edu.harvard.i2b2.eclipse.plugins.analysis.ontologyMessaging.SelectServiceDriver.java Source code

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Here is the source code for edu.harvard.i2b2.eclipse.plugins.analysis.ontologyMessaging.SelectServiceDriver.java

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/*
 * Copyright (c) 2006-2015 Massachusetts General Hospital 
 * All rights reserved. This program and the accompanying materials 
 * are made available under the terms of the i2b2 Software License v2.1 
 * which accompanies this distribution.  
 * 
 * Contributors:
 *       Lori Phillips
 *       Wensong Pan (ported it here from ontology plug-in)
 */
package edu.harvard.i2b2.eclipse.plugins.analysis.ontologyMessaging;

import java.util.Iterator;
import java.util.logging.Logger;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.jdom.output.XMLOutputter;
import org.w3c.dom.Document;

import edu.harvard.i2b2.analysis.queryClient.QueryClient;

/**
 * The SelectServiceDriver class controls calls to/from 
 *    the Select web service
 * @author Lori Phillips   
 */

public class SelectServiceDriver {

    public static final String THIS_CLASS_NAME = SelectServiceDriver.class.getName();
    private static final Log log = LogFactory.getLog(SelectServiceDriver.class);

    /**
     * The constructor
     */
    public SelectServiceDriver() {
    }

    /**
     * Makes call to the Select Web Service
     *
     * @param selectParameters   a document describing the input parameter to the Select Web service
     * @return a document containing the result of the Select web service transaction
     */

    public Document callSelects(Document selectParameters) {
        Document results = null;
        try {
            java.net.URL endpoint = new java.net.URL(System.getProperty("ontologywebservice"));

        } catch (Exception e) {
            Logger.getLogger(THIS_CLASS_NAME).severe(e.getMessage());
            e.printStackTrace();
        }
        return results;
    }

    /**
     * Generates input to the Select Web Service
     *
     * @param code   the concept code we are inquiring about
     * @return a document containing the input to send to the Select web service
     */

    public Document buildSelectParameters(String code) {
        Document selectParameters = null;
        try {
            org.jdom.Element selectElement = new org.jdom.Element("selectParameters");
            org.jdom.Document jqueryDoc = new org.jdom.Document(selectElement);
            org.jdom.Element dbElement = new org.jdom.Element("i2b2Mart");
            dbElement.setText("metadata");
            selectElement.addContent(dbElement);

            org.jdom.Element table = new org.jdom.Element("table");

            table.setText("i2b2");
            table.setAttribute("abbr", "l");
            table.setAttribute("numCols", "21");
            table.setAttribute("withBlob", "false");
            selectElement.addContent(table);
            org.jdom.Element where = new org.jdom.Element("where");
            String whereClause = "c_basecode = '" + code + "'";

            where.setText(whereClause);
            selectElement.addContent(where);
            org.jdom.Element orderBy = new org.jdom.Element("orderBy");
            orderBy.setText("c_name");
            selectElement.addContent(orderBy);

            org.jdom.output.DOMOutputter convertor = new org.jdom.output.DOMOutputter();
            selectParameters = convertor.output(jqueryDoc);
        } catch (Exception e) {
            Logger.getLogger(THIS_CLASS_NAME).severe(e.getMessage());
            e.printStackTrace();
        }

        return selectParameters;
    }

    /**
     * Test code to print the result document from the Select web service
     *   in XML format
     *
     * @param resultDoc   a document describing the results returned by the Select Web service
     * 
     */
    private void printResultsAsXML(org.w3c.dom.Document resultDoc) {
        try {
            org.jdom.input.DOMBuilder builder = new org.jdom.input.DOMBuilder();
            org.jdom.Document jresultDoc = builder.build(resultDoc);
            org.jdom.Namespace ns = jresultDoc.getRootElement().getNamespace();
            log.debug(new XMLOutputter().outputString(jresultDoc));
        } catch (Exception e) {
            Logger.getLogger(THIS_CLASS_NAME).severe(e.getMessage());
            e.printStackTrace();
        }
    }

    /**
     * Get the c_name returned from the Select web service result document
     *
     * @param resultDoc   a document describing the results returned by the Select Web service
     * @return  the c_name returned from the Select web service lookup
     * 
     */
    public String getNameFromDocument(org.w3c.dom.Document resultDoc) {
        String name = null;
        String code = null;
        try {
            org.jdom.input.DOMBuilder builder = new org.jdom.input.DOMBuilder();
            org.jdom.Document doc = builder.build(resultDoc);
            org.jdom.Element select = doc.getRootElement();
            org.jdom.Namespace ns = select.getNamespace();

            Iterator iterator = doc.getRootElement().getChildren("patientData", ns).iterator();
            while (iterator.hasNext()) {
                org.jdom.Element patientData = (org.jdom.Element) iterator.next();
                org.jdom.Element table = (org.jdom.Element) patientData.getChild("i2b2", ns).clone();
                name = table.getChildTextTrim("c_name", ns);
                code = table.getChildTextTrim("c_basecode", ns);
            }
        } catch (Exception e) {
            Logger.getLogger(THIS_CLASS_NAME).severe(e.getMessage());
            e.printStackTrace();
        }
        return name;
    }

    public static void main(String args[]) {
        System.setProperty("ontologywebservice", "http://localhost:8080/i2b2/services/Select");
        SelectServiceDriver driver = new SelectServiceDriver();
        Document input = driver.buildSelectParameters("I2B2");
        driver.printResultsAsXML(input);
    }
}