List of usage examples for com.vaadin.ui CheckBox setValue
@Override public void setValue(Boolean value)
From source file:dhbw.ka.mwi.businesshorizon2.ui.process.scenario.ScenarioViewImpl.java
License:Open Source License
/** * Die Methode fuegt der View ein Szenario hinzu. Sie baut hierzu saemtliche * notwendigen GUI-Elemente und entsprecheenden Listener hinzu. * //w ww .j a va 2 s . co m * @author Julius Hacker * @param rateReturnEquity Standardwert fuer die Renditeforderung Eigenkapital * @param rateReturnCapitalStock Standardwert fuer die Renditeforderung Fremdkapital * @param businessTax Standardwert fuer die Gewerbesteuer * @param corporateAndSolitaryTax Standardwert fuer die Koerperschaftssteuer mit Solidaritaetszuschlag. */ @Override public void addScenario(String rateReturnEquity, String rateReturnCapitalStock, String corporateAndSolitaryTax, String businessTax, boolean isIncludeInCalculation, final int number) { HashMap<String, AbstractComponent> scenarioComponents = new HashMap<String, AbstractComponent>(); Property.ValueChangeListener changeListener = new Property.ValueChangeListener() { private static final long serialVersionUID = 1L; @Override public void valueChange(ValueChangeEvent event) { presenter.updateScenario(number); logger.debug("TextChange ausgeloest"); logger.debug("ChangeListener " + System.identityHashCode(this)); } }; HorizontalLayout hlScenario = new HorizontalLayout(); hlScenario.setSizeFull(); FormLayout formLeft = new FormLayout(); FormLayout formRight = new FormLayout(); hlScenario.addComponent(formLeft); //hlScenario.addComponent(formRight); final Label scenarioName = new Label("<strong>Szenario " + number + "</strong>"); scenarioName.setContentMode(Label.CONTENT_XHTML); scenarioComponents.put("label", scenarioName); formLeft.addComponent(scenarioName); scenarioName.setWidth(Sizeable.SIZE_UNDEFINED, 0); final CheckBox cbBerechnungEinbezug = new CheckBox("In Berechnung einbeziehen"); cbBerechnungEinbezug.setValue(isIncludeInCalculation); cbBerechnungEinbezug.setImmediate(true); cbBerechnungEinbezug.addListener(new ClickListener() { private static final long serialVersionUID = 1L; @Override public void buttonClick(ClickEvent event) { presenter.updateScenario(number); logger.debug("ChangeListener " + System.identityHashCode(this)); } }); scenarioComponents.put("isIncludeInCalculation", cbBerechnungEinbezug); formLeft.addComponent(cbBerechnungEinbezug); final TextField tfEigenkapital = new TextField("Renditeforderung Eigenkapital: "); if (!"0.0".equals(rateReturnEquity)) { tfEigenkapital.setValue(rateReturnEquity); } tfEigenkapital.setImmediate(true); tfEigenkapital.addListener(changeListener); scenarioComponents.put("rateReturnEquity", tfEigenkapital); formLeft.addComponent(tfEigenkapital); final TextField tfFremdkapital = new TextField("Renditeforderung Fremdkapital: "); if (!"0.0".equals(rateReturnCapitalStock)) { tfFremdkapital.setValue(rateReturnCapitalStock); } tfFremdkapital.setImmediate(true); tfFremdkapital.addListener(changeListener); scenarioComponents.put("rateReturnCapitalStock", tfFremdkapital); formLeft.addComponent(tfFremdkapital); final TextField tfGewerbesteuer = new TextField("Gewerbesteuer: "); if (!"0.0".equals(businessTax)) { tfGewerbesteuer.setValue(businessTax); } tfGewerbesteuer.setImmediate(true); tfGewerbesteuer.addListener(changeListener); scenarioComponents.put("businessTax", tfGewerbesteuer); formLeft.addComponent(tfGewerbesteuer); final TextField tfKoerperschaftssteuer = new TextField( "K\u00F6rperschaftssteuer mit Solidarit\u00E4tszuschlag: "); if (!"0.0".equals(corporateAndSolitaryTax)) { tfKoerperschaftssteuer.setValue(corporateAndSolitaryTax); } tfKoerperschaftssteuer.setImmediate(true); tfKoerperschaftssteuer.addListener(changeListener); scenarioComponents.put("corporateAndSolitaryTax", tfKoerperschaftssteuer); formLeft.addComponent(tfKoerperschaftssteuer); final Button removeScenario = new Button("Szenario entfernen"); removeScenario.addListener(new ClickListener() { private static final long serialVersionUID = 1L; @Override public void buttonClick(ClickEvent event) { presenter.removeScenario(number); } }); formLeft.addComponent(removeScenario); formLeft.setWidth(Sizeable.SIZE_UNDEFINED, 0); formLeft.setWidth(Sizeable.SIZE_UNDEFINED, 0); scenarioComponents.put("scenario", hlScenario); this.scenarios.add(scenarioComponents); this.vlScenarios.addComponent(hlScenario); }
From source file:edu.cornell.qatarmed.planrnaseq.AnnotateRNAseqSQL.java
private void initDataAndSubcomponent() { rnaseqContainer = createMySQLContainer("study_summary", "dummy"); bioprojectSummaryTable.setContainerDataSource(rnaseqContainer); // bioprojectSummaryTable.setVisibleColumns(new String[] { studyName }); bioprojectSummaryTable.setSelectable(true); bioprojectSummaryTable.setImmediate(true); bioprojectSummaryTable.setColumnReorderingAllowed(true); bioprojectSummaryTable.setSortEnabled(true); bioprojectSummaryTable.setVisibleColumns( new Object[] { "Study", "title", "name", "Numsample", "Numexp", "Numrun", "Avgspots", "avgbases" }); //bioprojectSummaryTable.setVisibleColumns(new Object[] { "firstName", "lastName", "department", "phoneNumber", "street", "city", "zipCode" }); studyName.setValue(rnaseqContainer.firstItemId().toString()); bioprojectSummaryTable.addItemClickListener(new ItemClickEvent.ItemClickListener() { int custom_annotation_counter = 0; public void itemClick(ItemClickEvent event) { //<editor-fold defaultstate="collapsed" desc="filling study details on right panel"> Object selectedStudyObject = event.getItemId(); bioprojectSummaryTable.select(selectedStudyObject); tree.removeAllItems();/*from ww w . j a v a2 s . c o m*/ rightTopForm.removeAllComponents(); rightTopAnnotationForm.removeAllComponents(); myform.removeAllComponents(); String selectedStudy = selectedStudyObject.toString(); String studyTitle = (String) bioprojectSummaryTable .getContainerProperty(selectedStudyObject, "title").getValue(); String studyName = (String) bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "name") .getValue(); String studyNumsample = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numsample").getValue()); String studyNumexp = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numexp").getValue()); String studyNumrun = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numrun").getValue()); String studyAvgspots = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Avgspots").getValue()); String studyAvgbases = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "avgbases").getValue()); tree.addItem(selectedStudy); tree.setItemCaption(selectedStudy, "Study: " + selectedStudy); SQLContainer tempContainer = createMySQLContainer("study_extdb", selectedStudy); // In this table I will chaeck for the manual annotation status String extdbid = tempContainer.getItem(tempContainer.getIdByIndex(0)).getItemProperty("extdb") .getValue().toString(); Label labelStudyAcc = new Label("<b>SRA Study Accession : </b>" + selectedStudy, ContentMode.HTML); rightTopForm.addComponent(labelStudyAcc); Label labelStudyTitle = new Label("<b>Study Title: </b>" + studyTitle, ContentMode.HTML); rightTopForm.addComponent(labelStudyTitle); Label labelStudyName = new Label("<b>Study Name: </b>" + studyName, ContentMode.HTML); rightTopForm.addComponent(labelStudyName); Label labelStudyNumsample = new Label("<b>Total number of samples: </b>" + studyNumsample, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumsample); Label labelStudyNumexp = new Label( "<b>Total number of experiments (each experiment uses any one of the samples): </b>" + studyNumexp, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumexp); Label labelStudyNumrun = new Label( "<b>Total number of runs ( an experiment can have multiple runs) : </b>" + studyNumrun, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumrun); Label labelStudyAvgspots = new Label( "<b>Avg number of spots or reads (per run): </b>" + studyAvgspots, ContentMode.HTML); rightTopForm.addComponent(labelStudyAvgspots); Label labelStudyAvgbases = new Label("<b>Avg number of bases (per run): </b>" + studyAvgbases, ContentMode.HTML); rightTopForm.addComponent(labelStudyAvgbases); if (extdbid.startsWith("PRJ")) { //<editor-fold defaultstate="collapsed" desc="if PRJ"> tempContainer = createMySQLContainer("bioproject_details", extdbid); String bioproject_accession = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("BioprojectAccession").getValue().toString(); String bioproject_id = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("BioprojectId").getValue().toString(); String bioproject_name = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Name").getValue().toString(); String bioproject_title = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Title").getValue().toString(); String bioproject_description = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Description").getValue().toString(); String bioproject_capture = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Capture").getValue().toString(); String bioproject_material = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Material").getValue().toString(); String bioproject_method = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("MethodType").getValue().toString(); String bioproject_datatype = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("DataType").getValue().toString(); String bioproject_sampleScope = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("SampleScope").getValue().toString(); System.out.println(bioproject_description); Label labelBioprojectAccession = new Label( "<b>Bioproject Accession : </b>" + bioproject_accession, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectAccession); Label labelBioprojectId = new Label("<b>Bioproject Id : </b>" + bioproject_id, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectId); Label labelBioprojectTitle = new Label("<b>Bioproject Title : </b>" + bioproject_title, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectTitle); Label labelBioprojectName = new Label("<b>Bioproject Name : </b>" + bioproject_name, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectName); Label labelBioprojectDescription = new Label( "<b>Bioproject Description : </b>" + bioproject_description, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectDescription); Label labelBioprojectCapture = new Label("<b>Bioproject Capture : </b>" + bioproject_capture, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectCapture); Label labelBioprojectMaterial = new Label( "<b>Bioproject Material : </b>" + bioproject_material, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectMaterial); Label labelBioprojectMethod = new Label("<b>Bioproject Method : </b>" + bioproject_method, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectMethod); Label labelBioprojectDatatype = new Label( "<b>Bioproject Data Type : </b>" + bioproject_datatype, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectDatatype); Label labelBioprojectSampleScope = new Label( "<b>Bioproject Sample Scope : </b>" + bioproject_sampleScope, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectSampleScope); //</editor-fold> } if (extdbid.startsWith("GSE")) { //<editor-fold defaultstate="collapsed" desc="if GSE"> tempContainer = createMySQLContainer("study_gse_details", extdbid); String gse_accesion = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("gse").getValue().toString(); String gse_summary = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("summary").getValue().toString(); String gse_design = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("overall_design").getValue().toString(); System.out.println(gse_summary); Label labelGSE = new Label("<b>GEO Series Accession : </b>" + gse_accesion, ContentMode.HTML); rightTopForm.addComponent(labelGSE); Label labelGseSummary = new Label("<b>GSE Summary : </b>" + gse_summary, ContentMode.HTML); rightTopForm.addComponent(labelGseSummary); Label labelGseDesign = new Label("<b>GSE Design : </b>" + gse_design, ContentMode.HTML); rightTopForm.addComponent(labelGseDesign); //</editor-fold> } //</editor-fold> //SQLContainer tempContainer = createMySQLContainer("sra_rnaseq", selectedStudy); tempContainer = createMySQLContainer("sra_rnaseq", selectedStudy); // List<String> list = new ArrayList<String>(); Map expMap = new HashMap(); Map<String, String[]> expDetailMap = new HashMap<>(); Map<String, String[]> platformMap = new HashMap<>(); Map runMap = new HashMap(); HashSet<String> biosampleSet = new HashSet<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { //<editor-fold defaultstate="collapsed" desc="for loop"> String docid = tempContainer.getIdByIndex(i).toString(); String biosample = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Biosample_Acc_Id_SampleId").getValue().toString(); biosampleSet.add(biosample); String[] b_parts = biosample.split("\\|"); String exp = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Experiment_Acc_Ver_Status_Name").getValue().toString(); String[] exp_parts = exp.split("\\|"); String exp_acc = exp_parts[0]; expMap.put(exp_acc, b_parts[0]); expDetailMap.put(exp_acc, exp_parts); String sra_plaforms = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Platform_InstrumentModel").getValue().toString(); String[] sra_plaforms_parts = sra_plaforms.split("\\|"); platformMap.put(exp_acc, sra_plaforms_parts); String run = tempContainer.getItem(tempContainer.getIdByIndex(i)).getItemProperty("Runs") .getValue().toString(); String[] run_parts = run.split("\\|"); if (run_parts.length > 0) { for (int j = 0; j < run_parts.length; j++) { String temprun = run_parts[j]; String[] temprun_parts = temprun.split("\\,"); runMap.put(temprun_parts[0], exp_acc); } } //</editor-fold> } //<editor-fold defaultstate="collapsed" desc="Manual Annotaion"> tempContainer = createMySQLContainer("biosample_with_studyacc", selectedStudy); int count_cell_line = 0; int count_organism_part = 0; int count_tissue = 0; int count_disease = 0; Set<String> cell_lines_set = new HashSet(); Set<String> organism_part_set = new HashSet(); Set<String> tissue_set = new HashSet(); Set<String> disease_set = new HashSet(); Map<String, Integer> cell_line_stat_map = new HashMap<>(); Map<String, Integer> organism_part_stat_map = new HashMap<>(); Map<String, Integer> tissue_stat_map = new HashMap<>(); Map<String, Integer> disease_stat_map = new HashMap<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { //<editor-fold defaultstate="collapsed" desc="for biosample attributes"> String biosample_attr = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Attributes").getValue().toString(); String[] biosample_attr_parts = biosample_attr.split("\\:-"); if (biosample_attr_parts.length > 0) { String[] attr_names = biosample_attr_parts[0].split("\\|"); String[] attr_values = new String[] {}; if (biosample_attr_parts.length > 1) { attr_values = biosample_attr_parts[1].split("\\|"); } int atn_index = 0; for (String atn : attr_names) { if (atn.equalsIgnoreCase("cell line")) { count_cell_line = count_cell_line + 1; if (attr_values.length >= atn_index) { String cell_line_value = attr_values[atn_index]; cell_lines_set.add(cell_line_value); if (cell_line_stat_map.containsKey(cell_line_value)) { cell_line_stat_map.put(cell_line_value, cell_line_stat_map.get(cell_line_value) + 1); } else { cell_line_stat_map.put(cell_line_value, 1); } } } if (atn.equalsIgnoreCase("organism part")) { count_organism_part = count_organism_part + 1; if (attr_values.length >= atn_index) { String organism_part_value = attr_values[atn_index]; organism_part_set.add(organism_part_value); if (organism_part_stat_map.containsKey(organism_part_value)) { organism_part_stat_map.put(organism_part_value, organism_part_stat_map.get(organism_part_value) + 1); } else { organism_part_stat_map.put(organism_part_value, 1); } } } if (atn.contains("disease")) { count_disease = count_disease + 1; if (attr_values.length >= atn_index) { String disease_value = attr_values[atn_index]; disease_set.add(disease_value); if (disease_stat_map.containsKey(disease_value)) { disease_stat_map.put(disease_value, disease_stat_map.get(disease_value) + 1); } else { disease_stat_map.put(disease_value, 1); } } } if (atn.equalsIgnoreCase("tissue")) { count_tissue = count_tissue + 1; if (attr_values.length >= atn_index) { String tissue_value = attr_values[atn_index]; tissue_set.add(tissue_value); if (tissue_stat_map.containsKey(tissue_value)) { tissue_stat_map.put(tissue_value, tissue_stat_map.get(tissue_value) + 1); } else { tissue_stat_map.put(tissue_value, 1); } } } atn_index = atn_index + 1; } } //</editor-fold> } String suggestion_cell_line = ""; String suggestion_organism_part = ""; String suggestion_tissue = ""; String suggestion_disease = ""; String samplesType_from_sra = ""; String cell_line_confidence = ""; String organism_part_confidence = ""; String disease_confidence = ""; String tissue_confidence = ""; //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has cell line"> if (count_cell_line > 0) { if (Integer.parseInt(studyNumsample) == count_cell_line) { //good. all samples are from cell lines suggestion_cell_line = "Yes:"; String cell_line_value = cell_lines_set.iterator().next(); suggestion_cell_line = suggestion_cell_line + cell_line_value; cell_line_confidence = "100%. All " + cell_line_stat_map.get(cell_line_value).toString() + " Samples"; } else { suggestion_cell_line = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : cell_line_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_cell_line = suggestion_cell_line + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); cell_line_confidence = confidence_percent + "%"; for (Iterator<String> it = cell_lines_set.iterator(); it.hasNext();) { String cellLine = it.next(); if (cellLine.equals(maxEntry.getKey())) { //do nothing } else { suggestion_cell_line = suggestion_cell_line + ", " + cellLine + "(" + cell_line_stat_map.get(cellLine).toString() + ")"; } } } } else { suggestion_cell_line = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has organism part"> if (count_organism_part > 0) { if (Integer.parseInt(studyNumsample) == count_organism_part) { //good. all samples are from cell lines suggestion_organism_part = "Yes:"; String organism_part_value = organism_part_set.iterator().next(); suggestion_organism_part = suggestion_organism_part + organism_part_value; organism_part_confidence = "100%. All " + organism_part_stat_map.get(organism_part_value).toString() + " Samples"; } else { suggestion_organism_part = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : organism_part_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_organism_part = suggestion_organism_part + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); organism_part_confidence = confidence_percent + "%"; for (Iterator<String> it = organism_part_set.iterator(); it.hasNext();) { String organismPart = it.next(); if (organismPart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_organism_part = suggestion_organism_part + ", " + organismPart + "(" + organism_part_stat_map.get(organismPart).toString() + ")"; } } } } else { suggestion_organism_part = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has disease"> if (count_disease > 0) { if (Integer.parseInt(studyNumsample) == count_disease) { //good. all samples are from cell lines suggestion_disease = "Yes:"; String disease_value = disease_set.iterator().next(); suggestion_disease = suggestion_disease + disease_value; disease_confidence = "100%. All " + disease_stat_map.get(disease_value).toString() + " Samples"; } else { suggestion_disease = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : disease_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_disease = suggestion_disease + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); disease_confidence = confidence_percent + "%"; for (Iterator<String> it = disease_set.iterator(); it.hasNext();) { String diseasePart = it.next(); if (diseasePart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_disease = suggestion_disease + ", " + diseasePart + "(" + disease_stat_map.get(diseasePart).toString() + ")"; } } } } else { suggestion_disease = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has tissue"> if (count_tissue > 0) { if (Integer.parseInt(studyNumsample) == count_tissue) { //good. all samples are from cell lines suggestion_tissue = "Yes:"; String tissue_value = tissue_set.iterator().next(); suggestion_tissue = suggestion_tissue + tissue_value; tissue_confidence = "100%. All " + tissue_stat_map.get(tissue_value).toString() + " Samples"; } else { suggestion_tissue = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : tissue_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_tissue = suggestion_tissue + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); tissue_confidence = confidence_percent + "%"; for (Iterator<String> it = disease_set.iterator(); it.hasNext();) { String tissuePart = it.next(); if (tissuePart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_tissue = suggestion_tissue + ", " + tissuePart + "(" + tissue_stat_map.get(tissuePart).toString() + ")"; } } } } else { suggestion_tissue = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="filling right top manual annotation"> HorizontalLayout diseaseLayout = new HorizontalLayout(); CheckBox checkboxDiseaseYes = new CheckBox("Yes"); CheckBox checkboxDiseaseNo = new CheckBox("No"); String disease_from_biosample_attribute = ""; if (suggestion_disease.startsWith("Yes")) { disease_from_biosample_attribute = "From Biosample: " + suggestion_disease; } String disease_found = ""; String disease_text_parsed_confidence = ""; for (String disease : list_of_diseases) { if (StringUtils.containsIgnoreCase(studyName, disease) || StringUtils.containsIgnoreCase(studyTitle, disease)) { checkboxDiseaseYes.setValue(true); disease_found = disease_found + disease + " "; disease_text_parsed_confidence = "keyword found in Study or Title"; } } String diseaseLabelString = ""; if (disease_text_parsed_confidence.length() > 1) { diseaseLabelString = "<b><i>Suggestion: </i></b>" + disease_found + " <b> <i> Confidence: <i></b> " + disease_text_parsed_confidence; } if (disease_from_biosample_attribute.length() > 1) { diseaseLabelString = diseaseLabelString + "<b><i>Suggestion: </i></b>" + disease_from_biosample_attribute + " <b> <i> Confidence: <i></b> " + disease_confidence; } Label diseaseLabel = new Label(diseaseLabelString, ContentMode.HTML); Label diseaseTitle = new Label("<b>Disease: </b>", ContentMode.HTML); diseaseLayout.addComponent(diseaseTitle); diseaseLayout.addComponent(checkboxDiseaseNo); diseaseLayout.addComponent(checkboxDiseaseYes); diseaseLayout.addComponent(diseaseLabel); HorizontalLayout caseControlLayout = new HorizontalLayout(); CheckBox checkboxCaseControlYes = new CheckBox("Yes"); CheckBox checkboxCaseControlNo = new CheckBox("No"); checkboxDiseaseYes.setValue(true); Label caseControlTitle = new Label("<b>Case-Control: </b>", ContentMode.HTML); caseControlLayout.addComponent(caseControlTitle); caseControlLayout.addComponent(checkboxCaseControlYes); caseControlLayout.addComponent(checkboxCaseControlNo); HorizontalLayout timeSeriesLayout = new HorizontalLayout(); CheckBox checkboxTimeSerieslYes = new CheckBox("Yes"); CheckBox checkboxTimeSeriesNo = new CheckBox("No"); checkboxDiseaseYes.setValue(true); Label timeSeriesTitle = new Label("<b>Time Series: </b>", ContentMode.HTML); timeSeriesLayout.addComponent(timeSeriesTitle); timeSeriesLayout.addComponent(checkboxTimeSerieslYes); timeSeriesLayout.addComponent(checkboxTimeSeriesNo); HorizontalLayout diseaseCategoriesLayout = new HorizontalLayout(); Label diseaseCategoryLabel = new Label("<b><i>Suggestion: </i></b>" + disease_found + " <b> <i> Confidence: <i></b> " + disease_confidence, ContentMode.HTML); String[] diseaseCategories = new String[] { "Complex Disease", "Rare Disease", "Other", "Not Sure" }; List<String> diseaseCategoriesList = Arrays.asList(diseaseCategories); ComboBox diseaseCategoryComboBox = new ComboBox("Disease Category", diseaseCategoriesList); diseaseCategoriesLayout.addComponent(diseaseCategoryComboBox); diseaseCategoriesLayout.addComponent(diseaseCategoryLabel); String[] platforms = new String[] { "Illumina", "SOLID", "Roche 454", "PacBio", "Helicos", "Complete Genomics" }; List<String> platformsList = Arrays.asList(platforms); ComboBox platformsListComboBox = new ComboBox("Sequencing Platform", platformsList); Set<String> matchedPlatformSet = new HashSet(); String platform_from_sra = ""; String platorm_confidence = ""; int matchPlatformCount = 0; for (String[] val : platformMap.values()) { if (val.length > 1) { for (String pf : platforms) { if (val[0].equalsIgnoreCase(pf)) { matchedPlatformSet.add(pf); matchPlatformCount = matchPlatformCount + 1; } } } else { } } if (matchedPlatformSet.isEmpty()) { platform_from_sra = "Match Not Found"; } else { if (matchedPlatformSet.size() == matchPlatformCount) { //Ideally this shouldn't be the case. // This suggests that all experiments of this project are run on different platforms or // it has only one expriment if (matchedPlatformSet.size() == 1) { platform_from_sra = matchedPlatformSet.iterator().next().toString(); platformsListComboBox.select(platform_from_sra); } else { platform_from_sra = "Can't predict. All experiment on different Platforms"; } } else { if (matchedPlatformSet.size() == 1) { // Perfect platform_from_sra = matchedPlatformSet.iterator().next().toString(); platformsListComboBox.select(platform_from_sra); platorm_confidence = "100%"; } else { } } } HorizontalLayout platformLayout = new HorizontalLayout(); Label suggestedPlatformLabel = new Label("<b><i>Suggestion: </i></b>" + platform_from_sra + "<b> <i> Confidence: <i></b> " + platorm_confidence, ContentMode.HTML); platformLayout.addComponent(platformsListComboBox); platformLayout.addComponent(suggestedPlatformLabel); VerticalLayout sampleTypesLayout = new VerticalLayout(); CheckBox checkboxSampleTypeCellLine = new CheckBox("Cell Line"); CheckBox checkboxSampleTypeTissue = new CheckBox("Tissue"); CheckBox checkboxSampleTypeStemCells = new CheckBox("Stem Cells"); CheckBox checkboxSampleTypeWholeBlood = new CheckBox("Whole Blood"); CheckBox checkboxSampleTypePlasma = new CheckBox("Plasma"); String suggestedCellTypeLabelString = ""; if (suggestion_cell_line.startsWith("Yes")) { //sampleTypesListComboBox.select("Cell Lines"); checkboxSampleTypeCellLine.setValue(true); suggestedCellTypeLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_cell_line + " <b> <i> Confidence: <i></b> " + cell_line_confidence; } Label suggestedCellLineLabel = new Label(suggestedCellTypeLabelString, ContentMode.HTML); String suggestedTissueLabelString = ""; if (suggestion_organism_part.startsWith("Yes")) { checkboxSampleTypeTissue.setValue(true); suggestedTissueLabelString = suggestedTissueLabelString + "<b><i>Suggestion: </i></b>" + "Organism part --> " + suggestion_organism_part + " <b> <i> Confidence: <i></b> " + organism_part_confidence; } if (suggestion_tissue.startsWith("Yes")) { checkboxSampleTypeTissue.setValue(true); suggestedTissueLabelString = suggestedTissueLabelString + "<b><i>Suggestion: </i></b>" + "Tissue --> " + suggestion_tissue + " <b> <i> Confidence: <i></b> " + tissue_confidence; } Label suggestedTissueLabel = new Label(suggestedTissueLabelString, ContentMode.HTML); String suggestedStemCellString = ""; /* if (suggestion_stem_cell.startsWith("Yes")) { checkboxSampleTypeStemCells.setValue(true); suggestedCellTypeLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_stem_cell + " <b> <i> Confidence: <i></b> " + stem_cell_confidence; } */ Label suggestedStemCellLabel = new Label(suggestedStemCellString, ContentMode.HTML); String suggestedWholeBloodLabelString = ""; /* if (suggestion_whole_blood.startsWith("Yes")) { checkboxSampleTypeWholeBlood.setValue(true); suggestedWholeBloodLabelString = "<b><i>Suggestion: </i></b>" + "Whole Blood --> " + suggestion_whole_blood + " <b> <i> Confidence: <i></b> " + whole_blood_confidence; } */ Label suggestedWholeBloodLabel = new Label(suggestedWholeBloodLabelString, ContentMode.HTML); String suggestedPlasmaLabelString = ""; /* if (suggestion_plasma.startsWith("Yes")) { checkboxSampleTypePlasma.setValue(true); suggestedPlasmaLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_plasma + " <b> <i> Confidence: <i></b> " + plasma_confidence; } */ Label suggestedPlasmaLabel = new Label(suggestedPlasmaLabelString, ContentMode.HTML); HorizontalLayout CellLineLayout = new HorizontalLayout(); CellLineLayout.addComponent(checkboxSampleTypeCellLine); CellLineLayout.addComponent(suggestedCellLineLabel); HorizontalLayout TissueLayout = new HorizontalLayout(); TissueLayout.addComponent(checkboxSampleTypeTissue); TissueLayout.addComponent(suggestedTissueLabel); HorizontalLayout WholeBloodLayout = new HorizontalLayout(); WholeBloodLayout.addComponent(checkboxSampleTypeWholeBlood); WholeBloodLayout.addComponent(suggestedWholeBloodLabel); HorizontalLayout PlasmaLayout = new HorizontalLayout(); PlasmaLayout.addComponent(checkboxSampleTypePlasma); PlasmaLayout.addComponent(suggestedPlasmaLabel); sampleTypesLayout.addComponent(CellLineLayout); sampleTypesLayout.addComponent(TissueLayout); sampleTypesLayout.addComponent(WholeBloodLayout); sampleTypesLayout.addComponent(PlasmaLayout); Button addCustomAnnoButton = new Button("++ Custom Annotation"); addCustomAnnoButton.addClickListener(new Button.ClickListener() { public void buttonClick(ClickEvent event) { custom_annotation_counter = custom_annotation_counter + 1; HorizontalLayout customLayout = new HorizontalLayout(); TextField customAnnoName = new TextField("Custom Name"); customAnnoName.setId("customAnnoName" + custom_annotation_counter); TextField customAnnoValue = new TextField("Custom Value"); customLayout.addComponent(customAnnoName); customLayout.addComponent(customAnnoValue); customAnnoValue.setId("customAnnoValue" + custom_annotation_counter); int addCustomAnnoButtonIndex = rightTopAnnotationForm .getComponentIndex(addCustomAnnoButton); rightTopAnnotationForm.addComponent(customLayout, addCustomAnnoButtonIndex); } }); //<editor-fold defaultstate="collapsed" desc="Replicate Type"> HorizontalLayout replicatTypesLayout = new HorizontalLayout(); String replicateType_from_sra = ""; String replicateType_confidence = ""; Label suggestedreplicatTypeLabel = new Label("<b><i>Suggestion: </i></b>" + replicateType_from_sra + " <b> <i> Confidence: <i></b> " + replicateType_confidence, ContentMode.HTML); String[] replicatTypes = new String[] { "Biological -- different individuals", "Biological -- same individual but severe treatment to RNA", "Semi Biological/Technical -- mild treatment", "Technical -- machine parameter or buffer (very mild)" }; List<String> replicatTypesList = Arrays.asList(replicatTypes); ComboBox replicatTypesListComboBox = new ComboBox("Replicates Type ", replicatTypesList); replicatTypesLayout.addComponent(replicatTypesListComboBox); replicatTypesLayout.addComponent(suggestedreplicatTypeLabel); //</editor-fold> checkboxDiseaseYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxDiseaseNo.setValue(!checkboxDiseaseYes.getValue()); diseaseCategoryComboBox.setVisible(true); } }); checkboxDiseaseNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxDiseaseYes.setValue(!checkboxDiseaseNo.getValue()); diseaseCategoryComboBox.setVisible(false); } }); //<editor-fold defaultstate="collapsed" desc="CheckBox Annotation Ongoing or Completed "> CheckBox checkboxAnnotaionCompleted = new CheckBox("Annotaion Completed"); CheckBox checkboxAnnotaionOngoing = new CheckBox("Annotaion Ongoing"); checkboxAnnotaionOngoing.setValue(true); checkboxAnnotaionCompleted.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxAnnotaionOngoing.setValue(!checkboxAnnotaionCompleted.getValue()); } }); checkboxAnnotaionOngoing.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxAnnotaionCompleted.setValue(!checkboxAnnotaionOngoing.getValue()); } }); //</editor-fold> HorizontalLayout annotationStatusLayout = new HorizontalLayout(); annotationStatusLayout.addComponent(checkboxAnnotaionOngoing); annotationStatusLayout.addComponent(checkboxAnnotaionCompleted); Button submitButton = new Button("Submit"); submitButton.addClickListener(new Button.ClickListener() { public void buttonClick(ClickEvent event) { int diseaseBoolean = 0; if (checkboxDiseaseYes.getValue() && !checkboxDiseaseNo.getValue()) { diseaseBoolean = 1; } int caseControlBoolean = 0; if (checkboxCaseControlYes.getValue() && !checkboxCaseControlNo.getValue()) { caseControlBoolean = 1; } for (int j = 1; j <= custom_annotation_counter; j++) { if (findById(rightTopAnnotationForm, "customAnnoName" + j) instanceof TextField) { TextField tempTFname = (TextField) findById(rightTopAnnotationForm, "customAnnoName" + j); System.out.println(j + "custom name: " + tempTFname.getValue()); } if (findById(rightTopAnnotationForm, "customAnnoValue" + j) instanceof TextField) { TextField tempTFvalue = (TextField) findById(rightTopAnnotationForm, "customAnnoValue" + j); System.out.println(j + "custom value: " + tempTFvalue.getValue()); } } //Notification.show("Do not press this button again"); } }); rightTopAnnotationForm.addComponent(diseaseLayout); rightTopAnnotationForm.addComponent(caseControlLayout); rightTopAnnotationForm.addComponent(timeSeriesLayout); rightTopAnnotationForm.addComponent(diseaseCategoriesLayout); rightTopAnnotationForm.addComponent(platformLayout); rightTopAnnotationForm.addComponent(sampleTypesLayout); rightTopAnnotationForm.addComponent(replicatTypesLayout); rightTopAnnotationForm.addComponent(addCustomAnnoButton); rightTopAnnotationForm.addComponent(annotationStatusLayout); rightTopAnnotationForm.addComponent(submitButton); //</editor-fold> //</editor-fold> //<editor-fold defaultstate="collapsed" desc="fill tree in right bottom"> Iterator iterator = biosampleSet.iterator(); // check values while (iterator.hasNext()) { // System.out.println("Value: "+ iterator.next() + " "); String bsample = iterator.next().toString(); String[] biosample_parts = bsample.split("\\|"); String biosample_acc = biosample_parts[0]; tree.addItem(biosample_acc); tree.setParent(biosample_acc, selectedStudy); tree.setItemCaption(biosample_acc, "BioSample: " + biosample_acc); } Set expMap_entrset = expMap.entrySet(); Iterator it = expMap_entrset.iterator(); while (it.hasNext()) { Map.Entry me = (Map.Entry) it.next(); String[] expParts = expDetailMap.get(me.getKey()); String expTitle = ""; if (expParts.length > 3) { expTitle = expParts[3]; } tree.addItem(me.getKey()); tree.setParent(me.getKey(), me.getValue()); tree.setItemCaption(me.getKey(), "Experiment: " + me.getKey() + ": " + expTitle); } Set runMap_entrset = runMap.entrySet(); Iterator runit = runMap_entrset.iterator(); while (runit.hasNext()) { Map.Entry runEntry = (Map.Entry) runit.next(); tree.addItem(runEntry.getKey()); tree.setParent(runEntry.getKey(), runEntry.getValue()); tree.setItemCaption(runEntry.getKey(), "Run: " + runEntry.getKey()); } tree.expandItemsRecursively(selectedStudy); //</editor-fold> } }); tree.setSelectable(true); tree.setImmediate(true); tree.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { Object id = event.getProperty().getValue(); if (id != null) { String selectedTreeId = id.toString(); String selectedTreeItem = tree.getItemCaption(id).toString(); System.out.println("Tree event is fired: " + selectedTreeItem); if (selectedTreeItem.startsWith("BioSample")) { myform.removeAllComponents(); SQLContainer tempContainer = createMySQLContainer("biosample", selectedTreeId); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { String accessType = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("AccessType").getValue().toString(); String publicationDate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("PublicationDate").getValue().toString(); String lastUpdate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("LastUpdate").getValue().toString(); String accession = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Accession").getValue().toString(); String title = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Title").getValue().toString(); String taxonomy_id = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("TaxonomyId").getValue().toString(); String taxonomy_name = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("TaxonomyName").getValue().toString(); String samplePackage = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Package").getValue().toString(); String status = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Status").getValue().toString(); String statusTime = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("StatusTime").getValue().toString(); String sampleIds = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Ids").getValue().toString(); String attributes = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Attributes").getValue().toString(); String models = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Models").getValue().toString(); String submissionDate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("SubmissionDate").getValue().toString(); String owner = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Owner").getValue().toString(); String[] myfields = new String[] { accessType, publicationDate, lastUpdate, accession, title, taxonomy_id, taxonomy_name, samplePackage, status, statusTime, sampleIds, attributes, models, submissionDate, owner }; /* for (String fieldName : myfields) { Label tempLabl = new Label(""); } */ Label labelAccessType = new Label("Access Type: " + accessType); myform.addComponent(labelAccessType); Label labelPublicationDate = new Label("Publication Date: " + publicationDate); myform.addComponent(labelPublicationDate); Label labelLastUpdate = new Label("Last Update: " + lastUpdate); myform.addComponent(labelLastUpdate); Label labelAccession = new Label("Accession: " + accession); myform.addComponent(labelAccession); Label labelTitle = new Label("<b>Title: </b>" + title, ContentMode.HTML); myform.addComponent(labelTitle); Label labelTaxonomyId = new Label("Taxonomy Id: " + taxonomy_id); myform.addComponent(labelTaxonomyId); Label labelTaxonomyName = new Label("Taxonomy Name: " + taxonomy_name); myform.addComponent(labelTaxonomyName); Label labelPackage = new Label("Package: " + samplePackage); myform.addComponent(labelPackage); Label labelStatus = new Label("Status: " + status); myform.addComponent(labelStatus); Label labelStatusTime = new Label("Status Time: " + statusTime); myform.addComponent(labelStatusTime); Label labelOwner = new Label("Owner: " + owner); myform.addComponent(labelOwner); String[] id_parts = sampleIds.split("\\:\\-"); if (id_parts.length > 1) { String[] id_dbs = id_parts[0].split("\\|"); String[] id_values = id_parts[1].split("\\|"); for (int j = 0; j < id_dbs.length; j++) { Label tempLabel = new Label(id_dbs[j] + ": " + id_values[j]); myform.addComponent(tempLabel); } } String[] attribute_parts = attributes.split("\\:\\-"); if (attribute_parts.length > 1) { String[] attribute_names = attribute_parts[0].split("\\|"); String[] attribute_values = attribute_parts[1].split("\\|"); for (int j = 0; j < attribute_names.length; j++) { Label tempLabel = new Label( "<b>" + attribute_names[j] + ": </b>" + attribute_values[j], ContentMode.HTML); myform.addComponent(tempLabel); System.out.println("inside attributes "); } } // TextField field = new TextField(lastDpdate); // myform.addComponent(field); //field.setWidth("100%"); } } if (selectedTreeItem.startsWith("Experiment")) { SQLContainer tempContainer = createMySQLContainer("sra_rnaseq_exp", selectedTreeId); myform.removeAllComponents(); Map expMap = new HashMap(); Map<String, String[]> expDetailMap = new HashMap<>(); Map<String, String[]> libraryDetailMap = new HashMap<>(); Map<String, String[]> platformMap = new HashMap<>(); Map runMap = new HashMap(); HashSet<String> biosampleSet = new HashSet<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { String docid = tempContainer.getIdByIndex(i).toString(); String biosample = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Biosample_Acc_Id_SampleId").getValue().toString(); biosampleSet.add(biosample); String[] b_parts = biosample.split("\\|"); String exp = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Experiment_Acc_Ver_Status_Name").getValue().toString(); String[] exp_parts = exp.split("\\|"); String exp_acc = exp_parts[0]; expMap.put(exp_acc, b_parts[0]); expDetailMap.put(exp_acc, exp_parts); String library_string = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Library_Name_Strategy_Source_Selection_Layout").getValue() .toString(); String[] library_parts = library_string.split("\\|"); String library_name = ""; String library_strategy = ""; String library_source = ""; String library_selection = ""; String library_layout = ""; if (library_parts.length > 0) { library_name = library_parts[0]; } if (library_parts.length > 1) { library_strategy = "<b> <i> Strategy </i> </b>" + library_parts[1]; } if (library_parts.length > 2) { library_source = "<b> <i> Source </i> </b>" + library_parts[2]; } if (library_parts.length > 3) { library_selection = "<b> <i> Selection </i> </b>" + library_parts[3]; } if (library_parts.length > 4) { String tempLayout = library_parts[4]; tempLayout = tempLayout.replaceAll("<", ""); tempLayout = tempLayout.replaceAll("/>", ""); library_layout = "<b> <i> Layout </i> </b>" + tempLayout; } String[] tempStringArray = new String[] { library_strategy, library_source, library_selection, library_layout }; if (library_name.length() > 1) { libraryDetailMap.put(library_name, tempStringArray); } String sra_plaforms = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Platform_InstrumentModel").getValue().toString(); String[] sra_plaforms_parts = sra_plaforms.split("\\|"); platformMap.put(exp_acc, sra_plaforms_parts); String run = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Runs").getValue().toString(); String[] run_parts = run.split("\\|"); if (run_parts.length > 0) { for (int j = 0; j < run_parts.length; j++) { String temprun = run_parts[j]; String[] temprun_parts = temprun.split("\\,"); runMap.put(temprun_parts[0], exp_acc); } } } Label labelExperimentAcc = new Label("<b>Experiment Accession: </b>" + selectedTreeId, ContentMode.HTML); myform.addComponent(labelExperimentAcc); String libraryDetails = ""; for (Map.Entry<String, String[]> entry : libraryDetailMap.entrySet()) { libraryDetails = libraryDetails + entry.getKey(); String[] temp_library_details = entry.getValue(); for (String dt : temp_library_details) { libraryDetails = libraryDetails + dt; } } Label labelLibraryDetails = new Label("<b>Library Details: </b>" + libraryDetails, ContentMode.HTML); myform.addComponent(labelLibraryDetails); } } else { System.out.println("id is null"); } } }); bioprojectSummaryTable.addValueChangeListener(new Property.ValueChangeListener() { public void valueChange(ValueChangeEvent event) { Object contactId = bioprojectSummaryTable.getValue(); //Binding data //When a contact is selected from the list, we want to show that in our editor on the right. This is nicely done by the FieldGroup that binds all the fields to the corresponding Properties in our contact at once. if (contactId != null) // editorFields.setItemDataSource(bioprojectSummaryTable.getItem(contactId)); // editorLayout.setVisible(contactId != null); } }); }
From source file:edu.cornell.qatarmed.planrnaseq.AnnotateView.java
