cancervariants/metakb issues and pull requests

#291 - CIViC links appear to be broken.

Issue - State: closed - Opened by acoffman 7 months ago - 4 comments
Labels: bug

#290 - Create a batch get for the metakb API

Issue - State: closed - Opened by quinnwai 7 months ago - 2 comments
Labels: enhancement, priority:medium

#289 - Create service info endpoint

Issue - State: open - Opened by korikuzma 8 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 8 months ago
Labels: enhancement, priority:medium

#287 - Include additional normalizer data in CDM extensions

Issue - State: closed - Opened by korikuzma 8 months ago - 3 comments
Labels: enhancement, priority:high

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

Issue - State: closed - Opened by jsstevenson 9 months ago - 1 comment
Labels: priority:low, build

#285 - Add type annotations

Issue - State: closed - Opened by jsstevenson 9 months ago - 1 comment
Labels: priority:medium, technical debt

#284 - style: use ruff

Pull Request - State: closed - Opened by jsstevenson 9 months ago - 1 comment

#283 - Use MOA representative coordinate to create PSC members

Issue - State: closed - Opened by korikuzma 9 months ago - 1 comment
Labels: enhancement, priority:medium, gk-pilot

#282 - Streamline local set up

Issue - State: open - Opened by jsstevenson 9 months ago
Labels: priority:medium, documentation

#281 - tests: update civic + moa test data

Pull Request - State: closed - Opened by korikuzma 9 months ago
Labels: priority:medium, test

#280 - cicd: update elastic beanstalk commands

Pull Request - State: closed - Opened by korikuzma 9 months ago
Labels: priority:medium, ci/cd

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

Pull Request - State: closed - Opened by korikuzma 9 months ago - 6 comments
Labels: enhancement, priority:medium

#278 - Neo4J Driver DeprecationWarning

Issue - State: closed - Opened by korikuzma 9 months ago - 3 comments
Labels: priority:low, gk-pilot

#277 - Remove unused Delta class

Issue - State: closed - Opened by korikuzma 9 months ago - 1 comment
Labels: priority:low, chore

#276 - tests: update civic + moa test data

Pull Request - State: closed - Opened by korikuzma 9 months ago - 1 comment
Labels: priority:medium, test

#275 - fix: db should include gene aliases

Pull Request - State: closed - Opened by korikuzma 9 months ago
Labels: bug, priority:low

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

Issue - State: closed - Opened by korikuzma 9 months ago - 1 comment
Labels: enhancement, priority:high, gk-pilot

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

Issue - State: closed - Opened by korikuzma 9 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 9 months ago - 2 comments
Labels: enhancement, priority:low, gk-pilot, stale

#271 - Pagination for FastAPI endpoints

Issue - State: closed - Opened by korikuzma 10 months 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 10 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 10 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 10 months ago
Labels: enhancement, priority:low

#267 - fix: bugs in database code

Pull Request - State: closed - Opened by korikuzma 10 months ago
Labels: bug, priority:medium

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

Pull Request - State: closed - Opened by korikuzma 10 months ago - 5 comments
Labels: enhancement, priority:medium

#265 - fix: typo for CODING_KEYS in database module

Pull Request - State: closed - Opened by korikuzma 10 months ago - 1 comment
Labels: bug, priority:low

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

Pull Request - State: closed - Opened by korikuzma 10 months ago
Labels: enhancement, priority:medium

#263 - Create IDs for Method Documents

Issue - State: open - Opened by korikuzma 10 months ago - 2 comments
Labels: enhancement, priority:low, gk-pilot

#262 - test: update moa source 44 title

Pull Request - State: closed - Opened by korikuzma 10 months ago - 1 comment
Labels: priority:medium, test

#261 - Create test dataset for database

Issue - State: open - Opened by korikuzma 10 months 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 10 months ago
Labels: enhancement, priority:medium

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

Pull Request - State: closed - Opened by korikuzma 10 months ago
Labels: priority:medium, build

#258 - fix: key error in MoaHarvester _get_feature

Pull Request - State: closed - Opened by korikuzma 10 months ago
Labels: bug, priority:medium

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

Pull Request - State: closed - Opened by korikuzma 10 months ago
Labels: enhancement, priority:medium

#256 - Fix MoaHarvester key error

Issue - State: closed - Opened by korikuzma 10 months ago
Labels: bug, priority:medium, gk-pilot

#255 - Update therapy query handler instantiation

Issue - State: closed - Opened by korikuzma 10 months ago - 2 comments
Labels: bug, build, gk-pilot

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

Issue - State: closed - Opened by korikuzma 10 months ago
Labels: enhancement, priority:medium

#253 - Rename `Transform` instance variables

Issue - State: closed - Opened by korikuzma 10 months 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 10 months ago
Labels: bug, priority:medium

#251 - feat: add support for CombinationTherapy

Pull Request - State: closed - Opened by korikuzma 10 months ago
Labels: enhancement, priority:medium

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

Issue - State: open - Opened by korikuzma 10 months ago - 4 comments
Labels: enhancement, priority:medium, gk-pilot

#249 - feat: add support for TherapeuticSubstituteGroup in CIViC

Pull Request - State: closed - Opened by korikuzma 10 months ago
Labels: enhancement, priority:medium

