List of usage examples for org.dom4j DocumentHelper createDocument
public static Document createDocument()
From source file:gov.nih.nci.rembrandt.web.taglib.HCPlotReport.java
License:BSD License
public StringBuffer quickReporterReport(List<String> reporters, ArrayPlatformType arrayPlatform) { StringBuffer html = new StringBuffer(); Document document = DocumentHelper.createDocument(); Element table = document.addElement("table").addAttribute("id", "reportTable").addAttribute("class", "report"); Element tr = null;//from w ww. j a v a 2 s . c om 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 { Map reporterResultsetMap = AnnotationHandler.getAllAnnotationsFor(reporters, arrayPlatform); for (String reporterId : reporters) { if (reporterResultsetMap != null) { ReporterAnnotations ra = (ReporterAnnotations) reporterResultsetMap.get(reporterId); tr = table.addElement("tr").addAttribute("class", "data"); String reporter = ra.getReporterName() != null ? ra.getReporterName() : "N/A"; td = tr.addElement("td").addText(reporter); //html.append("ReporterID :" +reporterResultset.getReporter().getValue().toString() + "<br/>"); String geneSymbols = ra.getGeneSymbol(); String genes = ""; if (geneSymbols != null) genes = geneSymbols; td = tr.addElement("td").addText(genes); Collection genBank_AccIDS = ra.getAccessions(); String accs = ""; if (genBank_AccIDS != null) { accs = StringUtils.join(genBank_AccIDS.toArray(), ","); } td = tr.addElement("td").addText(accs); Collection locusLinkIDs = ra.getLocusLinks(); String ll = ""; if (locusLinkIDs != null) { ll = StringUtils.join(locusLinkIDs.toArray(), ","); } td = tr.addElement("td").addText(ll); /* Collection<String> goIds = (Collection<String>)reporterResultset.getAssociatedGOIds(); if(goIds != null){ for(String goId: goIds){ html.append("Associtaed GO Id :" +goId + "<br/>"); } } Collection<String> pathways = (Collection<String>)reporterResultset.getAssociatedPathways(); if(pathways != null){ for(String pathway: pathways){ html.append("Associated Pathway :" +pathway + "<br/>"); } } */ } } } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } //return html; return html.append(document.asXML()); }
From source file:gov.nih.nci.rembrandt.web.xml.ClassComparisonReport.java
License:BSD License
public static Document getReportXML(Finding finding, Map filterMapParams, boolean allAnnotations, ArrayList reporterIdFilter) { DecimalFormat resultFormat = new DecimalFormat("0.0000"); DecimalFormat sciFormat = new DecimalFormat("0.00E0"); DecimalFormat tmpsciFormat = new DecimalFormat("###0.0000#####################"); /*/*from w w w . j av a2 s. c o m*/ * 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"); report.addAttribute("helpLink", ContextSensitiveHelpTag.getHelpLink("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(); 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; //pvalue is fixed in the second column, essential for XSL 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(RembrandtConstants.PVALUE + 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("Group Avg"); 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>(); HashSet<String> reporterIdSet = null; if (reporterIdFilter != null) { reporterIdSet = new HashSet<String>(reporterIdFilter); } int index = 0; if (reporterIdFilter == null) { for (ClassComparisonResultEntry classComparisonResultEntry : classComparisonResultEntrys) { if (classComparisonResultEntry.getReporterId() != null) { reporterIds.add(classComparisonResultEntry.getReporterId()); } } } else { reporterIds = reporterIdFilter; } Map reporterResultsetMap = null; ArrayPlatformType arrayPlatform = ccdto.getArrayPlatformDE() != null ? ccdto.getArrayPlatformDE().getValueObjectAsArrayPlatformType() : ArrayPlatformType.AFFY_OLIGO_PLATFORM; if (allAnnotations) { //Map<String, ReporterAnnotations> reporterResultsetMap = null; try { reporterResultsetMap = AnnotationHandler.getAllAnnotationsFor(reporterIds, arrayPlatform); } catch (Exception e) { e.printStackTrace(); } } else { try { reporterResultsetMap = AnnotationHandler.getGeneSymbolsFor(reporterIds, arrayPlatform); } 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){} } */ boolean found = false; for (ClassComparisonResultEntry ccre : ccf.getResultEntries()) { if (reporterIdFilter != null) { found = reporterIdSet.contains(ccre.getReporterId()); //not found, then skip if (!found) continue; } 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", "header").addText(ccre.getReporterId()); 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"; BigDecimal bigd = new BigDecimal(ccre.getPvalue()); data = cell.addElement("Data").addAttribute("type", "header").addText(bigd.toPlainString()); 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", "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(); 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(); //ReporterResultset reporterResultset = reporterResultsetMap.get(reporterId); ReporterAnnotations ra = (ReporterAnnotations) reporterResultsetMap.get(reporterId); //Collection<String> geneSymbols = (Collection<String>)reporterResultset.getAssiciatedGeneSymbols(); String geneSymbols = ra.getGeneSymbol(); if (geneSymbols != null) genes = geneSymbols; /* if(geneSymbols != null){ genes = StringUtils.join(geneSymbols.toArray(), delim); } */ Collection<String> genBank_AccIDS = (Collection<String>) ra.getAccessions(); if (genBank_AccIDS != null) { accIds = StringUtils.join(genBank_AccIDS.toArray(), delim); } Collection<String> locusLinkIDs = (Collection<String>) ra.getLocusLinks(); 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.getPathways(); 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; }
From source file:gov.nih.nci.rembrandt.web.xml.ClinicalSampleReport.java
License:BSD License
@SuppressWarnings("unchecked") public Document getReportXML(Resultant resultant, Map filterMapParams) { //String theColors[] = { "B6C5F2","F2E3B5","DAE1F9","C4F2B5","819BE9", "E9CF81" }; DecimalFormat resultFormat = new DecimalFormat("0.0000"); String defaultV = "-"; Document document = DocumentHelper.createDocument(); try {/* w w w. j ava 2s. c o m*/ Element report = document.addElement("Report"); Element cell = null; Element data = null; Element dataRow = null; //add the atts report.addAttribute("reportType", "Clinical"); report.addAttribute("helpLink", ContextSensitiveHelpTag.getHelpLink("Clinical")); //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" : "")); boolean gLinks = false; boolean cLinks = false; StringBuffer sb = new StringBuffer(); ResultsContainer resultsContainer = resultant.getResultsContainer(); SampleViewResultsContainer sampleViewContainer = null; if (resultsContainer instanceof DimensionalViewContainer) { DimensionalViewContainer dimensionalViewContainer = (DimensionalViewContainer) resultsContainer; // Are we making hyperlinks? if (dimensionalViewContainer.getGeneExprSingleViewContainer() != null) { // show the geneExprHyperlinks gLinks = true; } if (dimensionalViewContainer.getCopyNumberSingleViewContainer() != null) { // show the copyNumberHyperlinks cLinks = true; } sampleViewContainer = dimensionalViewContainer.getSampleViewResultsContainer(); } else if (resultsContainer instanceof SampleViewResultsContainer) { sampleViewContainer = (SampleViewResultsContainer) resultsContainer; } Collection samples = sampleViewContainer.getSampleResultsets(); // set up the headers for this table Element headerRow = report.addElement("Row").addAttribute("name", "headerRow"); for (String h : ClinicalSampleReport.getClinicalHeaderValues()) { cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(h); data = null; cell = null; } //append these to header if necessary Iterator si = samples.iterator(); if (si.hasNext()) { SampleResultset sampleResultset = (SampleResultset) si.next(); if (sampleResultset.getGeneExprSingleViewResultsContainer() != null) { cell = headerRow.addElement("Cell").addAttribute("type", "header") .addAttribute("class", "header").addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("GeneExp"); data = null; cell = null; } if (sampleResultset.getCopyNumberSingleViewResultsContainer() != null) { cell = headerRow.addElement("Cell").addAttribute("type", "header") .addAttribute("class", "header").addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("CopyNumber"); data = null; cell = null; } } //DONE header row for (Iterator sampleIterator = samples.iterator(); sampleIterator.hasNext();) { SampleResultset sampleResultset = (SampleResultset) sampleIterator.next(); dataRow = report.addElement("Row").addAttribute("name", "dataRow"); List rows = new ArrayList(); rows = ClinicalSampleReport.getClinicalRowValues(sampleResultset); /* rows.add(sampleResultset.getSampleIDDE()); rows.add(sampleResultset.getAgeGroup()); if(!DEUtils.checkNV(sampleResultset.getGenderCode()).equalsIgnoreCase("O")) { rows.add(sampleResultset.getGenderCode()); } else { rows.add(defaultV); } rows.add(sampleResultset.getSurvivalLengthRange()); rows.add(sampleResultset.getDisease()); rows.add(sampleResultset.getWhoGrade()); rows.add(sampleResultset.getRaceDE()); rows.add(sampleResultset.getKarnofskyClinicalEvalDE()); rows.add(sampleResultset.getNeuroExamDescs()); rows.add(sampleResultset.getMriScoreDescs()); rows.add(sampleResultset.getFollowupMonths()); rows.add(sampleResultset.getSteroidDoseStatuses()); rows.add(sampleResultset.getAntiConvulsantStatuses()); rows.add(sampleResultset.getPriorRadiationRadiationSites()); rows.add(sampleResultset.getPriorRadiationFractionDoses()); rows.add(sampleResultset.getPriorRadiationFractionNumbers()); rows.add(sampleResultset.getPriorRadiationRadiationTypes()); rows.add(sampleResultset.getPriorChemoAgentNames()); rows.add(sampleResultset.getPriorChemoCourseCounts()); rows.add(sampleResultset.getPriorSurgeryProcedureTitles()); rows.add(sampleResultset.getPriorSurgeryTumorHistologys()); rows.add(sampleResultset.getPriorSurgerySurgeryOutcomes()); rows.add(sampleResultset.getOnStudyRadiationRadiationSites()); rows.add(sampleResultset.getOnStudyRadiationFractionDoses()); rows.add(sampleResultset.getOnStudyRadiationFractionNumbers()); rows.add(sampleResultset.getOnStudyRadiationNeurosisStatuses()); rows.add(sampleResultset.getOnStudyRadiationRadiationTypes()); rows.add(sampleResultset.getOnStudyChemoAgentNames()); rows.add(sampleResultset.getOnStudyChemoCourseCounts()); rows.add(sampleResultset.getOnStudySurgeryProcedureTitles()); rows.add(sampleResultset.getOnStudySurgeryIndications()); rows.add(sampleResultset.getOnStudySurgeryHistoDiagnoses()); rows.add(sampleResultset.getOnStudySurgerySurgeryOutcomes()); */ cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "sample"); data = cell.addElement("Data").addAttribute("type", "data").addText(DEUtils.checkNull(rows.get(0))); data = null; cell = null; for (int i = 1; i < rows.size(); i++) { cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "data") .addText(DEUtils.checkNull(rows.get(i))); data = null; cell = null; } if (sampleResultset.getGeneExprSingleViewResultsContainer() != null) { //TODO: create the links cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "data").addText("G"); data = null; cell = null; } if (sampleResultset.getCopyNumberSingleViewResultsContainer() != null) { // TODO: create the links cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "data").addText("C"); data = null; cell = null; } } } catch (Exception e) { System.out.println(e); } return document; }
From source file:gov.nih.nci.rembrandt.web.xml.CopyNumberGeneBasedSampleReport.java
License:BSD License
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 */ /*//www. j a v a 2 s.c o m 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; }
From source file:gov.nih.nci.rembrandt.web.xml.CopyNumberSampleReport.java
License:BSD License
public Document getReportXML(Resultant resultant, Map filterMapParams) { //String theColors[] = { "B6C5F2","F2E3B5","DAE1F9","C4F2B5","819BE9", "E9CF81" }; DecimalFormat resultFormat = new DecimalFormat("0.0000"); String delim = " | "; 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;/*from ww w . ja v a 2s. c o m*/ 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" : "")); StringBuffer sb = new StringBuffer(); int recordCount = 0; int totalSamples = 0; ResultsContainer resultsContainer = resultant.getResultsContainer(); CopyNumberSingleViewResultsContainer copyNumberContainer = null; if (resultsContainer instanceof DimensionalViewContainer) { DimensionalViewContainer dimensionalViewContainer = (DimensionalViewContainer) resultsContainer; if (dimensionalViewContainer != null) { copyNumberContainer = dimensionalViewContainer.getCopyNumberSingleViewContainer(); } } else if (resultsContainer instanceof CopyNumberSingleViewResultsContainer) { //for single copyNumberContainer = (CopyNumberSingleViewResultsContainer) resultsContainer; } if (copyNumberContainer != null) { if (copyNumberContainer.getCytobandResultsets().size() > 0) { Collection cytobands = copyNumberContainer.getCytobandResultsets(); Collection labels = copyNumberContainer.getGroupsLabels(); Collection sampleIds = null; StringBuffer header = new StringBuffer(); StringBuffer sampleNames = new StringBuffer(); StringBuffer stringBuffer = new StringBuffer(); /* sampleNames.append("<Tr>"); sampleNames.append("<Td> </td><Td> </td>"); header.append("<tr>"); header.append("<Td id=\"header\">Cytoband</td><td id=\"header\">Reporter</td>"); */ 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("Position"); 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("Genes"); 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("Segment ID"); data = null; cell = null; /* * Start annotations (csv only) * 1) Bp position * 2) associated genes (pipe delimimted list) */ cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("Bp Position"); 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("Genes"); data = null; 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", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText("z "); 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; //this nested loop generates the header row and the samples row for (Iterator labelIterator = labels.iterator(); labelIterator.hasNext();) { String label = (String) labelIterator.next(); sampleIds = copyNumberContainer.getBiospecimenLabels(label); 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>"); //theColspan += sampleIds.size(); } } //header.append("</tr>\n"); //sampleNames.append("</tr>\n"); /* done with the headerRow and SampleRow Elements, time to add data rows */ for (Iterator cytobandIterator = cytobands.iterator(); cytobandIterator.hasNext();) { CytobandResultset cytobandResultset = (CytobandResultset) cytobandIterator.next(); String cytoband = cytobandResultset.getCytoband().getValue().toString(); Collection reporters = copyNumberContainer.getRepoterResultsets(cytoband); // if(!filter_element.equals("cytoband") || (filter_element.equals("cytoband") && !filter_string.contains(cytoband))) { if (FilterHelper.checkFilter(filter_element, "cytoband", cytoband, filter_type, filter_string)) { recordCount += reporters.size(); for (Iterator reporterIterator = reporters.iterator(); reporterIterator.hasNext();) { ReporterResultset reporterResultset = (ReporterResultset) reporterIterator.next(); /* * * store our annotations * */ String bp_position = ""; try { bp_position = reporterResultset.getStartPhysicalLocation().getValue().toString(); } catch (Exception e) { } //there is a much better way to do this, but this is reused from 0.50 //this code will be cleaned up for 1.0 String genes = ""; try { if (reporterResultset.getAssiciatedGeneSymbols() != null) { HashSet geneSymbols = new HashSet(reporterResultset.getAssiciatedGeneSymbols()); genes = StringUtils.join(geneSymbols.toArray(), delim); } else { genes = "-"; } } catch (Exception e) { genes = "--"; } String reporterName = reporterResultset.getReporter().getValue().toString(); if (FilterHelper.checkFilter(filter_element, "reporter", reporterName, filter_type, filter_string)) { //if(!filter_element.equals("reporter") || (filter_element.equals("reporter") && !filter_string.contains(reporterName))) { dataRow = report.addElement("Row").addAttribute("name", "dataRow"); cell = dataRow.addElement("Cell").addAttribute("type", "data") .addAttribute("class", "cytoband").addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(cytoband); data = null; cell = null; cell = dataRow.addElement("Cell").addAttribute("type", "data") .addAttribute("class", "gene").addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(genes); 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>"+cytoband+"</td><td>"+reporterName+"</td>"); /* * * 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(bp_position); 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(genes); data = null; cell = null; for (Iterator labelIterator = labels.iterator(); labelIterator.hasNext();) { String label = (String) labelIterator.next(); ViewByGroupResultset groupResultset = (ViewByGroupResultset) reporterResultset .getGroupByResultset(label); sampleIds = copyNumberContainer.getBiospecimenLabels(label); String hClass = label; if (groupResultset != null) { for (Iterator sampleIdIterator = sampleIds.iterator(); sampleIdIterator .hasNext();) { BioSpecimenIdentifierDE sampleId = (BioSpecimenIdentifierDE) sampleIdIterator .next(); SampleCopyNumberValuesResultset sampleResultset2 = (SampleCopyNumberValuesResultset) groupResultset .getBioSpecimenResultset(sampleId.getSpecimenName()); if (sampleResultset2 != null) { //JB Begin: Add for GForge # 17783 - Advance Query Reports - Make the report more user friendly (Provide tool tip) String tooltip = "Position = " + cytoband + ", Gene = " + genes + ", Reporter = " + reporterName + ", Sample = " + sampleId.getSampleId() + " (" + sampleId.getSpecimenName() + ")"; //JB End: Add for GForge # 17783 - Advance Query Reports - Make the report more user friendly (Provide tool tip) if (sampleResultset2.isHighlighted()) hClass = "highlighted"; else hClass = label; Double ratio = (Double) sampleResultset2.getCopyNumber().getValue(); Double segMean = (Double) sampleResultset2.getSegmentMean() .getValue(); if (ratio != null && segMean != null) { //sb.append("<td class='"+label+"'>"+resultFormat.format(ratio)+"</td>"); 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) + "(" + resultFormat.format(segMean) + ")"); //JB End: Add for GForge # 17783 - Advance Query Reports - Make the report more user friendly (Provide tool tip) data = null; cell = null; } else { //sb.append("<td class='"+label+"'>-</td>"); 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; } } else { //sb.append("<td class='"+label+"'>-</td>"); 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; } } } 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"); } /* close reporter filter */ } //sb.append("<tr><td colspan=\""+theColspan+"\" class=\"geneSpacerStyle\"> </td></tr>\n"); } /* close cyto filter */ //sb.append("</table><Br><br>"); } } else { //TODO: handle these errs sb.append("<br><br>Copy Number container is empty"); } } else { //TODO: handle these errs sb.append("<br><br>Copy Number container is empty"); } return document; //return "<div class=\"rowCount\">"+ helpFul +recordCount+" records returned. "+ totalSamples + " samples returned. " + links +"</div>\n" + sb.toString(); }
From source file:gov.nih.nci.rembrandt.web.xml.CopyNumberSegmentReport.java
License:BSD License
@SuppressWarnings("unchecked") public Document getReportXML(Resultant resultant, Map filterMapParams) { //String theColors[] = { "B6C5F2","F2E3B5","DAE1F9","C4F2B5","819BE9", "E9CF81" }; DecimalFormat resultFormat = new DecimalFormat("0.0000"); String defaultV = "-"; Document document = DocumentHelper.createDocument(); try {/*from w w w . ja va 2s . c o m*/ 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" : "")); StringBuffer sb = new StringBuffer(); ResultsContainer resultsContainer = resultant.getResultsContainer(); CopyNumberSegmentViewResultsContainer segmentViewResultsContainer = null; if (resultsContainer instanceof DimensionalViewContainer) { DimensionalViewContainer dimensionalViewContainer = (DimensionalViewContainer) resultsContainer; segmentViewResultsContainer = dimensionalViewContainer.getCopyNumberSegmentViewResultsContainer(); } else if (resultsContainer instanceof CopyNumberSegmentViewResultsContainer) { segmentViewResultsContainer = (CopyNumberSegmentViewResultsContainer) resultsContainer; } Collection segments = segmentViewResultsContainer.getSampleCopyNumberValuesResultsets(); // set up the headers for this table Element headerRow = report.addElement("Row").addAttribute("name", "headerRow"); for (String h : CopyNumberSegmentReport.getCopyNumberSegmentHeaderValues()) { cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(h); data = null; cell = null; } for (Iterator sampleIterator = segments.iterator(); sampleIterator.hasNext();) { SampleCopyNumberValuesResultset sampleResultset = (SampleCopyNumberValuesResultset) sampleIterator .next(); dataRow = report.addElement("Row").addAttribute("name", "dataRow"); List rows = new ArrayList(); rows = CopyNumberSegmentReport.getClinicalRowValues(sampleResultset); cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "sample"); data = cell.addElement("Data").addAttribute("type", "data").addText(DEUtils.checkNull(rows.get(0))); data = null; cell = null; String tooltip = "Specimen = " + rows.get(0); for (int i = 1; i < rows.size(); i++) { switch (i) { case 1: tooltip = "Specimen = " + rows.get(0) + " (Chr No.)"; break; case 2: tooltip = "Specimen = " + rows.get(0) + " (Start Position)"; break; case 3: tooltip = "Specimen = " + rows.get(0) + " (End Position)"; break; case 4: tooltip = "Specimen = " + rows.get(0) + " (Number of Marks)"; break; case 5: tooltip = "Specimen = " + rows.get(0) + " (Segment Mean)"; break; default: tooltip = "Specimen = " + rows.get(0); break; } cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "data").addAttribute("datainfo", tooltip) .addText(DEUtils.checkNull(rows.get(i))); data = null; cell = null; } } } catch (Exception e) { System.out.println(e); } return document; }
From source file:gov.nih.nci.rembrandt.web.xml.FTestReport.java
License:BSD License
public static Document getReportXML(Finding finding, Map filterMapParams, boolean allAnnotations) { DecimalFormat resultFormat = new DecimalFormat("0.0000"); DecimalFormat sciFormat = new DecimalFormat("0.00E0"); DecimalFormat tmpsciFormat = new DecimalFormat("###0.0000#####################"); /*//from w w w . j a v a 2 s .c o m * 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"); report.addAttribute("helpLink", ContextSensitiveHelpTag.getHelpLink("Class Comparison")); //lets flag this as Ftest report.addAttribute("reportSubType", "FTEST"); //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 FTestFinding ccf = (FTestFinding) finding; //process the query details ArrayList<String> queryDetails = new ArrayList(); ClassComparisonQueryDTO ccdto = (ClassComparisonQueryDTO) ccf.getQueryDTO(); 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); 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); } 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; //pvalue is fixed in the second column, essential for XSL 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(RembrandtConstants.PVALUE + isAdj); data = null; cell = null; //one col for each group in the comparison List<String> groupNames = ccf.getGroupNames(); for (String n : groupNames) { cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header") .addAttribute("group", "header"); data = cell.addElement("Data").addAttribute("type", "header").addText(n + " Group Avg"); 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 */ List<FTestResultEntry> fTestResultEntrys = ccf.getResultEntries(); List<String> reporterIds = new ArrayList<String>(); for (FTestResultEntry fTestResultEntry : fTestResultEntrys) { if (fTestResultEntry.getReporterId() != null) { reporterIds.add(fTestResultEntry.getReporterId()); } } ArrayPlatformType arrayPlatform = ccdto.getArrayPlatformDE() != null ? ccdto.getArrayPlatformDE().getValueObjectAsArrayPlatformType() : ArrayPlatformType.AFFY_OLIGO_PLATFORM; Map reporterResultsetMap = null; if (allAnnotations) { //Map<String, ReporterAnnotations> reporterResultsetMap = null; try { reporterResultsetMap = AnnotationHandler.getAllAnnotationsFor(reporterIds, arrayPlatform); } catch (Exception e) { e.printStackTrace(); } } else { //Map<String, String> reporterResultsetMap = null; try { reporterResultsetMap = AnnotationHandler.getGeneSymbolsFor(reporterIds, arrayPlatform); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } for (FTestResultEntry 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", "header").addText(ccre.getReporterId()); 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"; BigDecimal bigd = new BigDecimal(ccre.getPvalue()); data = cell.addElement("Data").addAttribute("type", "header").addText(bigd.toPlainString()); data = null; cell = null; //one col for each group for (int i = 0; i < ccre.getGroupMeans().length; i++) { cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data") .addAttribute("group", "data"); data = cell.addElement("Data").addAttribute("type", "header") .addText(resultFormat.format(ccre.getGroupMeans()[i])); 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.getMaximumFoldChange()))); data = null; cell = null; //if only showing genes if (!allAnnotations && reporterResultsetMap != null) { String reporterId = ccre.getReporterId(); 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(); //ReporterResultset reporterResultset = reporterResultsetMap.get(reporterId); ReporterAnnotations ra = (ReporterAnnotations) reporterResultsetMap.get(reporterId); //Collection<String> geneSymbols = (Collection<String>)reporterResultset.getAssiciatedGeneSymbols(); String geneSymbols = ra.getGeneSymbol(); if (geneSymbols != null) genes = geneSymbols; /* if(geneSymbols != null){ genes = StringUtils.join(geneSymbols.toArray(), delim); } */ Collection<String> genBank_AccIDS = (Collection<String>) ra.getAccessions(); if (genBank_AccIDS != null) { accIds = StringUtils.join(genBank_AccIDS.toArray(), delim); } Collection<String> locusLinkIDs = (Collection<String>) ra.getLocusLinks(); 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.getPathways(); 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/>"); } logger.info(document.toString()); return document; }
From source file:gov.nih.nci.rembrandt.web.xml.GeneExprDiseaseReport.java
License:BSD License
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;//w w w.j av a2 s . com 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; }
From source file:gov.nih.nci.rembrandt.web.xml.GeneExprSampleReport.java
License:BSD License
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 */ /*/* w w w .ja v a2 s . c om*/ 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", "Gene Expression Sample"); report.addAttribute("helpLink", ContextSensitiveHelpTag.getHelpLink("Gene Expression Sample")); //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(); GeneExprSingleViewResultsContainer geneViewContainer = 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) { geneViewContainer = dimensionalViewContainer.getGeneExprSingleViewContainer(); } } else if (resultsContainer instanceof GeneExprSingleViewResultsContainer) { //for single geneViewContainer = (GeneExprSingleViewResultsContainer) resultsContainer; } if (geneViewContainer != null) { Collection genes = geneViewContainer.getGeneResultsets(); Collection labels = geneViewContainer.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"); 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; 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 = geneViewContainer.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 += reporters.size(); for (Iterator reporterIterator = reporters.iterator(); reporterIterator.hasNext();) { ReporterResultset reporterResultset = (ReporterResultset) reporterIterator.next(); Collection groupTypes = reporterResultset.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", reporterName, 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(reporterName); 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) reporterResultset .getGroupByResultset(label); sampleIds = geneViewContainer.getBiospecimenLabels(label); String hClass = label; if (groupResultset != null) { for (Iterator sampleIdIterator = sampleIds.iterator(); sampleIdIterator .hasNext();) { BioSpecimenIdentifierDE sampleId = (BioSpecimenIdentifierDE) sampleIdIterator .next(); SampleFoldChangeValuesResultset biospecimenResultset = (SampleFoldChangeValuesResultset) 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 + ", Reporter = " + reporterName + ", 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.getFoldChangeRatioValue() .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>Gene Container is empty<br>"); } //return "<div class=\"rowCount\">"+ helpFul +recordCount+" records returned. " + totalSamples +" samples returned. " + links + "</div>\n" + sb.toString(); return document; }
From source file:gr.abiss.calipso.util.XmlUtils.java
License:Open Source License
public static Document getNewDocument(String rootElementName) { Document d = DocumentHelper.createDocument(); d.addElement(rootElementName); return d; }