-normalizer -

  • Use ga4gh.vrsatile.pydantic classes
  • Fix one off bug in SequenceInterval

- Python
Published by korikuzma almost 5 years ago

gene-normalizer -

  • Set type in ChromosomeLocation and SequenceLocation
  • Cleaning up validators in schemas

- Python
Published by korikuzma almost 5 years ago

gene-normalizer -

  • Catch and log pydantic validation errors when loading sources
  • Only download Ensembl data file if version is not found

- Python
Published by korikuzma almost 5 years ago

gene-normalizer -

  • Add previous_symbols to extensions
  • Fix chromosome spelling / return dictionary for query instead of list

- Python
Published by korikuzma almost 5 years ago

gene-normalizer -

  • _id is optional field for Location

- Python
Published by korikuzma almost 5 years ago

gene-normalizer -

  • Adding validators to schemas

- Python
Published by korikuzma almost 5 years ago

gene-normalizer -

  • Add normalize endpoint
  • Update sources to extract most recent version

- Python
Published by korikuzma almost 5 years ago

gene-normalizer -

  • Add service meta to response
  • Search by xref
  • Add item type attribute
  • otherid -> xref, xref -> associatedwith
  • Capture previous gene identifiers from NCBI
  • Adds Dockerfile

- Python
Published by korikuzma almost 5 years ago

gene-normalizer -

  • Fix search endpoint with only partial sources loaded
  • Remove unused requirements to fix EB instance

- Python
Published by korikuzma about 5 years ago

gene-normalizer -

  • Fixing environment variables for production EB

- Python
Published by korikuzma about 5 years ago

gene-normalizer -

  • Add CLI Class back
  • Use one environment variable for production EB instance

- Python
Published by korikuzma about 5 years ago

gene-normalizer -

- Python
Published by korikuzma over 5 years ago