private void initDataAndSubcomponent() { rnaseqContainer = createMySQLContainer("study_summary", "dummy"); bioprojectSummaryTable.setContainerDataSource(rnaseqContainer); // bioprojectSummaryTable.setVisibleColumns(new String[] { studyName }); bioprojectSummaryTable.setSelectable(true); bioprojectSummaryTable.setImmediate(true); bioprojectSummaryTable.setColumnReorderingAllowed(true); bioprojectSummaryTable.setSortEnabled(true); bioprojectSummaryTable.setVisibleColumns( new Object[] { "Study", "title", "name", "Numsample", "Numexp", "Numrun", "Avgspots", "avgbases" }); //bioprojectSummaryTable.setVisibleColumns(new Object[] { "firstName", "lastName", "department", "phoneNumber", "street", "city", "zipCode" }); studyName.setValue(rnaseqContainer.firstItemId().toString()); bioprojectSummaryTable.addItemClickListener(new ItemClickEvent.ItemClickListener() { int custom_annotation_counter = 0; public void itemClick(ItemClickEvent event) { //<editor-fold defaultstate="collapsed" desc="filling study details on right panel"> Object selectedStudyObject = event.getItemId(); bioprojectSummaryTable.select(selectedStudyObject); tree.removeAllItems();/*from w w w .j av a 2s .co m*/ rightTopForm.removeAllComponents(); rightTopAnnotationForm.removeAllComponents(); myform.removeAllComponents(); String selectedStudy = selectedStudyObject.toString(); String studyTitle = (String) bioprojectSummaryTable .getContainerProperty(selectedStudyObject, "title").getValue(); String studyName = (String) bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "name") .getValue(); String studyNumsample = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numsample").getValue()); String studyNumexp = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numexp").getValue()); String studyNumrun = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numrun").getValue()); String studyAvgspots = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Avgspots").getValue()); String studyAvgbases = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "avgbases").getValue()); tree.addItem(selectedStudy); tree.setItemCaption(selectedStudy, "Study: " + selectedStudy); SQLContainer tempContainer = createMySQLContainer("study_extdb", selectedStudy); // In this table I will chaeck for the manual annotation status String extdbid = tempContainer.getItem(tempContainer.getIdByIndex(0)).getItemProperty("extdb") .getValue().toString(); Label labelStudyAcc = new Label("<b>SRA Study Accession : </b>" + selectedStudy, ContentMode.HTML); rightTopForm.addComponent(labelStudyAcc); Label labelStudyTitle = new Label("<b>Study Title: </b>" + studyTitle, ContentMode.HTML); rightTopForm.addComponent(labelStudyTitle); Label labelStudyName = new Label("<b>Study Name: </b>" + studyName, ContentMode.HTML); rightTopForm.addComponent(labelStudyName); Label labelStudyNumsample = new Label("<b>Total number of samples: </b>" + studyNumsample, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumsample); Label labelStudyNumexp = new Label( "<b>Total number of experiments (each experiment uses any one of the samples): </b>" + studyNumexp, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumexp); Label labelStudyNumrun = new Label( "<b>Total number of runs ( an experiment can have multiple runs) : </b>" + studyNumrun, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumrun); Label labelStudyAvgspots = new Label( "<b>Avg number of spots or reads (per run): </b>" + studyAvgspots, ContentMode.HTML); rightTopForm.addComponent(labelStudyAvgspots); Label labelStudyAvgbases = new Label("<b>Avg number of bases (per run): </b>" + studyAvgbases, ContentMode.HTML); rightTopForm.addComponent(labelStudyAvgbases); if (extdbid.startsWith("PRJ")) { //<editor-fold defaultstate="collapsed" desc="if PRJ"> tempContainer = createMySQLContainer("bioproject_details", extdbid); String bioproject_accession = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("BioprojectAccession").getValue().toString(); String bioproject_id = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("BioprojectId").getValue().toString(); String bioproject_name = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Name").getValue().toString(); String bioproject_title = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Title").getValue().toString(); String bioproject_description = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Description").getValue().toString(); String bioproject_capture = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Capture").getValue().toString(); String bioproject_material = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Material").getValue().toString(); String bioproject_method = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("MethodType").getValue().toString(); String bioproject_datatype = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("DataType").getValue().toString(); String bioproject_sampleScope = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("SampleScope").getValue().toString(); System.out.println(bioproject_description); Label labelBioprojectAccession = new Label( "<b>Bioproject Accession : </b>" + bioproject_accession, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectAccession); Label labelBioprojectId = new Label("<b>Bioproject Id : </b>" + bioproject_id, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectId); Label labelBioprojectTitle = new Label("<b>Bioproject Title : </b>" + bioproject_title, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectTitle); Label labelBioprojectName = new Label("<b>Bioproject Name : </b>" + bioproject_name, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectName); Label labelBioprojectDescription = new Label( "<b>Bioproject Description : </b>" + bioproject_description, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectDescription); Label labelBioprojectCapture = new Label("<b>Bioproject Capture : </b>" + bioproject_capture, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectCapture); Label labelBioprojectMaterial = new Label( "<b>Bioproject Material : </b>" + bioproject_material, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectMaterial); Label labelBioprojectMethod = new Label("<b>Bioproject Method : </b>" + bioproject_method, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectMethod); Label labelBioprojectDatatype = new Label( "<b>Bioproject Data Type : </b>" + bioproject_datatype, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectDatatype); Label labelBioprojectSampleScope = new Label( "<b>Bioproject Sample Scope : </b>" + bioproject_sampleScope, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectSampleScope); //</editor-fold> } if (extdbid.startsWith("GSE")) { //<editor-fold defaultstate="collapsed" desc="if GSE"> tempContainer = createMySQLContainer("study_gse_details", extdbid); String gse_accesion = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("gse").getValue().toString(); String gse_summary = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("summary").getValue().toString(); String gse_design = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("overall_design").getValue().toString(); System.out.println(gse_summary); Label labelGSE = new Label("<b>GEO Series Accession : </b>" + gse_accesion, ContentMode.HTML); rightTopForm.addComponent(labelGSE); Label labelGseSummary = new Label("<b>GSE Summary : </b>" + gse_summary, ContentMode.HTML); rightTopForm.addComponent(labelGseSummary); Label labelGseDesign = new Label("<b>GSE Design : </b>" + gse_design, ContentMode.HTML); rightTopForm.addComponent(labelGseDesign); //</editor-fold> } //</editor-fold> //SQLContainer tempContainer = createMySQLContainer("sra_rnaseq", selectedStudy); tempContainer = createMySQLContainer("sra_rnaseq", selectedStudy); // List<String> list = new ArrayList<String>(); Map expMap = new HashMap(); Map<String, String[]> expDetailMap = new HashMap<>(); Map<String, String[]> platformMap = new HashMap<>(); Map runMap = new HashMap(); HashSet<String> biosampleSet = new HashSet<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { //<editor-fold defaultstate="collapsed" desc="for loop"> String docid = tempContainer.getIdByIndex(i).toString(); String biosample = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Biosample_Acc_Id_SampleId").getValue().toString(); biosampleSet.add(biosample); String[] b_parts = biosample.split("\\|"); String exp = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Experiment_Acc_Ver_Status_Name").getValue().toString(); String[] exp_parts = exp.split("\\|"); String exp_acc = exp_parts[0]; expMap.put(exp_acc, b_parts[0]); expDetailMap.put(exp_acc, exp_parts); String sra_plaforms = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Platform_InstrumentModel").getValue().toString(); String[] sra_plaforms_parts = sra_plaforms.split("\\|"); platformMap.put(exp_acc, sra_plaforms_parts); String run = tempContainer.getItem(tempContainer.getIdByIndex(i)).getItemProperty("Runs") .getValue().toString(); String[] run_parts = run.split("\\|"); if (run_parts.length > 0) { for (int j = 0; j < run_parts.length; j++) { String temprun = run_parts[j]; String[] temprun_parts = temprun.split("\\,"); runMap.put(temprun_parts[0], exp_acc); } } //</editor-fold> } //<editor-fold defaultstate="collapsed" desc="Manual Annotaion"> tempContainer = createMySQLContainer("biosample_with_studyacc", selectedStudy); int count_cell_line = 0; int count_organism_part = 0; int count_tissue = 0; int count_disease = 0; Set<String> cell_lines_set = new HashSet(); Set<String> organism_part_set = new HashSet(); Set<String> tissue_set = new HashSet(); Set<String> disease_set = new HashSet(); Map<String, Integer> cell_line_stat_map = new HashMap<>(); Map<String, Integer> organism_part_stat_map = new HashMap<>(); Map<String, Integer> tissue_stat_map = new HashMap<>(); Map<String, Integer> disease_stat_map = new HashMap<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { //<editor-fold defaultstate="collapsed" desc="for biosample attributes"> String biosample_attr = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Attributes").getValue().toString(); String[] biosample_attr_parts = biosample_attr.split("\\:-"); if (biosample_attr_parts.length > 0) { String[] attr_names = biosample_attr_parts[0].split("\\|"); String[] attr_values = new String[] {}; if (biosample_attr_parts.length > 1) { attr_values = biosample_attr_parts[1].split("\\|"); } int atn_index = 0; for (String atn : attr_names) { if (atn.equalsIgnoreCase("cell line")) { count_cell_line = count_cell_line + 1; if (attr_values.length >= atn_index) { String cell_line_value = attr_values[atn_index]; cell_lines_set.add(cell_line_value); if (cell_line_stat_map.containsKey(cell_line_value)) { cell_line_stat_map.put(cell_line_value, cell_line_stat_map.get(cell_line_value) + 1); } else { cell_line_stat_map.put(cell_line_value, 1); } } } if (atn.equalsIgnoreCase("organism part")) { count_organism_part = count_organism_part + 1; if (attr_values.length >= atn_index) { String organism_part_value = attr_values[atn_index]; organism_part_set.add(organism_part_value); if (organism_part_stat_map.containsKey(organism_part_value)) { organism_part_stat_map.put(organism_part_value, organism_part_stat_map.get(organism_part_value) + 1); } else { organism_part_stat_map.put(organism_part_value, 1); } } } if (atn.contains("disease")) { count_disease = count_disease + 1; if (attr_values.length >= atn_index) { String disease_value = attr_values[atn_index]; disease_set.add(disease_value); if (disease_stat_map.containsKey(disease_value)) { disease_stat_map.put(disease_value, disease_stat_map.get(disease_value) + 1); } else { disease_stat_map.put(disease_value, 1); } } } if (atn.equalsIgnoreCase("tissue")) { count_tissue = count_tissue + 1; if (attr_values.length >= atn_index) { String tissue_value = attr_values[atn_index]; tissue_set.add(tissue_value); if (tissue_stat_map.containsKey(tissue_value)) { tissue_stat_map.put(tissue_value, tissue_stat_map.get(tissue_value) + 1); } else { tissue_stat_map.put(tissue_value, 1); } } } atn_index = atn_index + 1; } } //</editor-fold> } String suggestion_cell_line = ""; String suggestion_organism_part = ""; String suggestion_tissue = ""; String suggestion_disease = ""; String samplesType_from_sra = ""; String cell_line_confidence = ""; String organism_part_confidence = ""; String disease_confidence = ""; String tissue_confidence = ""; //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has cell line"> if (count_cell_line > 0) { if (Integer.parseInt(studyNumsample) == count_cell_line) { //good. all samples are from cell lines suggestion_cell_line = "Yes:"; String cell_line_value = cell_lines_set.iterator().next(); suggestion_cell_line = suggestion_cell_line + cell_line_value; cell_line_confidence = "100%. All " + cell_line_stat_map.get(cell_line_value).toString() + " Samples"; } else { suggestion_cell_line = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : cell_line_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_cell_line = suggestion_cell_line + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); cell_line_confidence = confidence_percent + "%"; for (Iterator<String> it = cell_lines_set.iterator(); it.hasNext();) { String cellLine = it.next(); if (cellLine.equals(maxEntry.getKey())) { //do nothing } else { suggestion_cell_line = suggestion_cell_line + ", " + cellLine + "(" + cell_line_stat_map.get(cellLine).toString() + ")"; } } } } else { suggestion_cell_line = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has organism part"> if (count_organism_part > 0) { if (Integer.parseInt(studyNumsample) == count_organism_part) { //good. all samples are from cell lines suggestion_organism_part = "Yes:"; String organism_part_value = organism_part_set.iterator().next(); suggestion_organism_part = suggestion_organism_part + organism_part_value; organism_part_confidence = "100%. All " + organism_part_stat_map.get(organism_part_value).toString() + " Samples"; } else { suggestion_organism_part = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : organism_part_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_organism_part = suggestion_organism_part + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); organism_part_confidence = confidence_percent + "%"; for (Iterator<String> it = organism_part_set.iterator(); it.hasNext();) { String organismPart = it.next(); if (organismPart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_organism_part = suggestion_organism_part + ", " + organismPart + "(" + organism_part_stat_map.get(organismPart).toString() + ")"; } } } } else { suggestion_organism_part = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has disease"> if (count_disease > 0) { if (Integer.parseInt(studyNumsample) == count_disease) { //good. all samples are from cell lines suggestion_disease = "Yes:"; String disease_value = disease_set.iterator().next(); suggestion_disease = suggestion_disease + disease_value; disease_confidence = "100%. All " + disease_stat_map.get(disease_value).toString() + " Samples"; } else { suggestion_disease = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : disease_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_disease = suggestion_disease + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); disease_confidence = confidence_percent + "%"; for (Iterator<String> it = disease_set.iterator(); it.hasNext();) { String diseasePart = it.next(); if (diseasePart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_disease = suggestion_disease + ", " + diseasePart + "(" + disease_stat_map.get(diseasePart).toString() + ")"; } } } } else { suggestion_disease = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has tissue"> if (count_tissue > 0) { if (Integer.parseInt(studyNumsample) == count_tissue) { //good. all samples are from cell lines suggestion_tissue = "Yes:"; String tissue_value = tissue_set.iterator().next(); suggestion_tissue = suggestion_tissue + tissue_value; tissue_confidence = "100%. All " + tissue_stat_map.get(tissue_value).toString() + " Samples"; } else { suggestion_tissue = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : tissue_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_tissue = suggestion_tissue + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); tissue_confidence = confidence_percent + "%"; for (Iterator<String> it = disease_set.iterator(); it.hasNext();) { String tissuePart = it.next(); if (tissuePart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_tissue = suggestion_tissue + ", " + tissuePart + "(" + tissue_stat_map.get(tissuePart).toString() + ")"; } } } } else { suggestion_tissue = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="filling right top manual annotation"> HorizontalLayout diseaseLayout = new HorizontalLayout(); CheckBox checkboxDiseaseYes = new CheckBox("Yes"); CheckBox checkboxDiseaseNo = new CheckBox("No"); String disease_from_biosample_attribute = ""; if (suggestion_disease.startsWith("Yes")) { disease_from_biosample_attribute = "From Biosample: " + suggestion_disease; } String disease_found = ""; String disease_text_parsed_confidence = ""; for (String disease : list_of_diseases) { if (StringUtils.containsIgnoreCase(studyName, disease) || StringUtils.containsIgnoreCase(studyTitle, disease)) { checkboxDiseaseYes.setValue(true); disease_found = disease_found + disease + " "; disease_text_parsed_confidence = "keyword found in Study or Title"; } } String diseaseLabelString = ""; if (disease_text_parsed_confidence.length() > 1) { diseaseLabelString = "<b><i>Suggestion: </i></b>" + disease_found + " <b> <i> Confidence: <i></b> " + disease_text_parsed_confidence; } if (disease_from_biosample_attribute.length() > 1) { diseaseLabelString = diseaseLabelString + "<b><i>Suggestion: </i></b>" + disease_from_biosample_attribute + " <b> <i> Confidence: <i></b> " + disease_confidence; } Label diseaseLabel = new Label(diseaseLabelString, ContentMode.HTML); Label diseaseTitle = new Label("<b>Disease: </b>", ContentMode.HTML); diseaseLayout.addComponent(diseaseTitle); diseaseLayout.addComponent(checkboxDiseaseNo); diseaseLayout.addComponent(checkboxDiseaseYes); diseaseLayout.addComponent(diseaseLabel); HorizontalLayout caseControlLayout = new HorizontalLayout(); CheckBox checkboxCaseControlYes = new CheckBox("Yes"); CheckBox checkboxCaseControlNo = new CheckBox("No"); checkboxDiseaseYes.setValue(true); Label caseControlTitle = new Label("<b>Case-Control: </b>", ContentMode.HTML); caseControlLayout.addComponent(caseControlTitle); caseControlLayout.addComponent(checkboxCaseControlYes); caseControlLayout.addComponent(checkboxCaseControlNo); HorizontalLayout timeSeriesLayout = new HorizontalLayout(); CheckBox checkboxTimeSerieslYes = new CheckBox("Yes"); CheckBox checkboxTimeSeriesNo = new CheckBox("No"); checkboxDiseaseYes.setValue(true); Label timeSeriesTitle = new Label("<b>Time Series: </b>", ContentMode.HTML); timeSeriesLayout.addComponent(timeSeriesTitle); timeSeriesLayout.addComponent(checkboxTimeSerieslYes); timeSeriesLayout.addComponent(checkboxTimeSeriesNo); HorizontalLayout diseaseCategoriesLayout = new HorizontalLayout(); Label diseaseCategoryLabel = new Label("<b><i>Suggestion: </i></b>" + disease_found + " <b> <i> Confidence: <i></b> " + disease_confidence, ContentMode.HTML); String[] diseaseCategories = new String[] { "Complex Disease", "Rare Disease", "Other", "Not Sure" }; List<String> diseaseCategoriesList = Arrays.asList(diseaseCategories); ComboBox diseaseCategoryComboBox = new ComboBox("Disease Category", diseaseCategoriesList); diseaseCategoriesLayout.addComponent(diseaseCategoryComboBox); diseaseCategoriesLayout.addComponent(diseaseCategoryLabel); String[] platforms = new String[] { "Illumina", "SOLID", "Roche 454", "PacBio", "Helicos", "Complete Genomics" }; List<String> platformsList = Arrays.asList(platforms); ComboBox platformsListComboBox = new ComboBox("Sequencing Platform", platformsList); Set<String> matchedPlatformSet = new HashSet(); String platform_from_sra = ""; String platorm_confidence = ""; int matchPlatformCount = 0; for (String[] val : platformMap.values()) { if (val.length > 1) { for (String pf : platforms) { if (val[0].equalsIgnoreCase(pf)) { matchedPlatformSet.add(pf); matchPlatformCount = matchPlatformCount + 1; } } } else { } } if (matchedPlatformSet.isEmpty()) { platform_from_sra = "Match Not Found"; } else { if (matchedPlatformSet.size() == matchPlatformCount) { //Ideally this shouldn't be the case. // This suggests that all experiments of this project are run on different platforms or // it has only one expriment if (matchedPlatformSet.size() == 1) { platform_from_sra = matchedPlatformSet.iterator().next().toString(); platformsListComboBox.select(platform_from_sra); } else { platform_from_sra = "Can't predict. All experiment on different Platforms"; } } else { if (matchedPlatformSet.size() == 1) { // Perfect platform_from_sra = matchedPlatformSet.iterator().next().toString(); platformsListComboBox.select(platform_from_sra); platorm_confidence = "100%"; } else { } } } HorizontalLayout platformLayout = new HorizontalLayout(); Label suggestedPlatformLabel = new Label("<b><i>Suggestion: </i></b>" + platform_from_sra + "<b> <i> Confidence: <i></b> " + platorm_confidence, ContentMode.HTML); platformLayout.addComponent(platformsListComboBox); platformLayout.addComponent(suggestedPlatformLabel); VerticalLayout sampleTypesLayout = new VerticalLayout(); CheckBox checkboxSampleTypeCellLine = new CheckBox("Cell Line"); CheckBox checkboxSampleTypeTissue = new CheckBox("Tissue"); CheckBox checkboxSampleTypeStemCells = new CheckBox("Stem Cells"); CheckBox checkboxSampleTypeWholeBlood = new CheckBox("Whole Blood"); CheckBox checkboxSampleTypePlasma = new CheckBox("Plasma"); String suggestedCellTypeLabelString = ""; if (suggestion_cell_line.startsWith("Yes")) { //sampleTypesListComboBox.select("Cell Lines"); checkboxSampleTypeCellLine.setValue(true); suggestedCellTypeLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_cell_line + " <b> <i> Confidence: <i></b> " + cell_line_confidence; } Label suggestedCellLineLabel = new Label(suggestedCellTypeLabelString, ContentMode.HTML); String suggestedTissueLabelString = ""; if (suggestion_organism_part.startsWith("Yes")) { checkboxSampleTypeTissue.setValue(true); suggestedTissueLabelString = suggestedTissueLabelString + "<b><i>Suggestion: </i></b>" + "Organism part --> " + suggestion_organism_part + " <b> <i> Confidence: <i></b> " + organism_part_confidence; } if (suggestion_tissue.startsWith("Yes")) { checkboxSampleTypeTissue.setValue(true); suggestedTissueLabelString = suggestedTissueLabelString + "<b><i>Suggestion: </i></b>" + "Tissue --> " + suggestion_tissue + " <b> <i> Confidence: <i></b> " + tissue_confidence; } Label suggestedTissueLabel = new Label(suggestedTissueLabelString, ContentMode.HTML); String suggestedStemCellString = ""; /* if (suggestion_stem_cell.startsWith("Yes")) { checkboxSampleTypeStemCells.setValue(true); suggestedCellTypeLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_stem_cell + " <b> <i> Confidence: <i></b> " + stem_cell_confidence; } */ Label suggestedStemCellLabel = new Label(suggestedStemCellString, ContentMode.HTML); String suggestedWholeBloodLabelString = ""; /* if (suggestion_whole_blood.startsWith("Yes")) { checkboxSampleTypeWholeBlood.setValue(true); suggestedWholeBloodLabelString = "<b><i>Suggestion: </i></b>" + "Whole Blood --> " + suggestion_whole_blood + " <b> <i> Confidence: <i></b> " + whole_blood_confidence; } */ Label suggestedWholeBloodLabel = new Label(suggestedWholeBloodLabelString, ContentMode.HTML); String suggestedPlasmaLabelString = ""; /* if (suggestion_plasma.startsWith("Yes")) { checkboxSampleTypePlasma.setValue(true); suggestedPlasmaLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_plasma + " <b> <i> Confidence: <i></b> " + plasma_confidence; } */ Label suggestedPlasmaLabel = new Label(suggestedPlasmaLabelString, ContentMode.HTML); HorizontalLayout CellLineLayout = new HorizontalLayout(); CellLineLayout.addComponent(checkboxSampleTypeCellLine); CellLineLayout.addComponent(suggestedCellLineLabel); HorizontalLayout TissueLayout = new HorizontalLayout(); TissueLayout.addComponent(checkboxSampleTypeTissue); TissueLayout.addComponent(suggestedTissueLabel); HorizontalLayout WholeBloodLayout = new HorizontalLayout(); WholeBloodLayout.addComponent(checkboxSampleTypeWholeBlood); WholeBloodLayout.addComponent(suggestedWholeBloodLabel); HorizontalLayout PlasmaLayout = new HorizontalLayout(); PlasmaLayout.addComponent(checkboxSampleTypePlasma); PlasmaLayout.addComponent(suggestedPlasmaLabel); sampleTypesLayout.addComponent(CellLineLayout); sampleTypesLayout.addComponent(TissueLayout); sampleTypesLayout.addComponent(WholeBloodLayout); sampleTypesLayout.addComponent(PlasmaLayout); Button addCustomAnnoButton = new Button("++ Custom Annotation"); addCustomAnnoButton.addClickListener(new Button.ClickListener() { public void buttonClick(ClickEvent event) { custom_annotation_counter = custom_annotation_counter + 1; HorizontalLayout customLayout = new HorizontalLayout(); TextField customAnnoName = new TextField("Custom Name"); customAnnoName.setId("customAnnoName" + custom_annotation_counter); TextField customAnnoValue = new TextField("Custom Value"); customLayout.addComponent(customAnnoName); customLayout.addComponent(customAnnoValue); customAnnoValue.setId("customAnnoValue" + custom_annotation_counter); int addCustomAnnoButtonIndex = rightTopAnnotationForm .getComponentIndex(addCustomAnnoButton); rightTopAnnotationForm.addComponent(customLayout, addCustomAnnoButtonIndex); } }); //<editor-fold defaultstate="collapsed" desc="Replicate Type"> HorizontalLayout replicatTypesLayout = new HorizontalLayout(); String replicateType_from_sra = ""; String replicateType_confidence = ""; Label suggestedreplicatTypeLabel = new Label("<b><i>Suggestion: </i></b>" + replicateType_from_sra + " <b> <i> Confidence: <i></b> " + replicateType_confidence, ContentMode.HTML); String[] replicatTypes = new String[] { "Biological -- different individuals", "Biological -- same individual but severe treatment to RNA", "Semi Biological/Technical -- mild treatment", "Technical -- machine parameter or buffer (very mild)" }; List<String> replicatTypesList = Arrays.asList(replicatTypes); ComboBox replicatTypesListComboBox = new ComboBox("Replicates Type ", replicatTypesList); replicatTypesLayout.addComponent(replicatTypesListComboBox); replicatTypesLayout.addComponent(suggestedreplicatTypeLabel); //</editor-fold> checkboxDiseaseYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxDiseaseNo.setValue(!checkboxDiseaseYes.getValue()); diseaseCategoryComboBox.setVisible(true); } }); checkboxDiseaseNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxDiseaseYes.setValue(!checkboxDiseaseNo.getValue()); diseaseCategoryComboBox.setVisible(false); } }); //<editor-fold defaultstate="collapsed" desc="CheckBox Annotation Ongoing or Completed "> CheckBox checkboxAnnotaionCompleted = new CheckBox("Annotaion Completed"); CheckBox checkboxAnnotaionOngoing = new CheckBox("Annotaion Ongoing"); checkboxAnnotaionOngoing.setValue(true); checkboxAnnotaionCompleted.