Java tutorial
/*L * Copyright (c) 2006 SAIC, SAIC-F. * * Distributed under the OSI-approved BSD 3-Clause License. * See http://ncip.github.com/rembrandt/LICENSE.txt for details. */ package gov.nih.nci.rembrandt.web.xml; import gov.nih.nci.caintegrator.dto.de.GeneIdentifierDE.GeneSymbol; import gov.nih.nci.rembrandt.queryservice.resultset.Resultant; import gov.nih.nci.rembrandt.queryservice.resultset.ResultsContainer; import gov.nih.nci.rembrandt.queryservice.resultset.gene.DiseaseGroupResultset; import gov.nih.nci.rembrandt.queryservice.resultset.gene.GeneExprResultsContainer; import gov.nih.nci.rembrandt.queryservice.resultset.gene.GeneResultset; import gov.nih.nci.rembrandt.queryservice.resultset.gene.ReporterResultset; import gov.nih.nci.rembrandt.util.ContextSensitiveHelpTag; import java.text.DecimalFormat; import java.util.Collection; import java.util.Iterator; import java.util.Map; import org.dom4j.Document; import org.dom4j.DocumentHelper; import org.dom4j.Element; /** * @author Landyr * Feb 8, 2005 * */ /** * caIntegrator License * * Copyright 2001-2005 Science Applications International Corporation ("SAIC"). * The software subject to this notice and license includes both human readable source code form and machine readable, * binary, object code form ("the caIntegrator Software"). The caIntegrator Software was developed in conjunction with * the National Cancer Institute ("NCI") by NCI employees and employees of SAIC. * To the extent government employees are authors, any rights in such works shall be subject to Title 17 of the United States * Code, section 105. * This caIntegrator Software License (the "License") is between NCI and You. "You (or "Your") shall mean a person or an * entity, and all other entities that control, are controlled by, or are under common control with the entity. "Control" * for purposes of this definition means (i) the direct or indirect power to cause the direction or management of such entity, * whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) * beneficial ownership of such entity. * This License is granted provided that You agree to the conditions described below. NCI grants You a non-exclusive, * worldwide, perpetual, fully-paid-up, no-charge, irrevocable, transferable and royalty-free right and license in its rights * in the caIntegrator Software to (i) use, install, access, operate, execute, copy, modify, translate, market, publicly * display, publicly perform, and prepare derivative works of the caIntegrator Software; (ii) distribute and have distributed * to and by third parties the caIntegrator Software and any modifications and derivative works thereof; * and (iii) sublicense the foregoing rights set out in (i) and (ii) to third parties, including the right to license such * rights to further third parties. For sake of clarity, and not by way of limitation, NCI shall have no right of accounting * or right of payment from You or Your sublicensees for the rights granted under this License. This License is granted at no * charge to You. * 1. Your redistributions of the source code for the Software must retain the above copyright notice, this list of conditions * and the disclaimer and limitation of liability of Article 6, below. Your redistributions in object code form must reproduce * the above copyright notice, this list of conditions and the disclaimer of Article 6 in the documentation and/or other materials * provided with the distribution, if any. * 2. Your end-user documentation included with the redistribution, if any, must include the following acknowledgment: "This * product includes software developed by SAIC and the National Cancer Institute." If You do not include such end-user * documentation, You shall include this acknowledgment in the Software itself, wherever such third-party acknowledgments * normally appear. * 3. You may not use the names "The National Cancer Institute", "NCI" "Science Applications International Corporation" and * "SAIC" to endorse or promote products derived from this Software. This License does not authorize You to use any * trademarks, service marks, trade names, logos or product names of either NCI or SAIC, except as required to comply with * the terms of this License. * 4. For sake of clarity, and not by way of limitation, You may incorporate this Software into Your proprietary programs and * into any third party proprietary programs. However, if You incorporate the Software into third party proprietary * programs, You agree that You are solely responsible for obtaining any permission from such third parties required to * incorporate the Software into such third party proprietary programs and for informing Your sublicensees, including * without limitation Your end-users, of their obligation to secure any required permissions from such third parties * before incorporating the Software into such third party proprietary software programs. In the event that You fail * to obtain such permissions, You agree to indemnify NCI for any claims against NCI by such third parties, except to * the extent prohibited by law, resulting from Your failure to obtain such permissions. * 5. For sake of clarity, and not by way of limitation, You may add Your own copyright statement to Your modifications and * to the derivative works, and You may provide additional or different license terms and conditions in Your sublicenses * of modifications of the Software, or any derivative works of the Software as a whole, provided Your use, reproduction, * and distribution of the Work otherwise complies with the conditions stated in this License. * 6. