cancervariants/metakb issues and pull requests

#324 - refactor!: update cli

Pull Request - State: closed - Opened by korikuzma 11 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 11 months ago
Labels: bug, priority:medium

#322 - Add support for civic ASH source in transformer

Issue - State: closed - Opened by korikuzma 11 months ago - 1 comment
Labels: bug, priority:medium

#321 - chore: remove unused files

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: priority:low, chore

#320 - chore: remove analysis dir

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: priority:low, chore

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

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: priority:medium, test

#318 - Update test data directory

Issue - State: closed - Opened by korikuzma 11 months ago - 1 comment
Labels: priority:medium, test

#317 - docs: refresh docs

Pull Request - State: closed - Opened by jsstevenson 11 months ago - 3 comments

#316 - cicd: adjust installation checks

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low

#315 - Remove unused files/code

Issue - State: closed - Opened by korikuzma 11 months ago - 3 comments
Labels: priority:low, chore

#314 - Tweak Python version distributions on install check action

Issue - State: closed - Opened by jsstevenson 11 months ago - 2 comments
Labels: priority:low, ci/cd

#313 - style: use ruff

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low

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

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: enhancement, priority:high

#311 - Streamline graph DB queries

Issue - State: open - Opened by jsstevenson 11 months ago - 4 comments
Labels: priority:low, technical debt

#310 - fix: creating location parameterized query string

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: bug, priority:medium

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

Issue - State: closed - Opened by korikuzma 11 months ago - 20 comments
Labels: enhancement, priority:medium

#308 - Add readthedocs

Issue - State: closed - Opened by korikuzma 11 months ago - 3 comments
Labels: priority:medium, documentation

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

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: priority:low, ci/cd

#306 - chore: remove unused delta class

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: priority:low, chore

#305 - add back missing models to openapi.json

Issue - State: closed - Opened by korikuzma 11 months ago - 1 comment
Labels: priority:high, technical debt

#304 - Use `SourceName` enum

Issue - State: closed - Opened by korikuzma 11 months ago - 1 comment
Labels: priority:low, technical debt

#303 - CivicPy cache wrapper for fetching relevant checkpoints

Issue - State: open - Opened by jsstevenson 11 months ago - 6 comments
Labels: enhancement, priority:low

#302 - test: update civicpy cache data

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: priority:medium, test

#301 - Replace StrEnum with str, Enum

Issue - State: closed - Opened by korikuzma 11 months ago - 1 comment
Labels: bug, priority:medium

#300 - build!: update dependencies and ga4gh digests

Pull Request - State: closed - Opened by korikuzma 11 months ago
Labels: priority:high, build

#299 - style: use ruff

Pull Request - State: closed - Opened by jsstevenson 11 months ago - 2 comments
Labels: priority:medium

#298 - build: configure setuptools in pyproject.toml

Pull Request - State: closed - Opened by jsstevenson 11 months ago - 2 comments
Labels: priority:medium

#297 - Add lab template CICD actions

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low

#296 - cicd: require priority label on PRs

Pull Request - State: closed - Opened by jsstevenson 11 months ago
Labels: priority:low

#295 - cicd: test in 3.12

Pull Request - State: closed - Opened by jsstevenson 11 months ago

#294 - style: use ruff

Pull Request - State: closed - Opened by jsstevenson 11 months ago - 1 comment

#293 - style: use ruff for formatting/linting

Pull Request - State: closed - Opened by jsstevenson 11 months ago

#292 - build: configure setuptools via pyproject.toml

Pull Request - State: closed - Opened by jsstevenson 11 months ago - 1 comment
Labels: priority:medium

#291 - CIViC links appear to be broken.

Issue - State: closed - Opened by acoffman 12 months ago - 4 comments
Labels: bug

#290 - Create a batch get for the metakb API

Issue - State: closed - Opened by quinnwai 12 months ago - 2 comments
Labels: enhancement, priority:medium

#289 - Create service info endpoint

Issue - State: open - Opened by korikuzma 12 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 about 1 year ago
Labels: enhancement, priority:medium

#287 - Include additional normalizer data in CDM extensions

Issue - State: closed - Opened by korikuzma about 1 year ago - 3 comments
Labels: enhancement, priority:high

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

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

#285 - Add type annotations

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

#284 - style: use ruff

Pull Request - State: closed - Opened by jsstevenson about 1 year ago - 1 comment

#283 - Use MOA representative coordinate to create PSC members

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

#282 - Streamline local set up

Issue - State: open - Opened by jsstevenson about 1 year ago
Labels: priority:medium, documentation

#281 - tests: update civic + moa test data

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: priority:medium, test

#280 - cicd: update elastic beanstalk commands

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: priority:medium, ci/cd

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

Pull Request - State: closed - Opened by korikuzma about 1 year ago - 6 comments
Labels: enhancement, priority:medium

#278 - Neo4J Driver DeprecationWarning

Issue - State: closed - Opened by korikuzma about 1 year ago - 3 comments
Labels: priority:low, gk-pilot

#277 - Remove unused Delta class

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

#276 - tests: update civic + moa test data

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

#275 - fix: db should include gene aliases

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: bug, priority:low

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

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

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

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

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

Issue - State: closed - Opened by korikuzma about 1 year ago - 2 comments
Labels: enhancement, priority:low, gk-pilot, stale

#271 - Pagination for FastAPI endpoints

Issue - State: closed - Opened by korikuzma about 1 year ago - 2 comments
Labels: enhancement, priority:low, technical debt, gk-pilot

#270 - Create enums for database node labels and relationships

Issue - State: open - Opened by korikuzma about 1 year 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 about 1 year 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 about 1 year ago
Labels: enhancement, priority:low