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxAnnotaionOngoing.setValue(!checkboxAnnotaionCompleted.getValue()); } }); checkboxAnnotaionOngoing.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxAnnotaionCompleted.setValue(!checkboxAnnotaionOngoing.getValue()); } }); //</editor-fold> HorizontalLayout annotationStatusLayout = new HorizontalLayout(); annotationStatusLayout.addComponent(checkboxAnnotaionOngoing); annotationStatusLayout.addComponent(checkboxAnnotaionCompleted); Button submitButton = new Button("Submit"); submitButton.addClickListener(new Button.ClickListener() { public void buttonClick(ClickEvent event) { int diseaseBoolean = 0; if (checkboxDiseaseYes.getValue() && !checkboxDiseaseNo.getValue()) { diseaseBoolean = 1; } int caseControlBoolean = 0; if (checkboxCaseControlYes.getValue() && !checkboxCaseControlNo.getValue()) { caseControlBoolean = 1; } for (int j = 1; j <= custom_annotation_counter; j++) { if (findById(rightTopAnnotationForm, "customAnnoName" + j) instanceof TextField) { TextField tempTFname = (TextField) findById(rightTopAnnotationForm, "customAnnoName" + j); System.out.println(j + "custom name: " + tempTFname.getValue()); } if (findById(rightTopAnnotationForm, "customAnnoValue" + j) instanceof TextField) { TextField tempTFvalue = (TextField) findById(rightTopAnnotationForm, "customAnnoValue" + j); System.out.println(j + "custom value: " + tempTFvalue.getValue()); } } //Notification.show("Do not press this button again"); } }); Button logout = new Button("Logout", new Button.ClickListener() { @Override public void buttonClick(ClickEvent event) { // "Logout" the user getSession().setAttribute("user", null); // Refresh this view, should redirect to login view getUI().getNavigator().navigateTo(ANNOTATIONVIEW); } }); HorizontalLayout userLayout = new HorizontalLayout(); userLayout.addComponent(userWelcome); userLayout.addComponent(logout); rightTopAnnotationForm.addComponent(userLayout); rightTopAnnotationForm.addComponent(diseaseLayout); rightTopAnnotationForm.addComponent(caseControlLayout); rightTopAnnotationForm.addComponent(timeSeriesLayout); rightTopAnnotationForm.addComponent(diseaseCategoriesLayout); rightTopAnnotationForm.addComponent(platformLayout); rightTopAnnotationForm.addComponent(sampleTypesLayout); rightTopAnnotationForm.addComponent(replicatTypesLayout); rightTopAnnotationForm.addComponent(addCustomAnnoButton); rightTopAnnotationForm.addComponent(annotationStatusLayout); rightTopAnnotationForm.addComponent(submitButton); //</editor-fold> //</editor-fold> //<editor-fold defaultstate="collapsed" desc="fill tree in right bottom"> Iterator iterator = biosampleSet.iterator(); // check values while (iterator.hasNext()) { // System.out.println("Value: "+ iterator.next() + " "); String bsample = iterator.next().toString(); String[] biosample_parts = bsample.split("\\|"); String biosample_acc = biosample_parts[0]; tree.addItem(biosample_acc); tree.setParent(biosample_acc, selectedStudy); tree.setItemCaption(biosample_acc, "BioSample: " + biosample_acc); } Set expMap_entrset = expMap.entrySet(); Iterator it = expMap_entrset.iterator(); while (it.hasNext()) { Map.Entry me = (Map.Entry) it.next(); String[] expParts = expDetailMap.get(me.getKey()); String expTitle = ""; if (expParts.length > 3) { expTitle = expParts[3]; } tree.addItem(me.getKey()); tree.setParent(me.getKey(), me.getValue()); tree.setItemCaption(me.getKey(), "Experiment: " + me.getKey() + ": " + expTitle); } Set runMap_entrset = runMap.entrySet(); Iterator runit = runMap_entrset.iterator(); while (runit.hasNext()) { Map.Entry runEntry = (Map.Entry) runit.next(); tree.addItem(runEntry.getKey()); tree.setParent(runEntry.getKey(), runEntry.getValue()); tree.setItemCaption(runEntry.getKey(), "Run: " + runEntry.getKey()); } tree.expandItemsRecursively(selectedStudy); //</editor-fold> } }); tree.setSelectable(true); tree.setImmediate(true); tree.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { Object id = event.getProperty().getValue(); if (id != null) { String selectedTreeId = id.toString(); String selectedTreeItem = tree.getItemCaption(id).toString(); System.out.println("Tree event is fired: " + selectedTreeItem); if (selectedTreeItem.startsWith("BioSample")) { myform.removeAllComponents(); SQLContainer tempContainer = createMySQLContainer("biosample", selectedTreeId); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { String accessType = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("AccessType").getValue().toString(); String publicationDate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("PublicationDate").getValue().toString(); String lastUpdate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("LastUpdate").getValue().toString(); String accession = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Accession").getValue().toString(); String title = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Title").getValue().toString(); String taxonomy_id = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("TaxonomyId").getValue().toString(); String taxonomy_name = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("TaxonomyName").getValue().toString(); String samplePackage = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Package").getValue().toString(); String status = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Status").getValue().toString(); String statusTime = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("StatusTime").getValue().toString(); String sampleIds = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Ids").getValue().toString(); String attributes = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Attributes").getValue().toString(); String models = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Models").getValue().toString(); String submissionDate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("SubmissionDate").getValue().toString(); String owner = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Owner").getValue().toString(); String[] myfields = new String[] { accessType, publicationDate, lastUpdate, accession, title, taxonomy_id, taxonomy_name, samplePackage, status, statusTime, sampleIds, attributes, models, submissionDate, owner }; /* for (String fieldName : myfields) { Label tempLabl = new Label(""); } */ Label labelAccessType = new Label("Access Type: " + accessType); myform.addComponent(labelAccessType); Label labelPublicationDate = new Label("Publication Date: " + publicationDate); myform.addComponent(labelPublicationDate); Label labelLastUpdate = new Label("Last Update: " + lastUpdate); myform.addComponent(labelLastUpdate); Label labelAccession = new Label("Accession: " + accession); myform.addComponent(labelAccession); Label labelTitle = new Label("<b>Title: </b>" + title, ContentMode.HTML); myform.addComponent(labelTitle); Label labelTaxonomyId = new Label("Taxonomy Id: " + taxonomy_id); myform.addComponent(labelTaxonomyId); Label labelTaxonomyName = new Label("Taxonomy Name: " + taxonomy_name); myform.addComponent(labelTaxonomyName); Label labelPackage = new Label("Package: " + samplePackage); myform.addComponent(labelPackage); Label labelStatus = new Label("Status: " + status); myform.addComponent(labelStatus); Label labelStatusTime = new Label("Status Time: " + statusTime); myform.addComponent(labelStatusTime); Label labelOwner = new Label("Owner: " + owner); myform.addComponent(labelOwner); String[] id_parts = sampleIds.split("\\:\\-"); if (id_parts.length > 1) { String[] id_dbs = id_parts[0].split("\\|"); String[] id_values = id_parts[1].split("\\|"); for (int j = 0; j < id_dbs.length; j++) { Label tempLabel = new Label(id_dbs[j] + ": " + id_values[j]); myform.addComponent(tempLabel); } } String[] attribute_parts = attributes.split("\\:\\-"); if (attribute_parts.length > 1) { String[] attribute_names = attribute_parts[0].split("\\|"); String[] attribute_values = attribute_parts[1].split("\\|"); for (int j = 0; j < attribute_names.length; j++) { Label tempLabel = new Label( "<b>" + attribute_names[j] + ": </b>" + attribute_values[j], ContentMode.HTML); myform.addComponent(tempLabel); System.out.println("inside attributes "); } } // TextField field = new TextField(lastDpdate); // myform.addComponent(field); //field.setWidth("100%"); } } if (selectedTreeItem.startsWith("Experiment")) { SQLContainer tempContainer = createMySQLContainer("sra_rnaseq_exp", selectedTreeId); myform.removeAllComponents(); Map expMap = new HashMap(); Map<String, String[]> expDetailMap = new HashMap<>(); Map<String, String[]> libraryDetailMap = new HashMap<>(); Map<String, String[]> platformMap = new HashMap<>(); Map runMap = new HashMap(); HashSet<String> biosampleSet = new HashSet<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { String docid = tempContainer.getIdByIndex(i).toString(); String biosample = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Biosample_Acc_Id_SampleId").getValue().toString(); biosampleSet.add(biosample); String[] b_parts = biosample.split("\\|"); String exp = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Experiment_Acc_Ver_Status_Name").getValue().toString(); String[] exp_parts = exp.split("\\|"); String exp_acc = exp_parts[0]; expMap.put(exp_acc, b_parts[0]); expDetailMap.put(exp_acc, exp_parts); String library_string = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Library_Name_Strategy_Source_Selection_Layout").getValue() .toString(); String[] library_parts = library_string.split("\\|"); String library_name = ""; String library_strategy = ""; String library_source = ""; String library_selection = ""; String library_layout = ""; if (library_parts.length > 0) { library_name = library_parts[0]; } if (library_parts.length > 1) { library_strategy = "<b> <i> Strategy </i> </b>" + library_parts[1]; } if (library_parts.length > 2) { library_source = "<b> <i> Source </i> </b>" + library_parts[2]; } if (library_parts.length > 3) { library_selection = "<b> <i> Selection </i> </b>" + library_parts[3]; } if (library_parts.length > 4) { String tempLayout = library_parts[4]; tempLayout = tempLayout.replaceAll("<", ""); tempLayout = tempLayout.replaceAll("/>", ""); library_layout = "<b> <i> Layout </i> </b>" + tempLayout; } String[] tempStringArray = new String[] { library_strategy, library_source, library_selection, library_layout }; if (library_name.length() > 1) { libraryDetailMap.put(library_name, tempStringArray); } String sra_plaforms = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Platform_InstrumentModel").getValue().toString(); String[] sra_plaforms_parts = sra_plaforms.split("\\|"); platformMap.put(exp_acc, sra_plaforms_parts); String run = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Runs").getValue().toString(); String[] run_parts = run.split("\\|"); if (run_parts.length > 0) { for (int j = 0; j < run_parts.length; j++) { String temprun = run_parts[j]; String[] temprun_parts = temprun.split("\\,"); runMap.put(temprun_parts[0], exp_acc); } } } Label labelExperimentAcc = new Label("<b>Experiment Accession: </b>" + selectedTreeId, ContentMode.HTML); myform.addComponent(labelExperimentAcc); String libraryDetails = ""; for (Map.Entry<String, String[]> entry : libraryDetailMap.entrySet()) { libraryDetails = libraryDetails + entry.getKey(); String[] temp_library_details = entry.getValue(); for (String dt : temp_library_details) { libraryDetails = libraryDetails + dt; } } Label labelLibraryDetails = new Label("<b>Library Details: </b>" + libraryDetails, ContentMode.HTML); myform.addComponent(labelLibraryDetails); } } else { System.out.println("id is null"); } } }); bioprojectSummaryTable.addValueChangeListener(new Property.ValueChangeListener() { public void valueChange(ValueChangeEvent event) { Object contactId = bioprojectSummaryTable.getValue(); //Binding data //When a contact is selected from the list, we want to show that in our editor on the right. This is nicely done by the FieldGroup that binds all the fields to the corresponding Properties in our contact at once. if (contactId != null) // editorFields.setItemDataSource(bioprojectSummaryTable.getItem(contactId)); // editorLayout.setVisible(contactId != null); } }); }
From source file:edu.cornell.qatarmed.planrnaseq.AnnotateViewLogin.java
private void initDataAndSubcomponent() { rnaseqContainer = createMySQLContainer("study_summary", "dummy"); bioprojectSummaryTable.setContainerDataSource(rnaseqContainer); // bioprojectSummaryTable.setVisibleColumns(new String[] { studyName }); bioprojectSummaryTable.setSelectable(true); bioprojectSummaryTable.setImmediate(true); bioprojectSummaryTable.setColumnReorderingAllowed(true); bioprojectSummaryTable.setSortEnabled(true); bioprojectSummaryTable.setVisibleColumns( new Object[] { "Study", "title", "name", "Numsample", "Numexp", "Numrun", "Avgspots", "avgbases" }); //bioprojectSummaryTable.setVisibleColumns(new Object[] { "firstName", "lastName", "department", "phoneNumber", "street", "city", "zipCode" }); studyName.setValue(rnaseqContainer.firstItemId().toString()); bioprojectSummaryTable.addItemClickListener(new ItemClickEvent.ItemClickListener() { int custom_annotation_counter = 0; public void itemClick(ItemClickEvent event) { //<editor-fold defaultstate="collapsed" desc="filling study details on right panel"> Object selectedStudyObject = event.getItemId(); bioprojectSummaryTable.select(selectedStudyObject); tree.removeAllItems();//from www . j a va 2 s . c om rightTopForm.removeAllComponents(); rightTopAnnotationForm.removeAllComponents(); myform.removeAllComponents(); String selectedStudy = selectedStudyObject.toString(); String studyTitle = (String) bioprojectSummaryTable .getContainerProperty(selectedStudyObject, "title").getValue(); String studyName = (String) bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "name") .getValue(); String studyNumsample = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numsample").getValue()); String studyNumexp = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numexp").getValue()); String studyNumrun = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numrun").getValue()); String studyAvgspots = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Avgspots").getValue()); String studyAvgbases = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "avgbases").getValue()); tree.addItem(selectedStudy); tree.setItemCaption(selectedStudy, "Study: " + selectedStudy); SQLContainer tempContainer = createMySQLContainer("study_extdb", selectedStudy); // In this table I will chaeck for the manual annotation status String extdbid = tempContainer.getItem(tempContainer.getIdByIndex(0)).getItemProperty("extdb") .getValue().toString(); Label labelStudyAcc = new Label("<b>SRA Study Accession : </b>" + selectedStudy, ContentMode.HTML); rightTopForm.addComponent(labelStudyAcc); Label labelStudyTitle = new Label("<b>Study Title: </b>" + studyTitle, ContentMode.HTML); rightTopForm.addComponent(labelStudyTitle); Label labelStudyName = new Label("<b>Study Name: </b>" + studyName, ContentMode.HTML); rightTopForm.addComponent(labelStudyName); Label labelStudyNumsample = new Label("<b>Total number of samples: </b>" + studyNumsample, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumsample); Label labelStudyNumexp = new Label( "<b>Total number of experiments (each experiment uses any one of the samples): </b>" + studyNumexp, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumexp); Label labelStudyNumrun = new Label( "<b>Total number of runs ( an experiment can have multiple runs) : </b>" + studyNumrun, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumrun); Label labelStudyAvgspots = new Label( "<b>Avg number of spots or reads (per run): </b>" + studyAvgspots, ContentMode.HTML); rightTopForm.addComponent(labelStudyAvgspots); Label labelStudyAvgbases = new Label("<b>Avg number of bases (per run): </b>" + studyAvgbases, ContentMode.HTML); rightTopForm.addComponent(labelStudyAvgbases); if (extdbid.startsWith("PRJ")) { //<editor-fold defaultstate="collapsed" desc="if PRJ"> tempContainer = createMySQLContainer("bioproject_details", extdbid); String bioproject_accession = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("BioprojectAccession").getValue().toString(); String bioproject_id = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("BioprojectId").getValue().toString(); String bioproject_name = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Name").getValue().toString(); String bioproject_title = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Title").getValue().toString(); String bioproject_description = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Description").getValue().toString(); String bioproject_capture = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Capture").getValue().toString(); String bioproject_material = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Material").getValue().toString(); String bioproject_method = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("MethodType").getValue().toString(); String bioproject_datatype = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("DataType").getValue().toString(); String bioproject_sampleScope = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("SampleScope").getValue().toString(); System.out.println(bioproject_description); Label labelBioprojectAccession = new Label( "<b>Bioproject Accession : </b>" + bioproject_accession, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectAccession); Label labelBioprojectId = new Label("<b>Bioproject Id : </b>" + bioproject_id, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectId); Label labelBioprojectTitle = new Label("<b>Bioproject Title : </b>" + bioproject_title, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectTitle); Label labelBioprojectName = new Label("<b>Bioproject Name : </b>" + bioproject_name, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectName); Label labelBioprojectDescription = new Label( "<b>Bioproject Description : </b>" + bioproject_description, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectDescription); Label labelBioprojectCapture = new Label("<b>Bioproject Capture : </b>" + bioproject_capture, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectCapture); Label labelBioprojectMaterial = new Label( "<b>Bioproject Material : </b>" + bioproject_material, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectMaterial); Label labelBioprojectMethod = new Label("<b>Bioproject Method : </b>" + bioproject_method, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectMethod); Label labelBioprojectDatatype = new Label( "<b>Bioproject Data Type : </b>" + bioproject_datatype, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectDatatype); Label labelBioprojectSampleScope = new Label( "<b>Bioproject Sample Scope : </b>" + bioproject_sampleScope, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectSampleScope); //</editor-fold> } if (extdbid.startsWith("GSE")) { //<editor-fold defaultstate="collapsed" desc="if GSE"> tempContainer = createMySQLContainer("study_gse_details", extdbid); String gse_accesion = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("gse").getValue().toString(); String gse_summary = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("summary").getValue().toString(); String gse_design = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("overall_design").getValue().toString(); System.out.println(gse_summary); Label labelGSE = new Label("<b>GEO Series Accession : </b>" + gse_accesion, ContentMode.HTML); rightTopForm.addComponent(labelGSE); Label labelGseSummary = new Label("<b>GSE Summary : </b>" + gse_summary, ContentMode.HTML); rightTopForm.addComponent(labelGseSummary); Label labelGseDesign = new Label("<b>GSE Design : </b>" + gse_design, ContentMode.HTML); rightTopForm.addComponent(labelGseDesign); //</editor-fold> } //</editor-fold> //SQLContainer tempContainer = createMySQLContainer("sra_rnaseq", selectedStudy); tempContainer = createMySQLContainer("sra_rnaseq", selectedStudy); // List<String> list = new ArrayList<String>(); Map expMap = new HashMap(); Map<String, String[]> expDetailMap = new HashMap<>(); Map<String, String[]> platformMap = new HashMap<>(); Map runMap = new HashMap(); HashSet<String> biosampleSet = new HashSet<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { //<editor-fold defaultstate="collapsed" desc="for loop"> String docid = tempContainer.getIdByIndex(i).toString(); String biosample = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Biosample_Acc_Id_SampleId").getValue().toString(); biosampleSet.add(biosample); String[] b_parts = biosample.split("\\|"); String exp = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Experiment_Acc_Ver_Status_Name").getValue().toString(); String[] exp_parts = exp.split("\\|"); String exp_acc = exp_parts[0]; expMap.put(exp_acc, b_parts[0]); expDetailMap.put(exp_acc, exp_parts); String sra_plaforms = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Platform_InstrumentModel").getValue().toString(); String[] sra_plaforms_parts = sra_plaforms.split("\\|"); platformMap.put(exp_acc, sra_plaforms_parts); String run = tempContainer.getItem(tempContainer.getIdByIndex(i)).getItemProperty("Runs") .getValue().toString(); String[] run_parts = run.split("\\|"); if (run_parts.length > 0) { for (int j = 0; j < run_parts.length; j++) { String temprun = run_parts[j]; String[] temprun_parts = temprun.split("\\,"); runMap.put(temprun_parts[0], exp_acc); } } //</editor-fold> } //<editor-fold defaultstate="collapsed" desc="Manual Annotaion"> tempContainer = createMySQLContainer("biosample_with_studyacc", selectedStudy); int count_cell_line = 0; int count_organism_part = 0; int count_tissue = 0; int count_disease = 0; Set<String> cell_lines_set = new HashSet(); Set<String> organism_part_set = new HashSet(); Set<String> tissue_set = new HashSet(); Set<String> disease_set = new HashSet(); Map<String, Integer> cell_line_stat_map = new HashMap<>(); Map<String, Integer> organism_part_stat_map = new HashMap<>(); Map<String, Integer> tissue_stat_map = new HashMap<>(); Map<String, Integer> disease_stat_map = new HashMap<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { //<editor-fold defaultstate="collapsed" desc="for biosample attributes"> String biosample_attr = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Attributes").getValue().toString(); String[] biosample_attr_parts = biosample_attr.split("\\:-"); if (biosample_attr_parts.length > 0) { String[] attr_names = biosample_attr_parts[0].split("\\|"); String[] attr_values = new String[] {}; if (biosample_attr_parts.length > 1) { attr_values = biosample_attr_parts[1].split("\\|"); } int atn_index = 0; for (String atn : attr_names) { if (atn.equalsIgnoreCase("cell line")) { count_cell_line = count_cell_line + 1; if (attr_values.length >= atn_index) { String cell_line_value = attr_values[atn_index]; cell_lines_set.add(cell_line_value); if (cell_line_stat_map.containsKey(cell_line_value)) { cell_line_stat_map.put(cell_line_value, cell_line_stat_map.get(cell_line_value) + 1); } else { cell_line_stat_map.put(cell_line_value, 1); } } } if (atn.equalsIgnoreCase("organism part")) { count_organism_part = count_organism_part + 1; if (attr_values.length >= atn_index) { String organism_part_value = attr_values[atn_index]; organism_part_set.add(organism_part_value); if (organism_part_stat_map.containsKey(organism_part_value)) { organism_part_stat_map.put(organism_part_value, organism_part_stat_map.get(organism_part_value) + 1); } else { organism_part_stat_map.put(organism_part_value, 1); } } } if (atn.contains("disease")) { count_disease = count_disease + 1; if (attr_values.length >= atn_index) { String disease_value = attr_values[atn_index]; disease_set.add(disease_value); if (disease_stat_map.containsKey(disease_value)) { disease_stat_map.put(disease_value, disease_stat_map.get(disease_value) + 1); } else { disease_stat_map.put(disease_value, 1); } } } if (atn.equalsIgnoreCase("tissue")) { count_tissue = count_tissue + 1; if (attr_values.length >= atn_index) { String tissue_value = attr_values[atn_index]; tissue_set.add(tissue_value); if (tissue_stat_map.containsKey(tissue_value)) { tissue_stat_map.put(tissue_value, tissue_stat_map.get(tissue_value) + 1); } else { tissue_stat_map.put(tissue_value, 1); } } } atn_index = atn_index + 1; } } //</editor-fold> } String suggestion_cell_line = ""; String suggestion_organism_part = ""; String suggestion_tissue = ""; String suggestion_disease = ""; String samplesType_from_sra = ""; String cell_line_confidence = ""; String organism_part_confidence = ""; String disease_confidence = ""; String tissue_confidence = ""; //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has cell line"> if (count_cell_line > 0) { if (Integer.parseInt(studyNumsample) == count_cell_line) { //good. all samples are from cell lines suggestion_cell_line = "Yes:"; String cell_line_value = cell_lines_set.iterator().next(); suggestion_cell_line = suggestion_cell_line + cell_line_value; cell_line_confidence = "100%. All " + cell_line_stat_map.get(cell_line_value).toString() + " Samples"; } else { suggestion_cell_line = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : cell_line_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_cell_line = suggestion_cell_line + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); cell_line_confidence = confidence_percent + "%"; for (Iterator<String> it = cell_lines_set.iterator(); it.hasNext();) { String cellLine = it.next(); if (cellLine.equals(maxEntry.getKey())) { //do nothing } else { suggestion_cell_line = suggestion_cell_line + ", " + cellLine + "(" + cell_line_stat_map.get(cellLine).toString() + ")"; } } } } else { suggestion_cell_line = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has organism part"> if (count_organism_part > 0) { if (Integer.parseInt(studyNumsample) == count_organism_part) { //good. all samples are from cell lines suggestion_organism_part = "Yes:"; String organism_part_value = organism_part_set.iterator().next(); suggestion_organism_part = suggestion_organism_part + organism_part_value; organism_part_confidence = "100%. All " + organism_part_stat_map.get(organism_part_value).toString() + " Samples"; } else { suggestion_organism_part = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : organism_part_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_organism_part = suggestion_organism_part + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); organism_part_confidence = confidence_percent + "%"; for (Iterator<String> it = organism_part_set.iterator(); it.hasNext();) { String organismPart = it.next(); if (organismPart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_organism_part = suggestion_organism_part + ", " + organismPart + "(" + organism_part_stat_map.get(organismPart).toString() + ")"; } } } } else { suggestion_organism_part = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has disease"> if (count_disease > 0) { if (Integer.parseInt(studyNumsample) == count_disease) { //good. all samples are from cell lines suggestion_disease = "Yes:"; String disease_value = disease_set.iterator().next(); suggestion_disease = suggestion_disease + disease_value; disease_confidence = "100%. All " + disease_stat_map.get(disease_value).toString() + " Samples"; } else { suggestion_disease = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : disease_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_disease = suggestion_disease + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); disease_confidence = confidence_percent + "%"; for (Iterator<String> it = disease_set.iterator(); it.hasNext();) { String diseasePart = it.next(); if (diseasePart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_disease = suggestion_disease + ", " + diseasePart + "(" + disease_stat_map.get(diseasePart).toString() + ")"; } } } } else { suggestion_disease = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has tissue"> if (count_tissue > 0) { if (Integer.parseInt(studyNumsample) == count_tissue) { //good. all samples are from cell lines suggestion_tissue = "Yes:"; String tissue_value = tissue_set.iterator().next(); suggestion_tissue = suggestion_tissue + tissue_value; tissue_confidence = "100%. All " + tissue_stat_map.get(tissue_value).toString() + " Samples"; } else { suggestion_tissue = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : tissue_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_tissue = suggestion_tissue + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); tissue_confidence = confidence_percent + "%"; for (Iterator<String> it = disease_set.iterator(); it.hasNext();) { String tissuePart = it.next(); if (tissuePart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_tissue = suggestion_tissue + ", " + tissuePart + "(" + tissue_stat_map.get(tissuePart).toString() + ")"; } } } } else { suggestion_tissue = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="filling right top manual annotation"> HorizontalLayout diseaseLayout = new HorizontalLayout(); CheckBox checkboxDiseaseYes = new CheckBox("Yes"); CheckBox checkboxDiseaseNo = new CheckBox("No"); String disease_from_biosample_attribute = ""; if (suggestion_disease.startsWith("Yes")) { disease_from_biosample_attribute = "From Biosample: " + suggestion_disease; } String disease_found = ""; String disease_text_parsed_confidence = ""; for (String disease : list_of_diseases) { if (StringUtils.containsIgnoreCase(studyName, disease) || StringUtils.containsIgnoreCase(studyTitle, disease)) { checkboxDiseaseYes.setValue(true); disease_found = disease_found + disease + " "; disease_text_parsed_confidence = "keyword found in Study or Title"; } } String diseaseLabelString = ""; if (disease_text_parsed_confidence.length() > 1) { diseaseLabelString = "<b><i>Suggestion: </i></b>" + disease_found + " <b> <i> Confidence: <i></b> " + disease_text_parsed_confidence; } if (disease_from_biosample_attribute.length() > 1) { diseaseLabelString = diseaseLabelString + "<b><i>Suggestion: </i></b>" + disease_from_biosample_attribute + " <b> <i> Confidence: <i></b> " + disease_confidence; } Label diseaseLabel = new Label(diseaseLabelString, ContentMode.HTML); Label diseaseTitle = new Label("<b>Disease: </b>", ContentMode.HTML); diseaseLayout.addComponent(diseaseTitle); diseaseLayout.addComponent(checkboxDiseaseNo); diseaseLayout.addComponent(checkboxDiseaseYes); diseaseLayout.addComponent(diseaseLabel); HorizontalLayout caseControlLayout = new HorizontalLayout(); CheckBox checkboxCaseControlYes = new CheckBox("Yes"); CheckBox checkboxCaseControlNo = new CheckBox("No"); checkboxDiseaseYes.setValue(true); Label caseControlTitle = new Label("<b>Case-Control: </b>", ContentMode.HTML); caseControlLayout.addComponent(caseControlTitle); caseControlLayout.addComponent(checkboxCaseControlYes); caseControlLayout.addComponent(checkboxCaseControlNo); HorizontalLayout timeSeriesLayout = new HorizontalLayout(); CheckBox checkboxTimeSerieslYes = new CheckBox("Yes"); CheckBox checkboxTimeSeriesNo = new CheckBox("No"); checkboxDiseaseYes.setValue(true); Label timeSeriesTitle = new Label("<b>Time Series: </b>", ContentMode.HTML); timeSeriesLayout.addComponent(timeSeriesTitle); timeSeriesLayout.addComponent(checkboxTimeSerieslYes); timeSeriesLayout.addComponent(checkboxTimeSeriesNo); HorizontalLayout diseaseCategoriesLayout = new HorizontalLayout(); Label diseaseCategoryLabel = new Label("<b><i>Suggestion: </i></b>" + disease_found + " <b> <i> Confidence: <i></b> " + disease_confidence, ContentMode.HTML); String[] diseaseCategories = new String[] { "Complex Disease", "Rare Disease", "Other", "Not Sure" }; List<String> diseaseCategoriesList = Arrays.asList(diseaseCategories); ComboBox diseaseCategoryComboBox = new ComboBox("Disease Category", diseaseCategoriesList); diseaseCategoriesLayout.addComponent(diseaseCategoryComboBox); diseaseCategoriesLayout.addComponent(diseaseCategoryLabel); String[] platforms = new String[] { "Illumina", "SOLID", "Roche 454", "PacBio", "Helicos", "Complete Genomics" }; List<String> platformsList = Arrays.asList(platforms); ComboBox platformsListComboBox = new ComboBox("Sequencing Platform", platformsList); Set<String> matchedPlatformSet = new HashSet(); String platform_from_sra = ""; String platorm_confidence = ""; int matchPlatformCount = 0; for (String[] val : platformMap.values()) { if (val.length > 1) { for (String pf : platforms) { if (val[0].equalsIgnoreCase(pf)) { matchedPlatformSet.add(pf); matchPlatformCount = matchPlatformCount + 1; } } } else { } } if (matchedPlatformSet.isEmpty()) { platform_from_sra = "Match Not Found"; } else { if (matchedPlatformSet.size() == matchPlatformCount) { //Ideally this shouldn't be the case. // This suggests that all experiments of this project are run on different platforms or // it has only one expriment if (matchedPlatformSet.size() == 1) { platform_from_sra = matchedPlatformSet.iterator().next().toString(); platformsListComboBox.select(platform_from_sra); } else { platform_from_sra = "Can't predict. All experiment on different Platforms"; } } else { if (matchedPlatformSet.size() == 1) { // Perfect platform_from_sra = matchedPlatformSet.iterator().next().toString(); platformsListComboBox.select(platform_from_sra); platorm_confidence = "100%"; } else { } } } HorizontalLayout platformLayout = new HorizontalLayout(); Label suggestedPlatformLabel = new Label("<b><i>Suggestion: </i></b>" + platform_from_sra + "<b> <i> Confidence: <i></b> " + platorm_confidence, ContentMode.HTML); platformLayout.addComponent(platformsListComboBox); platformLayout.addComponent(suggestedPlatformLabel); VerticalLayout sampleTypesLayout = new VerticalLayout(); CheckBox checkboxSampleTypeCellLine = new CheckBox("Cell Line"); CheckBox checkboxSampleTypeTissue = new CheckBox("Tissue"); CheckBox checkboxSampleTypeStemCells = new CheckBox("Stem Cells"); CheckBox checkboxSampleTypeWholeBlood = new CheckBox("Whole Blood"); CheckBox checkboxSampleTypePlasma = new CheckBox("Plasma"); String suggestedCellTypeLabelString = ""; if (suggestion_cell_line.startsWith("Yes")) { //sampleTypesListComboBox.select("Cell Lines"); checkboxSampleTypeCellLine.setValue(true); suggestedCellTypeLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_cell_line + " <b> <i> Confidence: <i></b> " + cell_line_confidence; } Label suggestedCellLineLabel = new Label(suggestedCellTypeLabelString, ContentMode.HTML); String suggestedTissueLabelString = ""; if (suggestion_organism_part.startsWith("Yes")) { checkboxSampleTypeTissue.setValue(true); suggestedTissueLabelString = suggestedTissueLabelString + "<b><i>Suggestion: </i></b>" + "Organism part --> " + suggestion_organism_part + " <b> <i> Confidence: <i></b> " + organism_part_confidence; } if (suggestion_tissue.startsWith("Yes")) { checkboxSampleTypeTissue.setValue(true); suggestedTissueLabelString = suggestedTissueLabelString + "<b><i>Suggestion: </i></b>" + "Tissue --> " + suggestion_tissue + " <b> <i> Confidence: <i></b> " + tissue_confidence; } Label suggestedTissueLabel = new Label(suggestedTissueLabelString, ContentMode.HTML); String suggestedStemCellString = ""; /* if (suggestion_stem_cell.startsWith("Yes")) { checkboxSampleTypeStemCells.setValue(true); suggestedCellTypeLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_stem_cell + " <b> <i> Confidence: <i></b> " + stem_cell_confidence; } */ Label suggestedStemCellLabel = new Label(suggestedStemCellString, ContentMode.HTML); String suggestedWholeBloodLabelString = ""; /* if (suggestion_whole_blood.startsWith("Yes")) { checkboxSampleTypeWholeBlood.setValue(true); suggestedWholeBloodLabelString = "<b><i>Suggestion: </i></b>" + "Whole Blood --> " + suggestion_whole_blood + " <b> <i> Confidence: <i></b> " + whole_blood_confidence; } */ Label suggestedWholeBloodLabel = new Label(suggestedWholeBloodLabelString, ContentMode.HTML); String suggestedPlasmaLabelString = ""; /* if (suggestion_plasma.startsWith("Yes")) { checkboxSampleTypePlasma.setValue(true); suggestedPlasmaLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_plasma + " <b> <i> Confidence: <i></b> " + plasma_confidence; } */ Label suggestedPlasmaLabel = new Label(suggestedPlasmaLabelString, ContentMode.HTML); HorizontalLayout CellLineLayout = new HorizontalLayout(); CellLineLayout.addComponent(checkboxSampleTypeCellLine); CellLineLayout.addComponent(suggestedCellLineLabel); HorizontalLayout TissueLayout = new HorizontalLayout(); TissueLayout.addComponent(checkboxSampleTypeTissue); TissueLayout.addComponent(suggestedTissueLabel); HorizontalLayout WholeBloodLayout = new HorizontalLayout(); WholeBloodLayout.addComponent(checkboxSampleTypeWholeBlood); WholeBloodLayout.addComponent(suggestedWholeBloodLabel); HorizontalLayout PlasmaLayout = new HorizontalLayout(); PlasmaLayout.addComponent(checkboxSampleTypePlasma); PlasmaLayout.addComponent(suggestedPlasmaLabel); sampleTypesLayout.addComponent(CellLineLayout); sampleTypesLayout.addComponent(TissueLayout); sampleTypesLayout.addComponent(WholeBloodLayout); sampleTypesLayout.addComponent(PlasmaLayout); Button addCustomAnnoButton = new Button("++ Custom Annotation"); addCustomAnnoButton.addClickListener(new Button.ClickListener() { public void buttonClick(ClickEvent event) { custom_annotation_counter = custom_annotation_counter + 1; HorizontalLayout customLayout = new HorizontalLayout(); TextField customAnnoName = new TextField("Custom Name"); customAnnoName.setId("customAnnoName" + custom_annotation_counter); TextField customAnnoValue = new TextField("Custom Value"); customLayout.addComponent(customAnnoName); customLayout.addComponent(customAnnoValue); customAnnoValue.setId("customAnnoValue" + custom_annotation_counter); int addCustomAnnoButtonIndex = rightTopAnnotationForm .getComponentIndex(addCustomAnnoButton); rightTopAnnotationForm.addComponent(customLayout, addCustomAnnoButtonIndex); } }); //<editor-fold defaultstate="collapsed" desc="Replicate Type"> HorizontalLayout replicatTypesLayout = new HorizontalLayout(); String replicateType_from_sra = ""; String replicateType_confidence = ""; Label suggestedreplicatTypeLabel = new Label("<b><i>Suggestion: </i></b>" + replicateType_from_sra + " <b> <i> Confidence: <i></b> " + replicateType_confidence, ContentMode.HTML); String[] replicatTypes = new String[] { "Biological -- different individuals", "Biological -- same individual but severe treatment to RNA", "Semi Biological/Technical -- mild treatment", "Technical -- machine parameter or buffer (very mild)" }; List<String> replicatTypesList = Arrays.asList(replicatTypes); ComboBox replicatTypesListComboBox = new ComboBox("Replicates Type ", replicatTypesList); replicatTypesLayout.addComponent(replicatTypesListComboBox); replicatTypesLayout.addComponent(suggestedreplicatTypeLabel); //</editor-fold> checkboxDiseaseYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxDiseaseNo.setValue(!checkboxDiseaseYes.getValue()); diseaseCategoryComboBox.setVisible(true); } }); checkboxDiseaseNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxDiseaseYes.setValue(!checkboxDiseaseNo.getValue()); diseaseCategoryComboBox.setVisible(false); } }); //<editor-fold defaultstate="collapsed" desc="CheckBox Annotation Ongoing or Completed "> CheckBox checkboxAnnotaionCompleted = new CheckBox("Annotaion Completed"); CheckBox checkboxAnnotaionOngoing = new CheckBox("Annotaion Ongoing"); checkboxAnnotaionOngoing.setValue(true); checkboxAnnotaionCompleted.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxAnnotaionOngoing.setValue(!checkboxAnnotaionCompleted.getValue()); } }); checkboxAnnotaionOngoing.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxAnnotaionCompleted.setValue(!checkboxAnnotaionOngoing.getValue()); } }); //</editor-fold> HorizontalLayout annotationStatusLayout = new HorizontalLayout(); annotationStatusLayout.addComponent(checkboxAnnotaionOngoing); annotationStatusLayout.addComponent(checkboxAnnotaionCompleted); Button submitButton = new Button("Submit"); submitButton.addClickListener(new Button.ClickListener() { public void buttonClick(ClickEvent event) { int diseaseBoolean = 0; if (checkboxDiseaseYes.getValue() && !checkboxDiseaseNo.getValue()) { diseaseBoolean = 1; } int caseControlBoolean = 0; if (checkboxCaseControlYes.getValue() && !checkboxCaseControlNo.getValue()) { caseControlBoolean = 1; } for (int j = 1; j <= custom_annotation_counter; j++) { if (findById(rightTopAnnotationForm, "customAnnoName" + j) instanceof TextField) { TextField tempTFname = (TextField) findById(rightTopAnnotationForm, "customAnnoName" + j); System.out.println(j + "custom name: " + tempTFname.getValue()); } if (findById(rightTopAnnotationForm, "customAnnoValue" + j) instanceof TextField) { TextField tempTFvalue = (TextField) findById(rightTopAnnotationForm, "customAnnoValue" + j); System.out.println(j + "custom value: " + tempTFvalue.getValue()); } } //Notification.show("Do not press this button again"); } }); Button loginButton = new Button("Login"); HorizontalLayout requestLoginLayout = new HorizontalLayout(); requestLoginLayout.addComponent(userWelcome); requestLoginLayout.addComponent(loginButton); rightTopAnnotationForm.addComponent(requestLoginLayout); VerticalLayout userPasswordLayout = new VerticalLayout(); loginButton.addClickListener(new Button.ClickListener() { @Override public void buttonClick(ClickEvent event) { if (event.getButton() == loginButton) { // Create the user input field user = new TextField("User:"); user.setWidth("300px"); user.setRequired(true); user.setInputPrompt("Your username (eg. joe@email.com)"); user.addValidator(new EmailValidator("Username must be an email address")); user.setInvalidAllowed(false); // Create the password input field password = new PasswordField("Password:"); password.setWidth("300px"); password.addValidator(new PasswordValidator()); password.setRequired(true); password.setValue(""); password.setNullRepresentation(""); // Create login button loginSubmitButton = new Button("Login", this); // Add both to a panel VerticalLayout fields = new VerticalLayout(user, password, loginSubmitButton); fields.setCaption("Please login to access the application. (test@test.com/passw0rd)"); fields.setSpacing(true); fields.setMargin(new MarginInfo(true, true, true, false)); fields.setSizeUndefined(); // The view root layout userPasswordLayout.addComponent(fields); int addUserLayoutIndex = rightTopAnnotationForm.getComponentIndex(requestLoginLayout); rightTopAnnotationForm.addComponent(userPasswordLayout, addUserLayoutIndex); rightTopAnnotationForm.removeComponent(requestLoginLayout); } loginSubmitButton.addClickListener(new Button.ClickListener() { @Override public void buttonClick(ClickEvent event) { if (event.getButton() == loginSubmitButton) { // // Validate the fields using the navigator. By using validors for the // fields we reduce the amount of queries we have to use to the database // for wrongly entered passwords // if (!user.isValid() || !password.isValid()) { return; } String username = user.getValue(); String entered_password = password.getValue(); // // Validate username and password with database here. For examples sake // I use a dummy username and password. // boolean isValid = username.equals("test@test.com") && entered_password.equals("passw0rd"); if (isValid) { System.out.println("User name and passoword : Both are correct"); // Store the current user in the service session getSession().setAttribute("user", username); userWelcome.setValue("Hello " + username); int userPasswordLayoutIndex = rightTopAnnotationForm .getComponentIndex(userPasswordLayout); rightTopAnnotationForm.addComponent(requestLoginLayout, userPasswordLayoutIndex); rightTopAnnotationForm.removeComponent(userPasswordLayout); loginButton.setCaption("Logout"); // Navigate to main view // getUI().getNavigator().navigateTo(AnnotateView.ANNOTATIONVIEW);// I guess there is no need to change the view // getUI().getNavigator().navigateTo(AnnotateViewLogin.ANNOTATIONVIEW); } else { // Wrong password clear the password field and refocuses it password.setValue(null); password.focus(); } // throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates. } } }); } }); /* loginSubmitButton.addClickListener(new Button.ClickListener() { @Override public void buttonClick(ClickEvent event) { if (event.getButton() == loginSubmitButton) { // // Validate the fields using the navigator. By using validors for the // fields we reduce the amount of queries we have to use to the database // for wrongly entered passwords // if (!user.isValid() || !password.isValid()) { return; } String username = user.getValue(); String entered_password = password.getValue(); // // Validate username and password with database here. For examples sake // I use a dummy username and password. // boolean isValid = username.equals("test@test.com") && entered_password.equals("passw0rd"); if (isValid) { // Store the current user in the service session getSession().setAttribute("user", username); // Navigate to main view getUI().getNavigator().navigateTo(AnnotateView.ANNOTATIONVIEW);// // getUI().getNavigator().navigateTo(AnnotateRNAseqSQL);// } else { // Wrong password clear the password field and refocuses it password.setValue(null); password.focus(); } throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates. } } }); */ rightTopAnnotationForm.addComponent(diseaseLayout); rightTopAnnotationForm.addComponent(caseControlLayout); rightTopAnnotationForm.addComponent(timeSeriesLayout); rightTopAnnotationForm.addComponent(diseaseCategoriesLayout); rightTopAnnotationForm.addComponent(platformLayout); rightTopAnnotationForm.addComponent(sampleTypesLayout); rightTopAnnotationForm.addComponent(replicatTypesLayout); rightTopAnnotationForm.addComponent(addCustomAnnoButton); rightTopAnnotationForm.addComponent(annotationStatusLayout); rightTopAnnotationForm.addComponent(submitButton); //</editor-fold> //</editor-fold> //<editor-fold defaultstate="collapsed" desc="fill tree in right bottom"> Iterator iterator = biosampleSet.iterator(); // check values while (iterator.hasNext()) { // System.out.println("Value: "+ iterator.next() + " "); String bsample = iterator.next().toString(); String[] biosample_parts = bsample.split("\\|"); String biosample_acc = biosample_parts[0]; tree.addItem(biosample_acc); tree.setParent(biosample_acc, selectedStudy); tree.setItemCaption(biosample_acc, "BioSample: " + biosample_acc); } Set expMap_entrset = expMap.entrySet(); Iterator it = expMap_entrset.iterator(); while (it.hasNext()) { Map.Entry me = (Map.Entry) it.next(); String[] expParts = expDetailMap.get(me.getKey()); String expTitle = ""; if (expParts.length > 3) { expTitle = expParts[3]; } tree.addItem(me.getKey()); tree.setParent(me.getKey(), me.getValue()); tree.setItemCaption(me.getKey(), "Experiment: " + me.getKey() + ": " + expTitle); } Set runMap_entrset = runMap.entrySet(); Iterator runit = runMap_entrset.iterator(); while (runit.hasNext()) { Map.Entry runEntry = (Map.Entry) runit.next(); tree.addItem(runEntry.getKey()); tree.setParent(runEntry.getKey(), runEntry.getValue()); tree.setItemCaption(runEntry.getKey(), "Run: " + runEntry.getKey()); } tree.expandItemsRecursively(selectedStudy); //</editor-fold> } }); tree.setSelectable(true); tree.setImmediate(true); tree.