You're Invited:Meet the Socket Team at BlackHat and DEF CON in Las Vegas, Aug 4-6.RSVP
Socket
Book a DemoInstallSign in
Socket

bedhost

Package Overview
Dependencies
Maintainers
2
Alerts
File Explorer

Advanced tools

Socket logo

Install Socket

Detect and block malicious and high-risk dependencies

Install

bedhost

A database server application that provides both a RESTful API and GUI for access to BED files and related basic statistics

0.2.0
pipPyPI
Maintainers
2

bedhost

Code style: black

bedhost is a Python FastAPI module for the API that powers BEDbase It needs a path to the bedbase configuration file, which can be provided either via -c/--config argument or read from $BEDBASE_CONFIG environment variable.

Running for development

Running with uvicorn provides auto-reload. To configure, this assumes you have previously set up databio/secrets.

  • Source .env file to populate the environment variables referenced in the configuration file.
  • Start bedhost using uvicorn and pass the configuration file via the BEDBASE_CONFIG env var.
source ../bedbase.org/environment/production.env
BEDBASE_CONFIG=../bedbase.org/config/api.bedbase.org.yaml uvicorn bedhost.main:app --reload

You can change the database you're connecting to by using a different config file:

  • Using a local config: BEDBASE_CONFIG=../bbconf/tests/data/config.yaml uvicorn bedhost.main:app --reload
  • With new database: BEDBASE_CONFIG=../bedbase.org/config/bedbase2.yaml uvicorn bedhost.main:app --reload

Now, you can access the service at http://127.0.0.1:8000. Example endpoints:

  • 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/img/open_chromatin
  • 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/img_path/open_chromatin
  • 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/file/bedfile
  • 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/file_path/bedfile
  • 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata
  • 127.0.0.1:8000/bed/78c0e4753d04b238fc07e4ebe5a02984/metadata?attr_ids=md5sum&attr_ids=genome

Running the server in Docker

Building image

  • Primary image: docker build -t databio/bedhost -f .Dockerfile .
  • Dev image docker build -t databio/bedhost:dev -f dev.Dockerfile .
  • Test image: docker build -t databio/bedhost:dev -f test.Dockerfile .

Existing images can be found at dockerhub.

Running container for development

Configuration settings and deployment instructions are in the bedbase.org repository.

Keywords

project

FAQs

Did you know?

Socket

Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.

Install

Related posts