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

https://github.com/clinical-genomics/schug - Switch to grch37.ensembl.org to download build 37 data

[1.12]

Changed

  • Download build 37 data using the https://grch37.ensembl.org/ BioMart, since the https://feb2014.archive.ensembl.org archive is offline now
  • Updated several libraries ### Fixed
  • Updated gunicorn and jinja2 libs, among others, to address security vulnerabilities

- Python
Published by northwestwitch about 1 year ago

https://github.com/clinical-genomics/schug - Reintroduce [success] lines, for downstream integrity checks

[1.11]

Changed

  • Reintroduce [success] lines in the streamed content, to simplify checks downstream

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/schug - Anti-timeout patch

[1.10.1]

Fixed

  • Refactor Ensembl data downloads to avoid timeout issues

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/schug - Gene type column and improved demo files

[1.10]

Added

  • An additional Gene Biotype (build 37) or Gene type (build 38) column when downloading genes to file. This allows downloading of non-coding genes ### Changed
  • Demo files genes_37.tsv and genes_38.tsv to reflect latest changes in genes downloaded files
  • Demo files contain now lines from the following genes: MTHFR, DHFR, FOLR1, SLC46A1, MT-TP (better integration with chanjo tests)

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/schug - Retry streaming files chunks and simpler Swagger docs

[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.

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/schug - Download resources without [success] lines and minor changes

[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

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/schug - Missing exons workaround and deprecate Python 3.8

[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)

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/schug - Missing build 38 exons using Ensembl v.113: using v.112 instead

[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.

- Python
Published by northwestwitch over 1 year ago

https://github.com/clinical-genomics/schug - Updated starlette, fastapi, urllib3 and certifi libs

[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

- Python
Published by northwestwitch almost 2 years ago

https://github.com/clinical-genomics/schug - Updated dependencies

[1.6]

Changed

  • Updated a number of libraries to address security alerts

- Python
Published by northwestwitch about 2 years ago

https://github.com/clinical-genomics/schug - Fix Docker RuntimeError: can't start new thread

[1.5.1]

Fixed

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

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/schug - Updates and deprecated code removal

[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

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/schug - Support Python >=3.8 and upgrade Pydantic to v2

[1.4]

Changed

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

- Python
Published by northwestwitch over 2 years ago

https://github.com/clinical-genomics/schug - Python 3.11 in Dockerfile plus fixes and lib updates

[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

- Python
Published by northwestwitch almost 3 years ago

https://github.com/clinical-genomics/schug - Include Mane transcripts info and support official genome build names

[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

- Python
Published by northwestwitch over 3 years ago

https://github.com/clinical-genomics/schug - Fixed PyPI push action and demo instance to use a memory database

[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

- Python
Published by northwestwitch over 3 years ago

https://github.com/clinical-genomics/schug - Proxy endpoints to Ensembl genes, exons and transcripts

[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

- Python
Published by northwestwitch over 3 years ago