Patientmatcher

Added
Changed
Fixed
- Liftover crashing when no end coordinate is not provided

Added
- Code for performing coordinate liftover using Ensembl REST API
- Variant liftover when comparing genotype features
Changed
- Using coloredlogs for app logs
Fixed
- removed unused docker folder

Added
Changed
- Install requirements in setup
- Improved Dockerfile and docker-compose files
Fixed
- Connection string to database when creating the app

Changed
- Pulling Docker images in docker-compose from clinicalgenomics Docker Hub
- Switched from Travis CI to github actions

Changed
- Display error message and raise exception when Ensembl Rest API is needed but offline
- New Dockerfile and instructions to run on docker
- Github action to build and push Docker image when a new software release is created
- Try to match patients based on gene symbol (gene._geneName) if gene.id doesn't match

Fixed
- Do not crash trying to convert genes when Ensembl REST API isn't available

Added
- Codeowners document

Fixed
- Avoid pymongo-related deprecated code
- Unblock pytest and mongomock dependencies

Modified
- Open up metrics endpoint for any request (no token needed)

Fixed
- Update HPO file name to reflect resource on compbio.charite.de/jenkins