Changelog

0.13.1

Released on 2026-05-13 - GitHub - PyPI

What's Changed

• feat: add dynamodb export db method by @korikuzma in #273
• build: update vrs-python by @jsstevenson in #270
• feat: add source provenance to dump file by @jsstevenson in #274
• chore: remove issue template overrides by @katie-perry in #275
• docs: update RTD build image by @jsstevenson in #276
• docs: add DOI badge and citation file by @jsstevenson in #277

New Contributors

• @katie-perry made their first contribution in #275

Full Changelog: 0.13.0...0.13.1

0.13.0

Released on 2026-01-06 - GitHub - PyPI

What's Changed

• feat: use config module for setting DB URL by @jsstevenson in #265
• fix: suppress and track keyerror from new sources by @jsstevenson in #267
• chore: add codeowners file by @korikuzma in #269
• cicd: update actions, ruff, etc by @jsstevenson in #271
• feat: add docker install instructions by @korikuzma in #272

Full Changelog: 0.12.0...0.13.0

0.12.0

Released on 2025-11-04 - GitHub - PyPI

What's Changed

• fix!: AwsEnvName should use values from ServiceEnvironment by @korikuzma in #264

Full Changelog: 0.11.3...0.12.0

0.11.3

Released on 2025-10-31 - GitHub - PyPI

What's Changed

• feat: add property blocklist by @jsstevenson in #250
• feat: capture cancer subset in DO by @jsstevenson in #251
• fix: guard against ETL dependency importerrors by @jsstevenson in #252
• feat: make mappings dump by @jsstevenson in #254
• cicd: use uv by @jsstevenson in #256
• feat: update configs and API by @jsstevenson in #257
• feat: no rats by @jsstevenson in #259
• feat: add cancer filter to disease mapping dump by @jsstevenson in #260

Full Changelog: 0.11.2...0.11.3

0.11.2

Released on 2025-07-21 - GitHub - PyPI

What's Changed

• chore: add pipfile + uv lock to gitignore by @korikuzma in #248
• build: bump wags-tails version by @korikuzma in #247

Full Changelog: 0.11.1...0.11.2

0.11.1

Released on 2025-07-10 - GitHub - PyPI

What's Changed

• chore: remove pipfile by @korikuzma in #241
• docs: update notes on how stuff works by @jsstevenson in #245
• build: tighten ga4gh.vrs version to >=2.1.3,<3.0 by @korikuzma in #246
• style: update ruff and precommit by @jsstevenson in #242

Full Changelog: 0.11.0...0.11.1

0.11.0

Released on 2025-04-22 - GitHub - PyPI

What's Changed

• test: fix version pattern by @jsstevenson in #234
• feat: add --version to cli by @jsstevenson in #236
• feat!: use VRS 2.0.1 models by @korikuzma in #239

Full Changelog: 0.10.0...0.11.0

0.10.0

Released on 2025-03-24 - GitHub - PyPI

What's Changed

• style: update ruff by @jsstevenson in #228
• cicd: update precommit by @jsstevenson in #227
• feat!: overhaul CLI by @jsstevenson in #230
• feat: add service_info endpoint, modularize logging and env management by @jsstevenson in #231
• build: update dependencies by @jsstevenson in #233

Full Changelog: 0.9.0...0.10.0

0.9.0

Released on 2025-02-13 - GitHub - PyPI

What's Changed

• build!: update ga4gh.vrs by @korikuzma in #225

Full Changelog: 0.8.0...0.9.0

0.8.0

Released on 2025-01-29 - GitHub - PyPI

What's Changed

• fix: correct P310 URI typo in NCIt extraction by @jsstevenson in #219
• fix!: xrefs should have exactMatch for ConceptMapping.relation by @korikuzma in #223
• fix!: use correct representation of Coding object in mappings by @korikuzma in #221

Full Changelog: 0.7.0...0.8.0

0.7.0

Released on 2025-01-02 - GitHub - PyPI

What's Changed

• fix: handle mondo xref annotation changes by @jsstevenson in #211
• feat!: update models to vrs 2.0.0 community review ballot by @korikuzma in #210
• feat!: use preferred formats for MappableConcept.mappings by @korikuzma in #215
• feat!: remove normalized_id and leverage MappableConcept.primaryCode by @korikuzma in #216

