cancervariants/disease-normalization issues and pull requests

#223 - fix!: `xrefs` should have `exactMatch` for `ConceptMapping.relation`

Pull Request - State: closed - Opened by korikuzma 15 days ago
Labels: bug, priority:medium

#222 - Sources we ingest should have `exactMatch` for `ConceptMapping.relation`

Issue - State: closed - Opened by korikuzma 15 days ago
Labels: bug, priority:high

#221 - fix!: use correct representation of Coding object in mappings

Pull Request - State: closed - Opened by korikuzma 25 days ago - 3 comments
Labels: bug, priority:medium

#220 - `Coding` object in mappings is not being represented correctly

Issue - State: closed - Opened by korikuzma 26 days ago
Labels: bug, priority:high

#219 - fix: correct P310 URI typo in NCIt extraction

Pull Request - State: closed - Opened by jsstevenson about 1 month ago - 4 comments
Labels: priority:low

#218 - ruff update

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

#217 - chore!: rename optional dependency

Pull Request - State: closed - Opened by korikuzma about 1 month ago - 4 comments
Labels: priority:low, chore

#216 - feat!: remove `normalized_id` and leverage `MappableConcept.primaryCode`

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

#215 - feat!: use preferred formats for `MappableConcept.mappings`

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

#214 - `NamespacePrefix` contains external sources that we don't capture

Issue - State: open - Opened by korikuzma about 2 months ago - 2 comments
Labels: question, priority:low

#213 - Remove `normalized_id` and leverage `MappableConcept.primaryCode`

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

#212 - Use preferred formats for `MappableConcept.mappings`

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

#211 - fix: handle mondo xref annotation changes

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

#210 - feat!: update models to vrs 2.0.0 community review ballot

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

#209 - Update models to VRS 2.0.0 Community Review Ballot

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

#208 - cicd: fix hook names

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

#207 - build!: require python >=3.11

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

#206 - chore: add acceptance criteria to issue templates

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

#205 - cicd: update precommit

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

#204 - style: update ruff configs

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

#203 - chore: update gitignore

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

#202 - build: fix test group name

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

#201 - Normalized concepts are borked

Issue - State: closed - Opened by jsstevenson 4 months ago - 1 comment
Labels: priority:high

#200 - feat: add oncologic disease parameter from mondo terms

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

#199 - Capture UniProt disease entries

Issue - State: open - Opened by jsstevenson 5 months ago
Labels: enhancement, priority:low, keep-alive

#198 - fix: update preferred OMIM prefix

Pull Request - State: closed - Opened by jsstevenson 6 months ago
Labels: priority:low

#197 - All mondo xrefs are broken

Issue - State: closed - Opened by jsstevenson 6 months ago - 2 comments
Labels: bug, priority:high

#196 - cicd: update workflows/templates from template repo

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

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

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

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

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

#193 - build!: update ga4gh.vrs version

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

#192 - style: update ruff to 0.5.0

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

#191 - build: require >= Python 3.10

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

#190 - Add `omim-directory` console entrypoint

Issue - State: open - Opened by jsstevenson 8 months ago - 1 comment
Labels: enhancement, priority:low, stale-exempt

#189 - fix: don't configure logging on library import

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

#188 - feat: add tqdm to track update progress

Pull Request - State: closed - Opened by jsstevenson 10 months ago
Labels: enhancement, priority:low

#187 - docs: fix readthedocs links

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

#186 - readthedocs in readme give 404

Issue - State: closed - Opened by korikuzma 11 months ago
Labels: bug, documentation, priority:low

#185 - docs: clean up README

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

#184 - docs: add RTD config

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

#183 - cicd: test on 3.12

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

#182 - cicd: add priority label requirement

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

#181 - build: update build metadata

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

#180 - Update OMIM refs in Disease Ontology

Issue - State: closed - Opened by jsstevenson 12 months ago - 1 comment
Labels: enhancement, priority:high, keep-alive

#179 - style: update ruff rules

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

#178 - docs: add docs skeleton

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

#177 - style: update ruff rules

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

#176 - Use Mondo ID instead of NCIt ID to designate normalized groups

Issue - State: open - Opened by jsstevenson about 1 year ago - 1 comment
Labels: enhancement, priority:medium, keep-alive

