Rhea Beacon

Knowledge beacon wrapper for https://www.rhea-db.org/

Hosted at https://kba.ncats.io/beacon/rhea/

Python Beacon client https://github.com/NCATS-Tangerine/tkbeacon-python-client

Getting started

The latest release of this project expects the use of Python 3.7, and it is advised that you use this version.

Create virtual environment

It is helpful to keep a local virtual environment in which all local dependencies as well as the application can be installed.

virtualenv -p python3.7 venv
source venv/bin/activate

Configuring

The config/config.yaml file can be modified to change some behaviours of this application.

Getting the data

Use data/Makefile for downloading and pre-processing the needed files. First enter the data directory, and then use the make setup command:

cd data
make setup

This will run execute the data/generate_ec_names.py script. It should clean up after itself, and leave behind two new files: ecc_names.csv, and rhea2xrefs.tsv. The application will use them to perform keyword searches on enzymes, and to look up xrefs for identifiers.

Installing the application

The Makefile in the root directory can be used to install the application. Make sure you are back in the root directory, and run it:

cd ..
make install

Note: if you make changes to config/config.yaml you will need to re-install the application for those results to be used. Alternatively, you can use the command make dev-install to avoid needing to re-install each time you make a change.

Running

The Makefile in the root directory can be used to run the application:

make run

View it at http://localhost:8080

Alternatively you can run the application within a Docker container:

make docker-build
make docker-run

View it at http://localhost:8079

To stop the docker container you can use the command:

make docker-stop

Project structure

The beacon package was generated with Swagger, and the beacon_controller package is where all the implementation details are kept.

The beacon package can be regenerated with the Make command. But first make sure to update the SPECIFICATION parameter in Makefile first if the specification file has a new name.

make regenerate

Alternatively, you can run swagger-codegen-cli.jar directly:

java -jar swagger-codegen-cli.jar generate -i <path-to-specification-file> -l python-flask -o beacon

Do a careful git diff review of the project after regenerating to make sure that nothing vital was overwritten, and to see all the changes made. Since we keep all implementation details in beacon_controller there shouldn't be much to worry about, and the only thing you will need to do is plug the beacon_controller package back in. Again, a git diff will show where this needs to be done.