Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / cancervariants/metakb issues and pull requests

#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 almost 2 years ago
Labels: priority:medium, ci/cd

#221 - refactor: remove LAST_UPDATED

Pull Request - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:low, technical debt

#220 - Refactor getting logger

Issue - State: closed - Opened by korikuzma almost 2 years ago - 2 comments
Labels: priority:low, technical debt

#219 - Refactor CLI to remove the class

Issue - State: closed - Opened by korikuzma almost 2 years ago - 1 comment
Labels: priority:low, technical debt

#218 - Remove LAST_UPDATED in version.py

Issue - State: closed - Opened by korikuzma almost 2 years ago
Labels: priority:low, technical debt

#217 - build!: update dependencies

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

#215 - Bump starlette from 0.22.0 to 0.25.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#214 - Bump ipython from 8.7.0 to 8.10.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#213 - Update civicpy to ~= 3.0.0

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

#212 - OncoKB analysis work

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

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

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

#210 - Consider updating CLI arguments

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

#209 - How to handle PubMed documents from various sources

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

#207 - neo4j driver close session deprecation

Issue - State: closed - Opened by korikuzma about 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] about 2 years ago - 2 comments

#205 - Unpin exact versions for dependencies

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

#204 - OncoKB add abstracts as documents

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

#203 - Update to neo4j cypher v5

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

#202 - Staging

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

#201 - build!: pin dependencies

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

#200 - Update gene-normalizer version

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

#199 - Add linting actions

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

#198 - Update readme

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

#197 - Pin vicc / ga4gh dependencies

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

#196 - feat: initial work for metaschema updates

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

#195 - ci: bump action versions

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

#194 - Capture civic phenotype data

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

#193 - Update queries to reflect gk pilot update

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

#191 - Bump oauthlib from 3.2.0 to 3.2.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 3 comments

#190 - Add support for TherapeuticSubstituteGroup

Issue - State: closed - Opened by korikuzma over 2 years ago - 3 comments
Labels: gk-pilot

#189 - Add support for CombinationTherapy

Issue - State: closed - Opened by korikuzma over 2 years ago - 3 comments
Labels: gk-pilot

#188 - Metaschema update

Issue - State: closed - Opened by korikuzma over 2 years ago - 2 comments
Labels: epic

#187 - Bump nbconvert from 6.5.0 to 6.5.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment

#186 - Consider restructuring CDM files

Issue - State: open - Opened by korikuzma over 2 years ago - 1 comment
Labels: technical debt, gk-pilot

#185 - Automate updates to data

Issue - State: open - Opened by korikuzma over 2 years ago - 1 comment
Labels: enhancement, requirement, priority:high

#184 - Bump mistune from 0.8.4 to 2.0.3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment

#183 - Test installation on different OS

Issue - State: open - Opened by korikuzma over 2 years ago
Labels: enhancement, build

#182 - Remove semicolons from file names in analysis directory

Issue - State: closed - Opened by korikuzma over 2 years ago - 1 comment
Labels: chore

#181 - Update civicpy cache

Issue - State: closed - Opened by korikuzma over 2 years ago - 1 comment
Labels: bug

#180 - Update source schemas for metaschema update

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

#179 - Don't hardcode versions

Issue - State: closed - Opened by korikuzma over 2 years ago - 2 comments
Labels: bug

#178 - Considering storing external dependency versions in harvest/cdm files

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

#177 - Bump lxml from 4.9.0 to 4.9.1

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

#176 - docs: update readme and add readme for cli

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

#175 - Staging

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

#174 - build: update variation normalizer + other requirements

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

#173 - Staging

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

#172 - build: update requirements

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

#171 - Bump pyjwt from 1.7.1 to 2.4.0

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

#170 - Add OncoKB as a source

Issue - State: open - Opened by korikuzma over 2 years ago - 6 comments
Labels: enhancement, requirement, priority:medium, gk-pilot, stale-exempt

#169 - feat: Add transformed regulatory_approval field from Therapy Normalizer

Pull Request - State: closed - Opened by korikuzma almost 3 years ago

#168 - Add FDA Approval field from Therapy Normalizer

Issue - State: closed - Opened by korikuzma almost 3 years ago - 1 comment

#167 - Staging

Pull Request - State: closed - Opened by korikuzma almost 3 years ago

#166 - Issue 162: Update variation normalizer dependency

Pull Request - State: closed - Opened by korikuzma almost 3 years ago

#165 - Have analysis dir pull from existing files

Issue - State: closed - Opened by korikuzma almost 3 years ago - 1 comment
Labels: enhancement

#164 - Error loading json files using --load_target_cdm

Issue - State: closed - Opened by wx115 almost 3 years ago - 4 comments
Labels: bug

