cancervariants/disease-normalization issues and pull requests

#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 almost 2 years ago

#120 - NCIt import issues

Issue - State: open - Opened by jsstevenson almost 2 years ago - 4 comments
Labels: bug, NCIt

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

Issue - State: open - Opened by jsstevenson almost 2 years ago - 1 comment
Labels: bug, priority:low, keep-alive

#118 - Remove therapy references due to copy/paste

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

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

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

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

Pull Request - State: closed - Opened by jsstevenson almost 2 years ago - 1 comment
Labels: priority:low

#115 - ci: overhaul test data

Pull Request - State: closed - Opened by jsstevenson almost 2 years ago
Labels: priority:low

#114 - ci: overhaul test data

Pull Request - State: closed - Opened by jsstevenson almost 2 years ago
Labels: priority:medium

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

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

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

Pull Request - State: closed - Opened by jsstevenson almost 2 years ago - 1 comment

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

Issue - State: open - Opened by korikuzma about 2 years ago - 3 comments
Labels: bug, NCIt

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

Issue - State: open - Opened by jsstevenson about 2 years ago - 2 comments
Labels: priority:low, performance, keep-alive

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

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

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

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

#107 - Overhaul test fixtures

Issue - State: closed - Opened by jsstevenson about 2 years ago
Labels: test

#106 - fix: MONDO latest version retrieval

Pull Request - State: closed - Opened by korikuzma about 2 years ago - 1 comment
Labels: bug, MONDO, priority:medium

#105 - fix: Catch ValueError during MONDO ETL

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

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

Issue - State: closed - Opened by korikuzma about 2 years ago
Labels: bug, MONDO

#103 - Use bioversions to get MONDO version

Issue - State: closed - Opened by korikuzma about 2 years ago - 4 comments
Labels: enhancement, MONDO

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

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

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

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

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

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

#99 - fix: click echo msg

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

#98 - fix: click echo msg

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

#97 - Cleanup click message format

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

#96 - Get GitHub Actions to pass

Issue - State: closed - Opened by korikuzma about 2 years ago
Labels: test

#95 - build: do not pin exact version for ga4gh.vrsatile.pydantic

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

#94 - Unpin exact ga4gh.vrsatile.pydantic version in main

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

#93 - Don't import obsolete MONDO/NCIt concepts

Issue - State: open - Opened by jsstevenson about 2 years ago - 1 comment
Labels: bug, MONDO, NCIt

#92 - Support lookup by context free OncoTree code

Issue - State: open - Opened by jsstevenson about 2 years ago
Labels: enhancement, OncoTree

#91 - Indicate whether term is oncologic

Issue - State: closed - Opened by jsstevenson about 2 years ago - 1 comment
Labels: enhancement, priority:medium, keep-alive

#90 - ci: update style and checks

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

#89 - ci: add python 3.11 checks

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

#88 - ci: use vanilla pip for tests

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

#86 - fix: stricter Mondo xref import rules

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

#85 - build: use latest version of ga4gh.vrsatile.pydantic

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

#84 - Staging

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

#83 - refactor!: changes to help with serverless (#82)

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

#82 - Transition to serverless

Issue - State: closed - Opened by korikuzma over 2 years ago - 5 comments

#81 - Only use MONDO:equivalentTo relationships for Mondo xrefs

Issue - State: closed - Opened by jsstevenson over 2 years ago - 1 comment
Labels: MONDO

#80 - Normalization wonkiness

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

#79 - feat: use most recent data

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

#78 - ci: update gh actions versioning

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

#77 - Unable to normalize MetaKB terms

Issue - State: closed - Opened by korikuzma over 2 years ago - 6 comments
Labels: OncoTree, priority:high, analysis, stale, closed-by-stale

#76 - refactor: disease_id --> disease

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

#75 - Staging

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

#74 - refactor: use DiseaseDescriptor from ga4gh.vrsatile.pydantic

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

#73 - Update ga4gh.vrsatile.pydantic to reflect schema changes

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

#72 - Capture SSSOM mappings from MONDO

Issue - State: open - Opened by jsstevenson almost 3 years ago - 2 comments
Labels: MONDO, priority:medium, stale-exempt

#71 - Staging

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

#70 - Update internal search/normalize API

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

#69 - Enable param entry in swaggerui by default

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

#68 - Return all matches in search/

Issue - State: open - Opened by jsstevenson about 3 years ago - 2 comments
Labels: enhancement, priority:medium, stale-exempt

