cancervariants/metakb issues and pull requests

#425 - feat!: move `ViccNormalizerDataExtension` to `mappings`

Pull Request - State: open - Opened by korikuzma 11 days ago
Labels: enhancement, priority:medium

#424 - feat!: change strength representation

Pull Request - State: open - Opened by korikuzma 12 days ago
Labels: enhancement, priority:high

#423 - Update vicc normalizers to pull in coding changes

Issue - State: open - Opened by korikuzma 12 days ago
Labels: priority:high, build

#422 - feat!: add support for civic assertions

Pull Request - State: open - Opened by korikuzma 12 days ago
Labels: enhancement, priority:medium

#421 - style: resolve ruff errors

Pull Request - State: closed - Opened by korikuzma 14 days ago
Labels: priority:medium

#420 - feat!: update models to ga4gh gks nov 2024 ballot releases

Pull Request - State: open - Opened by korikuzma 17 days ago - 1 comment
Labels: enhancement, priority:medium

#419 - Change `strength` representation

Issue - State: open - Opened by korikuzma 17 days ago
Labels: enhancement, priority:medium

#418 - `ViccNormalizerDataExtension` should be moved to `mappings`

Issue - State: open - Opened by korikuzma 18 days ago - 2 comments
Labels: enhancement, priority:medium

#417 - Transformers should include concepts that fail to normalize

Issue - State: open - Opened by korikuzma 18 days ago
Labels: enhancement, priority:medium

#416 - style: update ruff

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

#415 - Update transformers to use the Nov 2024 ballot releases

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

#414 - feat!: add support for transforming civic diagnostic evidence items

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

#413 - fix: aggregate moa oncotree concepts during transformation

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

#412 - feat: add option to cli to create neo4j db constraints

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

#411 - feat!: add support for moa prognostic assertions

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

#410 - Add ability to create MetaKB DB constraints in CLI

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

#409 - MOA disease unique contraint failed

Issue - State: closed - Opened by korikuzma about 2 months ago - 4 comments
Labels: bug, priority:high

#408 - Add support for MOA prognostic data

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

#407 - feat!: add support for transforming CIViC prognostic evidence

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

#406 - Implement GA4GH pagination guide

Issue - State: open - Opened by jsstevenson 2 months ago
Labels: priority:low

#405 - feat!: rename study --> study statement / statement

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

#404 - feat!: use cat-vrs-python + va-spec-python

Pull Request - State: closed - Opened by korikuzma 3 months ago - 1 comment
Labels: enhancement, priority:medium

#403 - build!: require python >= 3.11

Pull Request - State: closed - Opened by jsstevenson 3 months ago - 1 comment
Labels: priority:low

#402 - chore: add acceptance criteria to issue templates

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

#401 - cicd: update precommit configs

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

#400 - style: update ruff configs

Pull Request - State: closed - Opened by jsstevenson 3 months ago - 1 comment
Labels: priority:low

#399 - chore: update gitignore

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

#398 - cicd: warn when merging to main

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

#397 - fix: correct syntax error in `gene_id_constraint`

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

#396 - chore!: rename transform class and dirs to transformers

Pull Request - State: closed - Opened by korikuzma 3 months ago - 2 comments
Labels: priority:low, chore

#395 - Revise "Study" node type to "Statement"

Issue - State: closed - Opened by ahwagner 4 months ago - 7 comments

#394 - Provide data versioning/metadata

Issue - State: open - Opened by jsstevenson 4 months ago
Labels: priority:low

#393 - Rename `Transform` class to `Transformer` for naming consistency

Issue - State: closed - Opened by korikuzma 4 months ago - 1 comment
Labels: priority:low, chore

#392 - build(deps): bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 4 comments
Labels: dependencies, github_actions

#391 - Reconstruct repo as monorepo (client + server)

Issue - State: open - Opened by jsstevenson 5 months ago
Labels: chore

#390 - Add MOA fetcher from wags-tails 0.1.4

Issue - State: open - Opened by jsstevenson 6 months ago - 4 comments
Labels: priority:low

#389 - build!: update ga4gh.vrs + gene/variation normalizers

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

#388 - use cat-vrs-python and va-spec-python

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

#387 - feat!: rename env var for logging + cred handling

Pull Request - State: closed - Opened by korikuzma 7 months ago - 1 comment
Labels: enhancement, priority:low

#386 - build!: update normalizer + ga4gh.vrs depdencies

Pull Request - State: closed - Opened by korikuzma 7 months ago - 2 comments
Labels: priority:medium, build

#385 - chore: update seqrepo version to 2024-02-20

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

#384 - feat: enable pagination

Pull Request - State: closed - Opened by jsstevenson 7 months ago - 1 comment
Labels: priority:low

#383 - cicd: update actions versions, stalebot, + templates from template repo

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

#382 - feat: update pre-commit version + add more hooks

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

#381 - feat!: use setuptools-scm, capture version at package root

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

#380 - style: update ruff version + add more rules

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

#379 - Update normalizer/ga4gh dependencies

Issue - State: closed - Opened by korikuzma 7 months ago - 1 comment
Labels: priority:high, build

#378 - fix: catch TokenRetrievalError in ViccNormalizers + update log levels

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

#377 - feat!: refactor graph DB code, streamline unneeded query transaction usage

