de.document.umls.RetrieveCui.java Source code

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Here is the source code for de.document.umls.RetrieveCui.java

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package de.document.umls;

import com.jayway.jsonpath.Configuration;
import com.jayway.jsonpath.JsonPath;
import com.jayway.jsonpath.spi.mapper.JacksonMappingProvider;
import com.jayway.restassured.RestAssured;
import static com.jayway.restassured.RestAssured.given;
import com.jayway.restassured.response.Response;
import de.document.entity.RestTicketClient;
import org.junit.Test;
import com.codesnippets4all.json.parsers.JSONParser;
import org.junit.Test;
import com.jayway.jsonpath.Configuration;
import com.jayway.jsonpath.JsonPath;
import com.jayway.jsonpath.spi.mapper.JacksonMappingProvider;
import com.jayway.restassured.RestAssured;
import com.jayway.restassured.response.Response;
import static com.jayway.restassured.RestAssured.given;
import de.document.entity.Umls;
import java.math.BigInteger;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import java.util.Set;
import net.minidev.json.JSONObject;
import static com.jayway.restassured.RestAssured.given;
import static com.jayway.restassured.RestAssured.given;
import static com.jayway.restassured.RestAssured.given;
import static com.jayway.restassured.RestAssured.given;
//import static org.apache.commons.lang.StringUtils.join;

/**
 *
 * @author MyTEK
 */
public class RetrieveCui {

    String username = System.getProperty("username");
    String password = System.getProperty("password");
    //String id = "C0155502";
    String id;

    public RetrieveCui(String id) {
        this.id = id;
    }

    String version = System.getProperty("version");
    RestTicketClient ticketClient = new RestTicketClient("tmar01", "Master2016");
    RestTicketClient ticketClient2 = new RestTicketClient("tmar01", "Master2016");

    //get a ticket granting ticket for this session.
    String tgt = ticketClient.getTgt();
    String tgt2 = ticketClient2.getTgt();
    private static BigInteger nextId;

    public Umls RetCui(String id) {

        //if you omit the -Dversion parameter, use 'current' as the default.
        version = System.getProperty("version") == null ? "current" : System.getProperty("version");
        String path = "/rest/content/" + version + "/CUI/" + id;
        RestAssured.baseURI = "https://uts-ws.nlm.nih.gov";
        Response response = given()//.log().all()
                .request().with().param("ticket", ticketClient.getST(tgt)).expect().statusCode(200).when()
                .get(path);
        //response.then().log().all();;     
        String output = response.getBody().asString();

        Configuration config = Configuration.builder().mappingProvider(new JacksonMappingProvider()).build();
        ConceptLite conceptLite = JsonPath.using(config).parse(output).read("$.result", ConceptLite.class);

        System.out.println(conceptLite.getUi() + ": " + conceptLite.getName());
        //System.out.println("Semantic Type(s): "+ join(conceptLite.getSemanticTypes(),","));
        System.out.println("Number of Atoms: " + conceptLite.getAtomCount());
        System.out.println("Atoms: " + conceptLite.getAtoms());
        System.out.println("Relations: " + conceptLite.getRelations());
        //System.out.println("Highest Ranking Atom: "+conceptLite.getDefaultPreferredAtom());
        System.out.println("Definitions: " + conceptLite.getDefinitions());
        //System.out.println(ticketClient.getST(tgt));
        //ST-115269-Mvb5oLFpIgQElKaKWVsN-cas
        String s = conceptLite.getDefinitions();
        if (s.charAt(0) != 'N' && s.charAt(1) != 'O' && s.charAt(2) != 'N' && s.charAt(3) != 'E') {

            String path2 = "/rest/content/" + version + "/CUI/" + id + "/definitions?ticket="
                    + ticketClient.getST(tgt);
            RestAssured.baseURI = "https://uts-ws.nlm.nih.gov";
            Response response2 = given().log().all().request().with().param("ticket", ticketClient.getST(tgt))
                    .expect().statusCode(200).when().get(path2);
            //response.then().log().all();;     
            String output2 = response2.getBody().asString();

            // System.out.println(output2);
            //extract the definition 
            System.out.println(output2.substring(output2.indexOf("value") + 8, output2.indexOf(".\"}")));
            String def = output2.substring(output2.indexOf("value") + 8, output2.indexOf("\"}"));

            HashMap hm = conceptLite.getSemanticTypes().get(0);
            Set set = hm.entrySet();
            // Get an iterator
            Iterator i = set.iterator();
            // Display elements

            Map.Entry me = (Map.Entry) i.next();
            System.out.print(me.getKey() + ": ");
            System.out.println(me.getValue());

            // def =def + "\r\n"+"Semantic Type"+me.getKey() + ": "+me.getValue()+"\r\n"+"Number of Atoms: " + conceptLite.getAtomCount();

            Umls u = new Umls();
            //u.setNumberOfAtom(conceptLite.getAtomCount());
            u.setUi(id);
            u.setDefinition(def);
            u.setNumberOfAtom(conceptLite.getAtomCount());

            u.setSemanticType(me.getValue().toString());

            return u;
        } else {
            Umls u = new Umls();
            //u.setNumberOfAtom(conceptLite.getAtomCount());
            u.setUi("");
            u.setName("");
            u.setDefinition("There is no available definition");
            return u;

        }
    }
}