#248 - Consider removing analysis directory

Issue - State: closed - Opened by korikuzma 10 months ago - 4 comments
Labels: priority:low, chore

#247 - refactor!: fix class name casing

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

#246 - Fix class name casing

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

#244 - Update CLI

Issue - State: closed - Opened by korikuzma 11 months ago - 2 comments
Labels: priority:high, technical debt, gk-pilot

#243 - Add support for CNVs in Transformers

Issue - State: open - Opened by korikuzma 11 months ago - 1 comment
Labels: enhancement, priority:medium, gk-pilot

#242 - Add support for CIViC prognostic evidence

Issue - State: open - Opened by korikuzma 11 months ago - 3 comments
Labels: enhancement, priority:high, gk-pilot

#241 - Add support for CIViC diagnostic evidence

Issue - State: open - Opened by korikuzma 11 months ago - 3 comments
Labels: enhancement, priority:high, gk-pilot

#240 - Add CIViC assertions to CIViCTransform

Issue - State: open - Opened by korikuzma 11 months ago - 2 comments
Labels: enhancement, priority:high, gk-pilot

#239 - chore: remove requirements files

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

#238 - Upgrade AWS dev instance to python 3.11

Issue - State: closed - Opened by korikuzma 12 months ago - 1 comment
Labels: priority:medium, chore

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

Pull Request - State: closed - Opened by korikuzma 12 months ago
Labels: priority:low, ci/cd

#236 - Update release.yml to use trusted publisher

Issue - State: closed - Opened by korikuzma 12 months ago - 1 comment
Labels: priority:low, ci/cd

#235 - Replace flake8 with ruff

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

#234 - refactor: cleanup harvester classes

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

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

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

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

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

#231 - GK Pilot update

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

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

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

#228 - cicd: update sc_product_id

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

#227 - fix: civic transformer bugs

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

#226 - civic transform bugs

Issue - State: closed - Opened by korikuzma about 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

#224 - chore: update elastic beanstalk commands

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

#223 - ci: add GH action for installing deps + remove requirements

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

#222 - Create GH Action to install dependencies using different python versions

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

#221 - refactor: remove LAST_UPDATED

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

#220 - Refactor getting logger

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

#219 - Refactor CLI to remove the class

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

#218 - Remove LAST_UPDATED in version.py

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

#217 - build!: update dependencies

Pull Request - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: priority:medium, technical debt, build

#216 - Bump sqlparse from 0.4.3 to 0.4.4

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#215 - Bump starlette from 0.22.0 to 0.25.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#214 - Bump ipython from 8.7.0 to 8.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#213 - Update civicpy to ~= 3.0.0

Issue - State: closed - Opened by korikuzma over 1 year ago - 1 comment
Labels: requirement, priority:high, build

#212 - OncoKB analysis work

Issue - State: open - Opened by korikuzma almost 2 years ago
Labels: analysis

#211 - feat: add oncokb as a source (#170)

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#210 - Consider updating CLI arguments

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: enhancement

#209 - How to handle PubMed documents from various sources

Issue - State: open - Opened by korikuzma almost 2 years ago - 2 comments
Labels: question

#208 - Transform extract_harvester should use latest harvested data if harvester path not provided

Issue - State: open - Opened by korikuzma almost 2 years ago
Labels: enhancement

#207 - neo4j driver close session deprecation

Issue - State: closed - Opened by korikuzma almost 2 years ago - 2 comments
Labels: build

#206 - Bump certifi from 2022.9.24 to 2022.12.7

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments

#205 - Unpin exact versions for dependencies

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: bug, priority:high, build

#204 - OncoKB add abstracts as documents

Issue - State: open - Opened by korikuzma almost 2 years ago
Labels: enhancement

#203 - Update to neo4j cypher v5

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: enhancement

#202 - Staging

Pull Request - State: closed - Opened by korikuzma almost 2 years ago

#201 - build!: pin dependencies

Pull Request - State: closed - Opened by korikuzma almost 2 years ago - 1 comment

#200 - Update gene-normalizer version

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment

#199 - Add linting actions

Issue - State: closed - Opened by jsstevenson almost 2 years ago - 1 comment
Labels: good first issue, cleanup

#198 - Update readme

Issue - State: open - Opened by korikuzma almost 2 years ago - 1 comment
Labels: documentation

#197 - Pin vicc / ga4gh dependencies

Issue - State: closed - Opened by korikuzma almost 2 years ago

#196 - feat: initial work for metaschema updates

Pull Request - State: closed - Opened by korikuzma almost 2 years ago - 1 comment

#195 - ci: bump action versions

Pull Request - State: closed - Opened by jsstevenson almost 2 years ago

#194 - Capture civic phenotype data

Issue - State: open - Opened by korikuzma about 2 years ago - 1 comment
Labels: enhancement

#193 - Update queries to reflect gk pilot update

Issue - State: open - Opened by korikuzma about 2 years ago - 1 comment
Labels: enhancement, epic, requirement, priority:high, gk-pilot

#192 - Update database to reflect gk pilot update

Issue - State: closed - Opened by korikuzma about 2 years ago - 1 comment
Labels: enhancement, requirement, priority:high, gk-pilot

GitHub / cancervariants/metakb issues and pull requests