ArrayFile.java Source code

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Here is the source code for ArrayFile.java

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/*L
 *  Copyright SAIC
 *
 *  Distributed under the OSI-approved BSD 3-Clause License.
 *  See http://ncip.github.com/cabio/LICENSE.txt for details.
 */

import gov.nih.nci.cabio.annotations.ArrayAnnotationService;
import gov.nih.nci.cabio.annotations.ArrayAnnotationServiceImpl;
import gov.nih.nci.cabio.domain.ArrayReporter;
import gov.nih.nci.cabio.domain.ExpressionArrayReporter;
import gov.nih.nci.common.util.ReflectionUtils;
import gov.nih.nci.system.applicationservice.CaBioApplicationService;
import gov.nih.nci.system.client.ApplicationServiceProvider;

import java.io.FileWriter;
import java.io.PrintWriter;
import java.util.Collection;
import java.util.List;

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

/**
 * Sample caBIO-generated array annotation file.
 * 
 * @author <a href="mailto:rokickik@mail.nih.gov">Konrad Rokicki</a>
 */
public class ArrayFile {

    private static Log log = LogFactory.getLog(ArrayFile.class);

    public static void main(String[] args) throws Exception {

        PrintWriter out = new PrintWriter(new FileWriter("arrayfile.txt"));

        CaBioApplicationService appService = (CaBioApplicationService) ApplicationServiceProvider
                .getApplicationServiceFromUrl("http://cabioapi-qa.nci.nih.gov/cabio42");

        ArrayAnnotationService am = new ArrayAnnotationServiceImpl(appService);

        String arrayName = "HG-U133_Plus_2";

        Collection<ArrayReporter> reps = am.getReportersForPlatform(arrayName);

        out.println("Name\tSymbol\tHUGO Symbol\tUnigene Id\t" + "Sequence Type\tSequence Source\tTarget Id\t"
                + "Target Description\tCytoband\tChromosome\tStart\tEnd");

        int c = 0;
        for (ArrayReporter rep : reps) {

            ExpressionArrayReporter er = (ExpressionArrayReporter) rep;

            out.println(resolve(er, "name") + "\t" + resolve(er, "gene.symbol") + "\t"
                    + resolve(er, "gene.hugoSymbol") + "\t" + resolve(er, "gene.clusterId") + "\t"
                    + resolve(er, "sequenceType") + "\t" + resolve(er, "sequenceSource") + "\t"
                    + resolve(er, "targetId") + "\t" + resolve(er, "targetDescription") + "\t"
                    + resolve(er, "cytogeneticLocationCollection[0].startCytoband.name") + "\t"
                    + resolve(er, "physicalLocationCollection[0].chromosome.number") + "\t"
                    + resolve(er, "physicalLocationCollection[0].chromosomalStartPosition") + "\t"
                    + resolve(er, "physicalLocationCollection[0].chromosomalEndPosition"));

            if (c++ > 500)
                break;
        }

        out.close();
    }

    /**
     * Code borrowed from caBIO Portlet's ResultItem.
     * @param object
     * @param path
     * @return
     */
    private static Object resolve(Object object, String path) {

        if (object == null)
            return "";

        int d = path.indexOf('.');
        String attr = (d < 0) ? path : path.substring(0, d);

        int a = attr.indexOf('[');
        int b = attr.indexOf(']');
        int index = -1;
        if (a > 0) {
            index = Integer.parseInt(attr.substring(a + 1, b));
            attr = attr.substring(0, a);
        }

        Object nextObj;
        try {
            nextObj = ReflectionUtils.get(object, attr);
        } catch (Exception e) {
            log.error("Attribute error for " + path, e);
            return "ERROR";
        }

        if (d < 0) {
            // this is the target attribute
            return (nextObj == null) ? "" : nextObj;
        } else {
            String nextPath = path.substring(d + 1);
            if (nextObj instanceof List) {
                List nextList = (List) nextObj;

                // just need one element from the list
                if (index >= 0) {
                    try {
                        nextObj = nextList.get(index);
                    } catch (IndexOutOfBoundsException e) {
                        return "";
                    }
                    return resolve(nextObj, nextPath);
                }

                // aggregate all the elements in the list
                StringBuffer buf = new StringBuffer();
                int c = 0;
                for (Object e : (List) nextObj) {
                    if (c++ > 0)
                        buf.append(", ");
                    buf.append(resolve(e, nextPath));
                }
                return buf.toString();
            } else {
                return resolve(nextObj, nextPath);
            }
        }
    }

}