cancervariants/metakb issues and pull requests

#366 - refactor: use updated annotation API

Pull Request - State: closed - Opened by jsstevenson 18 days ago
Labels: priority:low, technical debt

#365 - fix!: querying studies based on therapeutic

Pull Request - State: open - Opened by korikuzma 19 days ago
Labels: bug, priority:medium

#363 - `METAKB_NORM_EB_PROD` -> `METAKB_EB_PROD`

Issue - State: open - Opened by jsstevenson 22 days ago
Labels: enhancement, priority:low

#362 - Normalizers fail silently

Issue - State: open - Opened by jsstevenson 22 days ago - 3 comments
Labels: bug, priority:medium

#361 - feat: add batch search by variations

Pull Request - State: closed - Opened by jsstevenson 23 days ago
Labels: enhancement, priority:medium

#360 - Work out intersection vs union issues in `_get_related_studies` query

Issue - State: open - Opened by jsstevenson 23 days ago - 4 comments
Labels: bug, priority:high

#359 - fix: don't use deprecated multi property semantics

Pull Request - State: closed - Opened by jsstevenson 23 days ago
Labels: bug, priority:low

#358 - test: remove marks from fixtures (they don't do anything)

Pull Request - State: closed - Opened by jsstevenson 23 days ago
Labels: priority:low, test

#357 - Database layer refactor

Issue - State: open - Opened by jsstevenson 24 days ago
Labels: priority:medium, technical debt

#356 - fix: don't use deprecated graph driver destructor

Pull Request - State: closed - Opened by jsstevenson 24 days ago
Labels: priority:medium, technical debt

#355 - Colon separator for relationship types is deprecated

Issue - State: closed - Opened by jsstevenson 24 days ago - 2 comments
Labels: bug, priority:medium

#354 - fix: use latest minor civicpy release to get correct schema

Pull Request - State: closed - Opened by jsstevenson 24 days ago
Labels: bug, priority:high

#353 - CIViC harvest fails

Issue - State: closed - Opened by jsstevenson 24 days ago - 1 comment
Labels: bug, priority:high

#352 - fix: use correct Disease model

Pull Request - State: closed - Opened by jsstevenson 26 days ago
Labels: bug, priority:medium

#351 - build: fix pipenv build

Pull Request - State: closed - Opened by jsstevenson 26 days ago
Labels: priority:high

#350 - pipenv build currently failing

Issue - State: closed - Opened by jsstevenson 26 days ago - 3 comments
Labels: bug, priority:high, build

#349 - test: optionally minimize connection debug logging

Pull Request - State: closed - Opened by jsstevenson 26 days ago
Labels: priority:medium, test

#348 - Don't apply marks to fixtures in tests

Issue - State: closed - Opened by jsstevenson 26 days ago - 1 comment
Labels: priority:low, technical debt

#347 - Resolve pydantic serializer warnings

Issue - State: closed - Opened by jsstevenson 26 days ago - 1 comment
Labels: bug, priority:medium

#346 - feat: perform better logging

Pull Request - State: closed - Opened by jsstevenson about 1 month ago
Labels: priority:low

#345 - Rewrite test_datebase.py tests as a validation job

Issue - State: open - Opened by jsstevenson about 1 month ago - 2 comments
Labels: priority:medium, test

#344 - feat!: break out CLI for more specific commands/more reasonable defaults

Pull Request - State: closed - Opened by jsstevenson about 2 months ago - 4 comments
Labels: priority:medium

#343 - docs: initial docs work

Pull Request - State: open - Opened by jsstevenson about 2 months ago - 1 comment

#342 - feat!: sharpen type annotation

Pull Request - State: closed - Opened by jsstevenson about 2 months ago
Labels: priority:medium

#341 - Remove `extract_harvester` call from `transform`

Issue - State: open - Opened by korikuzma about 2 months ago
Labels: priority:medium, technical debt

#340 - Revert "feat!: sharpen up type usage (#332)"

Pull Request - State: closed - Opened by jsstevenson about 2 months ago
Labels: priority:high, chore

#339 - feat: prevent usage of aws db instances in cli

Pull Request - State: closed - Opened by korikuzma about 2 months ago
Labels: enhancement, priority:medium

#338 - refactor!: clean up harvest method

Pull Request - State: closed - Opened by korikuzma about 2 months ago - 1 comment
Labels: priority:medium, technical debt

#337 - `metakb.harvesters.base.Harvester.create_json` shouldn't be reimplemented by child classes

Issue - State: closed - Opened by jsstevenson about 2 months ago - 2 comments
Labels: priority:low, technical debt

#336 - feat!: create_json accepts filepath arg and only creates composite file

Pull Request - State: closed - Opened by korikuzma about 2 months ago
Labels: enhancement, priority:medium

