bedhost

v0.2.0

A database server application that provides both a RESTful API and GUI for access to BED files and related basic statistics For more information about how to use this package see README

Latest version published 1 year ago

License: MIT

PyPI

GitHub

Package Health Score

61 / 100

security
Security review needed
popularity
Small
maintenance
Inactive
community
Active

Popularity

Small

GitHub Stars: 39.28K
Forks: 2.48K
Contributors: 440

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package bedhost, we found that it has been starred 39,277 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Dec 19, 2023
Direct Vulnerabilities: 0
C
0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 0
H
7
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

MIT

Security Policy

Yes

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Maintenance

Inactive

Commit Frequency

Open Issues: 363
Open PR: 27
Last Release: 1 year ago
Last Commit: 18 days ago

Further analysis of the maintenance status of bedhost based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Inactive.

An important project maintenance signal to consider for bedhost is that it hasn't seen any new versions released to PyPI in the past 12 months, and could be considered as a discontinued project, or that which receives low attention from its maintainers.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 440
Funding: No

A good and healthy external contribution signal for bedhost project, which invites more than one hundred open source maintainers to collaborate on the repository.

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Package

Python Versions Compatibility: ==3.10.*, ==3.11.*, ==3.8.*, ==3.9.*

Age: 4 years
Latest Release: 1 year ago
Dependencies: 9 Direct / 73 Total
Versions: 4
Maintainers: 0
Wheels: OS Independent

Readme

bedhost

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.

bedhost dependencies

bbconf fastapi geniml logmuse markdown requests setuptools uvicorn yacman

FAQs

What is bedhost?

A database server application that provides both a RESTful API and GUI for access to BED files and related basic statis... Visit Snyk Advisor to see a full health score report for bedhost, including popularity, security, maintenance & community analysis.

Is bedhost popular?

The python package bedhost receives a total of 92 weekly downloads. As such, bedhost popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is bedhost well maintained?

We found indications that bedhost is an Inactive project. See the full package health analysis to learn more about the package maintenance status.

Is bedhost safe to use?

While scanning the latest version of bedhost, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 17 December-2024, at 06:22 (UTC).

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Readme

bedhost

Running for development

Running the server in Docker

Building image

Running container for development

bedhost dependencies

FAQs

What is bedhost?

Is bedhost popular?

Is bedhost well maintained?

Is bedhost safe to use?

Build a secure application checklist

Select a recommended open source package

Scan your app for vulnerabilities

Source Code

Open Source

Container

Config

Fix identified vulnerabilities

Monitor for new issues