Java tutorial
/*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.xml; import gov.nih.nci.caintegrator.analysis.messaging.ClassComparisonResultEntry; import gov.nih.nci.caintegrator.application.service.annotation.GeneExprAnnotationService; import gov.nih.nci.caintegrator.application.service.annotation.ReporterAnnotation; import gov.nih.nci.caintegrator.dto.query.ClassComparisonQueryDTO; import gov.nih.nci.caintegrator.dto.query.ClinicalQueryDTO; import gov.nih.nci.caintegrator.service.findings.ClassComparisonFinding; import gov.nih.nci.caintegrator.service.findings.Finding; import gov.nih.nci.ispy.service.annotation.GeneExprAnnotationServiceFactory; import java.math.BigDecimal; import java.text.DecimalFormat; import java.util.ArrayList; import java.util.Collection; import java.util.List; 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 * */ public class ClassComparisonReport { /** * */ public ClassComparisonReport() { //super(); } public static Document getReportXML(Finding finding, Map filterMapParams) { //changed the sig to include an allannotation flag, hence this wrapper method is born return getReportXML(finding, filterMapParams, false); } /* (non-Javadoc) * @see gov.nih.nci.nautilus.ui.report.ReportGenerator#getTemplate(gov.nih.nci.nautilus.resultset.Resultant, java.lang.String) */ public static Document getReportXML(Finding finding, Map filterMapParams, boolean allAnnotations) { allAnnotations = true; //force this for now ISPY prerelease - RCL 3/2 DecimalFormat resultFormat = new DecimalFormat("0.0000"); DecimalFormat sciFormat = new DecimalFormat("0.00E0"); DecimalFormat tmpsciFormat = new DecimalFormat("###0.0000#####################"); /* * this is for filtering, we will want a p-value filter for CC */ 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"); String defaultV = "--"; String delim = " | "; Document document = DocumentHelper.createDocument(); Element report = document.addElement("Report"); Element cell = null; Element data = null; Element dataRow = null; //add the atts report.addAttribute("reportType", "Class Comparison"); //fudge these for now report.addAttribute("groupBy", "none"); String queryName = "none"; queryName = finding.getTaskId(); //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"); StringBuffer sb = new StringBuffer(); int recordCount = 0; int totalSamples = 0; //TODO: instance of ClassComparisonFinding ccf = (ClassComparisonFinding) finding; //process the query details ArrayList<String> queryDetails = new ArrayList(); ClassComparisonQueryDTO ccdto = (ClassComparisonQueryDTO) ccf.getQueryDTO(); String reporterType = ccdto.getArrayPlatformDE().getValueObject(); if (ccdto != null) { String tmp = ""; tmp = ccdto.getQueryName() != null ? ccdto.getQueryName() : ""; queryDetails.add("Query Name: " + tmp); tmp = ccdto.getArrayPlatformDE() != null ? ccdto.getArrayPlatformDE().getValue().toString() : ""; queryDetails.add("Array Platform: " + tmp); tmp = ""; List<ClinicalQueryDTO> grps = ccdto.getComparisonGroups() != null ? ccdto.getComparisonGroups() : new ArrayList(); Collection grs = new ArrayList(); for (ClinicalQueryDTO cdto : grps) { if (cdto.getQueryName() != null) grs.add(cdto.getQueryName()); } tmp += StringUtils.join(grs.toArray(), ", ") + " (baseline)"; queryDetails.add("Groups: " + tmp); /* noHTMLString = noHTMLString.replaceAll("<", "{"); noHTMLString = noHTMLString.replaceAll(">", "}"); noHTMLString = noHTMLString.replaceAll(" ", " "); */ tmp = ccdto.getExprFoldChangeDE() != null ? ccdto.getExprFoldChangeDE().getValue().toString() : ""; queryDetails.add("Fold Change: " + tmp); //queryDetails.add("Institutions: " + ccdto.getInstitutionDEs()); tmp = ccdto.getMultiGroupComparisonAdjustmentTypeDE() != null ? ccdto.getMultiGroupComparisonAdjustmentTypeDE().getValue().toString() : ""; queryDetails.add("Multi Group: " + tmp); tmp = ccdto.getStatisticalSignificanceDE() != null ? ccdto.getStatisticalSignificanceDE().getValue().toString() : ""; queryDetails.add("Stat Sig.: " + tmp); tmp = ccdto.getStatisticTypeDE() != null ? ccdto.getStatisticTypeDE().getValue().toString() : ""; queryDetails.add("Stat Type: " + tmp); } /* queryDetails.add("Analysis Result name: " + ccform.getAnalysisResultName()); queryDetails.add("Array Platform: " + ccform.getArrayPlatform()); queryDetails.add("Baseline group: " + ccform.getBaselineGroup()); queryDetails.add("Comparison Groups: " + ccform.getSelectedGroups()[0].toString()); queryDetails.add("Comparison Adjustment: " + ccform.getComparisonAdjustment()); //queryDetails.add("Comp. Adj. Coll: " + ccform.getComparisonAdjustmentCollection()); //queryDetails.add("Existing Groups: " + ccform.getExistingGroups()); //queryDetails.add("Existing group list: " + ccform.getExistingGroupsList()); //queryDetails.add("Fold Change: " + ccform.getFoldChange()); queryDetails.add("Fold Change auto: " + ccform.getFoldChangeAuto()); //queryDetails.add("Fold change auto list: " + ccform.getFoldChangeAutoList()); //queryDetails.add("Fold change manual: " + ccform.getFoldChangeManual()); queryDetails.add("Stastic: " + ccform.getStatistic()); queryDetails.add("Stastical method: " + ccform.getStatisticalMethod()); //queryDetails.add("Stastical method coll.: " + ccform.getStatisticalMethodCollection()); queryDetails.add("Stastical significance: " + ccform.getStatisticalSignificance()); */ String qd = ""; for (String q : queryDetails) { qd += q + " ||| "; } if (ccf != null) { Element details = report.addElement("Query_details"); cell = details.addElement("Data"); cell.addText(qd); cell = null; 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("Reporter"); 