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CHANGELOG.md

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Change Log

[1.9]

Changed

  • Added retry logic to stream_resource to handle failed chunk downloads with a configurable number of attempts and error handling.
  • Commented out in the code all endpoints that are not yet functioning.

[1.8]

Changed

  • Use custom issue and pull request templates in this repository
  • Remove old code once used for downloading data from Ensembl

Fixed

  • Do not include [success] lines in the streamed outfiles: genes, transcripts and exons

[1.7]

Changed

  • Do not download duplicated lines from Ensembl BioMart
  • Update Python version to v3.12 in Dockerfile
  • Update Python version in pyproject.toml

Fixed

  • Download data from Ensembl BioMart chromosome-wise, to avoid missing exons, for instance (see issue #74)

[1.6.2]

Fixed

  • Some exons are missing when downloading build 38 data using Ensembl v.113 (Oct 2024). Using v.112 (May 2024) until the problem is fixed. Build 37 not affected.

[1.6.1]

Fixed

  • Security issue related to starlette version by updating fastapi, starlette and some dependencies
  • Updated urlib to v.2.2.3 to address the urllib3's Proxy-Authorization request header isn't stripped during cross-origin redirects issue
  • Updated certifi to v.2024.7.4 to address the Certifi removes GLOBALTRUST root certificate issue

[1.6]

Changed

  • Updated a number of libraries to address security alerts

[1.5.1]

Fixed

  • Revert to python 3.8 in Dockerfile to avoid RuntimeError: can't start new thread issue

[1.5]

Changed

  • Updated version of external images used in GitHub actions
  • Updated Python version to v3.11 in tests GitHub action
  • Removed pytest from the package dependencies

Fixed

  • Converted deprecated Pydantic validators and Config into Pydantic 2 format

[1.4]

Changed

  • Updated Pydantic(^2.5.2) library and other dependencies
  • Support Python>=3.8

[1.3]

Fixed

  • Typo in instructions to download genes in README document

Changed

  • Code formatted with black and black check GitHub action
  • Renamed schug.load.ensembl.fetch_ensembl_exon_lines function to schug.load.ensembl.fetch_ensembl_exons
  • Upgraded Python version from 3.8 to 3.11 in Dockerfile
  • Updated several python libraries in poetry.lock

[1.2]

Added

  • Include also mane_plus_clinical and mane_select columns in transcripts file downloaded from Ensembl

Changed

  • Updated Uvicorn library
  • Accept also GRCh37 and GRCh38 as build values when downloading resources

[1.1]

Changed

  • Move the schug directory up in root dir folder

Fixed

  • Use a memory database as default database in demo instance
  • Issues flagged by SonarCloud
  • Publish to PyPI GitHub action

[1.0.0]

Added

  • Endpoint to Ensembl genes download
  • Endpoint to Ensembl transcripts download
  • Endpoint to Ensembl exons download
  • Dockerfile and docker-compose files
  • Push to Docker Hub -prod and stage- GitHub actions
  • Publish to PyPI GitHub actions
  • Run tests GitHub action
  • CHANGELOG file

Changed

  • Run the app with Python>=3.8

Fixed

  • Typing errors in fetch_ensembl_exons and fetch_genes_to_hpo_to_disease that prevented the app from starting