Added parsing of genomic coordinates and fixed parsing of multiple condition IDs

[2.1]

Added

• Parsing of variantType, referenceCopyNumber, copyNumber and chromosomeCoordinates fields from CSV/TSV files
• Genome assembly can be passed as an optional param to tsv_2_json and csv_to_json to create submission containing chromosome coordinates
• Link to demo service instance at clinical genomics

Fixed

• Parsing of multiple condition IDs from csv/tsv files

Fix parsing of condition ID type and HGVS

[2.0.1]

Fixed

• Parsing of Condition ID type
• Do not include HGVS field in submission if it is null

Changes reflecting ClinVar API updates and improvements

[2.0]

Added

• A new tsv_2_json endpoint to convert TSV files in json submission objects
• Keep a Changelog GitHub action
• Black GitHub action
• Flake8 Lint GitHub action
• Vulture GitHub action
• Woke GitHub action
• Badges showing the status of GitHub actions on README page
• File conversion endpoints accept optional parameters to set the following key/values: submissionName, clinvarSubmissionReleaseStatus, assertionCriteria

Changed

• New API schema introduced on 2022-11-21
• Modified file parsing code to create submission jsons compliant with the new API
• Renamed the old demo CSV files to FILENAME_before_221121.csv
• Demo json submission file to include submissionName and clinvarSubmissionReleaseStatus key/values

Fixed

• Do not crash when parsing Variant CSV files with no assertion criteria
• Simplify and fix CSV and TSV files parsing

Prevent StopIteration error when provided CSV files are empty

[1.0.2]

Fixed

• Prevent CSV file parsing StopIteration error when provided files are empty

Fixed COPY command error in Dockerfile

[unreleased]

• Fixed Dockerfile building error resulting in prod image release failed to be pushed to Docker Hub

CSV to json converter, validate and dry-run proxy endpoints

[1.0]

Added

• Poetry install
• main.py file with first functions
• .gitignore and CHANGELOG files
• json submission_schema and demo submission object
• tests folder
• Basic howto on README.md
• submission_from_csv endpoint and function to read csv files
• Add custom logging formatting
• Tests and coverage GitHub workflow
• Proxy endpoint to interrogate the submission dry run endpoint of ClinVar API
• Proxy endpoint to interrogate the submission validate endpoint of ClinVar API
• Dockerfile
• Docker-compose file
• GitHub actions to build Docker images (prod and stage) and push them to Docker Hub
• Codecov coverage badge
• Version number in CHANGELOG file and heartbeat endpoint

Changed

• Updated submission schema in resources following new release of schema by ClinVar (draft-07)
• Improved README files with description of endpoints and how to test it
• Increased test coverage
• Pass ClinVar API KEY as a form field and not a query argument

Fixed

• Parsing of CaseData csv with more than one individuals associated to the same variant
• dry-run enpoint, to return success when ClinVar returns a 204 successful response
• Dockerfile returning __call__() missing 1 required positional argument: 'send' error