README.md

factoid-converters

A java web server to convert biofactoid documents to BioPAX and SBGN models.

Build

./gradlew clean
./gradlew build

Run

java -jar build/libs/factoid-converters*.jar --server.port=8080

RESTful API (Swagger docs):

Once the app is built and running, the auto-generated OpenAPI/Swagger documentation is available at (ending with '/') http://localhost:8080/convert/

Docker

You can deploy the server to a docker container by following the steps below
(<PORT> - actual port number where the server will run).

docker build . -t pathwaycommons/factoid-converters
docker run -it --rm --name factoid-converters -p <PORT>:8080 pathwaycommons/factoid-converters 

Optionally, a member of 'pathwaycommons' group can now push (upload) the latest Docker image there: (BTW: the latest Docker image is built automatically by Dockerhub on every git push to the master branch)

docker login
docker push pathwaycommons/factoid-converters

So, other users could skip building from sources and simply run the app:

docker pull
docker run -p <PORT>:8080 -t pathwaycommons/factoid-converters

(you can Ctrl-c and quit the console; the container is still there running; check with docker ps)

Example queries

Using cUrl tool:

cd src/test/resources
curl -X POST -H 'Content-Type: application/json' -d @test2.json "http://localhost:8080/convert/v2/json-to-biopax"

Using a Node.js client:

let url = 'http://localhost:8080/convert/v2/json-to-biopax';
let content = fs.readFileSync('input/templates.json', 'utf8');
Promise.try( () => fetch( url, {
        method: 'POST',
        body:    content,
        headers: { 'Content-Type': 'application/json' }
    } ) )
    .then( res => res.text() )
    .then( res => {
      // we have biopax result here as a String
      console.log(res);
    } );