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("Group Avg"); data = null; cell = null; cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); String isAdj = ccf.arePvaluesAdjusted() ? " (Adjusted) " : ""; data = cell.addElement("Data").addAttribute("type", "header").addText("P-Value" + isAdj); 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("Fold Change"); 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("Gene Symbol"); data = null; cell = null; //starting annotations...get them only if allAnnotations == true if (allAnnotations) { 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("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("GO Id"); 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("Pathways"); data = null; cell = null; } /* done with the headerRow and SampleRow Elements, time to add data rows */ /* Map<String,ReporterResultset> reporterResultsetMap = null; reporterResultsetMap = ccf.getReporterAnnotationsMap(); */ List<ClassComparisonResultEntry> classComparisonResultEntrys = ccf.getResultEntries(); List<String> reporterIds = new ArrayList<String>(); for (ClassComparisonResultEntry classComparisonResultEntry : classComparisonResultEntrys) { if (classComparisonResultEntry.getReporterId() != null) { reporterIds.add(classComparisonResultEntry.getReporterId()); } } Map reporterResultsetMap = null; try { GeneExprAnnotationService geService = GeneExprAnnotationServiceFactory.getInstance(); reporterResultsetMap = geService.getAnnotationsMapForReporters(reporterIds); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } /* //new stuff AnnotationHandler h = new AnnotationHandler(); Map reporterResultsetMap = null; if(allAnnotations){ //Map<String, ReporterAnnotations> reporterResultsetMap = null; try { reporterResultsetMap = h.getAllAnnotationsFor(reporterIds); } catch (Exception e) { e.printStackTrace(); } } else { //Map<String, String> reporterResultsetMap = null; try { reporterResultsetMap = h.getGeneSymbolsFor(reporterIds); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } */ /* //this looks like a failsafe for the old method if(reporterResultsetMap == null) { try { reporterResultsetMap = GeneExprAnnotationService.getAnnotationsMapForReporters(reporterIds); } catch(Exception e){} } */ for (ClassComparisonResultEntry ccre : ccf.getResultEntries()) { dataRow = report.addElement("Row").addAttribute("name", "dataRow"); cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "reporter") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", reporterType).addText(ccre.getReporterId()); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header") .addText(resultFormat.format(ccre.getMeanGrp1()) + " / " + resultFormat.format(ccre.getMeanBaselineGrp())); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "pval").addAttribute("class", "data") .addAttribute("group", "data"); //String pv = (ccre.getPvalue() == null) ? String.valueOf(ccre.getPvalue()) : "N/A"; String pv = defaultV; BigDecimal bigd; try { bigd = new BigDecimal(ccre.getPvalue()); pv = bigd.toPlainString(); } catch (Exception e) { //missing value } data = cell.addElement("Data").addAttribute("type", "header").addText(pv); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header") .addText(String.valueOf(resultFormat.format(ccre.getFoldChange()))); data = null; cell = null; //if only showing genes if (!allAnnotations && reporterResultsetMap != null) { String reporterId = ccre.getReporterId().toUpperCase().trim(); String genes = reporterResultsetMap.get(reporterId) != null ? (String) reporterResultsetMap.get(reporterId) : defaultV; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(genes); data = null; cell = null; } else { //get the gene symbols for this reporter //ccre.getReporterId() String genes = defaultV; //start annotations String accIds = defaultV; String llink = defaultV; String go = defaultV; String pw = defaultV; if (reporterResultsetMap != null) { // && reporterIds != null //int count = 0; String reporterId = ccre.getReporterId().toUpperCase().trim(); //ReporterResultset reporterResultset = reporterResultsetMap.get(reporterId); ReporterAnnotation ra = (ReporterAnnotation) reporterResultsetMap.get(reporterId); //Collection<String> geneSymbols = (Collection<String>)reporterResultset.getAssiciatedGeneSymbols(); if (ra != null) { List geneSymbols = ra.getGeneSymbols(); //if(geneSymbols != null) // genes = geneSymbols.toString(); if (geneSymbols != null) { genes = StringUtils.join(geneSymbols.toArray(), delim); } Collection<String> genBank_AccIDS = (Collection<String>) ra.getGenbankAccessions(); if (genBank_AccIDS != null) { accIds = StringUtils.join(genBank_AccIDS.toArray(), delim); } Collection<String> locusLinkIDs = (Collection<String>) ra.getLocusLinkIds(); if (locusLinkIDs != null) { llink = StringUtils.join(locusLinkIDs.toArray(), delim); } Collection<String> goIds = (Collection<String>) ra.getGOIds(); if (goIds != null) { go = StringUtils.join(goIds.toArray(), delim); } Collection<String> pathways = (Collection<String>) ra.getPathwayIds(); if (pathways != null) { pw = StringUtils.join(pathways.toArray(), delim); } } } cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(genes); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(accIds); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(llink); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(go); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header").addText(pw); data = null; cell = null; } } } else { //TODO: handle this error sb.append("<br><Br>Class Comparison is empty<br>"); } return document; } }