Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of https://github.com/cancervariants/metakb

https://github.com/cancervariants/metakb - 2.0.0-a0

What's Changed

  • refactor: use SourceName enum by @korikuzma in https://github.com/cancervariants/metakb/pull/330
  • build: raise support to require python >=3.10 by @jsstevenson in https://github.com/cancervariants/metakb/pull/333
  • cicd: add issue templates, stalebot, and branch action by @korikuzma in https://github.com/cancervariants/metakb/pull/334
  • feat!: create_json accepts filepath arg and only creates composite file by @korikuzma in https://github.com/cancervariants/metakb/pull/336
  • feat: prevent usage of aws db instances in cli by @korikuzma in https://github.com/cancervariants/metakb/pull/339
  • refactor!: clean up harvest method by @korikuzma in https://github.com/cancervariants/metakb/pull/338
  • feat!: sharpen type annotation by @jsstevenson in https://github.com/cancervariants/metakb/pull/342
  • feat!: break out CLI for more specific commands/more reasonable defaults by @jsstevenson in https://github.com/cancervariants/metakb/pull/344
  • feat: perform better logging by @jsstevenson in https://github.com/cancervariants/metakb/pull/346
  • build: fix pipenv build by @jsstevenson in https://github.com/cancervariants/metakb/pull/351
  • fix: use correct Disease model by @jsstevenson in https://github.com/cancervariants/metakb/pull/352
  • test: optionally minimize connection debug logging by @jsstevenson in https://github.com/cancervariants/metakb/pull/349
  • fix: use latest minor civicpy release to get correct schema by @jsstevenson in https://github.com/cancervariants/metakb/pull/354
  • fix: don't use deprecated graph driver destructor by @jsstevenson in https://github.com/cancervariants/metakb/pull/356
  • fix: don't use deprecated multi property semantics by @jsstevenson in https://github.com/cancervariants/metakb/pull/359
  • test: remove marks from fixtures (they don't do anything) by @jsstevenson in https://github.com/cancervariants/metakb/pull/358
  • feat: add batch search by variations by @jsstevenson in https://github.com/cancervariants/metakb/pull/361
  • refactor: use updated annotation API by @jsstevenson in https://github.com/cancervariants/metakb/pull/366
  • build: temporarily pin ga4gh.vrs==2.0.0a6 by @korikuzma in https://github.com/cancervariants/metakb/pull/367
  • fix(tests): update testbatchsearch to apply PR (#361) suggestions by @korikuzma in https://github.com/cancervariants/metakb/pull/368
  • fix: querying studies based on therapeutic by @korikuzma in https://github.com/cancervariants/metakb/pull/365
  • docs: initial docs work by @jsstevenson in https://github.com/cancervariants/metakb/pull/343
  • refactor!: remove extract_harvester from transform method by @korikuzma in https://github.com/cancervariants/metakb/pull/370
  • refactor!: rename Transform instance variables by @korikuzma in https://github.com/cancervariants/metakb/pull/371
  • feat!: initialize query handler with graph, not graph credentials by @jsstevenson in https://github.com/cancervariants/metakb/pull/376
  • feat!: refactor graph DB code, streamline unneeded query transaction usage by @jsstevenson in https://github.com/cancervariants/metakb/pull/377
  • feat!: replace instance var lists with pydantic model by @korikuzma in https://github.com/cancervariants/metakb/pull/374
  • fix: catch TokenRetrievalError in ViccNormalizers + update log levels by @korikuzma in https://github.com/cancervariants/metakb/pull/378
  • feat: update pre-commit version + add more hooks by @korikuzma in https://github.com/cancervariants/metakb/pull/382
  • feat!: use setuptools-scm, capture version at package root by @korikuzma in https://github.com/cancervariants/metakb/pull/381
  • style: update ruff version + add more rules by @korikuzma in https://github.com/cancervariants/metakb/pull/380
  • cicd: update actions versions, stalebot, + templates from template repo by @korikuzma in https://github.com/cancervariants/metakb/pull/383
  • feat: enable pagination by @jsstevenson in https://github.com/cancervariants/metakb/pull/384
