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Recent Releases of https://github.com/cancervariants/disease-normalization

https://github.com/cancervariants/disease-normalization - 0.11.2

What's Changed

  • chore: add pipfile + uv lock to gitignore by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/248
  • build: bump wags-tails version by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/247

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/0.11.1...0.11.2

- Python
Published by korikuzma 8 months ago

https://github.com/cancervariants/disease-normalization - 0.11.1

What's Changed

  • chore: remove pipfile by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/241
  • docs: update notes on how stuff works by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/245
  • build: tighten ga4gh.vrs version to >=2.1.3,<3.0 by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/246
  • style: update ruff and precommit by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/242

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/0.11.0...0.11.1

- Python
Published by jsstevenson 8 months ago

https://github.com/cancervariants/disease-normalization - 0.11.0

What's Changed

  • test: fix version pattern by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/234
  • feat: add --version to cli by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/236
  • feat!: use VRS 2.0.1 models by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/239

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/0.10.0...0.11.0

- Python
Published by korikuzma 11 months ago

https://github.com/cancervariants/disease-normalization - 0.10.0

What's Changed

  • style: update ruff by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/228
  • cicd: update precommit by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/227
  • feat!: overhaul CLI by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/230
  • feat: add service_info endpoint, modularize logging and env management by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/231
  • build: update dependencies by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/233

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

- Python
Published by jsstevenson 12 months ago

https://github.com/cancervariants/disease-normalization - 0.9.0

What's Changed

  • build!: update ga4gh.vrs by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/225

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

- Python
Published by korikuzma about 1 year ago

https://github.com/cancervariants/disease-normalization - 0.8.0

What's Changed

  • fix: correct P310 URI typo in NCIt extraction by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/219
  • fix!: xrefs should have exactMatch for ConceptMapping.relation by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/223
  • fix!: use correct representation of Coding object in mappings by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/221

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

- Python
Published by korikuzma about 1 year ago

https://github.com/cancervariants/disease-normalization - 0.7.0

What's Changed

  • fix: handle mondo xref annotation changes by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/211
  • feat!: update models to vrs 2.0.0 community review ballot by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/210
  • feat!: use preferred formats for MappableConcept.mappings by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/215
  • feat!: remove normalized_id and leverage MappableConcept.primaryCode by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/216

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

- Python
Published by korikuzma about 1 year ago

https://github.com/cancervariants/disease-normalization - 0.6.0

What's Changed

  • cicd: update workflows/templates from template repo by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/196
  • fix: update preferred OMIM prefix by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/198
  • feat: add oncologic disease parameter from mondo terms by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/200
  • build: fix test group name by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/202
  • chore: update gitignore by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/203
  • build!: require python >=3.11 by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/207
  • chore: add acceptance criteria to issue templates by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/206
  • cicd: update precommit by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/205
  • style: update ruff configs by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/204
  • cicd: fix hook names by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/208

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

- Python
Published by korikuzma over 1 year ago

https://github.com/cancervariants/disease-normalization - 0.5.0

What's Changed

  • build: require >= Python 3.10 by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/191
  • style: update ruff to 0.5.0 by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/192
  • build!: update ga4gh.vrs version by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/193
  • feat!: use setuptools-scm, capture version at package root by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/194
  • feat: update pre-commit version + add more hooks by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/195

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/0.4.0.dev4...0.5.0

- Python
Published by korikuzma over 1 year ago

https://github.com/cancervariants/disease-normalization - 0.4.0.dev4

What's Changed

  • style: update ruff rules by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/177
  • style: update ruff rules by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/179
  • docs: add docs skeleton by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/178
  • docs: clean up README by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/185
  • docs: add RTD config by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/184
  • cicd: test on 3.12 by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/183
  • build: update build metadata by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/181
  • cicd: add priority label requirement by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/182
  • docs: fix readthedocs links by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/187
  • feat: add tqdm to track update progress by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/188
  • fix: don't configure logging on library import by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/189

