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PaxToolsAgent

Java servlet to convert SBGN-ML files into BioPAX Level 3 format. The tool depends on Paxtools (https://biopax.github.io/Paxtools/) libraries .

Installation

Install Maven and Apache Tomcat 8 first. Make sure the port 8080 is open for Tomcat.

git clone https://github.com/fdurupinar/PaxToolsAgent.git
cd PaxToolsAgent
mvn clean install

Deploying to Tomcat 8 Manually

Ubuntu

mkdir /opt/tomcat/paxtools
cd <Path to PaxToolsAgent>/PaxToolsAgent/out/artifacts/PCArtifact_war_exploded/WEB-INF
cp -R . /opt/tomcat/webapps/paxtools/WEB-INF <Path to PaxToolsAgent>/PaxToolsAgent/out/artifacts/PCArtifact_war_exploded/WEB-INF
  • In WEB-INF there is a classes directory with necessary classes and libraries and a web.xml file which includes the name of the server “PaxtoolsServlet".
  • You may need to put slf4j.jar additionally into the out/artifacts/PCArtifact_war_exploded/web-inf/lib folder.

Running the Servlet

The servlet runs at: localhost/paxtools/PaxtoolsServlet. You can POST http requests to "http://localhost/paxtools/PaxtoolsServlet".

The form parameters for the POST request are: {reqType:"biopax", content:}. The servlet will then return the SBGN model.

Using the Converter

You can use the converter separately if you don't need to provide this as a service. E.g. run the following piece of code to convert the sample SBGN file under src/main/resources:

 File fIn = new File("src/main/resources/testFile.xml");
 InputStream in = new FileInputStream(fIn);
 OutputStream out = new ByteArrayOutputStream();

 try {
     SBGNPDToL3Converter conv = new SBGNPDToL3Converter(); //get a new converter
     conv.writeL3(in, out);
 }
 catch (JAXBException e) {
     e.printStackTrace();
 }

 resultStr = out.toString();
 

You can see the output of texFile.xml in testOut.owl.

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