  • chore: update seqrepo version to 2024-02-20 by @korikuzma in https://github.com/cancervariants/metakb/pull/385
  • feat!: rename env var for logging + cred handling by @korikuzma in https://github.com/cancervariants/metakb/pull/387
  • build!: update normalizer + ga4gh.vrs depdencies by @korikuzma in https://github.com/cancervariants/metakb/pull/386
  • build!: update ga4gh.vrs + gene/variation normalizers by @korikuzma in https://github.com/cancervariants/metakb/pull/389
  • chore!: rename transform class and dirs to transformers by @korikuzma in https://github.com/cancervariants/metakb/pull/396
  • fix: correct syntax error in gene_id_constraint by @korikuzma in https://github.com/cancervariants/metakb/pull/397
  • feat!: use cat-vrs-python + va-spec-python by @korikuzma in https://github.com/cancervariants/metakb/pull/404
  • feat!: rename study --> study statement / statement by @korikuzma in https://github.com/cancervariants/metakb/pull/405
  • feat!: add support for transforming CIViC prognostic evidence by @korikuzma in https://github.com/cancervariants/metakb/pull/407
  • feat: add option to cli to create neo4j db constraints by @korikuzma in https://github.com/cancervariants/metakb/pull/412
  • feat!: add support for moa prognostic assertions by @korikuzma in https://github.com/cancervariants/metakb/pull/411
  • fix: aggregate moa oncotree concepts during transformation by @korikuzma in https://github.com/cancervariants/metakb/pull/413
  • feat!: add support for transforming civic diagnostic evidence items by @korikuzma in https://github.com/cancervariants/metakb/pull/414
  • build!: require python >= 3.11 by @jsstevenson in https://github.com/cancervariants/metakb/pull/403
  • cicd: warn when merging to main by @jsstevenson in https://github.com/cancervariants/metakb/pull/398
  • style: resolve ruff errors by @korikuzma in https://github.com/cancervariants/metakb/pull/421
  • feat!: update models to ga4gh gks nov 2024 ballot releases by @korikuzma in https://github.com/cancervariants/metakb/pull/420
  • feat!: add support for civic assertions by @korikuzma in https://github.com/cancervariants/metakb/pull/422
  • feat!: change strength representation by @korikuzma in https://github.com/cancervariants/metakb/pull/424
  • feat!: move ViccNormalizerDataExtension to mappings by @korikuzma in https://github.com/cancervariants/metakb/pull/425
  • feat!: add support for transforming concepts that fail to normalize by @korikuzma in https://github.com/cancervariants/metakb/pull/427
  • fix!: resolve conflicts where moa therapies resolve to same concept by @korikuzma in https://github.com/cancervariants/metakb/pull/429
  • feat!: moa disease conflict resolution should follow therapy conflict resolution by @korikuzma in https://github.com/cancervariants/metakb/pull/430
  • build!: update vicc normalizers to pull in gks coding changes by @korikuzma in https://github.com/cancervariants/metakb/pull/432
  • chore: add acceptance criteria to issue templates by @korikuzma in https://github.com/cancervariants/metakb/pull/458
  • feat!: use system identifiers from source for normalization by @korikuzma in https://github.com/cancervariants/metakb/pull/433
  • build!: update gks and normalizer versions by @korikuzma in https://github.com/cancervariants/metakb/pull/434
  • test: update test data by @korikuzma in https://github.com/cancervariants/metakb/pull/435
  • feat!: change civic classification.primaryCode to use clinvar enum by @korikuzma in https://github.com/cancervariants/metakb/pull/455
  • fix: store variation aliases in aliases not extensions by @korikuzma in https://github.com/cancervariants/metakb/pull/460
  • refactor: transform into monorepo by @katiestahl in https://github.com/cancervariants/metakb/pull/474
  • feat!: update models to VA-Spec 1.0.0-ballot.2025-03.4 by @korikuzma in https://github.com/cancervariants/metakb/pull/479
  • cicd: update ruff, precommit by @jsstevenson in https://github.com/cancervariants/metakb/pull/473
  • fix(ci): fix deployment, remove pipfile + update seqrepo version by @korikuzma in https://github.com/cancervariants/metakb/pull/485
  • merge: staging changes to main by @korikuzma in https://github.com/cancervariants/metakb/pull/487