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { Object id = event.getProperty().getValue(); if (id != null) { String selectedTreeId = id.toString(); String selectedTreeItem = tree.getItemCaption(id).toString(); System.out.println("Tree event is fired: " + selectedTreeItem); if (selectedTreeItem.startsWith("BioSample")) { myform.removeAllComponents(); SQLContainer tempContainer = createMySQLContainer("biosample", selectedTreeId); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { String accessType = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("AccessType").getValue().toString(); String publicationDate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("PublicationDate").getValue().toString(); String lastUpdate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("LastUpdate").getValue().toString(); String accession = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Accession").getValue().toString(); String title = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Title").getValue().toString(); String taxonomy_id = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("TaxonomyId").getValue().toString(); String taxonomy_name = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("TaxonomyName").getValue().toString(); String samplePackage = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Package").getValue().toString(); String status = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Status").getValue().toString(); String statusTime = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("StatusTime").getValue().toString(); String sampleIds = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Ids").getValue().toString(); String attributes = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Attributes").getValue().toString(); String models = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Models").getValue().toString(); String submissionDate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("SubmissionDate").getValue().toString(); String owner = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Owner").getValue().toString(); String[] myfields = new String[] { accessType, publicationDate, lastUpdate, accession, title, taxonomy_id, taxonomy_name, samplePackage, status, statusTime, sampleIds, attributes, models, submissionDate, owner }; /* for (String fieldName : myfields) { Label tempLabl = new Label(""); } */ Label labelAccessType = new Label("Access Type: " + accessType); myform.addComponent(labelAccessType); Label labelPublicationDate = new Label("Publication Date: " + publicationDate); myform.addComponent(labelPublicationDate); Label labelLastUpdate = new Label("Last Update: " + lastUpdate); myform.addComponent(labelLastUpdate); Label labelAccession = new Label("Accession: " + accession); myform.addComponent(labelAccession); Label labelTitle = new Label("<b>Title: </b>" + title, ContentMode.HTML); myform.addComponent(labelTitle); Label labelTaxonomyId = new Label("Taxonomy Id: " + taxonomy_id); myform.addComponent(labelTaxonomyId); Label labelTaxonomyName = new Label("Taxonomy Name: " + taxonomy_name); myform.addComponent(labelTaxonomyName); Label labelPackage = new Label("Package: " + samplePackage); myform.addComponent(labelPackage); Label labelStatus = new Label("Status: " + status); myform.addComponent(labelStatus); Label labelStatusTime = new Label("Status Time: " + statusTime); myform.addComponent(labelStatusTime); Label labelOwner = new Label("Owner: " + owner); myform.addComponent(labelOwner); String[] id_parts = sampleIds.split("\\:\\-"); if (id_parts.length > 1) { String[] id_dbs = id_parts[0].split("\\|"); String[] id_values = id_parts[1].split("\\|"); for (int j = 0; j < id_dbs.length; j++) { Label tempLabel = new Label(id_dbs[j] + ": " + id_values[j]); myform.addComponent(tempLabel); } } String[] attribute_parts = attributes.split("\\:\\-"); if (attribute_parts.length > 1) { String[] attribute_names = attribute_parts[0].split("\\|"); String[] attribute_values = attribute_parts[1].split("\\|"); for (int j = 0; j < attribute_names.length; j++) { Label tempLabel = new Label( "<b>" + attribute_names[j] + ": </b>" + attribute_values[j], ContentMode.HTML); myform.addComponent(tempLabel); System.out.println("inside attributes "); } } // TextField field = new TextField(lastDpdate); // myform.addComponent(field); //field.setWidth("100%"); } } if (selectedTreeItem.startsWith("Experiment")) { SQLContainer tempContainer = createMySQLContainer("sra_rnaseq_exp", selectedTreeId); myform.removeAllComponents(); Map expMap = new HashMap(); Map<String, String[]> expDetailMap = new HashMap<>(); Map<String, String[]> libraryDetailMap = new HashMap<>(); Map<String, String[]> platformMap = new HashMap<>(); Map runMap = new HashMap(); HashSet<String> biosampleSet = new HashSet<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { String docid = tempContainer.getIdByIndex(i).toString(); String biosample = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Biosample_Acc_Id_SampleId").getValue().toString(); biosampleSet.add(biosample); String[] b_parts = biosample.split("\\|"); String exp = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Experiment_Acc_Ver_Status_Name").getValue().toString(); String[] exp_parts = exp.split("\\|"); String exp_acc = exp_parts[0]; expMap.put(exp_acc, b_parts[0]); expDetailMap.put(exp_acc, exp_parts); String library_string = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Library_Name_Strategy_Source_Selection_Layout").getValue() .toString(); String[] library_parts = library_string.split("\\|"); String library_name = ""; String library_strategy = ""; String library_source = ""; String library_selection = ""; String library_layout = ""; if (library_parts.length > 0) { library_name = library_parts[0]; } if (library_parts.length > 1) { library_strategy = "<b> <i> Strategy </i> </b>" + library_parts[1]; } if (library_parts.length > 2) { library_source = "<b> <i> Source </i> </b>" + library_parts[2]; } if (library_parts.length > 3) { library_selection = "<b> <i> Selection </i> </b>" + library_parts[3]; } if (library_parts.length > 4) { String tempLayout = library_parts[4]; tempLayout = tempLayout.replaceAll("<", ""); tempLayout = tempLayout.replaceAll("/>", ""); library_layout = "<b> <i> Layout </i> </b>" + tempLayout; } String[] tempStringArray = new String[] { library_strategy, library_source, library_selection, library_layout }; if (library_name.length() > 1) { libraryDetailMap.put(library_name, tempStringArray); } String sra_plaforms = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Platform_InstrumentModel").getValue().toString(); String[] sra_plaforms_parts = sra_plaforms.split("\\|"); platformMap.put(exp_acc, sra_plaforms_parts); String run = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Runs").getValue().toString(); String[] run_parts = run.split("\\|"); if (run_parts.length > 0) { for (int j = 0; j < run_parts.length; j++) { String temprun = run_parts[j]; String[] temprun_parts = temprun.split("\\,"); runMap.put(temprun_parts[0], exp_acc); } } } Label labelExperimentAcc = new Label("<b>Experiment Accession: </b>" + selectedTreeId, ContentMode.HTML); myform.addComponent(labelExperimentAcc); String libraryDetails = ""; for (Map.Entry<String, String[]> entry : libraryDetailMap.entrySet()) { libraryDetails = libraryDetails + entry.getKey(); String[] temp_library_details = entry.getValue(); for (String dt : temp_library_details) { libraryDetails = libraryDetails + dt; } } Label labelLibraryDetails = new Label("<b>Library Details: </b>" + libraryDetails, ContentMode.HTML); myform.addComponent(labelLibraryDetails); } } else { System.out.println("id is null"); } } }); bioprojectSummaryTable.addValueChangeListener(new Property.ValueChangeListener() { public void valueChange(ValueChangeEvent event) { Object contactId = bioprojectSummaryTable.getValue(); //Binding data //When a contact is selected from the list, we want to show that in our editor on the right. This is nicely done by the FieldGroup that binds all the fields to the corresponding Properties in our contact at once. if (contactId != null) // editorFields.setItemDataSource(bioprojectSummaryTable.getItem(contactId)); // editorLayout.setVisible(contactId != null); } }); }
From source file:edu.cornell.qatarmed.planrnaseq.BrowseAndAnnotate.java
private void initDataAndSubcomponent() { //<editor-fold defaultstate="collapsed" desc="populating project/study summary table"> rnaseqContainer = createMySQLContainer("study_summary", "dummy"); bioprojectSummaryTable.setContainerDataSource(rnaseqContainer); // bioprojectSummaryTable.setVisibleColumns(new String[] { studyName }); bioprojectSummaryTable.setCurrentPageFirstItemIndex(300); bioprojectSummaryTable.setSelectable(true); bioprojectSummaryTable.setImmediate(true); bioprojectSummaryTable.setColumnReorderingAllowed(true); bioprojectSummaryTable.setSortEnabled(true); bioprojectSummaryTable.setVisibleColumns( new Object[] { "Study", "title", "Numsample", "Numexp", "Numrun", "Avgspots", "avgbases", "name" }); //bioprojectSummaryTable.setVisibleColumns(new Object[] { "firstName", "lastName", "department", "phoneNumber", "street", "city", "zipCode" }); studyName.setValue(rnaseqContainer.firstItemId().toString()); bioprojectSummaryTable.setCellStyleGenerator(new Table.CellStyleGenerator() { @Override//from w w w. ja v a2 s . co m public String getStyle(Table table, Object itemId, Object propertyId) { String mynullreturn = ""; if (propertyId == null) { // Styling for row // Item item = bioprojectSummaryTable.getItem(itemId); Item item = table.getItem(itemId); String annotatus_status = ""; if (item == null) { // checking this is important in lazy loading table. Otherwise it produces null pointer exception while scrolling down the table. // System.out.println("It's null"); return mynullreturn; } else { if (item.getItemProperty("annotation_status").getValue() != null) { annotatus_status = (String) item.getItemProperty("annotation_status").getValue(); } } // String annotatus_status = (String) item.getItemProperty("annotation_status").getValue(); if (annotatus_status.toLowerCase().startsWith("ongoing")) { // System.out.println(annotatus_status); return "highlight-orange"; } else if (annotatus_status.toLowerCase().startsWith("completed")) { return "highlight-green"; } else { return mynullreturn; } } else { // styling for column propertyId return mynullreturn; } } }); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Upon clicking any project from the project/study summary table"> bioprojectSummaryTable.addItemClickListener(new ItemClickEvent.ItemClickListener() { int custom_annotation_counter = 0; public void itemClick(ItemClickEvent event) { rightTopTabsheet.setSelectedTab(rightTopForm); //<editor-fold defaultstate="collapsed" desc="filling study details on right panel"> Object selectedStudyObject = event.getItemId(); bioprojectSummaryTable.select(selectedStudyObject); tree.removeAllItems(); rightTopForm.removeAllComponents(); rightTopAnnotationForm.removeAllComponents(); myform.removeAllComponents(); String selectedStudy = selectedStudyObject.toString(); String studyTitle = (String) bioprojectSummaryTable .getContainerProperty(selectedStudyObject, "title").getValue(); String studyName = (String) bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "name") .getValue(); String studyNumsample = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numsample").getValue()); String studyNumexp = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numexp").getValue()); String studyNumrun = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Numrun").getValue()); String studyAvgspots = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "Avgspots").getValue()); String studyAvgbases = String.valueOf( bioprojectSummaryTable.getContainerProperty(selectedStudyObject, "avgbases").getValue()); tree.addItem(selectedStudy); tree.setItemCaption(selectedStudy, "Study: " + selectedStudy); SQLContainer tempContainer = createMySQLContainer("study_extdb", selectedStudy); // In this table I will chaeck for the manual annotation status String extdbid = tempContainer.getItem(tempContainer.getIdByIndex(0)).getItemProperty("extdb") .getValue().toString(); HorizontalLayout studyAccLinkLayout = new HorizontalLayout(); Label labelStudyAcc = new Label( "<b>SRA Study Accession : </b>" + selectedStudy + " ", ContentMode.HTML); String ncbi_sra_study_link = "http://www.ncbi.nlm.nih.gov/Traces/sra/?study=" + selectedStudy; Link link = new Link("NCBI SRA Link", new ExternalResource(ncbi_sra_study_link)); // Open the URL in a new window/tab link.setTargetName("_blank"); // Indicate visually that it opens in a new window/tab link.setIcon(new ThemeResource("icons/external-link.png")); link.addStyleName("icon-after-caption"); studyAccLinkLayout.addComponent(labelStudyAcc); studyAccLinkLayout.addComponent(link); rightTopForm.addComponent(studyAccLinkLayout); Label labelStudyTitle = new Label("<b>Study Title: </b>" + studyTitle, ContentMode.HTML); rightTopForm.addComponent(labelStudyTitle); Label labelStudyName = new Label("<b>Study Name: </b>" + studyName, ContentMode.HTML); rightTopForm.addComponent(labelStudyName); tempContainer = null; tempContainer = createMySQLContainer("study_abstracts", selectedStudy); // In this table I will chaeck for the manual annotation status if (tempContainer.size() > 0) { Item tempItem = tempContainer.getItem(tempContainer.getIdByIndex(0)); if (!(tempItem.getItemProperty("abstract").getValue() == null)) { String abstr = tempItem.getItemProperty("abstract").getValue().toString(); String xref = tempItem.getItemProperty("xref").getValue().toString(); if (abstr.length() > 3) { Label labelStudyAbstract = new Label("<b>Abstract: </b>" + abstr, ContentMode.HTML); rightTopForm.addComponent(labelStudyAbstract); } if ((xref.length() > 3) & (xref.contains("pubmed"))) { HorizontalLayout pubLinkLayout = new HorizontalLayout(); Label labelPubmed = new Label("<b>Pubmed Id : </b>" + " ", ContentMode.HTML); pubLinkLayout.addComponent(labelPubmed); String[] pub = xref.split("\\|"); if (pub.length > 0) { for (String p : pub) { String[] pid = p.split("\\:-"); if (pid[0].startsWith("pubmed")) { Label tempPubLabel = new Label(" ", ContentMode.HTML); String pubmed_link = "http://www.ncbi.nlm.nih.gov/pubmed/" + pid[1]; Link linkpub = new Link(pid[1], new ExternalResource(pubmed_link)); linkpub.setTargetName("_blank"); linkpub.setIcon(new ThemeResource("icons/external-link.png")); linkpub.addStyleName("icon-after-caption"); pubLinkLayout.addComponent(tempPubLabel); pubLinkLayout.addComponent(linkpub); } } } rightTopForm.addComponent(pubLinkLayout); } } } Label labelStudyNumsample = new Label("<b>Total number of samples: </b>" + studyNumsample, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumsample); Label labelStudyNumexp = new Label( "<b>Total number of experiments (each experiment uses any one of the samples): </b>" + studyNumexp, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumexp); Label labelStudyNumrun = new Label( "<b>Total number of runs ( an experiment can have multiple runs) : </b>" + studyNumrun, ContentMode.HTML); rightTopForm.addComponent(labelStudyNumrun); Label labelStudyAvgspots = new Label( "<b>Avg number of spots or reads (per run): </b>" + studyAvgspots, ContentMode.HTML); rightTopForm.addComponent(labelStudyAvgspots); Label labelStudyAvgbases = new Label("<b>Avg number of bases (per run): </b>" + studyAvgbases, ContentMode.HTML); rightTopForm.addComponent(labelStudyAvgbases); if (extdbid.startsWith("PRJ")) { //<editor-fold defaultstate="collapsed" desc="if PRJ"> tempContainer = createMySQLContainer("bioproject_details", extdbid); String bioproject_accession = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("BioprojectAccession").getValue().toString(); String bioproject_id = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("BioprojectId").getValue().toString(); String bioproject_name = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Name").getValue().toString(); String bioproject_title = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Title").getValue().toString(); String bioproject_description = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Description").getValue().toString(); String bioproject_capture = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Capture").getValue().toString(); String bioproject_material = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("Material").getValue().toString(); String bioproject_method = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("MethodType").getValue().toString(); String bioproject_datatype = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("DataType").getValue().toString(); String bioproject_sampleScope = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("SampleScope").getValue().toString(); System.out.println(bioproject_description); Label labelBioprojectAccession = new Label( "<b>Bioproject Accession : </b>" + bioproject_accession, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectAccession); Label labelBioprojectId = new Label("<b>Bioproject Id : </b>" + bioproject_id, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectId); Label labelBioprojectTitle = new Label("<b>Bioproject Title : </b>" + bioproject_title, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectTitle); Label labelBioprojectName = new Label("<b>Bioproject Name : </b>" + bioproject_name, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectName); Label labelBioprojectDescription = new Label( "<b>Bioproject Description : </b>" + bioproject_description, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectDescription); Label labelBioprojectCapture = new Label("<b>Bioproject Capture : </b>" + bioproject_capture, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectCapture); Label labelBioprojectMaterial = new Label( "<b>Bioproject Material : </b>" + bioproject_material, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectMaterial); Label labelBioprojectMethod = new Label("<b>Bioproject Method : </b>" + bioproject_method, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectMethod); Label labelBioprojectDatatype = new Label( "<b>Bioproject Data Type : </b>" + bioproject_datatype, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectDatatype); Label labelBioprojectSampleScope = new Label( "<b>Bioproject Sample Scope : </b>" + bioproject_sampleScope, ContentMode.HTML); rightTopForm.addComponent(labelBioprojectSampleScope); //</editor-fold> } if (extdbid.startsWith("GSE")) { //<editor-fold defaultstate="collapsed" desc="if GSE"> tempContainer = createMySQLContainer("study_gse_details", extdbid); String gse_accesion = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("gse").getValue().toString(); String gse_summary = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("summary").getValue().toString(); String gse_design = tempContainer.getItem(tempContainer.getIdByIndex(0)) .getItemProperty("overall_design").getValue().toString(); // System.out.println(gse_summary); Label labelGSE = new Label("<b>GEO Series Accession : </b>" + gse_accesion, ContentMode.HTML); rightTopForm.addComponent(labelGSE); Label labelGseSummary = new Label("<b>GSE Summary : </b>" + gse_summary, ContentMode.HTML); rightTopForm.addComponent(labelGseSummary); Label labelGseDesign = new Label("<b>GSE Design : </b>" + gse_design, ContentMode.HTML); rightTopForm.addComponent(labelGseDesign); //</editor-fold> } try { String search_query = " SELECT * FROM manual_annotation " + "where annotation_status = 'completed' " + " AND studyid = '" + selectedStudy + "'"; rnaseqContainer = createMySQLContainer("suggestion_by_manual_annotation", search_query); if (rnaseqContainer.getItemIds().size() > 0) { Label ManualAnnotationLabelStart = new Label("<b>Manual Annotaion </b>", ContentMode.HTML); rightTopForm.addComponent(ManualAnnotationLabelStart); for (int i = 0; i < rnaseqContainer.getItemIds().size(); i++) { Item tempItem = rnaseqContainer.getItem(rnaseqContainer.getIdByIndex(i)); int annotation_count = i + 1; String stringManualAnnotationDetails = "------------ Manual Annotaion " + annotation_count + " ------------"; System.out.println("Item is " + tempItem); if (!(tempItem.getItemProperty("isDisease").getValue() == null)) { if (tempItem.getItemProperty("isDisease").getValue().toString().equals("1")) { stringManualAnnotationDetails = stringManualAnnotationDetails + "<br></br> Disease = Yes "; } } String stringStudyTypes = ""; if (!(tempItem.getItemProperty("isCaseControl").getValue() == null)) { if (tempItem.getItemProperty("isCaseControl").getValue().toString().equals("1")) { stringStudyTypes = stringStudyTypes + "<br> Case-Control = Yes "; } } if (!(tempItem.getItemProperty("isTimeSeries").getValue() == null)) { if (tempItem.getItemProperty("isTimeSeries").getValue().toString().equals("1")) { stringStudyTypes = stringStudyTypes + "<br> Time Series = Yes "; } } if (!(tempItem.getItemProperty("isTreatment").getValue() == null)) { if (tempItem.getItemProperty("isTreatment").getValue().toString().equals("1")) { stringStudyTypes = stringStudyTypes + "<br> Treatment = Yes "; } } if (stringStudyTypes.length() > 2) { stringManualAnnotationDetails = stringManualAnnotationDetails + "<br></br> <i> **** Study Types ****</i> " + stringStudyTypes; } String stringSampleTypes = ""; if (!(tempItem.getItemProperty("isCellLine").getValue() == null)) { if (tempItem.getItemProperty("isCellLine").getValue().toString().equals("1")) { stringSampleTypes = stringSampleTypes + "<br> Cell Line = Yes "; } } if (!(tempItem.getItemProperty("isPrimaryCells").getValue() == null)) { if (tempItem.getItemProperty("isPrimaryCells").getValue().toString().equals("1")) { stringSampleTypes = stringSampleTypes + "<br> Primary Cells = Yes "; } } if (!