Fix gunicorn execution in Dockerfile

[2.7.1]

Fixed

• Replace the CMD step of the Dockerfile with an ENTRYPOINT that uses /bin/sh -c to evaluates the shell commands and expand environment variables.

Delete submissions, code updates and updated submission schema

[2.7]

Added

• Delete submission endpoint, with json example (under demo files) and test

Changed

• Updated API submission schema to the latest available on ncbi/clinvar GitHub pages
• Modified the json submission example to use one from the ClinVar GitHib repo (sample_clinical_significance_hgvs_submission.json)
• Removed the example of an old json submission (before 2022-11-21)
• Updated actions using the latest base images and to run using Python 3.9
• Docker image uses Python 3.11 instead of 3.8
• Replaced deprecated app "on event" with app lifespan

Fixed

• Updated issue templates
• Updated a number of libraries to address all current security advisories
• Warnings in the Dockerfile

status and apitest-status endpoints

[2.6]

Added

• An endpoint /apitest-status that returns a response containing the status of a test submission, with link to the eventual json file with the submissions data errors
• An endpoint /status that returns a response containing the status of a submission (submitted, processing, processed, error), with eventual error details

Changed

• Renamed /validate endpoint to /apitest

Fix broken Codecov action and lowercase multipleConditionExplanation

[2.5.2]

Fixed

• Upload to Codecov step in tests_n_coverage.yml action
• Fix multipleConditionExplanation to be lowercase

Patch app not launching via gunicorn

[2.5.1]

Fixed

• Avoid "/bin/sh: 1: gunicorn: not found" error by using poetry <1.8 in Dockerfile

Updated API submission schema, vulnerability fix and parsing of MultipleConditionExplanation

[2.5]

Changed

• Updated submission schema to the latest API schema (01-03-2024)
• Switched from Draft3Validator to Draft7Validator in validate.py
• Updated fastapi lib to fix security vulnerability
• Parse conditionSet.MultipleConditionExplanation value from Explanation for multiple conditions column of variants file

Fixes to reflect changes in ClinVar submission schema & maintenance

[2.4]

Changed

• Updated version of external images in GitHub actions
• Updated API submission schema to the latest
• Demo variant to take care of "Somatic mutation" no longer available among Mode of inheritance choices
• clinicalSignificance.clinicalSignificanceDescription value extracted from Clinical significance or Germline classification column
• clinicalSignificance.comment values extracted from Comment on clinical significance or Comment on classification column

Fixed

• Bump certifi from 2022.12.7 to 2023.7.22
• Description of the response returned by dry run endpoint in README file
• Migrate from deprecated pkg_resources lib to importlib_resources
• Updated python-multipart from 0.0.5 to 0.0.7 to address security alert by dependabot

HGVS format fix

[2.3.1]

Fixed

• Combine Reference sequence and HGVS fields from Variant file to create the hgvs field in json submission object

Fix uppercase/lowercase letters for non-compliant clinsig terms

[2.3]

Changed

• Fix uppercase/lowercase letters when parsing clinsig terms from files

Removed parsing of Accession field and URL to prod running instance of README

[2.2]

Changed

• Provide the URL to the prod service running on the Clinical Genomics server instead of the stage one on README page

Fixed

• Do not parse dbSNP IDs as Accession key/values