factoid-to-biopax-server

A java servlet based web-server to convert factoid document to BioPAX. It uses Paxtools to generate a biopax model.

Installation

git clone https://github.com/metincansiper/factoid-to-biopax-server.git
cd factoid-to-biopax-server
mvn clean install

Deploying to Tomcat7

The project uses Tomcat7 Maven Plugin to automate deployment process. You should have Apache Tomcat running on port 8080. You should have a user authenticated for both Tomcat and Maven. You would like to see "Tomcat Authentication" and "Maven Authentication" steps of this tutorial for "Tomcat 7 example" if you have not authenticated a user yet. Server id in your settings.xml must be same with tomcat.server.name property in pom.xml, otherwise you would like to overwrite or override (if possible not sure yet) this property.

After creating an authorized user you can run mvn tomcat7:deploy , mvn tomcat7:undeploy and mvn tomcat7:redeploy to manage deployment process.

Deploying to Docker Container

You can deploy the server to a docker container by following the steps below. "" must be replaced by the port number where the server is expected to be run.

docker build -f Dockerfile -t factoid-to-biopax .
docker run -it --rm --name factoid-to-biopax --publish <PORT>:8080 factoid-to-biopax 

To create the war file with another name than "FactoidToBiopaxServer"(war name affects where the service is deployed) add --build-arg TARGET_WAR_NAME=<WAR_NAME> to the build command.

Consuming the Service

After completing installation and deployment steps the server will be up and running at "http://localhost:8080/FriesToBiopaxServer" (You should update port number and path in case you use another ones). You can send a post request to "http://localhost:8080/FactoidToBiopaxServer/ConvertToOwl" to consume the service.

The service takes a String in JSON array format (see Input section below), converts it to BioPax format and returns a String to represent it.

The following is a sample Node.js client

let url = 'http://localhost:8080/FactoidToBiopaxServer/ConvertToOwl';
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);
    } );

Input

TODO: Fill here with a sample input JSON array