Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
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