#335 - create_json should accept a path to file

Issue - State: closed - Opened by korikuzma about 2 months ago - 1 comment
Labels: enhancement, priority:low

#334 - cicd: add issue templates, stalebot, and branch action

Pull Request - State: closed - Opened by korikuzma about 2 months ago
Labels: priority:low, ci/cd

#333 - build: raise support to require python >=3.10

Pull Request - State: closed - Opened by jsstevenson about 2 months ago - 1 comment
Labels: priority:medium

#332 - feat!: sharpen up type usage

Pull Request - State: closed - Opened by jsstevenson about 2 months ago
Labels: priority:medium

#331 - Make sure CLI can't overwrite cloud normalizer DBs

Issue - State: closed - Opened by jsstevenson about 2 months ago - 2 comments
Labels: enhancement

#330 - refactor: use `SourceName` enum

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, technical debt

#329 - incorporate staging changes into main

Pull Request - State: closed - Opened by korikuzma 3 months ago - 4 comments
Labels: priority:high

#328 - fix: replace `StrEnum` with `Enum`

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: bug, priority:medium

#327 - incorporate staging changes into main

Pull Request - State: closed - Opened by korikuzma 3 months ago - 2 comments

#326 - cicd: fix elastic beanstalk deployment

Pull Request - State: closed - Opened by korikuzma 3 months ago - 2 comments
Labels: priority:high, ci/cd

#325 - cicd: add action for closing issue when merged into staging

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, ci/cd

#324 - refactor!: update cli

Pull Request - State: closed - Opened by korikuzma 3 months ago - 4 comments
Labels: priority:medium, technical debt

#323 - fix: add support for civic ash source type

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: bug, priority:medium

#322 - Add support for civic ASH source in transformer

Issue - State: closed - Opened by korikuzma 3 months ago - 1 comment
Labels: bug, priority:medium

#321 - chore: remove unused files

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, chore

#320 - chore: remove analysis dir

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, chore

#319 - test: fix test data dir + update param name change

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:medium, test

#318 - Update test data directory

Issue - State: closed - Opened by korikuzma 3 months ago - 1 comment
Labels: priority:medium, test

#317 - docs: refresh docs

Pull Request - State: closed - Opened by jsstevenson 3 months ago - 3 comments

#316 - cicd: adjust installation checks

Pull Request - State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low

#315 - Remove unused files/code

Issue - State: closed - Opened by korikuzma 3 months ago - 3 comments
Labels: priority:low, chore

#314 - Tweak Python version distributions on install check action

Issue - State: closed - Opened by jsstevenson 3 months ago - 2 comments
Labels: priority:low, ci/cd

#313 - style: use ruff

Pull Request - State: closed - Opened by jsstevenson 3 months ago
Labels: priority:low

#312 - feat: use MOA representative coordinate to create PSC members

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: enhancement, priority:high

#311 - Streamline graph DB queries

Issue - State: open - Opened by jsstevenson 3 months ago - 2 comments
Labels: priority:medium, technical debt

#310 - fix: creating location parameterized query string

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: bug, priority:medium

#309 - Move `variant.definingContext.expressions` to `variant.members`

Issue - State: open - Opened by korikuzma 3 months ago - 1 comment
Labels: enhancement, priority:medium

#308 - Add readthedocs

Issue - State: open - Opened by korikuzma 3 months ago - 1 comment
Labels: priority:medium, documentation

#307 - cicd: update release.yml (publish python distribution to pypi)

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, ci/cd

#306 - chore: remove unused delta class

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:low, chore

#305 - add back missing models to openapi.json

Issue - State: open - Opened by korikuzma 3 months ago
Labels: priority:high, technical debt

#304 - Use `SourceName` enum

Issue - State: closed - Opened by korikuzma 3 months ago - 1 comment
Labels: priority:low, technical debt

#303 - CivicPy cache wrapper for fetching relevant checkpoints

Issue - State: open - Opened by jsstevenson 3 months ago - 6 comments
Labels: enhancement, priority:low

#302 - test: update civicpy cache data

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:medium, test

#301 - Replace StrEnum with str, Enum

Issue - State: closed - Opened by korikuzma 3 months ago - 1 comment
Labels: bug, priority:medium

#300 - build!: update dependencies and ga4gh digests

Pull Request - State: closed - Opened by korikuzma 3 months ago
Labels: priority:high, build

#299 - style: use ruff

Pull Request - State: closed - Opened by jsstevenson 4 months ago - 2 comments
Labels: priority:medium

#298 - build: configure setuptools in pyproject.toml

Pull Request - State: closed - Opened by jsstevenson 4 months ago - 2 comments
Labels: priority:medium

#297 - Add lab template CICD actions

Pull Request - State: closed - Opened by jsstevenson 4 months ago
Labels: priority:low

#296 - cicd: require priority label on PRs

Pull Request - State: closed - Opened by jsstevenson 4 months ago
Labels: priority:low

#295 - cicd: test in 3.12

Pull Request - State: closed - Opened by jsstevenson 4 months ago

#294 - style: use ruff

Pull Request - State: closed - Opened by jsstevenson 4 months ago - 1 comment

#293 - style: use ruff for formatting/linting

Pull Request - State: closed - Opened by jsstevenson 4 months ago

#292 - build: configure setuptools via pyproject.toml

Pull Request - State: closed - Opened by jsstevenson 4 months ago - 1 comment
Labels: priority:medium

#291 - CIViC links appear to be broken.

