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.BioSpecimenIdentifierDE; import gov.nih.nci.caintegrator.dto.de.GeneIdentifierDE.GeneSymbol; import gov.nih.nci.rembrandt.queryservice.resultset.DimensionalViewContainer; import gov.nih.nci.rembrandt.queryservice.resultset.Resultant; import gov.nih.nci.rembrandt.queryservice.resultset.ResultsContainer; import gov.nih.nci.rembrandt.queryservice.resultset.copynumber.CopyNumberGeneViewResultsContainer; import gov.nih.nci.rembrandt.queryservice.resultset.copynumber.SampleCopyNumberValuesResultset; import gov.nih.nci.rembrandt.queryservice.resultset.gene.GeneExprSingleViewResultsContainer; import gov.nih.nci.rembrandt.queryservice.resultset.gene.GeneResultset; import gov.nih.nci.rembrandt.queryservice.resultset.gene.ReporterResultset; import gov.nih.nci.rembrandt.queryservice.resultset.gene.SampleFoldChangeValuesResultset; import gov.nih.nci.rembrandt.queryservice.resultset.gene.ViewByGroupResultset; import gov.nih.nci.rembrandt.util.ContextSensitiveHelpTag; import gov.nih.nci.rembrandt.web.helper.FilterHelper; import java.text.DecimalFormat; import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; import java.util.Iterator; import java.util.Map; import org.apache.commons.lang.StringUtils; 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 CopyNumberGeneBasedSampleReport implements ReportGenerator { /** * */ public CopyNumberGeneBasedSampleReport() { 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) { DecimalFormat resultFormat = new DecimalFormat("0.0000"); String delim = " | "; /* testing hardcoded vals - these will be params of this method soon */ /* ArrayList g = new ArrayList(); g.add("EGFR"); g.add("VEGF"); String tmp_filter_type = "hide"; String tmp_filter_element = "gene"; HashMap filterMapParams = new HashMap(); filterMapParams.put("filter_string", g); filterMapParams.put("filter_type", tmp_filter_type); filterMapParams.put("filter_element", tmp_filter_element); */ ArrayList filter_string = new ArrayList(); // hashmap of genes | reporters | cytobands String filter_type = "show"; // show | hide String filter_element = "none"; // none | gene | reporter | cytoband if (filterMapParams.containsKey("filter_string") && filterMapParams.get("filter_string") != null) filter_string = (ArrayList) filterMapParams.get("filter_string"); if (filterMapParams.containsKey("filter_type") && filterMapParams.get("filter_type") != null) filter_type = (String) filterMapParams.get("filter_type"); if (filterMapParams.containsKey("filter_element") && filterMapParams.get("filter_element") != null) filter_element = (String) filterMapParams.get("filter_element"); Document document = DocumentHelper.createDocument(); Element report = document.addElement("Report"); Element cell = null; Element data = null; Element dataRow = null; //add the atts report.addAttribute("reportType", "Copy Number"); report.addAttribute("helpLink", ContextSensitiveHelpTag.getHelpLink("Copy Number")); //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(); CopyNumberGeneViewResultsContainer copyNumberGeneViewContainer = null; StringBuffer sb = new StringBuffer(); //String helpFul = helpLink + "?sect=sample" + helpLinkClose; DimensionalViewContainer dimensionalViewContainer = null; int recordCount = 0; int totalSamples = 0; if (resultsContainer instanceof DimensionalViewContainer) { dimensionalViewContainer = (DimensionalViewContainer) resultsContainer; if (dimensionalViewContainer != null) { copyNumberGeneViewContainer = dimensionalViewContainer.getCopyNumberGeneViewResultsContainer(); } } else if (resultsContainer instanceof CopyNumberGeneViewResultsContainer) { //for single copyNumberGeneViewContainer = (CopyNumberGeneViewResultsContainer) resultsContainer; } if (copyNumberGeneViewContainer != null) { Collection genes = copyNumberGeneViewContainer.getGeneResultsets(); Collection labels = copyNumberGeneViewContainer.getGroupsLabels(); Collection sampleIds = null; StringBuffer header = new StringBuffer(); //header.append("<table cellpadding=\"0\" cellspacing=\"0\">\n<tr>\n"); StringBuffer sampleNames = new StringBuffer(); StringBuffer stringBuffer = new StringBuffer(); 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; //starting annotations cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Locus link"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("GenBank Acc"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("GO Id"); cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Pathways"); cell = null; Element sampleRow = report.addElement("Row").addAttribute("name", "sampleRow"); cell = sampleRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(" "); data = null; cell = null; cell = sampleRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(" "); data = null; cell = null; cell = sampleRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(" "); data = null; cell = null; cell = sampleRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(" "); data = null; cell = null; cell = sampleRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(" "); data = null; cell = null; cell = sampleRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(" "); data = null; cell = null; //set up the header for the table //header.append("<Td id=\"header\">Gene</td>\n<td id=\"header\">Reporter</td>\n"); //sampleNames.append("<tr><Td> </td><Td> </tD>"); for (Iterator labelIterator = labels.iterator(); labelIterator.hasNext();) { String label = (String) labelIterator.next(); sampleIds = copyNumberGeneViewContainer.getBiospecimenLabels(label); // theColspan += sampleIds.size(); totalSamples += sampleIds.size(); cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", label) .addAttribute("group", label); data = cell.addElement("Data").addAttribute("type", "header").addText(label + " Samples"); data = null; cell = null; //header.append("<td colspan="+sampleIds.size()+" class='"+label+"' id=\"header\">"+label+" Samples</td>"); for (Iterator sampleIdIterator = sampleIds.iterator(); sampleIdIterator.hasNext();) { BioSpecimenIdentifierDE bioSpecimenIdentifierDE = (BioSpecimenIdentifierDE) sampleIdIterator .next(); cell = sampleRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", label) .addAttribute("group", label) .addAttribute("sampleId", bioSpecimenIdentifierDE.getSampleId()); //cell = sampleRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", label).addAttribute("group", label).addAttribute("specimen", bioSpecimenIdentifierDE.getSpecimenName()); //data = cell.addElement("Data").addAttribute("type", "header").addText(s.substring(2)); if (bioSpecimenIdentifierDE.getSpecimenName() != null) { data = cell.addElement("Data").addAttribute("type", "header") .addText(bioSpecimenIdentifierDE.getSpecimenName()); } else { data = cell.addElement("Data").addAttribute("type", "header") .addText(bioSpecimenIdentifierDE.getSampleId()); } data = null; cell = null; //sampleNames.append("<td class='"+label+"' id=\"header\"><a href=\"report.do?s="+s+"&report=ss\">"+s.substring(2)+"</a></td>"); //header.append("\t"); } //header.deleteCharAt(header.lastIndexOf("\t")); } //sampleNames.append("</tr>"); //header.append("</tr>"); /* done with the headerRow and SampleRow Elements, time to add data rows */ for (Iterator geneIterator = genes.iterator(); geneIterator.hasNext();) { GeneResultset geneResultset = (GeneResultset) geneIterator.next(); //Collection reporters = geneResultset.getReporterResultsets(); String the_gene = ""; /* hard code filter for now */ if (geneResultset.getGeneSymbol() != null) { the_gene = geneResultset.getGeneSymbol().getValueObject().toString(); } //if(!the_gene.equalsIgnoreCase(filter_string)) { if (FilterHelper.checkFilter(filter_element, "gene", the_gene, filter_type, filter_string)) { //if(!filter_element.equals("gene") || (filter_element.equals("gene") && !filter_string.contains(the_gene))) { recordCount += genes.size(); //for (Iterator reporterIterator = reporters.iterator(); reporterIterator.hasNext();) { // ReporterResultset reporterResultset = (ReporterResultset)reporterIterator.next(); Collection groupTypes = geneResultset.getGroupByResultsets(); //String reporterName = reporterResultset.getReporter().getValue().toString(); /* test filtration by reporter */ //if(!filter_element.equals("reporter") || (filter_element.equals("reporter") && !filter_string.contains(reporterName))) { if (FilterHelper.checkFilter(filter_element, "reporter", geneResultset.getGeneSymbol().getValueObject().toString(), filter_type, filter_string)) { GeneSymbol gene = geneResultset.getGeneSymbol(); //String geneSymbol = " "; String geneSymbol = "-"; if (gene != null) { geneSymbol = geneResultset.getGeneSymbol().getValueObject().toString(); } 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(" ");//reporter data = null; cell = null; //sb.append("<tr><td>"+geneSymbol+"</td><td>"+reporterName+"</td>"); /* * adding our 4 annotations. this code needs to be cleaned up... * * I will pull all this logic out into a seperate Annotations Class ... * or something like that ASAP * * RCL * */ // String ll = ""; // try { // HashSet locusLinkIds = new HashSet(reporterResultset.getAssiciatedLocusLinkIDs()); // if(locusLinkIds != null){ // ll = StringUtils.join(locusLinkIds.toArray(), delim); // } // else { // ll = "-"; // } // } // catch(Exception e){ // ll = "--"; // } // // // String acc = ""; // try { // HashSet accNumbers = new HashSet(reporterResultset.getAssiciatedGenBankAccessionNos()); // if(accNumbers!=null) { // acc = StringUtils.join(accNumbers.toArray(), delim); // } // else { // acc = "-"; // } // } // catch(Exception e){ } // // String go_ids = ""; // try { // HashSet go_idsHS = new HashSet(reporterResultset.getAssociatedGOIds()); // if(go_idsHS!=null) { // go_ids = StringUtils.join(go_idsHS.toArray(), delim); // } // else { // go_ids = "-"; // } // } // catch(Exception e){ } // // String pathways = ""; // try { // HashSet pathwaysHS = new HashSet(reporterResultset.getAssociatedPathways()); // if(pathwaysHS!