edu.harvard.hms.dbmi.i2b2.api.samples.FactoryTraversePaths.java Source code

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Here is the source code for edu.harvard.hms.dbmi.i2b2.api.samples.FactoryTraversePaths.java

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/*
 *  This file is part of i2b2-Java-API.
 *
 *  The i2b2-Java-API is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation, either version 3 of the License, or
 *  (at your option) any later version.
 *
 *  i2b2-Java-API is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with i2b2-Java-API.  If not, see <http://www.gnu.org/licenses/>.
 */
package edu.harvard.hms.dbmi.i2b2.api.samples;

import java.io.IOException;

import javax.xml.bind.JAXBException;

import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.HttpClient;
import org.apache.http.impl.client.HttpClients;

import edu.harvard.hms.dbmi.i2b2.api.I2B2Factory;
import edu.harvard.hms.dbmi.i2b2.api.exception.I2B2InterfaceException;
import edu.harvard.hms.dbmi.i2b2.api.ont.ONTCell;
import edu.harvard.hms.dbmi.i2b2.api.ont.xml.ConceptType;
import edu.harvard.hms.dbmi.i2b2.api.ont.xml.ConceptsType;

/**
 * Provides an example of i2b2-Java-API for traversing paths
 * 
 * A simple example would be the following:
 * 
 * java TraversePaths i2b2demo demo demouser http://192.168.56.101:9090/i2b2/services/PMService/getServices Demo 2
 * 
 * @author Jeremy R. Easton-Marks
 *
 */
public class FactoryTraversePaths {
    private ONTCell ontCell = new ONTCell();
    private int totalCount = 0;

    /**
     * Runs the traverse paths example.
     * 
     * Requires 6 parameters:
     * domain userName password ontologyCellURL project depth
     * 
     * @param args
     *            arguments
     */
    public static void main(String[] args) {
        if (args.length != 6) {
            System.out.println("Invalid number of arguments.");
            System.out.println("java TraversePaths domain userName password cellURL project depth");
        }
        String domain = args[0];
        String userName = args[1];
        String password = args[2];
        String ontologyCellURL = args[3];
        String project = args[4];
        int depth = Integer.parseInt(args[5]);

        FactoryTraversePaths traversePaths = new FactoryTraversePaths();
        try {
            traversePaths.setup(userName, domain, password, ontologyCellURL, project);

            HttpClient httpClient = HttpClients.createDefault();

            traversePaths.printPath(httpClient, null, 0, depth);

        } catch (I2B2InterfaceException | JAXBException | IOException e) {
            System.out.println("An error occurred traverse the paths");
            e.printStackTrace();
        }
        System.out.println("\nFinished with " + traversePaths.getTotalCount() + " returned in total");
    }

    /**
     * Prints the current path and continues
     * 
     * @param httpClient
     *            HTTP client
     * @param currentConcept
     *            Current concept
     * @param currentDepth
     *            Current position
     * @param max
     *            Max distance to traverse
     * @throws ClientProtocolException
     *             A client protocol exception occurred
     * @throws JAXBException
     *             An XML exception occurred
     * @throws IOException
     *             An IO exception occurred
     * @throws I2B2InterfaceException
     *             An exception occurred on the I2B2 server
     */
    private void printPath(HttpClient httpClient, ConceptType currentConcept, int currentDepth, int max)
            throws ClientProtocolException, JAXBException, IOException, I2B2InterfaceException {
        ConceptsType conceptsType = null;
        // If we are at the base level we get categories
        // All other levels we get children
        if (currentConcept == null) {
            conceptsType = ontCell.getCategories(httpClient, false, false, true, "core");
            currentDepth = 0;
        } else {
            // Print some tabs for display
            for (int i = 0; i < currentDepth; i++) {
                System.out.print("\t");
            }
            // Print the name
            System.out.println("|-----> " + currentConcept.getName() + "\t" + currentConcept.getKey());
            // Increase the depth we are at
            currentDepth++;

            // Get all children if they will be needed
            if (currentDepth < max) {
                conceptsType = ontCell.getChildren(httpClient, currentConcept.getKey(), false, false, false, -1,
                        "core");
            }
        }
        // Traverse through the children
        if (currentDepth < max) {
            for (ConceptType conceptType : conceptsType.getConcept()) {
                totalCount++;
                printPath(httpClient, conceptType, currentDepth, max);
            }
        }

    }

    /**
     * Sets up the Ontology cell
     * 
     * @param userName
     *            User name
     * @param domain
     *            Domain
     * @param password
     *            Password
     * @param ontologyCellURL
     *            Ontology cell URL
     * @param project
     *            Project
     * @throws JAXBException
     *             An XML exception occurred
     * @throws I2B2InterfaceException 
     */
    private void setup(String userName, String domain, String password, String connectionURL, String project)
            throws I2B2InterfaceException {
        I2B2Factory i2b2Factory = new I2B2Factory();
        i2b2Factory.setup();
        i2b2Factory.login(connectionURL, domain, userName, password, false);

        ontCell = (ONTCell) i2b2Factory.getCell("ONT", project, true);
    }

    /**
     * Returns the total count of entries traversed
     * 
     * @return Total count
     */
    private int getTotalCount() {
        return totalCount;
    }

}