New Contributors

  • @katiestahl made their first contribution in https://github.com/cancervariants/metakb/pull/474

Full Changelog: https://github.com/cancervariants/metakb/compare/2.0.0-dev0...2.0.0-a0

- Python
Published by korikuzma about 1 year ago

https://github.com/cancervariants/metakb - 2.0.0-dev1

What's Changed

  • refactor: use SourceName enum by @korikuzma in https://github.com/cancervariants/metakb/pull/330
  • build: raise support to require python >=3.10 by @jsstevenson in https://github.com/cancervariants/metakb/pull/333
  • cicd: add issue templates, stalebot, and branch action by @korikuzma in https://github.com/cancervariants/metakb/pull/334
  • feat!: create_json accepts filepath arg and only creates composite file by @korikuzma in https://github.com/cancervariants/metakb/pull/336
  • feat: prevent usage of aws db instances in cli by @korikuzma in https://github.com/cancervariants/metakb/pull/339
  • refactor!: clean up harvest method by @korikuzma in https://github.com/cancervariants/metakb/pull/338
  • feat!: sharpen type annotation by @jsstevenson in https://github.com/cancervariants/metakb/pull/342
  • feat!: break out CLI for more specific commands/more reasonable defaults by @jsstevenson in https://github.com/cancervariants/metakb/pull/344
  • feat: perform better logging by @jsstevenson in https://github.com/cancervariants/metakb/pull/346
  • build: fix pipenv build by @jsstevenson in https://github.com/cancervariants/metakb/pull/351
  • fix: use correct Disease model by @jsstevenson in https://github.com/cancervariants/metakb/pull/352
  • test: optionally minimize connection debug logging by @jsstevenson in https://github.com/cancervariants/metakb/pull/349
  • fix: use latest minor civicpy release to get correct schema by @jsstevenson in https://github.com/cancervariants/metakb/pull/354
  • fix: don't use deprecated graph driver destructor by @jsstevenson in https://github.com/cancervariants/metakb/pull/356
  • fix: don't use deprecated multi property semantics by @jsstevenson in https://github.com/cancervariants/metakb/pull/359
  • test: remove marks from fixtures (they don't do anything) by @jsstevenson in https://github.com/cancervariants/metakb/pull/358
  • feat: add batch search by variations by @jsstevenson in https://github.com/cancervariants/metakb/pull/361
  • refactor: use updated annotation API by @jsstevenson in https://github.com/cancervariants/metakb/pull/366
  • build: temporarily pin ga4gh.vrs==2.0.0a6 by @korikuzma in https://github.com/cancervariants/metakb/pull/367
  • fix(tests): update testbatchsearch to apply PR (#361) suggestions by @korikuzma in https://github.com/cancervariants/metakb/pull/368
  • fix: querying studies based on therapeutic by @korikuzma in https://github.com/cancervariants/metakb/pull/365
  • docs: initial docs work by @jsstevenson in https://github.com/cancervariants/metakb/pull/343
  • refactor!: remove extract_harvester from transform method by @korikuzma in https://github.com/cancervariants/metakb/pull/370
  • refactor!: rename Transform instance variables by @korikuzma in https://github.com/cancervariants/metakb/pull/371
  • feat!: initialize query handler with graph, not graph credentials by @jsstevenson in https://github.com/cancervariants/metakb/pull/376
  • feat!: refactor graph DB code, streamline unneeded query transaction usage by @jsstevenson in https://github.com/cancervariants/metakb/pull/377
  • feat!: replace instance var lists with pydantic model by @korikuzma in https://github.com/cancervariants/metakb/pull/374
  • fix: catch TokenRetrievalError in ViccNormalizers + update log levels by @korikuzma in https://github.com/cancervariants/metakb/pull/378
  • feat: update pre-commit version + add more hooks by @korikuzma in https://github.com/cancervariants/metakb/pull/382
  • feat!: use setuptools-scm, capture version at package root by @korikuzma in https://github.com/cancervariants/metakb/pull/381
  • style: update ruff version + add more rules by @korikuzma in https://github.com/cancervariants/metakb/pull/380
  • cicd: update actions versions, stalebot, + templates from template repo by @korikuzma in https://github.com/cancervariants/metakb/pull/383
  • feat: enable pagination by @jsstevenson in https://github.com/cancervariants/metakb/pull/384