=null) { // pathways = StringUtils.join(pathwaysHS.toArray(), delim); // } // else { // pathways = "-"; // } // } // catch(Exception e){ } /* * * actually add the annotations to the report * */ // cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv").addAttribute("group", "header"); // data = cell.addElement("Data").addAttribute("type", "header").addText(ll); // data = null; // cell = null; // cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv").addAttribute("group", "header"); // data = cell.addElement("Data").addAttribute("type", "header").addText(acc); // data = null; // cell = null; // cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv").addAttribute("group", "header"); // data = cell.addElement("Data").addAttribute("type", "header").addText(go_ids); // data = null; // cell = null; // cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv").addAttribute("group", "header"); // data = cell.addElement("Data").addAttribute("type", "header").addText(pathways); // data = null; // cell = null; for (Iterator labelIterator = labels.iterator(); labelIterator.hasNext();) { String label = (String) labelIterator.next(); ViewByGroupResultset groupResultset = (ViewByGroupResultset) geneResultset .getGroupByResultset(label); sampleIds = copyNumberGeneViewContainer.getBiospecimenLabels(label); String hClass = label; if (groupResultset != null) { for (Iterator sampleIdIterator = sampleIds.iterator(); sampleIdIterator .hasNext();) { BioSpecimenIdentifierDE sampleId = (BioSpecimenIdentifierDE) sampleIdIterator .next(); SampleCopyNumberValuesResultset biospecimenResultset = (SampleCopyNumberValuesResultset) groupResultset .getBioSpecimenResultset(sampleId.getSpecimenName()); if (biospecimenResultset != null) { //JB Begin: Add for GForge # 17783 - Advance Query Reports - Make the report more user friendly (Provide tool tip) String tooltip = "Gene = " + geneSymbol + ", Sample = " + sampleId.getSampleId() + " (" + sampleId.getSpecimenName() + ")"; //JB End: Add for GForge # 17783 - Advance Query Reports - Make the report more user friendly (Provide tool tip) if (biospecimenResultset.isHighlighted()) hClass = "highlighted"; else hClass = label; Double ratio = (Double) biospecimenResultset.getSegmentMean().getValue(); if (ratio != null) { cell = dataRow.addElement("Cell").addAttribute("type", "data") .addAttribute("class", hClass).addAttribute("group", label); //JB Begin: Add for GForge # 17783 - Advance Query Reports - Make the report more user friendly (Provide tool tip) //data = cell.addElement("Data").addAttribute("type", "data").addText(resultFormat.format(ratio)); data = cell.addElement("Data").addAttribute("type", "data") .addAttribute("datainfo", tooltip) .addText(resultFormat.format(ratio)); //JB End: Add for GForge # 17783 - Advance Query Reports - Make the report more user friendly (Provide tool tip) data = null; cell = null; //sb.append("<Td class='"+label+"'>"+resultFormat.format(ratio)+" </td>"); } else { cell = dataRow.addElement("Cell").addAttribute("type", "data") .addAttribute("class", hClass).addAttribute("group", label); data = cell.addElement("Data").addAttribute("type", "data") .addText("-"); data = null; cell = null; //sb.append("<td class='"+label+"'>-</td>"); } } else { cell = dataRow.addElement("Cell").addAttribute("type", "data") .addAttribute("class", hClass).addAttribute("group", label); data = cell.addElement("Data").addAttribute("type", "data").addText("-"); data = null; cell = null; //sb.append("<td class='"+label+"'>-</td>"); } } } else { for (int s = 0; s < sampleIds.size(); s++) { cell = dataRow.addElement("Cell").addAttribute("type", "data") .addAttribute("class", hClass).addAttribute("group", label); data = cell.addElement("Data").addAttribute("type", "data").addText("-"); data = null; cell = null; //sb.append("<td class='"+label+"'>-</td>"); } } } //sb.append("</tr>\n"); } /* end reporter filter */ //sb.append("<tr><td colspan=\""+theColspan+"\" class=\"geneSpacerStyle\"> </td></tr>\n"); //} } /* end gene filter */ //sb.append("</table>"); } } else { //TODO: handle this error sb.append("<br><Br>Copy Number Container is empty<br>"); } //return "<div class=\"rowCount\">"+ helpFul +recordCount+" records returned. " + totalSamples +" samples returned. " + links + "</div>\n" + sb.toString(); return document; } /* public boolean checkFilter(String filter_element, String f_element, String name, String filter_type, ArrayList filter_string) { if(filter_type.equals("hide") && (!filter_element.equals(f_element) || (filter_element.equals(f_element) && !filter_string.contains(name)))) return true; else if(filter_type.equals("show") && (!filter_element.equals(f_element) || (filter_element.equals(f_element) && filter_string.contains(name)))) return true; else if(!filter_type.equals("show") && !filter_type.equals("hide")) return true; else return false; } */ }