#163 - Bump notebook from 6.4.8 to 6.4.10

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 2 comments

#162 - Update variation normalizer dependency

Issue - State: closed - Opened by korikuzma almost 3 years ago

#161 - Bump jupyter-server from 1.13.4 to 1.15.4

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago

#160 - Issue 48

Pull Request - State: closed - Opened by jsstevenson almost 3 years ago

#158 - Add param to filter query results by source

Issue - State: open - Opened by korikuzma almost 3 years ago
Labels: enhancement, good first issue

#153 - Remove warnings during transform

Issue - State: closed - Opened by korikuzma about 3 years ago - 1 comment

#139 - Query hard-to-search variation concepts

Issue - State: open - Opened by jsstevenson about 3 years ago
Labels: enhancement

#137 - Have warnings for supported_by evidence show even when detail is not set to true

Issue - State: open - Opened by korikuzma about 3 years ago
Labels: enhancement

#128 - TherapeuticResponsePropositions should allow more than 1 object

Issue - State: closed - Opened by korikuzma about 3 years ago - 6 comments
Labels: epic, gk-pilot

#126 - Use better caching strategies for searches

Issue - State: open - Opened by korikuzma about 3 years ago
Labels: enhancement, performance

#125 - Better exception raising/handling

Issue - State: open - Opened by jsstevenson about 3 years ago
Labels: enhancement, technical debt

#124 - Add SVIP-O resource

Issue - State: open - Opened by ahwagner about 3 years ago
Labels: enhancement

#123 - Use ruff and black

Issue - State: closed - Opened by korikuzma over 3 years ago - 2 comments
Labels: cleanup

#118 - Add Categorical Variation

Issue - State: closed - Opened by korikuzma over 3 years ago - 2 comments
Labels: enhancement

#116 - Extendability concerns

Issue - State: open - Opened by richardhj over 3 years ago
Labels: question

#104 - Extend harvester/normalizer process to BioThings Studio

Issue - State: closed - Opened by MayLiu27 over 3 years ago - 1 comment
Labels: enhancement

#102 - Add PharmGKB

Issue - State: open - Opened by jsstevenson over 3 years ago
Labels: enhancement, requirement

#96 - Add CIViC Pathogenicity Statements

Issue - State: open - Opened by korikuzma almost 4 years ago
Labels: enhancement

#75 - Maps mounted data dependencies to normalizer packages

Pull Request - State: closed - Opened by bwalsh almost 4 years ago - 2 comments

#66 - Identify and resolve normalization misses

Issue - State: open - Opened by jsstevenson almost 4 years ago - 5 comments
Labels: bug, requirement, analysis

#61 - Optimize Neo4j schema

Issue - State: open - Opened by jsstevenson almost 4 years ago - 3 comments
Labels: enhancement

#51 - therapeutic response data model

Issue - State: closed - Opened by ahwagner about 4 years ago - 2 comments
Labels: enhancement

#48 - Establish logging protocol and consistency

Issue - State: closed - Opened by jsstevenson about 4 years ago - 3 comments
Labels: enhancement

#44 - #32: PMKB Harvester

Pull Request - State: closed - Opened by jsstevenson about 4 years ago - 6 comments

#39 - Biomedical Knowledge Graph Resources

Issue - State: closed - Opened by ahwagner about 4 years ago
Labels: enhancement

#38 - Virtual environment management

Issue - State: closed - Opened by ahwagner about 4 years ago - 2 comments
Labels: enhancement

#37 - Consider producing Kafka streams for incremental updates

Issue - State: open - Opened by ahwagner about 4 years ago
Labels: enhancement

#35 - Consider ES as a solution for type ahead

Issue - State: open - Opened by bwalsh about 4 years ago
Labels: enhancement

#33 - Write loader / harvester for COSMIC Actionability

Issue - State: open - Opened by ahwagner about 4 years ago - 1 comment
Labels: enhancement

#32 - Write loader / harvester for PMKB

Issue - State: open - Opened by ahwagner about 4 years ago
Labels: enhancement

#29 - Update documentation

Issue - State: closed - Opened by ahwagner over 4 years ago - 1 comment
Labels: good first issue

#21 - data downloaders

Issue - State: open - Opened by ahwagner about 6 years ago - 1 comment
Labels: enhancement

#12 - determining oncogenecity

Issue - State: open - Opened by ahwagner about 6 years ago - 7 comments
Labels: enhancement

#11 - collect interface requirements

Issue - State: open - Opened by ahwagner about 6 years ago - 7 comments
Labels: enhancement

#8 - consider branding

Issue - State: open - Opened by ahwagner about 6 years ago
Labels: enhancement

#6 - sequence features

Issue - State: open - Opened by ahwagner about 6 years ago - 8 comments
Labels: enhancement

#5 - search requirements

Issue - State: open - Opened by ahwagner about 6 years ago - 2 comments
Labels: enhancement

#4 - resources to add

Issue - State: open - Opened by ahwagner about 6 years ago - 12 comments
Labels: enhancement

#3 - data model requirements

Issue - State: open - Opened by ahwagner about 6 years ago - 5 comments
Labels: enhancement