Ecosyste.ms: Issues

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

GitHub / Clinical-Genomics/patientMatcher issues and pull requests

#345 - Build & Push to Docker Hub failing

Issue - State: closed - Opened by northwestwitch 5 months ago

#344 - remove many info logs

Issue - State: open - Opened by northwestwitch 8 months ago

#343 - Bump tj-actions/branch-names from 5 to 7.0.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 2 comments
Labels: dependencies

#341 - Gunicorn worker not booting

Issue - State: closed - Opened by northwestwitch 11 months ago - 3 comments
Labels: bug

#340 - Minor release 4.5

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

#339 - generalize mongodb version in tests and docker-compose

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

#338 - Unfreeze PyMongo and run tests and docker-compose using MongoDB 7.0.2

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 3 comments

#337 - unfreeze PyMongo

Issue - State: closed - Opened by northwestwitch 11 months ago - 1 comment
Labels: enhancement

#336 - Option to rename a connected node to something else

Issue - State: open - Opened by northwestwitch about 1 year ago
Labels: enhancement

#334 - How to use docker image to run commands for interacting with the database

Issue - State: closed - Opened by northwestwitch about 1 year ago - 1 comment

#333 - Modify node documents to include link to institute

Issue - State: open - Opened by northwestwitch about 1 year ago
Labels: enhancement

#332 - Minor release v4.4

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 3 comments

#331 - Fix gunicorn workers boot by replacing python base in Dockerfile

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 7 comments

#330 - Gunicorn workers not loading

Issue - State: closed - Opened by northwestwitch about 1 year ago - 1 comment
Labels: bug

#329 - Display connected nodes info on index page

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 3 comments

#328 - Fix parsing of disease file and update resources

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 3 comments

#327 - Newest resource file not correctly parsed

Issue - State: closed - Opened by northwestwitch about 1 year ago - 1 comment
Labels: bug

#326 - Fixed broken Build and publish to Docker stage badge

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

#325 - Display connected details on landing page

Issue - State: closed - Opened by dnil over 1 year ago - 2 comments
Labels: enhancement

#324 - Broken badge on readme page

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

#323 - Minor version 4.3

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

#322 - Abort if phenotype terms are not correctly parsed from files

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments

#321 - Replace deprecated version of Ubuntu in GitHub actions

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

#320 - Switch from phenotype_annotation.tab to phenotype.hpoa

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

#319 - Do not start the server if resource files can't be parsed properly

Issue - State: closed - Opened by northwestwitch over 1 year ago
Labels: enhancement, easy

#318 - Can't download phenotype_annotation.tab

Issue - State: closed - Opened by northwestwitch over 1 year ago - 2 comments
Labels: bug

#317 - Deprecated Ubuntu version 18.04 in GitHub actions

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

#316 - Version 4.2

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

#315 - Fix many code smells reported by SonarCloud

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

#314 - Display correct number of parsed diseases when server starts

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

#313 - Parsed 0 disease/phenotypes from resource file

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

#312 - Fix sonarcloud bugz

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

#311 - Decreased vulnerability by removing some server log messages

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

#310 - Fix link to phenotype_annotation.tab

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

#309 - Phenotype annotations link is not working any more

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

#308 - Fix security hotspots

Pull Request - State: closed - Opened by northwestwitch about 2 years ago - 5 comments

#307 - Add this repo to Sonarcloud

Issue - State: closed - Opened by northwestwitch about 2 years ago - 3 comments

#306 - Prepare version 4.1

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

#305 - Added docs on how to update phenotype resource files

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

#304 - Automatic download of phenotye resources when app starts

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

#302 - Docs link doesn't work

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

#301 - New major release 4.0

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

#300 - Move documentation to dedicated mkdocs pages

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

#299 - Fixed ports used by app served using docker-compose in readme

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

#298 - Wrong port serving the app in readme file

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

#297 - Removed support for async requests/responses - major release change

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

#296 - Remove asynchronous responses from server views

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

#295 - Update database (diagnoses and phenotypes) both for demo and prod instances

Issue - State: closed - Opened by northwestwitch over 2 years ago - 1 comment
Labels: Clinical Genomics Solna instance only

#294 - New minor version 3.4

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

#293 - Remove critical issues -- HTTP-related concerns --

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

#292 - Upgrade black vesion in GitHub action

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

#291 - cannot import name '_unicodefun' from 'click'

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

#290 - Created codecov config file

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

#288 - Update codecov action to version 2

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

#287 - Codecov action v.1 got deprecated, switch to v.2

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

#286 - Prepare version 3.3

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

#285 - Favicon

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

#284 - Add favicon to index page

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

#283 - Add cite info on index page

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

#282 - Update citation to point to paper

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

#281 - Modify references to point to our new paper

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

#280 - Include db name in crash email report

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

#278 - Move documentation to dedicated docs pages (mkdocs)

Issue - State: closed - Opened by northwestwitch over 2 years ago
Labels: enhancement

#277 - Test admin notifications when app crashes

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

#276 - Email notifications triggered by server errors are not tested

Issue - State: closed - Opened by northwestwitch over 2 years ago - 1 comment
Labels: bug, enhancement

#275 - Prepare new minor version 3.2

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

#274 - Changed colors and upgraded icons of landing page

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

#273 - Prepare patch version 3.1.2

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

#272 - Improve email error debugging

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

#270 - Version 3.1.1

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

#269 - Fix env vars parsing

Pull Request - State: closed - Opened by northwestwitch over 2 years ago - 3 comments

#267 - Prepare minor version 3.1

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

#266 - Mock ALL web services in tests -- FINAL

Pull Request - State: closed - Opened by northwestwitch over 2 years ago - 2 comments
Labels: refactor

#264 - Mock the download of files containing phenotype resources in tests

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

#263 - Mock Ensembl services (gene conversion and liftover) used in patient parsing tests

Pull Request - State: closed - Opened by northwestwitch over 2 years ago - 3 comments

#262 - Speed-up CI tests by caching installation of libs and splitting tests into groups

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

#261 - Prepare new major version 3.0

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 1 comment

#260 - Refactor cli and relative documentation --MAJOR RELEASE--

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 1 comment

#258 - Speed up tests

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

#257 - Include software version in email notifications

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 1 comment

#256 - Fixed parsing of admins emails list when provided using env vars

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 2 comments

#255 - Created a landing page for PatientMatcher

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 2 comments

#253 - Fix metrics

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 1 comment

#252 - Same number of matches sent and matches received in metrics

Issue - State: closed - Opened by northwestwitch almost 3 years ago
Labels: bug

#251 - Refactor cli options and params to be compliant with the GNU coding standards

Issue - State: closed - Opened by northwestwitch almost 3 years ago
Labels: enhancement

#250 - New minor version 2.13

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

#249 - Improved initial debug messages

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

#248 - Dockerfile for pmatcher + Dockerfile for server

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 2 comments

#247 - Docker deploy stage

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 2 comments

#246 - Fix app wsgi and run Docker prod app via Gunicorn

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 8 comments

#245 - Deprecated werkzeug.contrib error with werkzeug>=1.0.0

Issue - State: closed - Opened by northwestwitch almost 3 years ago - 1 comment
Labels: bug