  • chore: update seqrepo version to 2024-02-20 by @korikuzma in https://github.com/cancervariants/metakb/pull/385
  • feat!: rename env var for logging + cred handling by @korikuzma in https://github.com/cancervariants/metakb/pull/387
  • build!: update normalizer + ga4gh.vrs depdencies by @korikuzma in https://github.com/cancervariants/metakb/pull/386
  • build!: update ga4gh.vrs + gene/variation normalizers by @korikuzma in https://github.com/cancervariants/metakb/pull/389
  • chore!: rename transform class and dirs to transformers by @korikuzma in https://github.com/cancervariants/metakb/pull/396
  • fix: correct syntax error in gene_id_constraint by @korikuzma in https://github.com/cancervariants/metakb/pull/397
  • feat!: use cat-vrs-python + va-spec-python by @korikuzma in https://github.com/cancervariants/metakb/pull/404
  • feat!: rename study --> study statement / statement by @korikuzma in https://github.com/cancervariants/metakb/pull/405
  • feat!: add support for transforming CIViC prognostic evidence by @korikuzma in https://github.com/cancervariants/metakb/pull/407
  • feat: add option to cli to create neo4j db constraints by @korikuzma in https://github.com/cancervariants/metakb/pull/412
  • feat!: add support for moa prognostic assertions by @korikuzma in https://github.com/cancervariants/metakb/pull/411
  • fix: aggregate moa oncotree concepts during transformation by @korikuzma in https://github.com/cancervariants/metakb/pull/413
  • feat!: add support for transforming civic diagnostic evidence items by @korikuzma in https://github.com/cancervariants/metakb/pull/414
  • build!: require python >= 3.11 by @jsstevenson in https://github.com/cancervariants/metakb/pull/403
  • cicd: warn when merging to main by @jsstevenson in https://github.com/cancervariants/metakb/pull/398
  • style: resolve ruff errors by @korikuzma in https://github.com/cancervariants/metakb/pull/421
  • feat!: update models to ga4gh gks nov 2024 ballot releases by @korikuzma in https://github.com/cancervariants/metakb/pull/420
  • feat!: add support for civic assertions by @korikuzma in https://github.com/cancervariants/metakb/pull/422
  • feat!: change strength representation by @korikuzma in https://github.com/cancervariants/metakb/pull/424
  • feat!: move ViccNormalizerDataExtension to mappings by @korikuzma in https://github.com/cancervariants/metakb/pull/425
  • feat!: add support for transforming concepts that fail to normalize by @korikuzma in https://github.com/cancervariants/metakb/pull/427
  • fix!: resolve conflicts where moa therapies resolve to same concept by @korikuzma in https://github.com/cancervariants/metakb/pull/429
  • feat!: moa disease conflict resolution should follow therapy conflict resolution by @korikuzma in https://github.com/cancervariants/metakb/pull/430
  • build!: update vicc normalizers to pull in gks coding changes by @korikuzma in https://github.com/cancervariants/metakb/pull/432
  • chore: add acceptance criteria to issue templates by @korikuzma in https://github.com/cancervariants/metakb/pull/458
  • feat!: use system identifiers from source for normalization by @korikuzma in https://github.com/cancervariants/metakb/pull/433
  • build!: update gks and normalizer versions by @korikuzma in https://github.com/cancervariants/metakb/pull/434
  • test: update test data by @korikuzma in https://github.com/cancervariants/metakb/pull/435
  • feat!: change civic classification.primaryCode to use clinvar enum by @korikuzma in https://github.com/cancervariants/metakb/pull/455
  • fix: store variation aliases in aliases not extensions by @korikuzma in https://github.com/cancervariants/metakb/pull/460
  • refactor: transform into monorepo by @katiestahl in https://github.com/cancervariants/metakb/pull/474
  • feat!: update models to VA-Spec 1.0.0-ballot.2025-03.4 by @korikuzma in https://github.com/cancervariants/metakb/pull/479
  • cicd: update ruff, precommit by @jsstevenson in https://github.com/cancervariants/metakb/pull/473
  • fix(ci): fix deployment, remove pipfile + update seqrepo version by @korikuzma in https://github.com/cancervariants/metakb/pull/485
  • merge: staging changes to main by @korikuzma in https://github.com/cancervariants/metakb/pull/487

