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Recent Releases of https://github.com/clinical-genomics/preclinvar

https://github.com/clinical-genomics/preclinvar - Remap chromosome 'M' to 'MT'

[2.8.1]

Fixed

  • Remap chromosome M to MT, which is the accepted format from ClinVar API

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/preclinvar - json validate endpoint and fixes

[2.8]

Added

  • validate endpoint, accepting germline or somatic json submissions and supporting validation against the official schema ### Changed
  • Improve README and endpoint descriptions specifying that tsv_2_json and csv_2_json endpoints support only conversion for germline submission files
  • PR template to be more compact and user friendly ### Fixed
  • GitHub action to use poetry v.1.7.1

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/preclinvar - 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.

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/preclinvar - 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

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/preclinvar - 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

- Python
Published by northwestwitch about 2 years ago

https://github.com/clinical-genomics/preclinvar - 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

- Python
Published by northwestwitch about 2 years ago

https://github.com/clinical-genomics/preclinvar - 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

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/preclinvar - 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

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/preclinvar - 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

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/preclinvar - 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

- Python
Published by northwestwitch over 3 years ago

https://github.com/clinical-genomics/preclinvar - Fix uppercase/lowercase letters for non-compliant clinsig terms

[2.3]

Changed

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

- Python
Published by northwestwitch over 3 years ago

https://github.com/clinical-genomics/preclinvar - 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

- Python
Published by northwestwitch over 3 years ago

https://github.com/clinical-genomics/preclinvar - 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 tsv2json and csvtojson to create submission containing chromosome coordinates
  • Link to demo service instance at clinical genomics ### Fixed
  • Parsing of multiple condition IDs from csv/tsv files

- Python
Published by northwestwitch over 3 years ago

https://github.com/clinical-genomics/preclinvar - 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

- Python
Published by northwestwitch over 3 years ago

https://github.com/clinical-genomics/preclinvar - Changes reflecting ClinVar API updates and improvements

[2.0]

Added

  • A new tsv2json 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 FILENAMEbefore221121.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

- Python
Published by northwestwitch over 3 years ago

https://github.com/clinical-genomics/preclinvar - Prevent StopIteration error when provided CSV files are empty

[1.0.2]

Fixed

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

- Python
Published by northwestwitch over 3 years ago

https://github.com/clinical-genomics/preclinvar - Fixed COPY command error in Dockerfile

[unreleased]

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

- Python
Published by northwestwitch almost 4 years ago

https://github.com/clinical-genomics/preclinvar - 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
  • submissionfromcsv 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

- Python
Published by northwestwitch almost 4 years ago