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, * THE IMPLIED WARRANTIES OF MERCHANTABILITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE) ARE DISCLAIMED. * IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE, SAIC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE * GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * */ public class GeneExprDiseaseReport implements ReportGenerator { /** * */ public GeneExprDiseaseReport() { super(); // TODO Auto-generated constructor stub } /* (non-Javadoc) * @see gov.nih.nci.nautilus.ui.report.ReportGenerator#getTemplate(gov.nih.nci.nautilus.resultset.Resultant, java.lang.String) */ public Document getReportXML(Resultant resultant, Map filterMapParams) { // have setter or put in props file //String theColors[] = { "B6C5F2","F2E3B5","DAE1F9","C4F2B5","819BE9", "E9CF81" }; DecimalFormat resultFormat = new DecimalFormat("0.0000"); Document document = DocumentHelper.createDocument(); Element report = document.addElement("Report"); Element cell = null; Element data = null; Element dataRow = null; //add the atts report.addAttribute("reportType", "Gene Expression Disease"); report.addAttribute("helpLink", ContextSensitiveHelpTag.getHelpLink("Gene Expression Disease")); //fudge these for now report.addAttribute("groupBy", "none"); String queryName = resultant.getAssociatedQuery().getQueryName(); //set the queryName to be unique for session/cache access report.addAttribute("queryName", queryName); report.addAttribute("sessionId", "the session id"); report.addAttribute("creationTime", "right now"); //hold a message to display on the report report.addAttribute("msg", (resultant.isOverLimit() ? "over limit" : "")); ResultsContainer resultsContainer = resultant.getResultsContainer(); StringBuffer sb = new StringBuffer(); //String helpFul = helpLink + "?sect=diseaseGroup" + helpLinkClose; GeneExprResultsContainer geneExprDiseaseContainer = (GeneExprResultsContainer) resultsContainer; /* if(resultsContainer instanceof DimensionalViewContainer) { DimensionalViewContainer dimensionalViewContainer = (DimensionalViewContainer) resultsContainer; if(dimensionalViewContainer != null) { geneExprDiseaseContainer = dimensionalViewContainer.; } } else if(resultsContainer instanceof CopyNumberSingleViewResultsContainer) { //for single geneExprDiseaseContainer = (CopyNumberSingleViewResultsContainer) resultsContainer; } */ StringBuffer css = new StringBuffer(); int recordCount = 0; if (geneExprDiseaseContainer != null) { Collection genes = geneExprDiseaseContainer.getGeneResultsets(); Collection labels = geneExprDiseaseContainer.getGroupsLabels(); Collection sampleIds = null; //get group size (as Disease or Agegroup )from label.size String label = null; //sb.append("<table cellpadding=\"0\" cellspacing=\"0\">\n"); //set up the header for the table Element headerRow = report.addElement("Row").addAttribute("name", "headerRow"); cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Gene"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Reporter"); data = null; cell = null; //sb.append("<tr><Td id=\"header\">Gene</td><td id=\"header\">Reporter</td>"); for (Iterator labelIterator = labels.iterator(); labelIterator.hasNext();) { label = (String) labelIterator.next(); cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", label) .addAttribute("group", label); data = cell.addElement("Data").addAttribute("type", "header").addText(label); data = null; cell = null; //sb.append("<Td id=\"header\" class=\""+label+"\">"+label+"</td>"); } //sb.append("</tr>\n"); for (Iterator geneIterator = genes.iterator(); geneIterator.hasNext();) { GeneResultset geneResultset = (GeneResultset) geneIterator.next(); Collection reporters = geneResultset.getReporterResultsets(); for (Iterator reporterIterator = reporters.iterator(); reporterIterator.hasNext();) { recordCount += reporters.size(); ReporterResultset reporterResultset = (ReporterResultset) reporterIterator.next(); Collection groupTypes = reporterResultset.getGroupByResultsets(); String reporterName = "-"; try { reporterName = reporterResultset.getReporter().getValue().toString(); } catch (Exception e) { reporterName = "-"; } GeneSymbol gene = geneResultset.getGeneSymbol(); String geneSymbol = "-"; if (gene != null) { try { geneSymbol = geneResultset.getGeneSymbol().getValueObject().toString(); } catch (Exception e) { geneSymbol = " - "; } //logger.debug("Gene Symbol: "+ geneSymbol); } //start the new data row dataRow = report.addElement("Row").addAttribute("name", "dataRow"); cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(geneSymbol); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "reporter") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(reporterName); data = null; cell = null; //sb.append("<tr><td>"+geneSymbol+"</td><td>" + reporterName + "</td>"); for (Iterator labelIterator = labels.iterator(); labelIterator.hasNext();) { sb = new StringBuffer(); label = (String) labelIterator.next(); DiseaseGroupResultset diseaseResultset = (DiseaseGroupResultset) reporterResultset .getGroupByResultset(label); if (diseaseResultset != null) { cell = dataRow.addElement("Cell").addAttribute("type", "data") .addAttribute("class", label).addAttribute("group", label); //sb.append("<td class=\""+label+"\">"); try { Double ratio = (Double) diseaseResultset.getFoldChangeRatioValue().getValue(); sb.append(resultFormat.format(ratio)); } catch (Exception e) { sb.append("-"); } try { Double pvalue = (Double) diseaseResultset.getRatioPval().getValue(); sb.append(" (" + resultFormat.format(pvalue) + ")"); } catch (Exception e) { sb.append("-"); } data = cell.addElement("Data").addAttribute("type", "data").addText(sb.toString()); data = null; cell = null; //sb.append("</td>"); } else { cell = dataRow.addElement("Cell").addAttribute("type", "data") .addAttribute("class", label).addAttribute("group", label); data = cell.addElement("Data").addAttribute("type", "data").addText("-"); data = null; cell = null; //sb.append("<Td class=\""+label+"\">-</td>"); } } //sb.append("</tr>"); } // add the line between genes //sb.append("<tr><td colspan=\""+(labels.size() + 2)+"\" class=\"geneSpacerStyle\"> </td></tr>\n"); } //sb.append("</table>\n\n"); } else { sb.append("<br/><br/>Gene Disease View container is empty"); //TODO: something fancy here w/errors } //return "<div class=\"rowCount\">"+helpFul +recordCount+" records returned " + links + "</div>\n" + css.toString() + sb.toString(); return document; } }