Pull Request - State: closed - Opened by jsstevenson 7 months ago
Labels: priority:medium

#376 - feat!: initialize query handler with graph, not graph credentials

Pull Request - State: closed - Opened by jsstevenson 7 months ago - 1 comment
Labels: priority:low

#375 - `QueryHandler` should take graph DB instance as arg

Issue - State: closed - Opened by jsstevenson 7 months ago - 1 comment
Labels: priority:medium, technical debt

#374 - feat!: replace instance var lists with pydantic model

Pull Request - State: closed - Opened by korikuzma 7 months ago - 1 comment
Labels: priority:medium, technical debt

#373 - Refactor graph/DB methods

Issue - State: closed - Opened by jsstevenson 8 months ago - 1 comment
Labels: priority:medium, technical debt

#372 - Batch-upload objects using `UNWIND`

Issue - State: open - Opened by jsstevenson 8 months ago
Labels: priority:low, performance

#371 - refactor!: rename `Transform` instance variables

Pull Request - State: closed - Opened by korikuzma 8 months ago - 1 comment
Labels: priority:low, technical debt

#370 - refactor!: remove `extract_harvester` from `transform` method

Pull Request - State: closed - Opened by korikuzma 8 months ago - 1 comment
Labels: priority:low, technical debt

#369 - log file has wrong name

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

#368 - fix(tests): update test_batch_search to apply PR (#361) suggestions

Pull Request - State: closed - Opened by korikuzma 8 months ago
Labels: bug, priority:low, test

#367 - build: temporarily pin ga4gh.vrs==2.0.0a6

Pull Request - State: closed - Opened by korikuzma 8 months ago
Labels: priority:high, build

#366 - refactor: use updated annotation API

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: priority:low, technical debt

#365 - fix: querying studies based on therapeutic

Pull Request - State: closed - Opened by korikuzma 8 months ago - 2 comments
Labels: bug, priority:medium

#363 - `METAKB_NORM_EB_PROD` -> `METAKB_EB_PROD`

Issue - State: closed - Opened by jsstevenson 8 months ago - 2 comments
Labels: enhancement, priority:low

#362 - Normalizers fail silently

Issue - State: closed - Opened by jsstevenson 8 months ago - 4 comments
Labels: bug, priority:medium

#361 - feat: add batch search by variations

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: enhancement, priority:medium

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

Issue - State: closed - Opened by jsstevenson 8 months ago - 5 comments
Labels: bug, priority:high

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

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: bug, priority:low

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

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: priority:low, test

#357 - Database layer refactor

Issue - State: open - Opened by jsstevenson 8 months ago
Labels: priority:medium, technical debt

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

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: priority:medium, technical debt

#355 - Colon separator for relationship types is deprecated

Issue - State: closed - Opened by jsstevenson 8 months 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 8 months ago
Labels: bug, priority:high

#353 - CIViC harvest fails

Issue - State: closed - Opened by jsstevenson 8 months ago - 1 comment
Labels: bug, priority:high

#352 - fix: use correct Disease model

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: bug, priority:medium

#351 - build: fix pipenv build

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: priority:high

#350 - pipenv build currently failing

Issue - State: closed - Opened by jsstevenson 8 months ago - 3 comments
Labels: bug, priority:high, build

#349 - test: optionally minimize connection debug logging

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: priority:medium, test

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

Issue - State: closed - Opened by jsstevenson 8 months ago - 1 comment
Labels: priority:low, technical debt

#347 - Resolve pydantic serializer warnings

Issue - State: closed - Opened by jsstevenson 8 months ago - 1 comment
Labels: bug, priority:medium

#346 - feat: perform better logging

Pull Request - State: closed - Opened by jsstevenson 8 months ago
Labels: priority:low

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

Issue - State: open - Opened by jsstevenson 8 months 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 9 months ago - 4 comments
Labels: priority:medium

#343 - docs: initial docs work

Pull Request - State: closed - Opened by jsstevenson 9 months ago
Labels: priority:low, documentation

#342 - feat!: sharpen type annotation

Pull Request - State: closed - Opened by jsstevenson 9 months ago
Labels: priority:medium

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

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

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

Pull Request - State: closed - Opened by jsstevenson 9 months ago
Labels: priority:high, chore

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

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

#338 - refactor!: clean up harvest method

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

#335 - create_json should accept a path to file

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

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

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

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

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

#332 - feat!: sharpen up type usage

Pull Request - State: closed - Opened by jsstevenson 9 months ago
Labels: priority:medium

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

Issue - State: closed - Opened by jsstevenson 9 months ago - 2 comments
Labels: enhancement

#330 - refactor: use `SourceName` enum

Pull Request - State: closed - Opened by korikuzma 10 months ago
Labels: priority:low, technical debt

#329 - incorporate staging changes into main

Pull Request - State: closed - Opened by korikuzma 10 months ago - 4 comments
Labels: priority:high

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

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

#327 - incorporate staging changes into main

Pull Request - State: closed - Opened by korikuzma 10 months ago - 2 comments

#326 - cicd: fix elastic beanstalk deployment

Pull Request - State: closed - Opened by korikuzma 10 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 10 months ago
Labels: priority:low, ci/cd

GitHub / cancervariants/metakb issues and pull requests