New Contributors

  • @katiestahl made their first contribution in https://github.com/cancervariants/metakb/pull/474

Full Changelog: https://github.com/cancervariants/metakb/compare/2.0.0-dev0...2.0.0-dev1

- Python
Published by korikuzma about 1 year ago

https://github.com/cancervariants/metakb - 2.0.0-dev0

What's Changed

  • cicd: update scproductid by @korikuzma in https://github.com/cancervariants/metakb/pull/228
  • build!: update civicpy build to 3.x.x by @korikuzma in https://github.com/cancervariants/metakb/pull/233
  • refactor: cleanup harvester classes by @korikuzma in https://github.com/cancervariants/metakb/pull/234
  • chore: remove requirements files by @korikuzma in https://github.com/cancervariants/metakb/pull/239
  • feat!: update transformers to use vrs 2-alpha and gk-pilot schemas by @korikuzma in https://github.com/cancervariants/metakb/pull/245
  • refactor!: fix class name casing by @korikuzma in https://github.com/cancervariants/metakb/pull/247
  • feat: add support for TherapeuticSubstituteGroup in CIViC by @korikuzma in https://github.com/cancervariants/metakb/pull/249
  • feat: add support for CombinationTherapy by @korikuzma in https://github.com/cancervariants/metakb/pull/251
  • fix: civic variant aliases should be a list + pydantic warning by @korikuzma in https://github.com/cancervariants/metakb/pull/252
  • change: snp ids should not be in civic aliases during transform by @korikuzma in https://github.com/cancervariants/metakb/pull/257
  • build: update thera-py + fix TherapyQueryHandler instantiation by @korikuzma in https://github.com/cancervariants/metakb/pull/259
  • fix: key error in MoaHarvester getfeature by @korikuzma in https://github.com/cancervariants/metakb/pull/258
  • change: snp ids should not be in civic mp aliases during transform by @korikuzma in https://github.com/cancervariants/metakb/pull/260
  • test: update moa source 44 title by @korikuzma in https://github.com/cancervariants/metakb/pull/262
  • tests: update civic + moa test data by @korikuzma in https://github.com/cancervariants/metakb/pull/276
  • feat: include additional therapy/disease normalizer data in CDM by @korikuzma in https://github.com/cancervariants/metakb/pull/288
  • build!: update dependencies and ga4gh digests by @korikuzma in https://github.com/cancervariants/metakb/pull/300
  • test: update civicpy cache data by @korikuzma in https://github.com/cancervariants/metakb/pull/302
  • chore: remove unused delta class by @korikuzma in https://github.com/cancervariants/metakb/pull/306
  • feat!: update database to reflect schema changes by @korikuzma in https://github.com/cancervariants/metakb/pull/266
  • cicd: update release.yml (publish python distribution to pypi) by @korikuzma in https://github.com/cancervariants/metakb/pull/307
  • fix: creating location parameterized query string by @korikuzma in https://github.com/cancervariants/metakb/pull/310
  • feat!: update /search/studies endpoint by @korikuzma in https://github.com/cancervariants/metakb/pull/279
  • cicd: update elastic beanstalk commands by @korikuzma in https://github.com/cancervariants/metakb/pull/280
  • Add lab template CICD actions by @jsstevenson in https://github.com/cancervariants/metakb/pull/297
  • build: configure setuptools in pyproject.toml by @jsstevenson in https://github.com/cancervariants/metakb/pull/298
  • style: use ruff by @jsstevenson in https://github.com/cancervariants/metakb/pull/313
  • cicd: adjust installation checks by @jsstevenson in https://github.com/cancervariants/metakb/pull/316
  • test: fix test data dir + update param name change by @korikuzma in https://github.com/cancervariants/metakb/pull/319
  • chore: remove unused files by @korikuzma in https://github.com/cancervariants/metakb/pull/321
  • fix: add support for civic ash source type by @korikuzma in https://github.com/cancervariants/metakb/pull/323
  • chore: remove analysis dir by @korikuzma in https://github.com/cancervariants/metakb/pull/320
  • feat: use MOA representative coordinate to create PSC members by @korikuzma in https://github.com/cancervariants/metakb/pull/312
  • cicd: add action for closing issue when merged into staging by @korikuzma in https://github.com/cancervariants/metakb/pull/325
  • cicd: fix elastic beanstalk deployment by @korikuzma in https://github.com/cancervariants/metakb/pull/326
  • fix: replace StrEnum with Enum by @korikuzma in https://github.com/cancervariants/metakb/pull/328
  • refactor!: update cli by @korikuzma in https://github.com/cancervariants/metakb/pull/324