#67 - Add url to openapi contact info

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

#66 - Handling grade in cancers

Issue - State: open - Opened by jsstevenson about 3 years ago - 2 comments
Labels: enhancement, priority:low, stale-exempt

#65 - Staging

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

#64 - Issue 63

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

#63 - update vrsatile-pydantic dependency

Issue - State: closed - Opened by jsstevenson about 3 years ago

#62 - Issue 61

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

#61 - Get app logs to show in EB

Issue - State: closed - Opened by korikuzma over 3 years ago
Labels: bug

#60 - Issue 59

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

#59 - Add tests for api endpoints for schema validation

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

#58 - Issue 55

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

#57 - EB use python 3.8

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

#56 - emergency

Issue - State: closed - Opened by jsstevenson over 3 years ago

#55 - Use ga4gh.vrsatile.pydantic models

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

#54 - Capture MTHU terms from OMIM

Issue - State: open - Opened by jsstevenson over 3 years ago
Labels: OMIM

#53 - Create release.yml

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

#52 - Automate pypi release using GH Actions

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

#51 - Improve error description if OMIM file is missing

Issue - State: closed - Opened by jsstevenson over 3 years ago - 2 comments
Labels: OMIM, priority:medium, ux, stale

#50 - Cleanup

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

#49 - Handle missing merge ref

Issue - State: closed - Opened by jsstevenson almost 4 years ago

#48 - Issue 47

Pull Request - State: closed - Opened by jsstevenson almost 4 years ago - 1 comment

#47 - other_id -> xref, xref -> associated_with

Issue - State: closed - Opened by jsstevenson almost 4 years ago

#46 - Issue 13

Pull Request - State: closed - Opened by jsstevenson almost 4 years ago

#45 - Issue 39

Pull Request - State: closed - Opened by jsstevenson almost 4 years ago

#44 - Issue 43

Pull Request - State: closed - Opened by korikuzma almost 4 years ago

#43 - Rename Value Object IDs

Issue - State: closed - Opened by korikuzma almost 4 years ago

#42 - Adds Dockerfile

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

#41 - Dockerfile

Issue - State: closed - Opened by bwalsh almost 4 years ago - 3 comments
Labels: enhancement, priority:low, stale, closed-by-stale

#40 - Resolve NCIT/UMLS identifier confusions

Issue - State: closed - Opened by jsstevenson almost 4 years ago

#39 - Enable search by associated_with fields

Issue - State: closed - Opened by jsstevenson almost 4 years ago

#38 - Issue 37

Pull Request - State: closed - Opened by jsstevenson almost 4 years ago - 1 comment

#37 - Add service meta to response

Issue - State: closed - Opened by jsstevenson almost 4 years ago

#36 - Add EB files back for CI/CD

Pull Request - State: closed - Opened by jsstevenson almost 4 years ago

#35 - add codebuild files

Pull Request - State: closed - Opened by korikuzma almost 4 years ago

#34 - Fix search on partial sources loaded bug

Pull Request - State: closed - Opened by korikuzma almost 4 years ago

#33 - Error when searching without all sources loaded

Issue - State: closed - Opened by korikuzma almost 4 years ago

#32 - Env var

Pull Request - State: closed - Opened by korikuzma almost 4 years ago

#31 - Cli tests

Pull Request - State: closed - Opened by jsstevenson almost 4 years ago

#30 - Wrong error message for failure to include Mondo in merge update command

Issue - State: closed - Opened by jsstevenson almost 4 years ago

#29 - only use one env var for eb

Pull Request - State: closed - Opened by korikuzma almost 4 years ago

#28 - Fix case

Pull Request - State: closed - Opened by jsstevenson almost 4 years ago

#27 - Clean OMIMPS xref values

Issue - State: closed - Opened by jsstevenson almost 4 years ago - 1 comment
Labels: enhancement

#26 - Initial draft of DB updates

Pull Request - State: closed - Opened by jsstevenson almost 4 years ago

#23 - Handle OMIM deprecated concepts

Issue - State: closed - Opened by korikuzma almost 4 years ago - 2 comments
Labels: enhancement, OMIM, priority:medium, stale

#20 - Issue 12 gh

Pull Request - State: closed - Opened by jsstevenson almost 4 years ago

#13 - Load Disease Ontology from local file

Issue - State: closed - Opened by jsstevenson almost 4 years ago
Labels: bug

GitHub / cancervariants/disease-normalization issues and pull requests