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/0.4.0.dev3...0.4.0.dev4

- Python
Published by korikuzma almost 2 years ago

https://github.com/cancervariants/disease-normalization - 0.4.0.dev3

What's Changed

  • fix: ensure consistent source meta schema typing by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/175

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/0.4.0.dev2...0.4.0.dev3

- Python
Published by jsstevenson about 2 years ago

https://github.com/cancervariants/disease-normalization - 0.4.0.dev2

What's Changed

  • feat!: use OBO release for Mondo by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/171

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/0.4.0.dev1...0.4.0.dev2

- Python
Published by jsstevenson over 2 years ago

https://github.com/cancervariants/disease-normalization - 0.4.0.dev1

What's Changed

  • feat: add getallrecords DB method by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/160
  • build: use pyproject.toml for build configuration by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/161
  • feat!: merge concepts and source dynamodb tables by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/162
  • feat!: remove search result formatting options by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/164
  • chore: remove unused configs by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/166
  • fix: catch ETL module import errors by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/165
  • test: add basic route tests by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/167
  • cicd: use ruff for formatting by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/168
  • feat!: use wags-tails for managing data by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/163
  • style: fix ruff settings by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/170
  • test: suppress noisy boto logs by default by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/169

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/0.4.0.dev0...0.4.0.dev1

- Python
Published by korikuzma over 2 years ago

https://github.com/cancervariants/disease-normalization - 0.4.0.dev0

What's Changed

  • fix: resolve the ETL problems of the week by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/113
  • ci: overhaul test data by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/115
  • feat!: support PostgreSQL as optional storage backend by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/121
  • build: remove requirements.txt files by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/124
  • fix: remove therapy refs by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/128
  • feat!: use vrs 2.0-alpha models in /normalize by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/140
  • cicd: update style checks and test coverage dependencies by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/145
  • cicd: update release.yml (publish python distribution to pypi) by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/150
  • fix!: use better name for CLI source option by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/153
  • feat: optionally define dynamo table names via env variable by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/152
  • test: update test data by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/151

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/v0.3.1...0.4.0.dev0

- Python
Published by jsstevenson over 2 years ago

https://github.com/cancervariants/disease-normalization - 0.2.21dev0

What's Changed

  • feat!: support PostgreSQL as optional storage backend by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/116

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/0.2.20...0.2.21dev0

- Python
Published by jsstevenson almost 3 years ago

https://github.com/cancervariants/disease-normalization - 0.2.20

What's Changed

  • fix: resolve the ETL problems of the week by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/112
  • ci: overhaul test data by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/114
  • build: pin owlready2==0.40 in Pipfile by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/117

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/v0.2.19...0.2.20

- Python
Published by korikuzma almost 3 years ago

https://github.com/cancervariants/disease-normalization - v0.3.1

What's Changed

  • fix: stricter Mondo xref import rules by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/86
  • ci: update style and checks by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/90
  • fix: click echo msg by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/99
  • fix: Catch ValueError during MONDO ETL (staging) by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/108
  • fix: MONDO latest version retrieval (staging) by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/109

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/v0.3.0...v0.3.1

- Python
Published by korikuzma about 3 years ago

https://github.com/cancervariants/disease-normalization - v0.2.19

What's Changed

  • fix: Catch ValueError during MONDO ETL by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/105
  • fix: MONDO latest version retrieval by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/106

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/v0.2.18...v0.2.19

- Python
Published by korikuzma about 3 years ago

https://github.com/cancervariants/disease-normalization - v0.2.18

What's Changed

  • fix: DiseaseDescriptor.disease --> DiseaseDescriptor.disease_id (main) by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/101
  • fix(mondo): stricter xref import rules by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/102 (originally done by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/79)

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/v0.2.17...v0.2.18

- Python
Published by korikuzma about 3 years ago

https://github.com/cancervariants/disease-normalization - v0.2.17

What's Changed

  • build: do not pin exact version for ga4gh.vrsatile.pydantic by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/95
  • fix: click echo msg by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/98

