Ecosyste.ms: Issues

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GitHub / cancervariants/disease-normalization issues and pull requests

#199 - Capture UniProt disease entries

Issue - State: open - Opened by jsstevenson 24 days ago
Labels: enhancement, priority:low, keep-alive

#198 - fix: update preferred OMIM prefix

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

#197 - All mondo xrefs are broken

Issue - State: open - Opened by jsstevenson 2 months ago
Labels: bug, priority:high

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

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

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

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

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

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

#193 - build!: update ga4gh.vrs version

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

#192 - style: update ruff to 0.5.0

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

#191 - build: require >= Python 3.10

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

#190 - Add `omim-directory` console entrypoint

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

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

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

#188 - feat: add tqdm to track update progress

Pull Request - State: closed - Opened by jsstevenson 5 months ago
Labels: enhancement, priority:low

#187 - docs: fix readthedocs links

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

#186 - readthedocs in readme give 404

Issue - State: closed - Opened by korikuzma 6 months ago
Labels: bug, documentation, priority:low

#185 - docs: clean up README

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

#184 - docs: add RTD config

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

#183 - cicd: test on 3.12

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

#182 - cicd: add priority label requirement

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

#181 - build: update build metadata

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

#180 - Update OMIM refs in Disease Ontology

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

#179 - style: update ruff rules

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

#178 - docs: add docs skeleton

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

#177 - style: update ruff rules

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

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

Issue - State: open - Opened by jsstevenson 8 months ago - 1 comment
Labels: enhancement, priority:medium, keep-alive

#175 - fix: ensure consistent source meta schema typing

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

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

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

#173 - Refine `Base.load_disease()`

Issue - State: open - Opened by jsstevenson 10 months ago - 1 comment
Labels: bug, priority:low, keep-alive

#172 - Pickier ingest of xrefs/associated_with

Issue - State: open - Opened by jsstevenson 10 months ago - 2 comments
Labels: priority:medium, keep-alive

#171 - feat!: use OBO release for Mondo

Pull Request - State: closed - Opened by jsstevenson 10 months ago

#170 - style: fix ruff settings

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

#169 - test: suppress noisy boto logs by default

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

#168 - cicd: use ruff for formatting

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

#167 - test: add basic route tests

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

#166 - chore: remove unused configs

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

#165 - fix: catch ETL module import errors

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

#164 - feat!: remove search result formatting options

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

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

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

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

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

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

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

#160 - feat: add get_all_records DB method

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

#159 - Use pyproject.toml for setup/build

Issue - State: closed - Opened by jsstevenson 12 months ago - 1 comment
Labels: priority:low, build

#158 - Add basic route tests

Issue - State: open - Opened by jsstevenson 12 months ago - 1 comment
Labels: priority:medium, test

#157 - Catch ETL import errors in CLI

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

#156 - Remove format option in /search

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

#155 - merge concepts + metadata tables

Issue - State: closed - Opened by korikuzma 12 months ago - 1 comment
Labels: priority:low, technical debt

#154 - build: modernize build config

Pull Request - State: closed - Opened by jsstevenson 12 months ago

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

Pull Request - State: closed - Opened by jsstevenson 12 months ago

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

Pull Request - State: closed - Opened by jsstevenson 12 months ago

#151 - test: update test data

Pull Request - State: closed - Opened by jsstevenson 12 months ago
Labels: priority:medium

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

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

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

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

#148 - cicd: make unused import fixable

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

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

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

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

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

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

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

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

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

#143 - fix `_record_order` priority

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

#142 - TypeError while loading Mondo

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

#141 - Replace bioversions dependency

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

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

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

#137 - Update dynamo table usage

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

#136 - Add get_all_records DB method

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

#134 - Remove remaining flake8-associated materials

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

#133 - Remove search result formatting options

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

#132 - Add documentation

Issue - State: open - Opened by jsstevenson about 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 about 1 year ago

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

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

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

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

#128 - fix: remove therapy refs

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

#127 - test: update test data

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

#126 - test

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

#125 - fix: remove therapy references

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

#124 - build: remove requirements.txt files

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

#123 - build: remove requirements.txt files

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

#122 - ci: test in 3.11

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

#121 - feat!: support PostgreSQL as optional storage backend

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

#120 - NCIt import issues

Issue - State: open - Opened by jsstevenson over 1 year ago - 4 comments
Labels: bug, NCIt

#119 - Include descendants of MONDO_0021178 ("injury")

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

#118 - Remove therapy references due to copy/paste

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

#117 - build: pin owlready2==0.40 in Pipfile

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

#116 - feat!: support PostgreSQL as optional storage backend

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

#115 - ci: overhaul test data

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

#114 - ci: overhaul test data

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

#113 - fix: resolve the ETL problems of the week

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

#112 - fix: resolve the ETL problems of the week

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

#111 - Fourth Ventricle Ependymal Tumor (ncit:C131593) returns no match

Issue - State: open - Opened by korikuzma over 1 year ago - 3 comments
Labels: bug, NCIt

#110 - Only create normalized groups for sizes n > 1

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

#109 - fix: MONDO latest version retrieval (staging)

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

#108 - fix: Catch ValueError during MONDO ETL (staging)

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

#107 - Overhaul test fixtures

Issue - State: closed - Opened by jsstevenson over 1 year ago
Labels: test

#106 - fix: MONDO latest version retrieval

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

#105 - fix: Catch ValueError during MONDO ETL

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

#104 - MONDO `_get_concept_id` raises ValueError when `ref=MESH:MESH:1622152`

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

#103 - Use bioversions to get MONDO version

Issue - State: closed - Opened by korikuzma over 1 year ago - 4 comments
Labels: enhancement, MONDO

#102 - fix(mondo): stricter xref import rules

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

#101 - fix: DiseaseDescriptor.disease --> DiseaseDescriptor.disease_id (main)

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

#100 - Revert `DiseaseDescriptor.disease` to `DiseaseDescriptor.disease_id` in main

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