Issue - State: closed - Opened by acoffman 4 months ago - 4 comments
Labels: bug

#290 - Create a batch get for the metakb API

Issue - State: closed - Opened by quinnwai 4 months ago - 2 comments
Labels: enhancement, priority:medium

#289 - Create service info endpoint

Issue - State: open - Opened by korikuzma 5 months ago - 6 comments
Labels: enhancement, priority:medium

#288 - feat: include additional therapy/disease normalizer data in CDM

Pull Request - State: closed - Opened by korikuzma 5 months ago
Labels: enhancement, priority:medium

#287 - Include additional normalizer data in CDM extensions

Issue - State: closed - Opened by korikuzma 5 months ago - 3 comments
Labels: enhancement, priority:high

#286 - Consolidate configs/build system in `pyproject.toml`

Issue - State: closed - Opened by jsstevenson 6 months ago - 1 comment
Labels: priority:low, build

#285 - Add type annotations

Issue - State: closed - Opened by jsstevenson 6 months ago - 1 comment
Labels: priority:medium, technical debt

#284 - style: use ruff

Pull Request - State: closed - Opened by jsstevenson 6 months ago - 1 comment

#283 - Use MOA representative coordinate to create PSC members

Issue - State: closed - Opened by korikuzma 6 months ago - 1 comment
Labels: enhancement, priority:medium, gk-pilot

#282 - Streamline local set up

Issue - State: open - Opened by jsstevenson 6 months ago
Labels: priority:medium, documentation

#281 - tests: update civic + moa test data

Pull Request - State: closed - Opened by korikuzma 6 months ago
Labels: priority:medium, test

#280 - cicd: update elastic beanstalk commands

Pull Request - State: closed - Opened by korikuzma 6 months ago
Labels: priority:medium, ci/cd

#279 - feat!: update `/search/studies` endpoint

Pull Request - State: closed - Opened by korikuzma 6 months ago - 6 comments
Labels: enhancement, priority:medium

#278 - Neo4J Driver DeprecationWarning

Issue - State: closed - Opened by korikuzma 6 months ago - 3 comments
Labels: priority:low, gk-pilot

#277 - Remove unused Delta class

Issue - State: closed - Opened by korikuzma 6 months ago - 1 comment
Labels: priority:low, chore

#276 - tests: update civic + moa test data

Pull Request - State: closed - Opened by korikuzma 6 months ago - 1 comment
Labels: priority:medium, test

#275 - fix: db should include gene aliases

Pull Request - State: closed - Opened by korikuzma 6 months ago
Labels: bug, priority:low

#274 - Update `/search` endpoint for gk-pilot schemas

Issue - State: open - Opened by korikuzma 6 months ago
Labels: enhancement, priority:high, gk-pilot

#273 - Create `/search/studies` endpoint for gk-pilot schemas

Issue - State: closed - Opened by korikuzma 6 months ago - 1 comment
Labels: enhancement, priority:high, gk-pilot

#272 - Update `search/{id}` endpoint for gk-pilot schemas

Issue - State: closed - Opened by korikuzma 6 months ago - 2 comments
Labels: enhancement, priority:low, gk-pilot, stale

#271 - Pagination for FastAPI endpoints

Issue - State: open - Opened by korikuzma 7 months ago - 1 comment
Labels: enhancement, priority:low, technical debt, gk-pilot

#270 - Create enums for database node labels and relationships

Issue - State: open - Opened by korikuzma 7 months ago - 2 comments
Labels: enhancement, priority:low, technical debt, gk-pilot

#269 - Add ability to provide source object ID in search endpoints

Issue - State: open - Opened by korikuzma 7 months ago - 2 comments
Labels: enhancement, priority:low, gk-pilot

#268 - feat: include type in nodes representing VRS objects

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: enhancement, priority:low

#267 - fix: bugs in database code

Pull Request - State: closed - Opened by korikuzma 7 months ago
Labels: bug, priority:medium

#266 - feat!: update database to reflect schema changes

Pull Request - State: closed - Opened by korikuzma 7 months ago - 5 comments
Labels: enhancement, priority:medium

GitHub / cancervariants/metakb issues and pull requests