(tempItem.getItemProperty("isTissue").getValue() == null)) { if (tempItem.getItemProperty("isTissue").getValue().toString().equals("1")) { stringSampleTypes = stringSampleTypes + "<br> Tissue = Yes "; } } if (!(tempItem.getItemProperty("isWholeBlood").getValue() == null)) { if (tempItem.getItemProperty("isWholeBlood").getValue().toString().equals("1")) { stringSampleTypes = stringSampleTypes + "<br> Blood = Yes "; } } if (!(tempItem.getItemProperty("isPlasma").getValue() == null)) { if (tempItem.getItemProperty("isPlasma").getValue().toString().equals("1")) { stringSampleTypes = stringSampleTypes + "<br> Plasma = Yes "; } } if (stringSampleTypes.length() > 2) { stringManualAnnotationDetails = stringManualAnnotationDetails + "<br></br> <i>**** Sample Types ****</i> " + stringSampleTypes; } if (!(tempItem.getItemProperty("sequencing_platform").getValue() == null)) { String sequencing_platform = tempItem.getItemProperty("sequencing_platform") .getValue().toString(); String[] annotated_platforms = sequencing_platform.split("\\;"); stringManualAnnotationDetails = stringManualAnnotationDetails + "<br></br> Sequencing Platform = " + sequencing_platform; } if (!(tempItem.getItemProperty("replicate_type").getValue() == null)) { String replicate_type = tempItem.getItemProperty("replicate_type").getValue() .toString(); stringManualAnnotationDetails = stringManualAnnotationDetails + "<br></br> Replicate Type = " + replicate_type; } if (!(tempItem.getItemProperty("disease_category").getValue() == null)) { String annotated_disease_category = tempItem.getItemProperty("disease_category") .getValue().toString(); String[] annotated_disease_categories = annotated_disease_category.split("\\;"); String string_disease_cat = ""; for (String cat : annotated_disease_categories) { if (cat.startsWith("complex_disease")) { String[] cat_parts = cat.split("\\|"); if (string_disease_cat.contains("complex_disease")) { string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(50) + " ---- " + cat_parts[1]; string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(57) + " ---- " + cat_parts[2]; } else { string_disease_cat = string_disease_cat + " Complex Disease "; string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(50) + " ---- " + cat_parts[1]; string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(57) + " ---- " + cat_parts[2]; } } if (cat.startsWith("rare_disease")) { String[] cat_parts = cat.split("\\|"); if (string_disease_cat.contains("rare_disease")) { string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(50) + " ---- " + cat_parts[1]; string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(57) + " ---- " + cat_parts[2]; } else { if (string_disease_cat.contains("complex_disease")) { string_disease_cat = string_disease_cat + "<br> "; } else { string_disease_cat = string_disease_cat + " Rare Disease "; } string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(50) + " ---- " + cat_parts[1]; string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(57) + " ---- " + cat_parts[2]; } } if (cat.startsWith("other_disease")) { String[] cat_parts = cat.split("\\|"); if (string_disease_cat.contains("other_disease")) { string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(50) + " ---- " + cat_parts[1]; string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(57) + " ---- " + cat_parts[2]; } else { if (string_disease_cat.contains("complex_disease") || string_disease_cat.contains("rare_disease")) { string_disease_cat = string_disease_cat + "<br> "; } else { string_disease_cat = string_disease_cat + " Other Disease "; } string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(50) + " ---- " + cat_parts[1]; string_disease_cat = string_disease_cat + "<br> " + createHTMLspaces(57) + " ---- " + cat_parts[2]; } } } stringManualAnnotationDetails = stringManualAnnotationDetails + "<br></br> Disease Category = " + string_disease_cat; } if (!(tempItem.getItemProperty("annotator").getValue() == null)) { String annotator = tempItem.getItemProperty("annotator").getValue().toString(); stringManualAnnotationDetails = stringManualAnnotationDetails + "<br></br> Annotator = " + annotator; } stringManualAnnotationDetails = stringManualAnnotationDetails + "<br></br>-----------------------------------"; Label tempManualAnnotationDetails = new Label(stringManualAnnotationDetails, ContentMode.HTML); rightTopForm.addComponent(tempManualAnnotationDetails); } // Label ManualAnnotationLabelEnd = new Label("<b>Manual Annotaion </b>", ContentMode.HTML); // rightTopForm.addComponent(ManualAnnotationLabelEnd); } } catch (Exception e) { } //</editor-fold> //SQLContainer tempContainer = createMySQLContainer("sra_rnaseq", selectedStudy); tempContainer = createMySQLContainer("sra_rnaseq", selectedStudy); // List<String> list = new ArrayList<String>(); Map expMap = new HashMap(); Map<String, String[]> expDetailMap = new HashMap<>(); Map<String, String[]> platformMap = new HashMap<>(); Map runMap = new HashMap(); HashSet<String> biosampleSet = new HashSet<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { //<editor-fold defaultstate="collapsed" desc="for loop"> String docid = tempContainer.getIdByIndex(i).toString(); String biosample = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Biosample_Acc_Id_SampleId").getValue().toString(); biosampleSet.add(biosample); String[] b_parts = biosample.split("\\|"); String exp = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Experiment_Acc_Ver_Status_Name").getValue().toString(); String[] exp_parts = exp.split("\\|"); String exp_acc = exp_parts[0]; expMap.put(exp_acc, b_parts[0]); expDetailMap.put(exp_acc, exp_parts); String sra_plaforms = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Platform_InstrumentModel").getValue().toString(); String[] sra_plaforms_parts = sra_plaforms.split("\\|"); platformMap.put(exp_acc, sra_plaforms_parts); String run = tempContainer.getItem(tempContainer.getIdByIndex(i)).getItemProperty("Runs") .getValue().toString(); String[] run_parts = run.split("\\|"); if (run_parts.length > 0) { for (int j = 0; j < run_parts.length; j++) { String temprun = run_parts[j]; String[] temprun_parts = temprun.split("\\,"); runMap.put(temprun_parts[0], exp_acc); } } //</editor-fold> } //<editor-fold defaultstate="collapsed" desc="Manual Annotaion"> tempContainer = createMySQLContainer("biosample_with_studyacc", selectedStudy); int count_cell_line = 0; int count_organism_part = 0; int count_tissue = 0; int count_disease = 0; Set<String> cell_lines_set = new HashSet(); Set<String> organism_part_set = new HashSet(); Set<String> tissue_set = new HashSet(); Set<String> disease_set = new HashSet(); Map<String, Integer> cell_line_stat_map = new HashMap<>(); Map<String, Integer> organism_part_stat_map = new HashMap<>(); Map<String, Integer> tissue_stat_map = new HashMap<>(); Map<String, Integer> disease_stat_map = new HashMap<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { //<editor-fold defaultstate="collapsed" desc="for biosample attributes"> String biosample_attr = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Attributes").getValue().toString(); String[] biosample_attr_parts = biosample_attr.split("\\:-"); if (biosample_attr_parts.length > 0) { String[] attr_names = biosample_attr_parts[0].split("\\|"); String[] attr_values = new String[] {}; if (biosample_attr_parts.length > 1) { attr_values = biosample_attr_parts[1].split("\\|"); } int atn_index = 0; for (String atn : attr_names) { if (atn.equalsIgnoreCase("cell line")) { count_cell_line = count_cell_line + 1; if (attr_values.length >= atn_index) { String cell_line_value = attr_values[atn_index]; cell_lines_set.add(cell_line_value); if (cell_line_stat_map.containsKey(cell_line_value)) { cell_line_stat_map.put(cell_line_value, cell_line_stat_map.get(cell_line_value) + 1); } else { cell_line_stat_map.put(cell_line_value, 1); } } } if (atn.equalsIgnoreCase("organism part")) { count_organism_part = count_organism_part + 1; if (attr_values.length >= atn_index) { String organism_part_value = attr_values[atn_index]; organism_part_set.add(organism_part_value); if (organism_part_stat_map.containsKey(organism_part_value)) { organism_part_stat_map.put(organism_part_value, organism_part_stat_map.get(organism_part_value) + 1); } else { organism_part_stat_map.put(organism_part_value, 1); } } } if (atn.contains("disease")) { count_disease = count_disease + 1; if (attr_values.length >= atn_index) { String disease_value = attr_values[atn_index]; disease_set.add(disease_value); if (disease_stat_map.containsKey(disease_value)) { disease_stat_map.put(disease_value, disease_stat_map.get(disease_value) + 1); } else { disease_stat_map.put(disease_value, 1); } } } if (atn.equalsIgnoreCase("tissue")) { count_tissue = count_tissue + 1; if (attr_values.length >= atn_index) { String tissue_value = attr_values[atn_index]; tissue_set.add(tissue_value); if (tissue_stat_map.containsKey(tissue_value)) { tissue_stat_map.put(tissue_value, tissue_stat_map.get(tissue_value) + 1); } else { tissue_stat_map.put(tissue_value, 1); } } } atn_index = atn_index + 1; } } //</editor-fold> } String suggestion_cell_line = ""; String suggestion_organism_part = ""; String suggestion_tissue = ""; String suggestion_disease = ""; String samplesType_from_sra = ""; String cell_line_confidence = ""; String organism_part_confidence = ""; String disease_confidence = ""; String tissue_confidence = ""; //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has cell line"> if (count_cell_line > 0) { if (Integer.parseInt(studyNumsample) == count_cell_line) { //good. all samples are from cell lines suggestion_cell_line = "Yes:"; String cell_line_value = cell_lines_set.iterator().next(); suggestion_cell_line = suggestion_cell_line + cell_line_value; cell_line_confidence = "100%. All " + cell_line_stat_map.get(cell_line_value).toString() + " Samples"; } else { suggestion_cell_line = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : cell_line_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_cell_line = suggestion_cell_line + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); cell_line_confidence = confidence_percent + "%"; for (Iterator<String> it = cell_lines_set.iterator(); it.hasNext();) { String cellLine = it.next(); if (cellLine.equals(maxEntry.getKey())) { //do nothing } else { suggestion_cell_line = suggestion_cell_line + ", " + cellLine + "(" + cell_line_stat_map.get(cellLine).toString() + ")"; } } } } else { suggestion_cell_line = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has organism part"> if (count_organism_part > 0) { if (Integer.parseInt(studyNumsample) == count_organism_part) { //good. all samples are from cell lines suggestion_organism_part = "Yes:"; String organism_part_value = organism_part_set.iterator().next(); suggestion_organism_part = suggestion_organism_part + organism_part_value; organism_part_confidence = "100%. All " + organism_part_stat_map.get(organism_part_value).toString() + " Samples"; } else { suggestion_organism_part = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : organism_part_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_organism_part = suggestion_organism_part + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); organism_part_confidence = confidence_percent + "%"; for (Iterator<String> it = organism_part_set.iterator(); it.hasNext();) { String organismPart = it.next(); if (organismPart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_organism_part = suggestion_organism_part + ", " + organismPart + "(" + organism_part_stat_map.get(organismPart).toString() + ")"; } } } } else { suggestion_organism_part = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has disease"> if (count_disease > 0) { if (Integer.parseInt(studyNumsample) == count_disease) { //good. all samples are from cell lines suggestion_disease = "Yes:"; String disease_value = disease_set.iterator().next(); suggestion_disease = suggestion_disease + disease_value; disease_confidence = "100%. All " + disease_stat_map.get(disease_value).toString() + " Samples"; } else { suggestion_disease = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : disease_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_disease = suggestion_disease + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); disease_confidence = confidence_percent + "%"; for (Iterator<String> it = disease_set.iterator(); it.hasNext();) { String diseasePart = it.next(); if (diseasePart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_disease = suggestion_disease + ", " + diseasePart + "(" + disease_stat_map.get(diseasePart).toString() + ")"; } } } } else { suggestion_disease = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="if else biosmaple attr has tissue"> if (count_tissue > 0) { if (Integer.parseInt(studyNumsample) == count_tissue) { //good. all samples are from cell lines suggestion_tissue = "Yes:"; String tissue_value = tissue_set.iterator().next(); suggestion_tissue = suggestion_tissue + tissue_value; tissue_confidence = "100%. All " + tissue_stat_map.get(tissue_value).toString() + " Samples"; } else { suggestion_tissue = "Yes:"; Map.Entry<String, Integer> maxEntry = null; for (Map.Entry<String, Integer> entry : tissue_stat_map.entrySet()) { if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) { maxEntry = entry; } } suggestion_tissue = suggestion_tissue + maxEntry.getKey() + "(" + maxEntry.getValue().toString() + " samples)"; int confidence_percent = (int) (maxEntry.getValue() * 100.0f) / (Integer.parseInt(studyNumsample)); tissue_confidence = confidence_percent + "%"; for (Iterator<String> it = tissue_set.iterator(); it.hasNext();) { String tissuePart = it.next(); if (tissuePart.equals(maxEntry.getKey())) { //do nothing } else { suggestion_tissue = suggestion_tissue + ", " + tissuePart + "(" + tissue_stat_map.get(tissuePart).toString() + ")"; } } } } else { suggestion_tissue = " No"; } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="filling right top manual annotation"> //<editor-fold defaultstate="collapsed" desc="disease layout (Manual Annotation"> HorizontalLayout diseaseLayout = new HorizontalLayout(); CheckBox checkboxDiseaseYes = new CheckBox("Yes"); CheckBox checkboxDiseaseNo = new CheckBox("No"); String disease_from_biosample_attribute = ""; if (suggestion_disease.startsWith("Yes")) { disease_from_biosample_attribute = "From Biosample: " + suggestion_disease; } String disease_found = ""; String disease_text_parsed_confidence = ""; for (String disease : list_of_diseases) { if (StringUtils.containsIgnoreCase(studyName, disease) || StringUtils.containsIgnoreCase(studyTitle, disease)) { checkboxDiseaseYes.setValue(true); disease_found = disease_found + disease + " "; disease_text_parsed_confidence = "keyword found in Study or Title"; } } String diseaseLabelString = ""; if (disease_text_parsed_confidence.length() > 1) { diseaseLabelString = "<b><i>Suggestion: </i></b>" + disease_found + " <b> <i> Confidence: <i></b> " + disease_text_parsed_confidence; } if (disease_from_biosample_attribute.length() > 1) { diseaseLabelString = diseaseLabelString + "<b><i>Suggestion: </i></b>" + disease_from_biosample_attribute + " <b> <i> Confidence: <i></b> " + disease_confidence; } Label diseaseLabel = new Label(" " + diseaseLabelString, ContentMode.HTML); Label diseaseTitle = new Label("<b>Disease: </b>", ContentMode.HTML); diseaseLayout.addComponent(diseaseTitle); diseaseLayout.addComponent(checkboxDiseaseNo); diseaseLayout.addComponent(checkboxDiseaseYes); diseaseLayout.addComponent(diseaseLabel); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="study types layout (Manual Annotation)"> Panel studyTypesPanel = new Panel("Sample Types"); HorizontalLayout studyTypesLayout = new HorizontalLayout(); HorizontalLayout caseControlLayout = new HorizontalLayout(); CheckBox checkboxCaseControlYes = new CheckBox("Yes"); CheckBox checkboxCaseControlNo = new CheckBox("No"); // checkboxCaseControlYes.setValue(true); Label caseControlTitle = new Label("<b>Case-Control: </b>", ContentMode.HTML); caseControlLayout.addComponent(caseControlTitle); caseControlLayout.addComponent(checkboxCaseControlYes); caseControlLayout.addComponent(checkboxCaseControlNo); HorizontalLayout timeSeriesLayout = new HorizontalLayout(); CheckBox checkboxTimeSeriesYes = new CheckBox("Yes"); CheckBox checkboxTimeSeriesNo = new CheckBox("No"); //checkboxTimeSeriesYes.setValue(true); Label timeSeriesTitle = new Label("<b>Time Series: </b>", ContentMode.HTML); timeSeriesLayout.addComponent(timeSeriesTitle); timeSeriesLayout.addComponent(checkboxTimeSeriesYes); timeSeriesLayout.addComponent(checkboxTimeSeriesNo); HorizontalLayout treatementLayout = new HorizontalLayout(); CheckBox checkboxTreatmentYes = new CheckBox("Yes"); CheckBox checkboxTreatmentNo = new CheckBox("No"); // checkboxTreatmentYes.setValue(true); Label treatmentTitle = new Label("<b>Treatment: </b>", ContentMode.HTML); treatementLayout.addComponent(treatmentTitle); treatementLayout.addComponent(checkboxTreatmentYes); treatementLayout.addComponent(checkboxTreatmentNo); studyTypesLayout.addComponent(caseControlLayout); Label emptyLabel = new Label(" ", ContentMode.HTML); studyTypesLayout.addComponent(emptyLabel); studyTypesLayout.addComponent(timeSeriesLayout); Label emptyLabel0 = new Label(" ", ContentMode.HTML); studyTypesLayout.addComponent(emptyLabel0); studyTypesLayout.addComponent(treatementLayout); studyTypesLayout.setSizeFull(); studyTypesPanel.setContent(studyTypesLayout); studyTypesPanel.setWidth(Sizeable.SIZE_UNDEFINED, Unit.PERCENTAGE); studyTypesPanel.addStyleName("panelborder"); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Disease Category Layout"> Panel diseaseCategoryPanel = new Panel("Disease Category"); HorizontalLayout diseaseCategoriesLayout = new HorizontalLayout(); //Complex Disease ListSelect complexDisease = new ListSelect("Complex Disease"); complexDisease.setMultiSelect(true); for (String disease : complexDiseaseArray) { complexDisease.addItem(disease); } diseaseCategoriesLayout.addComponent(complexDisease); Label emptyLabel2 = new Label(" ", ContentMode.HTML); diseaseCategoriesLayout.addComponent(emptyLabel2); // Rare disease ListSelect rareDisease = new ListSelect("Rare Diseases"); rareDisease.setMultiSelect(true); for (String disease : rareDiseaseArray) { rareDisease.addItem(disease); } diseaseCategoriesLayout.addComponent(rareDisease); Label emptyLabel3 = new Label(" ", ContentMode.HTML); diseaseCategoriesLayout.addComponent(emptyLabel3); // Other diseases ListSelect otherDisease = new ListSelect("Other Diseases"); otherDisease.setMultiSelect(true); for (String disease : otherDiseaseArray) { otherDisease.addItem(disease); } diseaseCategoriesLayout.addComponent(otherDisease); // Label emptyLabel4 = new Label(" ", ContentMode.HTML); // diseaseCategoriesLayout.addComponent(emptyLabel4); diseaseCategoryPanel.setContent(diseaseCategoriesLayout); diseaseCategoryPanel.setWidth(Sizeable.SIZE_UNDEFINED, Unit.PERCENTAGE); diseaseCategoryPanel.addStyleName("panelborder"); /* HorizontalLayout diseaseCategoriesLayout = new HorizontalLayout(); Label diseaseCategoryLabel = new Label("<b><i>Suggestion: </i></b>" + disease_found + " <b> <i> Confidence: <i></b> " + disease_confidence, ContentMode.HTML); String[] diseaseCategories = new String[]{"Complex Disease", "Rare Disease", "Other", "Not Sure"}; List<String> diseaseCategoriesList = Arrays.asList(diseaseCategories); ComboBox diseaseCategoryComboBox = new ComboBox("Disease Category", diseaseCategoriesList); diseaseCategoriesLayout.addComponent(diseaseCategoryComboBox); diseaseCategoriesLayout.addComponent(diseaseCategoryLabel); */ //</editor-fold> //<editor-fold defaultstate="collapsed" desc="platform layout (manual annotation)"> // List<String> platformsList = Arrays.asList(platforms); // ComboBox platformsListSelect = new ComboBox("Sequencing Platform", platformsList); ListSelect platformsListSelect = new ListSelect("Sequencing Platform"); platformsListSelect.setMultiSelect(true); for (String platform : platforms) { platformsListSelect.addItem(platform); } Set<String> matchedPlatformSet = new HashSet(); String platform_from_sra = ""; String platorm_confidence = ""; int matchPlatformCount = 0; for (String[] val : platformMap.values()) { if (val.length > 1) { for (String pf : platforms) { if (val[0].equalsIgnoreCase(pf)) { matchedPlatformSet.add(pf); matchPlatformCount = matchPlatformCount + 1; } } } else { } } if (matchedPlatformSet.isEmpty()) { platform_from_sra = "Match Not Found"; } else { if (matchedPlatformSet.size() == matchPlatformCount) { if (matchedPlatformSet.size() == 1) { platform_from_sra = matchedPlatformSet.iterator().next().toString(); for (Iterator i = platformsListSelect.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (platform_from_sra.equalsIgnoreCase(temp)) { platformsListSelect.select(iid); } } } else { platform_from_sra = "Can't predict. All experiment on different Platforms"; } } else { if (matchedPlatformSet.size() == 1) { // Perfect platform_from_sra = matchedPlatformSet.iterator().next().toString(); for (Iterator i = platformsListSelect.