Cgbeacon2

Fixed
- Modified the Beacon API version from `1.0` to `1.0.1`

Added
- Explicit `/apiv1.0/info` endpoint
Fixed
- Response errors compliant with API
- Validation errors against GA4GH's OpenAPI specification and CSCfi JSON schemas
- Make sure that dataset version created via API is of type string

Added
- Load genes when initializing demo application
- Instructions on how to load/update genes in database to filter uploaded VCFs by genes
- Added an add_dataset endpoint to create or update datasets via the API
- Return error if provided VCF path is not found before extracting genomic intervals of interest
Fixed
- Fixed code to remove all deprecation warnings
- Dockerfile worker owns the workdir to prevent permission denied when writing temp filtered VCF file
- Adding and removing variants in background after API calls
Changed
- `add` and `delete` endpoints return response code 202 (accepted) instead of 200 (success)

Added
- Redirect to query form page when user lands on / endpoint
- Software version on query form page
- Database name and general stats on landing page
- Tooltips on query form explaining that coordinates are 0-based
- Clicking on number of datasets in query form expands dataset description window
- Codecov config file
- Push gunicorn server image to Docker Hub on new release event
Changed
- / endpoint redirects to info endpoint returning json beacon info
- Refactored HTML query form to be more user friendly
- Refactored query form page to better display dataset-specific results
- Refactored cli options and params to be compliant with the GNU coding standards
- Moved code checking parameters used to create a new dataset in a dedicated function under utils/add.py
- Removed optional consent codes when creating a new dataset, as they are not required and complicate code
Fixed
- Return dataset-specific info even if allele is not found
- Instructions on how to deploy the beacon with podman as a systemd service
- Updated Black version used in GitHub action's to 22.3.0, to fix linting error in CI due to new Click release
- Dataset version is saved as a string

Fixed
- Long description error in setup.py file causing an error on twine before PyPI push
- Switch to codecov action v.2, since v.1 is deprecated

Added
- Push to PyPI when a new release is created
- Dockerfile-server to serve the prod app via gunicorn
- Notify admins via email when app crashes
- Queries using fuzzy string searching (allow Ns in search pattern)
- Return type annotation to all python functions
Changed
- Install required libs from requirements.txt directly in setup.py
- Dockerfile-server image pushed to Docker Hub (cgbeacon2-server-stage) when a PR is opened or updated
- Refactored code in server/blueprints/api_v1/controllers.py
Fixed
- Error returned when query contains non-existent dataset IDs
- Serve images as static files otherwise nginx doesn't show them