Full Changelog: 0.6.0...0.7.0

0.6.0

Released on 2024-11-29 - GitHub - PyPI

What's Changed

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

Full Changelog: 0.5.0...0.6.0

0.5.0

Released on 2024-07-15 - GitHub - PyPI

What's Changed

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

Full Changelog: 0.4.0.dev4...0.5.0

0.4.0.dev4

Released on 2024-06-07 - GitHub - PyPI

What's Changed

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

Full Changelog: 0.4.0.dev3...0.4.0.dev4

0.4.0.dev3

Released on 2023-12-20 - GitHub - PyPI

What's Changed

• fix: ensure consistent source meta schema typing by @jsstevenson in #175

Full Changelog: 0.4.0.dev2...0.4.0.dev3

0.4.0.dev2

Released on 2023-12-04 - GitHub - PyPI

What's Changed

• feat!: use OBO release for Mondo by @jsstevenson in #171

Full Changelog: 0.4.0.dev1...0.4.0.dev2

0.4.0.dev1

Released on 2023-11-28 - GitHub - PyPI

What's Changed

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

Full Changelog: 0.4.0.dev0...0.4.0.dev1

0.4.0.dev0

Released on 2023-10-25 - GitHub - PyPI

What's Changed

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

Full Changelog: v0.3.1...0.4.0.dev0

0.2.21dev0

Released on 2023-05-12 - GitHub - PyPI

What's Changed

• feat!: support PostgreSQL as optional storage backend by @jsstevenson in #116

Full Changelog: 0.2.20...0.2.21dev0

0.2.20

Released on 2023-05-07 - GitHub - PyPI

What's Changed

• fix: resolve the ETL problems of the week by @jsstevenson in #112
• ci: overhaul test data by @jsstevenson in #114
• build: pin owlready2==0.40 in Pipfile by @korikuzma in #117

Full Changelog: v0.2.19...0.2.20

v0.3.1

Released on 2023-01-11 - GitHub - PyPI

What's Changed

• fix: stricter Mondo xref import rules by @jsstevenson in #86
• ci: update style and checks by @jsstevenson in #90
• fix: click echo msg by @korikuzma in #99
• fix: Catch ValueError during MONDO ETL (staging) by @korikuzma in #108
• fix: MONDO latest version retrieval (staging) by @korikuzma in #109

Full Changelog: v0.3.0...v0.3.1

v0.2.19

Released on 2023-01-11 - GitHub - PyPI

What's Changed

• fix: Catch ValueError during MONDO ETL by @korikuzma in #105
• fix: MONDO latest version retrieval by @korikuzma in #106

Full Changelog: v0.2.18...v0.2.19

v0.2.18

Released on 2023-01-10 - GitHub - PyPI

What's Changed

• fix: DiseaseDescriptor.disease --> DiseaseDescriptor.disease_id (main) by @korikuzma in #101
• fix(mondo): stricter xref import rules by @korikuzma in #102 (originally done by @jsstevenson in #79)

Full Changelog: v0.2.17...v0.2.18

v0.2.17

Released on 2023-01-06 - GitHub - PyPI

What's Changed

• build: do not pin exact version for ga4gh.vrsatile.pydantic by @korikuzma in #95
• fix: click echo msg by @korikuzma in #98

Full Changelog: v0.2.16...v0.2.17

v0.2.16

Released on 2022-11-02 - GitHub - PyPI

What's Changed

• ci: update gh actions versioning by @jsstevenson in #78
• feat: use most recent data by @jsstevenson in #79
• Staging by @jsstevenson in #84

Full Changelog: v0.2.15...v0.2.16

v0.3.0

Released on 2022-11-02 - GitHub - PyPI

What's Changed

• build: use latest version of ga4gh.vrsatile.pydantic by @korikuzma in #85
• The v0.3.x versions use the latest metaschema updates

v0.2.15

Released on 2022-10-31 - GitHub - PyPI

What's Changed

• refactor!: changes to help with serverless (#82) by @korikuzma in #83

Full Changelog: v0.2.14...v0.2.15

v0.2.14

Released on 2022-09-23 - GitHub - PyPI

What's Changed

• refactor: use DiseaseDescriptor from ga4gh.vrsatile.pydantic by @korikuzma in #74
• refactor: disease_id --> disease by @korikuzma in #76

Full Changelog: v0.2.12...v0.2.14

v0.2.13:

Released on 2022-08-24 - GitHub - PyPI

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

v0.2.12:

Released on 2022-01-24 - GitHub - PyPI

• 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

v0.2.11:

Released on 2021-11-18 - GitHub - PyPI

• Update ElasticBeanstalk logging
• Update vrsatile-pydantic version requirement

v0.2.10:

Released on 2021-09-07 - GitHub - PyPI

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

v0.2.9:

Released on 2021-09-07 - GitHub - PyPI

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

v0.2.7

Released on 2021-04-15 - GitHub - PyPI

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

v0.2.4:

Released on 2021-03-31 - GitHub - PyPI

• Fix search endpoint with only partial sources loaded

v0.2.3:

Released on 2021-03-30 - GitHub - PyPI

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

v0.2.2

Released on 2021-03-29 - GitHub - PyPI

• CLI description/error message fixes

v0.2.1

Released on 2021-03-17 - GitHub - PyPI

• Fix merge update bug in CLI

v0.2.0

Released on 2021-03-12 - GitHub - PyPI

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

v0.1.0

Released on 2021-02-26 - GitHub - PyPI