edu.pitt.dbmi.ipm.service.EnterpriseAnalytics.java Source code

Introduction

Here is the source code for edu.pitt.dbmi.ipm.service.EnterpriseAnalytics.java

Source

package edu.pitt.dbmi.ipm.service;

import java.io.File;
import java.io.FileInputStream;
import java.util.Properties;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.json.JSONObject;

import edu.pitt.dbmi.ipm.service.storage.StorageFactory;

/**
 * Copyright (C) 2015  University of Pittsburgh
 * This program 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 2
 * of the License, or (at your option) any later version.
 * 
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA. 
 * 
 * 
 * Returns analytical data requested be web server.
 * 
 * @author opm1
 * @version 1
 * @since Dec 11, 2015
 *
 */

public class EnterpriseAnalytics {
    private static Log log = LogFactory.getLog(EnterpriseAnalytics.class);

    private static String count_patients_by_tss_Q = null;
    private static boolean hasParams = false;

    /**
     * Initializes parameters from *.conf file based on selected storage
     * parameter 'useVitOrPostgre' in jQueryPostgres.conf file
     */
    private static void initParams() {
        if (!hasParams) {
            hasParams = true;
            try {
                StorageFactory.getStorage().initParameters();
                hasParams = true;
                Properties params = new Properties();
                params.load(new FileInputStream(System.getProperty("user.dir") + File.separator + "resources"
                        + File.separator + StorageFactory.getStorage().getConfFileName()));

                String prefix_name = params.getProperty("prefix_name");
                String prefix = params.getProperty("prefix");

                count_patients_by_tss_Q = DataSelection
                        .queryInitReplace(params.getProperty("count_patients_by_tss"), prefix_name, prefix);
            } catch (Exception ex) {
                System.out.println(ex.getMessage());
            }
        }
    }

    /**
     * 
     * @param diseaseAbbr
     *            - example: "brca", "ov", "hnsc"
     * @param tssName
     *            - name of tissue source site for ex.
     *            "University of Pittsburgh"
     * @return number of patients for a particular disease and tss as JsonObject
     * @throws QueryException
     */
    public static JSONObject countPatientsByTSS(String diseaseAbbr, String tssName) throws QueryException {
        initParams();

        String q = count_patients_by_tss_Q.replace("<diseaseAbbr>", diseaseAbbr.toLowerCase());
        q = q.replace("<tssName>", tssName);
        try {
            return StorageFactory.getStorage().getJSONResult(StorageFactory.getStorage().getSparqlURL(), q);
        } catch (QueryException e) {
            throw e;
        }

    }

    /**
     * @param args
     */
    public static void main(String[] args) {

        try {
            EnterpriseAnalytics.initParams();
            // number of UPMC patients with brca cancer
            System.out.println("number of Patients: "
                    + EnterpriseAnalytics.countPatientsByTSS("brca", "University of Pittsburgh"));
        } catch (QueryException e) {
            e.printStackTrace();
        }

    }

}