Ecosyste.ms: Issues

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GitHub / Clinical-Genomics/cgbeacon2 issues and pull requests

#269 - Fix Gunicorn workers by using python-slim-bullseye in Dockerfiles

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 4 comments

#268 - Service eating up CPU

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

#267 - Minor release 4.5

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

#266 - Unfreeze pymongo and use MongoDB 7 in docker-compose file

Pull Request - State: closed - Opened by northwestwitch 11 months ago - 6 comments

#265 - unfreeze PyMongo

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

#264 - Prepare minor version 4.4

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

#263 - Updated GitHub actions

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

#262 - Deprecated Ubuntu version 18.04 in GitHub actions

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

#261 - Prepare version 4.3

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

#260 - Fix security hotspots

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

#259 - Remove return type from function

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

#258 - Fix all SonarCloud major issues

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

#257 - Refactor query controllers and simplify function

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

#256 - Rafactor code to remove SonarCloud critical issues

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

#255 - Add this repo to SonarCloud

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

#254 - Create a new user to interface Scout to the prod beacon instance

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

#253 - Document user add

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

#252 - SVs extracted from SVs VCF are saved as SNPs or INDELs

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

#250 - Load demo data temporary in prod server

Issue - State: closed - Opened by northwestwitch over 2 years ago - 6 comments
Labels: Clinical Genomics Solna instance only

#249 - Prepare release version 4.2.2

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

#248 - Beacon createDateTime collected from config file or from events collection

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

#247 - createDateTime is none when beacon doesn't contain data

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

#246 - Patch version 4.2.1

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

#245 - Fixed API version from 1.0 to 1.0.1

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

#244 - API version is 1.0.1 and not 1.0

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

#243 - Prepare version 4.2

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

#242 - Set response headers to disable caching in Flask app

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

#241 - Force API to create dataset version of type string

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

#240 - Make response errors compliant with API

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

#239 - Fixed all specification errors

Pull Request - State: closed - Opened by northwestwitch over 2 years ago - 4 comments

#238 - Validation tests for Beacon API v1

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

#237 - Specify an explicit 'info' endpoint

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

#236 - Switch from Beacon v1 to Beacon v2 using the beacon verifier software

Issue - State: open - Opened by northwestwitch over 2 years ago - 3 comments
Labels: enhancement

#235 - Validate standard queries

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

#234 - Registration form

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

#233 - Prepare version 4.1

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

#232 - Add an endpoint that returns the list of available datasets (with respective genome build)

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

#231 - Tentative speed up loading vars

Pull Request - State: closed - Opened by northwestwitch over 2 years ago - 4 comments

#230 - Adding variants using the API takes too much time

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

#228 - Fix dockerfiles so containerized app worker is owner of workdir

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

#227 - Error while creating VCF iterator from variant file

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

#226 - Response timeout when adding variants and filtering by thousands of genes

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

#225 - Introduce an index for genes

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

#224 - Remove all deprecated code

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

#223 - Deprecation warnings to be addressed

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

#222 - create/update a dataset via POST requests

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

#220 - Fix CI linting not working after latest Click update

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

#219 - ImportError: cannot import name '_unicodefun' from 'click'

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

#218 - Refactor dataset add function by moving data validation to a function outside the cli

Pull Request - State: closed - Opened by northwestwitch over 2 years ago - 6 comments

#217 - Create a new endpoint to create datasets via authenticated post requests

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

#216 - Instructions on how to populate db with gene data

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

#215 - Add genes together with demo data

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

#214 - Add update genes command in the containerized demo app

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

#213 - Add documentation about updating genes

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

#212 - Prepare major version 4.0

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

#211 - Fix podman systemd docs

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

#210 - Push gunicorn server image to Docker hub on new release event

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

#208 - Add Codecov config file

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

#207 - Remove codecov patch check in GitHub actions

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

#205 - Return dataset-specific info even if allele is not found and search improvements

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

#204 - Improve landing page

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

#203 - Dataset WITHOUT hits search doesn't work in search form

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

#202 - Update genes on a VM by launching a container with podman

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

#201 - Add info that this beacon contains 0-based coordinates

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

#200 - Expand description of datasets on landing page

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

#199 - Test PR: Show request content in add endpoint

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

#198 - Add stats and software version on landing page

Pull Request - State: closed - Opened by northwestwitch over 2 years ago - 4 comments

#197 - Create favicon for web page

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

#196 - Create a redirect to query form endpoint

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

#195 - Fix permission denied when mounting volumes in image filesystem

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

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

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

#193 - Permission denied while trying loading conf file from running container

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

#192 - Update the podman deployment part in the user guide

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

#191 - Launching a container shell to create a new dataset and user for Scout cases on cg-vm1 and cg-prod-services

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

#190 - Prepare patch version 3.3.1

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

#189 - Update codecov action to v.2

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

#188 - Fix long description error in setup.py file causing an error on twine

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

#187 - Display software version on the query form page

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

#186 - Build and Publish to PyPI action is failing

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

#185 - Release version 3.3

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

#184 - Fix relative images path

Pull Request - State: closed - Opened by northwestwitch over 2 years ago - 4 comments

#183 - All images missing from query form page

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

#182 - Provide a config file located on a custom dir

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

#181 - Add return type annotation to all python functions

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

#178 - Use Docker-compose to simulate and test the Elixir AAI-OAuth2

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

#177 - Match queries containing N bases using regular expressions

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

#176 - Crash email

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

#175 - Add app errors email handling

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

#174 - Push Dockerfile with gunicorn to Docker Hub on PR open or modify

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

#173 - Gunicorn serve

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

#172 - Option to use a config file placed in a custom location

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

#171 - Reintroduce install requirements in setup file

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

#170 - Install required libs directly from setup file

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