Full Changelog: https://github.com/cancervariants/metakb/compare/1.2.0-dev0...2.0.0-dev0

- Python
Published by korikuzma over 2 years ago

https://github.com/cancervariants/metakb - 1.2.0-dev0

What's Changed

  • feat: add oncokb as a source (#170) by @korikuzma in https://github.com/cancervariants/metakb/pull/211
  • build!: update dependencies by @korikuzma in https://github.com/cancervariants/metakb/pull/217
  • refactor: remove LAST_UPDATED by @korikuzma in https://github.com/cancervariants/metakb/pull/221
  • ci: add GH action for installing deps + remove requirements by @korikuzma in https://github.com/cancervariants/metakb/pull/223
  • chore: update elastic beanstalk commands by @korikuzma in https://github.com/cancervariants/metakb/pull/224

Full Changelog: https://github.com/cancervariants/metakb/compare/v1.1.0...1.2.0-dev0

- Python
Published by korikuzma about 3 years ago

https://github.com/cancervariants/metakb - v1.1.0

What's Changed

  • Bump lxml from 4.9.0 to 4.9.1 by @dependabot in https://github.com/cancervariants/metakb/pull/177
  • docs: update readme and add readme for cli by @korikuzma in https://github.com/cancervariants/metakb/pull/176
  • ci: bump action versions by @jsstevenson in https://github.com/cancervariants/metakb/pull/195
  • build!: pin dependencies by @korikuzma in https://github.com/cancervariants/metakb/pull/201
  • Staging by @korikuzma in https://github.com/cancervariants/metakb/pull/202

Full Changelog: https://github.com/cancervariants/metakb/compare/v1.1.0a9...v1.1.0

- Python
Published by korikuzma over 3 years ago

https://github.com/cancervariants/metakb -

  • Update variation normalizer + other dependencies

- Python
Published by korikuzma about 4 years ago

https://github.com/cancervariants/metakb -

  • Update requirements to remove security vulnerabilities

- Python
Published by korikuzma about 4 years ago

https://github.com/cancervariants/metakb -

  • Add transformed regulatory_approval field from thera-py to therapy descriptor extensions

- Python
Published by korikuzma about 4 years ago

https://github.com/cancervariants/metakb -

  • Clean up CLI log/click messages
  • Update dependencies
    • Variation Normalizer now uses latest version of MANE transcripts

- Python
Published by korikuzma over 4 years ago

https://github.com/cancervariants/metakb -

  • Bump jupyter-server from 1.13.5 to 1.15.4

- Python
Published by korikuzma over 4 years ago

https://github.com/cancervariants/metakb -

  • Replace response_datetime with last_updated in ServiceMeta
  • Remove extra node from diagnostic propositions
  • Created versioned data files
  • Add url to openapi contact info
  • Remove duplicate descriptors from response
  • Always enable Try it out param in FastAPI
  • Use hashed digests for arbitrary ID values instead of incremental numbering (eg for Propositions and some Documents)
  • Updated CLI option names + added option to load single CDM file
  • Refactor tests to improve runtime

- Python
Published by korikuzma over 4 years ago