#175 - fix: ensure consistent source meta schema typing

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

#174 - Expected `SourceMeta` but got `dict` - serialized value may not be as expected

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

#173 - Refine `Base.load_disease()`

Issue - State: open - Opened by jsstevenson about 1 year ago - 1 comment
Labels: bug, priority:low, keep-alive

#172 - Pickier ingest of xrefs/associated_with

Issue - State: open - Opened by jsstevenson about 1 year ago - 2 comments
Labels: priority:medium, keep-alive

#171 - feat!: use OBO release for Mondo

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

#170 - style: fix ruff settings

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

#169 - test: suppress noisy boto logs by default

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

#168 - cicd: use ruff for formatting

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

#167 - test: add basic route tests

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#166 - chore: remove unused configs

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

#165 - fix: catch ETL module import errors

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#164 - feat!: remove search result formatting options

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#163 - feat!: use wags-tails for managing data

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#162 - feat!: merge concepts and source dynamodb tables

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#161 - build: use pyproject.toml for build configuration

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

#160 - feat: add get_all_records DB method

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

#159 - Use pyproject.toml for setup/build

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

#158 - Add basic route tests

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

#157 - Catch ETL import errors in CLI

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

#156 - Remove format option in /search

Issue - State: open - Opened by jsstevenson over 1 year ago - 1 comment
Labels: enhancement, priority:medium, keep-alive

#155 - merge concepts + metadata tables

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

#154 - build: modernize build config

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

#153 - fix!: use better name for CLI source option

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

#152 - feat: optionally define dynamo table names via env variable

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

#151 - test: update test data

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:medium

#150 - 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

#149 - 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

#148 - cicd: make unused import fixable

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

#147 - feat: optionally define dynamo table names via environment variable

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

#146 - fix: use correct source priority in normalize resolution

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

#145 - cicd: update style checks and test coverage dependencies

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

#144 - fix: use correct source priority in normalize resolution

Pull Request - State: closed - Opened by jsstevenson over 1 year ago - 2 comments

#143 - fix `_record_order` priority

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

#142 - TypeError while loading Mondo

Issue - State: closed - Opened by jsstevenson over 1 year ago - 6 comments
Labels: bug, priority:high, technical debt

#141 - Replace bioversions dependency

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

#140 - feat!: use vrs 2.0-alpha models in /normalize

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

#139 - Add methods to fetch parent/child/sibling terms

Issue - State: open - Opened by jsstevenson over 1 year ago - 1 comment
Labels: enhancement, priority:low, keep-alive

#138 - Add deprecated oncotree terms and a "deprecated term" match type

Issue - State: open - Opened by jsstevenson over 1 year ago - 1 comment
Labels: enhancement, priority:medium, keep-alive

#137 - Update dynamo table usage

Issue - State: closed - Opened by jsstevenson over 1 year ago
Labels: enhancement, priority:medium

#136 - Add get_all_records DB method

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

#135 - Update pydantic to v2 + remove ga4gh.vrsatile.pydantic dependency

Issue - State: closed - Opened by jsstevenson over 1 year ago - 2 comments
Labels: priority:high, technical debt, build

#134 - Remove remaining flake8-associated materials

Issue - State: closed - Opened by jsstevenson over 1 year ago - 2 comments
Labels: priority:low, chore, stale

#133 - Remove search result formatting options

Issue - State: open - Opened by jsstevenson over 1 year ago - 1 comment
Labels: enhancement, priority:low, keep-alive

#132 - Add documentation

Issue - State: open - Opened by jsstevenson over 1 year ago - 2 comments
Labels: documentation, priority:medium, keep-alive

#131 - cicd: update style checks and test coverage dependencies

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

#130 - feat: optionally define dynamo table names via environment variable

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#129 - fix!: use better name for CLI source option

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#128 - fix: remove therapy refs

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#127 - test: update test data

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#126 - test

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

#125 - fix: remove therapy references

Pull Request - State: closed - Opened by jsstevenson over 1 year ago
Labels: priority:low

#124 - build: remove requirements.txt files

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

GitHub / cancervariants/disease-normalization issues and pull requests