edu.usd.btl.ontology.ToolTree.java Source code

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Here is the source code for edu.usd.btl.ontology.ToolTree.java

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/*
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package edu.usd.btl.ontology;

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectWriter;
import edu.usd.btl.toolTree.OntoToTree;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;

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

    public static void main(String[] args) throws Exception {
        try {
            //File ontoInput = new File(".\\ontology_files\\EDAM_1.3.owl");
            ObjectMapper mapper = new ObjectMapper();
            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 = mapper.writer().withDefaultPrettyPrinter();
            String edamJSON = mapper.writeValueAsString(nodeList);

            JsonNode rootNode = mapper.readValue(edamJSON, JsonNode.class);
            System.out.println("IsNull" + rootNode.toString());

            OntSearch ontSearch = new OntSearch();
            System.out.println(nodeList.get(0).getURI());
            String result = ontSearch.searchElementByURI("http://edamontology.org/topic_2817");
            System.out.println("RESULT = " + result);

            String topicSearchResult = ontSearch.findAllTopics();
            System.out.println("Topics Result = " + topicSearchResult);

            File ontFile = new File(".\\ontology_files\\EDAM_1.3.owl");
            String searchFromFileResult = ontSearch.searchNodeFromFile("http://edamontology.org/topic_2817",
                    ".\\ontology_files\\EDAM_1.3.owl");
            System.out.println("File Response = " + searchFromFileResult.toString());
        } catch (IOException e) {
            System.out.println(e.getMessage());
        }

        //Hashmap stuff
        //        OntologyFileRead ontFileRead = new OntologyFileRead();
        //        ArrayList<edu.usd.btl.ontology.BioPortalElement> nodeList = ontFileRead.readFile(".\\ontology_files\\EDAM_1.3.owl");
        //        
        //        HashMap hm = new HashMap();
        //        
        //        //find topics
        //        ArrayList<OntologyNode> ontoTopicList = new ArrayList();
        //        
        //        for(BioPortalElement node : nodeList){
        //            //System.out.println("****" + node.getURI());
        //            hm.put(node.getURI(), node.getName());
        //        }
        //        
        //        Set set = hm.entrySet();
        //        Iterator i = set.iterator();
        //        while(i.hasNext()){
        //            Map.Entry me = (Map.Entry)i.next();
        //            System.out.println(me.getKey() + ": " + me.getValue());
        //        }
        //        System.out.println("HashMap Size = " + hm.size());
    }
}