gov.nih.nci.ispy.web.reports.quick.QuickReporterReport.java Source code

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Here is the source code for gov.nih.nci.ispy.web.reports.quick.QuickReporterReport.java

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

package gov.nih.nci.ispy.web.reports.quick;

import gov.nih.nci.caintegrator.application.service.annotation.GeneExprAnnotationService;
import gov.nih.nci.caintegrator.application.service.annotation.ReporterAnnotation;
import gov.nih.nci.ispy.service.annotation.GeneExprAnnotationServiceFactory;

import java.util.Collection;
import java.util.List;

import org.apache.commons.lang.StringUtils;
import org.dom4j.Document;
import org.dom4j.DocumentHelper;
import org.dom4j.Element;

public class QuickReporterReport {

    public static StringBuffer quickReporterReport(List<String> reporters, String session, String taskId) {
        StringBuffer html = new StringBuffer();
        Document document = DocumentHelper.createDocument();
        Element table = document.addElement("table").addAttribute("id", "reportTable").addAttribute("class",
                "report");
        Element tr = null;
        Element td = null;

        tr = table.addElement("tr").addAttribute("class", "header");
        td = tr.addElement("td").addAttribute("class", "header").addText("Reporter");
        td = tr.addElement("td").addAttribute("class", "header").addText("Gene Symbol");
        td = tr.addElement("td").addAttribute("class", "header").addText("GenBank AccId");
        td = tr.addElement("td").addAttribute("class", "header").addText("LocusLink");

        if (reporters != null) {
            try {
                GeneExprAnnotationService geService = GeneExprAnnotationServiceFactory.getInstance();

                List<ReporterAnnotation> reporterAnnotations = geService.getAnnotationsListForReporters(reporters);
                for (ReporterAnnotation reporterAnnotation : reporterAnnotations) {
                    if (reporterAnnotation != null) {

                        tr = table.addElement("tr").addAttribute("class", "data");

                        //String reporter = reporterAnnotation.getReporter()!=null ? reporterAnnotation.getReporter().getValue().toString() : "N/A";
                        td = tr.addElement("td").addText(reporterAnnotation.getReporterId());
                        //html.append("ReporterID :" +reporterResultset.getReporter().getValue().toString() + "<br/>");
                        Collection<String> geneSymbols = (Collection<String>) reporterAnnotation.getGeneSymbols();
                        String genes = "";
                        if (geneSymbols != null) {
                            genes = StringUtils.join(geneSymbols.toArray(), ",");
                        }
                        if (!genes.equals("")) {
                            td = tr.addElement("td").addText(genes).addAttribute("class", "gene")
                                    .addAttribute("name", "gene").addAttribute("id", genes).addElement("input")
                                    .addAttribute("type", "checkbox").addAttribute("name", "checkable")
                                    .addAttribute("class", "saveElement").addAttribute("value", genes);
                        } else {
                            td = tr.addElement("td").addText(genes).addAttribute("class", "gene")
                                    .addAttribute("name", "gene").addAttribute("id", genes);
                        }
                        Collection<String> genBank_AccIDS = (Collection<String>) reporterAnnotation
                                .getGenbankAccessions();
                        String accs = "";
                        if (genBank_AccIDS != null) {
                            accs = StringUtils.join(genBank_AccIDS.toArray(), ",");
                        }

                        td = tr.addElement("td").addText(accs);

                        Collection<String> locusLinkIDs = (Collection<String>) reporterAnnotation.getLocusLinkIds();
                        String ll = "";
                        if (locusLinkIDs != null) {
                            ll = StringUtils.join(locusLinkIDs.toArray(), ",");
                        }

                        td = tr.addElement("td").addText(ll);
                    }
                }
            } catch (Exception e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
        }
        //return html;
        return html.append(document.asXML());
    }
}