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/v0.2.16...v0.2.17

- Python
Published by korikuzma about 3 years ago

https://github.com/cancervariants/disease-normalization - v0.3.0

What's Changed

  • build: use latest version of ga4gh.vrsatile.pydantic by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/85
  • The v0.3.x versions use the latest metaschema updates

- Python
Published by korikuzma over 3 years ago

https://github.com/cancervariants/disease-normalization - v0.2.16

What's Changed

  • ci: update gh actions versioning by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/78
  • feat: use most recent data by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/79
  • Staging by @jsstevenson in https://github.com/cancervariants/disease-normalization/pull/84

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/v0.2.15...v0.2.16

- Python
Published by korikuzma over 3 years ago

https://github.com/cancervariants/disease-normalization - v0.2.15

What's Changed

  • refactor!: changes to help with serverless (#82) by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/83

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/v0.2.14...v0.2.15

- Python
Published by korikuzma over 3 years ago

https://github.com/cancervariants/disease-normalization - v0.2.14

What's Changed

  • refactor: use DiseaseDescriptor from ga4gh.vrsatile.pydantic by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/74
  • refactor: disease_id --> disease by @korikuzma in https://github.com/cancervariants/disease-normalization/pull/76

Full Changelog: https://github.com/cancervariants/disease-normalization/compare/v0.2.12...v0.2.14

- Python
Published by korikuzma over 3 years ago

https://github.com/cancervariants/disease-normalization -

  • refactor: update ga4gh.vrsatile.pydantic models to use DiseaseDescriptor
  • refactor: add condition for using nonprod db

- Python
Published by korikuzma over 3 years ago

https://github.com/cancervariants/disease-normalization -

  • Add metadata to openapi.json to ensure adherence with openAPI standards
  • Enable parameter entry by default in SwaggerUI
  • Query methods return Pydantic objects, not dicts

- Python
Published by jsstevenson about 4 years ago

https://github.com/cancervariants/disease-normalization -

• Update ElasticBeanstalk logging • Update vrsatile-pydantic version requirement

- Python
Published by jsstevenson over 4 years ago

https://github.com/cancervariants/disease-normalization -

  • Use v0.0.3 for ga4gh.vrsatile.pydantic to allow for extra fields in VOD
  • Return pydantic class as a dict for searchgroups and searchsources

- Python
Published by korikuzma over 4 years ago

https://github.com/cancervariants/disease-normalization -

  • Use ga4gh.vrsatile.pydantic models
  • value_object_descriptor --> disease_descriptor, value (disease value object) --> disease_id

- Python
Published by korikuzma over 4 years ago

https://github.com/cancervariants/disease-normalization - v0.2.7

  • Rename ID field in Value Object Descriptors
  • Enable search by associated_with field
  • Add service_meta info to responses

- Python
Published by jsstevenson almost 5 years ago

https://github.com/cancervariants/disease-normalization -

  • Fix search endpoint with only partial sources loaded

- Python
Published by korikuzma almost 5 years ago

https://github.com/cancervariants/disease-normalization -

  • Updating database environment variables for EB
  • More descriptive database click messages

- Python
Published by korikuzma almost 5 years ago

https://github.com/cancervariants/disease-normalization - v0.2.2

  • CLI description/error message fixes

- Python
Published by jsstevenson almost 5 years ago

https://github.com/cancervariants/disease-normalization - v0.2.1

  • Fix merge update bug in CLI

- Python
Published by jsstevenson almost 5 years ago

https://github.com/cancervariants/disease-normalization - v0.2.0

  • Output normalization endpoint as Value Object Descriptor
  • Include non-Mondo concept groups in normalization endpoint
  • Add OMIM data
  • Enable lookup by other_id reference

- Python
Published by jsstevenson-tmp almost 5 years ago

https://github.com/cancervariants/disease-normalization - v0.1.0

- Python
Published by jsstevenson about 5 years ago