edu.usd.btl.toolTree.OntoToTree.java Source code

Introduction

Here is the source code for edu.usd.btl.toolTree.OntoToTree.java

Source

/*
 * To change this license header, choose License Headers in Project Properties.
 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
package edu.usd.btl.toolTree;

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectWriter;
import edu.usd.btl.ontology.OntologyFileRead;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

/**
 *
 * @author Tyler
 */
public class OntoToTree {

    /*
    Convert EDAM.owl file ArrayList to JSON
     */
    public static String getOntoJson() throws Exception {
        ObjectMapper treeMapper = new ObjectMapper(); //create new Jackson Mapper
        OntologyFileRead ontFileRead = new OntologyFileRead();
        ArrayList<edu.usd.btl.ontology.BioPortalElement> nodeList = ontFileRead
                .readFile(".\\ontology_files\\EDAM_1.3.owl");

        //write nodelist to JSON string
        ObjectWriter treeWriter = treeMapper.writer().withDefaultPrettyPrinter();
        String edamJSON = treeMapper.writeValueAsString(nodeList);
        System.out.println("**** EDAM ONTOLOGY JSON ****" + edamJSON);

        return edamJSON;
    }

    /*
     This section reads from a local JSON file, similar to the one above.'
     Converts JSON to Java Objects
     */
    public String jsonToJava(String input) throws Exception {
        try {
            //File input = new File("C:\\Users\\Tyler\\Documents\\GitHub\\BTL\\src\\ontology_files\\testEdam.json");

            /*
             CONVERT JSON TO JAVA OBJECTS
             */
            //map EDAM ontology JSON to List of objects
            ObjectMapper treeMapper = new ObjectMapper(); //create new Jackson Mapper
            ObjectWriter treeWriter = treeMapper.writer().withDefaultPrettyPrinter();
            List<EDAMNode> ontologyNodes = treeMapper.readValue(input,
                    treeMapper.getTypeFactory().constructCollectionType(List.class, EDAMNode.class));
            System.out.println("********SIZE OF ontologyNodes*********" + ontologyNodes.size());
            for (EDAMNode node : ontologyNodes) { //for each ontology node
                System.out.println(node.getName());
                //build tree from ontology nodes

            }
            JsonNode rootNode = treeMapper.readValue(getOntoJson(), JsonNode.class);
            JsonNode tool = rootNode.get("name");

            System.out.println("\n\n\n\n****************************" + tool.toString());
            System.out.println("**** ONTOLOGY SIZE *****" + ontologyNodes.size());
            String jsonOutput = treeWriter.writeValueAsString(ontologyNodes.get(0));
            System.out.println("\n\n****ONTOLOGY JSON OUPUT*****+\n" + jsonOutput);

            //            IplantV1 iplantOutput = BETSConverter.toIplant(betsTool);
            //            String iplantOutputJson = iplantWriter.writeValueAsString(iplantOutput); //write Json as String
        } catch (IOException e) {
            System.out.println(e.getMessage());
        }
        return "jsonToJava success";
    }
}