#267 - fix: bugs in database code

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: bug, priority:medium

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

Pull Request - State: closed - Opened by korikuzma about 1 year ago - 5 comments
Labels: enhancement, priority:medium

#265 - fix: typo for CODING_KEYS in database module

Pull Request - State: closed - Opened by korikuzma about 1 year ago - 1 comment
Labels: bug, priority:low

#264 - (OLD) feat!: update database to reflect schema changes

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: enhancement, priority:medium

#263 - Create IDs for Method Documents

Issue - State: open - Opened by korikuzma about 1 year ago - 2 comments
Labels: enhancement, priority:low, gk-pilot

#262 - test: update moa source 44 title

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

#261 - Create test dataset for database

Issue - State: open - Opened by korikuzma about 1 year ago - 1 comment
Labels: priority:low, test

#260 - change: snp ids should not be in civic mp aliases during transform

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: enhancement, priority:medium

#259 - build: update thera-py + fix TherapyQueryHandler instantiation

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: priority:medium, build

#258 - fix: key error in MoaHarvester _get_feature

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: bug, priority:medium

#257 - change: snp ids should not be in civic aliases during transform

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: enhancement, priority:medium

#256 - Fix MoaHarvester key error

Issue - State: closed - Opened by korikuzma about 1 year ago
Labels: bug, priority:medium, gk-pilot

#255 - Update therapy query handler instantiation

Issue - State: closed - Opened by korikuzma about 1 year ago - 2 comments
Labels: bug, build, gk-pilot

#254 - Don't store civic snp IDs as aliases

Issue - State: closed - Opened by korikuzma about 1 year ago
Labels: enhancement, priority:medium

#253 - Rename `Transform` instance variables

Issue - State: closed - Opened by korikuzma about 1 year ago - 2 comments
Labels: priority:low, technical debt, gk-pilot

#252 - fix: civic variant aliases should be a list + pydantic warning

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: bug, priority:medium

#251 - feat: add support for CombinationTherapy

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: enhancement, priority:medium

#250 - Handling multiple MOA therapy objects (`Hormone` and `Chemotherapy`)

Issue - State: open - Opened by korikuzma about 1 year ago - 4 comments
Labels: enhancement, priority:medium, gk-pilot

#249 - feat: add support for TherapeuticSubstituteGroup in CIViC

Pull Request - State: closed - Opened by korikuzma about 1 year ago
Labels: enhancement, priority:medium

#248 - Consider removing analysis directory

Issue - State: closed - Opened by korikuzma about 1 year ago - 4 comments
Labels: priority:low, chore

#247 - refactor!: fix class name casing

Pull Request - State: closed - Opened by korikuzma about 1 year ago - 1 comment
Labels: priority:low, technical debt

#246 - Fix class name casing

Issue - State: closed - Opened by korikuzma about 1 year ago - 1 comment
Labels: priority:low, technical debt, gk-pilot

#245 - feat!: update transformers to use vrs 2-alpha and gk-pilot schemas

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: enhancement, priority:medium, gk-pilot

#244 - Update CLI

Issue - State: closed - Opened by korikuzma over 1 year ago - 2 comments
Labels: priority:high, technical debt, gk-pilot

#243 - Add support for CNVs in Transformers

Issue - State: open - Opened by korikuzma over 1 year ago - 1 comment
Labels: enhancement, priority:medium, gk-pilot

#242 - Add support for CIViC prognostic evidence

Issue - State: closed - Opened by korikuzma over 1 year ago - 4 comments
Labels: enhancement, priority:high, gk-pilot

#241 - Add support for CIViC diagnostic evidence

Issue - State: closed - Opened by korikuzma over 1 year ago - 4 comments
Labels: enhancement, priority:high, gk-pilot

#240 - Add CIViC assertions to CIViCTransform

Issue - State: open - Opened by korikuzma over 1 year ago - 2 comments
Labels: enhancement, priority:high, gk-pilot

#239 - chore: remove requirements files

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:high, chore

#238 - Upgrade AWS dev instance to python 3.11

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: priority:medium, chore

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

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:low, ci/cd

#236 - Update release.yml to use trusted publisher

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: priority:low, ci/cd

#235 - Replace flake8 with ruff

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: cleanup, gk-pilot

#234 - refactor: cleanup harvester classes

Pull Request - State: closed - Opened by korikuzma over 1 year ago

#233 - build!: update civicpy build to 3.x.x

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:high, build

#232 - GK Pilot: Use civicpy 3.0.0 + update harvester

Issue - State: closed - Opened by korikuzma over 1 year ago

#231 - GK Pilot update

Issue - State: closed - Opened by korikuzma over 1 year ago - 2 comments
Labels: epic, priority:high, gk-pilot

#230 - Transformers use VRS 2.0-alpha for updated gk pilot data

Issue - State: closed - Opened by korikuzma over 1 year ago
Labels: enhancement, priority:high, gk-pilot

#229 - Stabilize how required resources (i.e. normalizers) are constructed

Issue - State: open - Opened by jsstevenson over 1 year ago
Labels: priority:low, technical debt

#228 - cicd: update sc_product_id

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: priority:medium, ci/cd

#227 - fix: civic transformer bugs

Pull Request - State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:low

#226 - civic transform bugs

Issue - State: closed - Opened by korikuzma over 1 year ago
Labels: bug, priority:low

#225 - CIViC variant names that have `c.` in them should be using genomic representation

Issue - State: open - Opened by korikuzma over 1 year ago - 1 comment
Labels: bug, priority:low

GitHub / cancervariants/metakb issues and pull requests