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (platform_from_sra.equalsIgnoreCase(temp)) { platformsListSelect.select(iid); } } platorm_confidence = "100%"; } else { } } } HorizontalLayout platformLayout = new HorizontalLayout(); Label suggestedPlatformLabel = new Label("<b><i>Suggestion: </i></b>" + platform_from_sra + "<b> <i> Confidence: <i></b> " + platorm_confidence, ContentMode.HTML); platformsListSelect.setHeight(platformsListSelect.size() + 2, Unit.EM); platformLayout.addComponent(platformsListSelect); platformLayout.addComponent(suggestedPlatformLabel); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Sample types Panel (Manual Annotation)"> Panel sampleTypesPanel = new Panel("Sample Types"); VerticalLayout sampleTypesLayout = new VerticalLayout(); CheckBox checkboxSampleTypeCellLine = new CheckBox("Cell Line"); CheckBox checkboxSampleTypeTissue = new CheckBox("Tissue"); CheckBox checkboxSampleTypePrimaryCells = new CheckBox("Primary Cells"); CheckBox checkboxSampleTypeWholeBlood = new CheckBox("Blood"); CheckBox checkboxSampleTypePlasma = new CheckBox("Plasma"); String suggestedCellTypeLabelString = ""; if (suggestion_cell_line.startsWith("Yes")) { //sampleTypesListComboBox.select("Cell Lines"); checkboxSampleTypeCellLine.setValue(true); suggestedCellTypeLabelString = "<b><i> Suggestion: </i></b>" + "Cell Lines --> " + suggestion_cell_line + " <b> <i> Confidence: <i></b> " + cell_line_confidence; } Label suggestedCellLineLabel = new Label(suggestedCellTypeLabelString, ContentMode.HTML); String suggestedTissueLabelString = ""; if (suggestion_organism_part.startsWith("Yes")) { checkboxSampleTypeTissue.setValue(true); suggestedTissueLabelString = suggestedTissueLabelString + "<b><i> Suggestion: </i></b>" + "Organism part --> " + suggestion_organism_part + " <b> <i> Confidence: <i></b> " + organism_part_confidence; } if (suggestion_tissue.startsWith("Yes")) { checkboxSampleTypeTissue.setValue(true); suggestedTissueLabelString = suggestedTissueLabelString + "<b><i> Suggestion: </i></b>" + "Tissue --> " + suggestion_tissue + " <b> <i> Confidence: <i></b> " + tissue_confidence; } Label suggestedTissueLabel = new Label(suggestedTissueLabelString, ContentMode.HTML); String suggestedStemCellString = ""; /* if (suggestion_stem_cell.startsWith("Yes")) { checkboxSampleTypeStemCells.setValue(true); suggestedCellTypeLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_stem_cell + " <b> <i> Confidence: <i></b> " + stem_cell_confidence; } */ Label suggestedStemCellLabel = new Label(suggestedStemCellString, ContentMode.HTML); String suggestedWholeBloodLabelString = ""; /* if (suggestion_whole_blood.startsWith("Yes")) { checkboxSampleTypeWholeBlood.setValue(true); suggestedWholeBloodLabelString = "<b><i>Suggestion: </i></b>" + "Whole Blood --> " + suggestion_whole_blood + " <b> <i> Confidence: <i></b> " + whole_blood_confidence; } */ Label suggestedWholeBloodLabel = new Label(suggestedWholeBloodLabelString, ContentMode.HTML); String suggestedPlasmaLabelString = ""; /* if (suggestion_plasma.startsWith("Yes")) { checkboxSampleTypePlasma.setValue(true); suggestedPlasmaLabelString = "<b><i>Suggestion: </i></b>" + "Cell Lines --> " + suggestion_plasma + " <b> <i> Confidence: <i></b> " + plasma_confidence; } */ Label suggestedPlasmaLabel = new Label(suggestedPlasmaLabelString, ContentMode.HTML); HorizontalLayout CellLineLayout = new HorizontalLayout(); CellLineLayout.addComponent(checkboxSampleTypeCellLine); CellLineLayout.addComponent(suggestedCellLineLabel); HorizontalLayout PrimaryCellsLayout = new HorizontalLayout(); PrimaryCellsLayout.addComponent(checkboxSampleTypePrimaryCells); // PrimaryCellsLayout.addComponent(suggestedPrimaryCellsLabel); HorizontalLayout TissueLayout = new HorizontalLayout(); TissueLayout.addComponent(checkboxSampleTypeTissue); TissueLayout.addComponent(suggestedTissueLabel); HorizontalLayout WholeBloodLayout = new HorizontalLayout(); WholeBloodLayout.addComponent(checkboxSampleTypeWholeBlood); WholeBloodLayout.addComponent(suggestedWholeBloodLabel); HorizontalLayout PlasmaLayout = new HorizontalLayout(); PlasmaLayout.addComponent(checkboxSampleTypePlasma); PlasmaLayout.addComponent(suggestedPlasmaLabel); sampleTypesLayout.addComponent(CellLineLayout); sampleTypesLayout.addComponent(PrimaryCellsLayout); sampleTypesLayout.addComponent(TissueLayout); sampleTypesLayout.addComponent(WholeBloodLayout); sampleTypesLayout.addComponent(PlasmaLayout); sampleTypesPanel.setContent(sampleTypesLayout); sampleTypesPanel.setWidth(Sizeable.SIZE_UNDEFINED, Unit.PERCENTAGE); sampleTypesPanel.addStyleName("panelborder"); //</editor-fold> Button addCustomAnnoButton = new Button("++ Custom Annotation"); addCustomAnnoButton.addClickListener(new Button.ClickListener() { public void buttonClick(ClickEvent event) { custom_annotation_counter = custom_annotation_counter + 1; HorizontalLayout customLayout = new HorizontalLayout(); TextField customAnnoName = new TextField("Custom Name"); customAnnoName.setId("customAnnoName" + custom_annotation_counter); TextField customAnnoValue = new TextField("Custom Value"); customLayout.addComponent(customAnnoName); customLayout.addComponent(customAnnoValue); customAnnoValue.setId("customAnnoValue" + custom_annotation_counter); int addCustomAnnoButtonIndex = rightTopAnnotationForm .getComponentIndex(addCustomAnnoButton); rightTopAnnotationForm.addComponent(customLayout, addCustomAnnoButtonIndex); } }); //<editor-fold defaultstate="collapsed" desc="Replicate Type"> HorizontalLayout replicatTypesLayout = new HorizontalLayout(); String replicateType_from_sra = ""; String replicateType_confidence = ""; Label suggestedreplicatTypeLabel = new Label("<b><i>Suggestion: </i></b>" + replicateType_from_sra + " <b> <i> Confidence: <i></b> " + replicateType_confidence, ContentMode.HTML); String[] replicatTypes = new String[] { "Biological -- different individuals", "Biological -- same individual but severe treatment to RNA", "Semi Biological/Technical -- mild treatment", "Technical -- machine parameter or buffer (very mild)" }; List<String> replicatTypesList = Arrays.asList(replicatTypes); ComboBox replicatTypesListComboBox = new ComboBox("Replicates Type ", replicatTypesList); replicatTypesLayout.addComponent(replicatTypesListComboBox); replicatTypesLayout.addComponent(suggestedreplicatTypeLabel); //</editor-fold> checkboxCaseControlYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxCaseControlYes.getValue()) { checkboxCaseControlNo.setValue(!checkboxCaseControlYes.getValue()); } } }); checkboxCaseControlNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxCaseControlNo.getValue()) { checkboxCaseControlYes.setValue(!checkboxCaseControlNo.getValue()); } } }); checkboxTimeSeriesYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxTimeSeriesYes.getValue()) { checkboxTimeSeriesNo.setValue(!checkboxTimeSeriesYes.getValue()); } } }); checkboxTimeSeriesNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxTimeSeriesNo.getValue()) { checkboxTimeSeriesYes.setValue(!checkboxTimeSeriesNo.getValue()); } } }); checkboxTreatmentYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxTreatmentYes.getValue()) { checkboxTreatmentNo.setValue(!checkboxTreatmentYes.getValue()); } } }); checkboxTreatmentNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxTreatmentNo.getValue()) { checkboxTreatmentYes.setValue(!checkboxTreatmentNo.getValue()); } } }); checkboxDiseaseYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxDiseaseNo.setValue(!checkboxDiseaseYes.getValue()); diseaseCategoryPanel.setVisible(true); } }); checkboxDiseaseNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxDiseaseYes.setValue(!checkboxDiseaseNo.getValue()); diseaseCategoryPanel.setVisible(false); } }); //<editor-fold defaultstate="collapsed" desc="Annotation Status Ongoing or Completed "> Panel annotationStatusPanel = new Panel("Annotation Status"); CheckBox checkboxAnnotaionCompleted = new CheckBox("Annotaion Completed"); CheckBox checkboxAnnotaionOngoing = new CheckBox("Annotaion Ongoing"); checkboxAnnotaionOngoing.setValue(true); checkboxAnnotaionCompleted.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxAnnotaionOngoing.setValue(!checkboxAnnotaionCompleted.getValue()); } }); checkboxAnnotaionOngoing.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { checkboxAnnotaionCompleted.setValue(!checkboxAnnotaionOngoing.getValue()); } }); HorizontalLayout annotationStatusLayout = new HorizontalLayout(); annotationStatusLayout.addComponent(checkboxAnnotaionOngoing); Label emptyLabel_1 = new Label(" ", ContentMode.HTML); annotationStatusLayout.addComponent(emptyLabel_1); annotationStatusLayout.addComponent(checkboxAnnotaionCompleted); annotationStatusPanel.setContent(annotationStatusLayout); annotationStatusPanel.setWidth(Sizeable.SIZE_UNDEFINED, Unit.PERCENTAGE); annotationStatusPanel.addStyleName("panelborder"); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="login, sign in, register, and suggestion by manual annotation if logged "> Button loginButton = new Button("Sign In"); Button registerButton = new Button("Register"); HorizontalLayout requestLoginLayout = new HorizontalLayout(); requestLoginLayout.addComponent(userWelcome); requestLoginLayout.addComponent(loginButton); requestLoginLayout.addComponent(registerButton); rightTopAnnotationForm.addComponent(requestLoginLayout); VerticalLayout userPasswordLayout = new VerticalLayout(); VerticalLayout registerLayout = new VerticalLayout(); loginButton.addClickListener(new Button.ClickListener() { @Override public void buttonClick(ClickEvent event) { if (event.getButton() == loginButton) { if (loginButton.getCaption() == "Sign In") { // Create the user input field user = new TextField("User:"); user.setWidth("300px"); user.setRequired(true); user.setInputPrompt("Your username (eg. joe@email.com)"); user.addValidator(new EmailValidator("Username must be an email address")); user.setInvalidAllowed(false); // Create the password input field password = new PasswordField("Password:"); password.setWidth("300px"); password.addValidator(new PasswordValidator()); password.setRequired(true); password.setValue(""); password.setNullRepresentation(""); // Create login button loginSubmitButton = new Button("Login", this); loginSubmitButton.addClickListener(new Button.ClickListener() { @Override public void buttonClick(ClickEvent event) { if (event.getButton() == loginSubmitButton) { if (!user.isValid() || !password.isValid()) { return; } String username = user.getValue(); String entered_password = password.getValue(); boolean isChecked = false; try { // check user details in the database SQLContainer checkContainer = createMySQLContainer( "annotation_users", "dummy"); Item id = checkContainer .getItem(new RowId(new Object[] { username })); if (id != null) { user.setCaption("User"); if (entered_password.equals( id.getItemProperty("password").getValue().toString())) { isChecked = true; } else { password.setCaption("Password (wrong password entered)"); System.out.println( "Password can not be validated. Please re-enter or Register"); System.out.println( "Fetched password for user : " + id.toString() + " is " + id.getItemProperty("password") .getValue().toString()); } } else { user.setCaption( "User (wrong username entered. Enter your email again or register)"); password.setCaption("Password"); System.out.println( "User name can not be validated. Please re-enter or Register"); } } catch (Exception e) { isChecked = false; System.out.println( "Problem in validating login details using database. Either user or password is wrong"); } boolean isValid = username.equals("test@test.com") && entered_password.equals("passw0rd"); if (isChecked) { // System.out.println("User name and passoword : Both are correct"); // Store the current user in the service session getSession().setAttribute("user", username); userWelcome.setValue("Hello " + username); int userPasswordLayoutIndex = rightTopAnnotationForm .getComponentIndex(userPasswordLayout); requestLoginLayout.removeComponent(registerButton); rightTopAnnotationForm.addComponent(requestLoginLayout, userPasswordLayoutIndex); rightTopAnnotationForm.removeComponent(userPasswordLayout); userPasswordLayout.removeAllComponents(); loginButton.setCaption("Logout"); } else { // Wrong password clear the password field and refocuses it password.setValue(null); password.focus(); } // throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates. } } }); // Add both to a panel VerticalLayout fields = new VerticalLayout(user, password, loginSubmitButton); fields.setCaption( "Please login to access the application. (test@test.com/passw0rd)"); fields.setSpacing(true); fields.setMargin(new MarginInfo(true, true, true, false)); fields.setSizeUndefined(); // The view root layout userPasswordLayout.addComponent(fields); int addUserLayoutIndex = rightTopAnnotationForm .getComponentIndex(requestLoginLayout); rightTopAnnotationForm.addComponent(userPasswordLayout, addUserLayoutIndex); rightTopAnnotationForm.removeComponent(requestLoginLayout); } else if (loginButton.getCaption() == "Logout") { getSession().setAttribute("user", null); userWelcome.setValue("Anonymous "); loginButton.setCaption("Sign In"); requestLoginLayout.addComponent(registerButton); } } } }); registerButton.addClickListener(new Button.ClickListener() { @Override public void buttonClick(ClickEvent event) { if (event.getButton() == registerButton) { // Create the user input field TextField newUser = new TextField("User:"); newUser.setWidth("300px"); newUser.setRequired(true); newUser.setInputPrompt("Your username (eg. joe@email.com)"); newUser.addValidator(new EmailValidator("Username must be an email address")); newUser.setInvalidAllowed(false); // Create the password input field PasswordField setPassword = new PasswordField("Set Password:"); setPassword.setWidth("300px"); setPassword.addValidator(new PasswordValidator()); setPassword.setRequired(true); setPassword.setValue(""); setPassword.setNullRepresentation(""); // Create login button Button registerSubmitButton = new Button("Register me", this); registerSubmitButton.addClickListener(new Button.ClickListener() { @Override public void buttonClick(ClickEvent event) { if (event.getButton() == registerSubmitButton) { if (!newUser.isValid() || !setPassword.isValid()) { return; } String username = newUser.getValue(); String entered_password = setPassword.getValue(); String insert_user = "'" + username + "' , '" + entered_password + "'"; boolean isInserted = true; try { // Insert new user details in the database SQLContainer insertContainer = createMySQLContainer("annotation_users", insert_user); Object id = insertContainer.addItem(); insertContainer.getContainerProperty(id, "user").setValue(username); insertContainer.getContainerProperty(id, "password") .setValue(entered_password); insertContainer.commit(); } catch (Exception e) { isInserted = false; System.out.println( "Problem in registering new user while inserting into the database"); } if (isInserted) { userWelcome.setValue( "Registered Successfulle. Please Sign in to annotate. "); int registerLayoutIndex = rightTopAnnotationForm .getComponentIndex(registerLayout); rightTopAnnotationForm.addComponent(requestLoginLayout, registerLayoutIndex); rightTopAnnotationForm.removeComponent(registerLayout); registerLayout.removeAllComponents(); requestLoginLayout.removeComponent(registerButton); } else { // Wrong password clear the password field and refocuses it password.setValue(null); password.focus(); } // throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates. } } }); // Add both to a panel VerticalLayout registerFields = new VerticalLayout(newUser, setPassword, registerSubmitButton); registerFields .setCaption("Please login to access the application. (test@test.com/passw0rd)"); registerFields.setSpacing(true); registerFields.setMargin(new MarginInfo(true, true, true, false)); registerFields.setSizeUndefined(); registerLayout.addComponent(registerFields); int requestLoginLayoutIndex = rightTopAnnotationForm .getComponentIndex(requestLoginLayout); rightTopAnnotationForm.addComponent(registerLayout, requestLoginLayoutIndex); rightTopAnnotationForm.removeComponent(requestLoginLayout); } } }); boolean isLoggedIn = getSession().getAttribute("user") != null; if (isLoggedIn) { // System.out.println("user attribute" + String.valueOf(getSession().getAttribute("user"))); String logged_user = String.valueOf(getSession().getAttribute("user")); userWelcome.setValue("Hello " + logged_user); loginButton.setCaption("Logout"); requestLoginLayout.removeComponent(registerButton); try { String search_query = " SELECT * FROM manual_annotation " + "where annotator = '" + logged_user + "'" + " AND studyid = '" + selectedStudy + "'"; rnaseqContainer = createMySQLContainer("suggestion_by_manual_annotation", search_query); //rnaseqContainer.removeAllContainerFilters(); Item lastItem = rnaseqContainer.getItem(rnaseqContainer.lastItemId()); System.out.println("Item is " + lastItem); // String annotated_disease_category = lastItem.getItemProperty("disease_category").getValue().toString(); String isDisease = "1"; if (!(lastItem.getItemProperty("isDisease").getValue() == null)) { isDisease = lastItem.getItemProperty("isDisease").getValue().toString(); // System.out.println("disease is not null" + isDisease); if (isDisease.equals("1")) { checkboxDiseaseYes.setValue(true); } else if (isDisease.equals("0")) { checkboxDiseaseNo.setValue(true); } } else { checkboxDiseaseYes.setValue(true); // System.out.println("disease is null"); } if (!(lastItem.getItemProperty("isCaseControl").getValue() == null)) { if (lastItem.getItemProperty("isCaseControl").getValue().toString().equals("1")) { checkboxCaseControlYes.setValue(true); } else if (lastItem.getItemProperty("isCaseControl").getValue().toString() .equals("0")) { checkboxCaseControlNo.setValue(true); } } if (!(lastItem.getItemProperty("isTimeSeries").getValue() == null)) { if (lastItem.getItemProperty("isTimeSeries").getValue().toString().equals("1")) { checkboxTimeSeriesYes.setValue(true); } else if (lastItem.getItemProperty("isTimeSeries").getValue().toString().equals("0")) { checkboxTimeSeriesNo.setValue(true); } } if (!(lastItem.getItemProperty("isTreatment").getValue() == null)) { if (lastItem.getItemProperty("isTreatment").getValue().toString().equals("1")) { checkboxTreatmentYes.setValue(true); } else if (lastItem.getItemProperty("isTreatment").getValue().toString().equals("0")) { checkboxTreatmentNo.setValue(true); } } if (!(lastItem.getItemProperty("isCellLine").getValue() == null)) { if (lastItem.getItemProperty("isCellLine").getValue().toString().equals("1")) { checkboxSampleTypeCellLine.setValue(true); } else if (lastItem.getItemProperty("isCellLine").getValue().toString().equals("0")) { checkboxSampleTypeCellLine.setValue(false); } } if (!(lastItem.getItemProperty("isPrimaryCells").getValue() == null)) { if (lastItem.getItemProperty("isPrimaryCells").getValue().toString().equals("1")) { checkboxSampleTypePrimaryCells.setValue(true); } else if (lastItem.getItemProperty("isPrimaryCells").getValue().toString() .equals("0")) { checkboxSampleTypePrimaryCells.setValue(false); } } if (!(lastItem.getItemProperty("isTissue").getValue() == null)) { if (lastItem.getItemProperty("isTissue").getValue().toString().equals("1")) { checkboxSampleTypeTissue.setValue(true); } else if (lastItem.getItemProperty("isTissue").getValue().toString().equals("0")) { checkboxSampleTypeTissue.setValue(false); } } if (!(lastItem.getItemProperty("isWholeBlood").getValue() == null)) { if (lastItem.getItemProperty("isWholeBlood").getValue().toString().equals("1")) { checkboxSampleTypeWholeBlood.setValue(true); } else if (lastItem.getItemProperty("isWholeBlood").getValue().toString().equals("0")) { checkboxSampleTypeWholeBlood.setValue(false); } } if (!(lastItem.getItemProperty("isPlasma").getValue() == null)) { if (lastItem.getItemProperty("isPlasma").getValue().toString().equals("1")) { checkboxSampleTypePlasma.setValue(true); } else if (lastItem.getItemProperty("isPlasma").getValue().toString().equals("0")) { checkboxSampleTypePlasma.setValue(false); } } if (!(lastItem.getItemProperty("sequencing_platform").getValue() == null)) { String sequencing_platform = lastItem.getItemProperty("sequencing_platform").getValue() .toString(); String[] annotated_platforms = sequencing_platform.split("\\;"); for (Iterator i = platformsListSelect.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (annotated_platforms.length > 0) { for (String pf : annotated_platforms) { if (pf.equalsIgnoreCase(temp)) { platformsListSelect.select(iid); } } } } } if (!(lastItem.getItemProperty("replicate_type").getValue() == null)) { String replicate_type = lastItem.getItemProperty("replicate_type").getValue() .toString(); for (Iterator i = replicatTypesListComboBox.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (replicate_type.equalsIgnoreCase(temp)) { replicatTypesListComboBox.select(iid); } } } if (!(lastItem.getItemProperty("annotation_status").getValue() == null)) { if (lastItem.getItemProperty("annotation_status").getValue().toString() .equals("ongoing")) { checkboxAnnotaionOngoing.setValue(true); } else if (lastItem.getItemProperty("annotation_status").getValue().toString() .equals("completed")) { checkboxAnnotaionCompleted.setValue(true); } } String annotated_disease_category = lastItem.getItemProperty("disease_category").getValue() .toString(); String[] annotated_disease_categories = annotated_disease_category.split("\\;"); String main_disease = ""; for (Iterator i = complexDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String selected_disease_category = ""; String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "complex_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + "," + "complex_disease|" + main_disease + "|" + temp; } } else { if (selected_disease_category.isEmpty()) { selected_disease_category = "complex_disease|" + main_disease + "|" + "-- Any"; } else { selected_disease_category = selected_disease_category + "," + "complex_disease|" + main_disease + "|" + "-- Any"; } } if (annotated_disease_categories.length > 0) { for (String cat : annotated_disease_categories) { // System.out.println(cat + selected_disease_category); if (cat.equals(selected_disease_category)) { complexDisease.select(iid); } } } } main_disease = ""; for (Iterator i = rareDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String selected_disease_category = ""; String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "rare_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + "," + "rare_disease|" + main_disease + "|" + temp; } } else { if (selected_disease_category.isEmpty()) { selected_disease_category = "rare_disease|" + main_disease + "|" + "-- Any"; } else { selected_disease_category = selected_disease_category + "," + "rare_disease|" + main_disease + "|" + "-- Any"; } } if (annotated_disease_categories.length > 0) { for (String cat : annotated_disease_categories) { // System.out.println(cat + selected_disease_category); if (cat.equals(selected_disease_category)) { rareDisease.select(iid); } } } } main_disease = ""; for (Iterator i = otherDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String selected_disease_category = ""; String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "other_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + "," + "other_disease|" + main_disease + "|" + temp; } } else { if (selected_disease_category.isEmpty()) { selected_disease_category = "other_disease|" + main_disease + "|" + "-- Any"; } else { selected_disease_category = selected_disease_category + "," + "other_disease|" + main_disease + "|" + "-- Any"; } } if (annotated_disease_categories.length > 0) { for (String cat : annotated_disease_categories) { // System.out.println(cat + selected_disease_category); if (cat.equals(selected_disease_category)) { otherDisease.select(iid); } } } } } catch (Exception e) { } } //</editor-fold> Button submitButton = new Button("Submit"); submit_manual_count = 0; Label manualSubmitStatus = new Label(""); submitButton.addClickListener(new Button.ClickListener() { public void buttonClick(ClickEvent event) { if (event.getButton() == submitButton) { submit_manual_count = submit_manual_count + 1; int isDisease = 0; if (checkboxDiseaseYes.getValue() && !checkboxDiseaseNo.getValue()) { isDisease = 1; } String selected_disease_category = ""; String main_disease = ""; for (Iterator i = complexDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (complexDisease.isSelected(iid)) { // System.out.println("Selected" + temp); if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "complex_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + ";" + "complex_disease|" + main_disease + "|" + temp; } } else { //main disease is selected // selected_disease_main = main_disease; if (selected_disease_category.isEmpty()) { selected_disease_category = "complex_disease|" + main_disease + "|" + "Any"; } else { selected_disease_category = selected_disease_category + ";" + "complex_disease|" + main_disease + "|" + "Any"; } } } } main_disease = ""; for (Iterator i = rareDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (rareDisease.isSelected(iid)) { // System.out.println("Selected" + temp); if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "rare_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + ";" + "rare_disease|" + main_disease + "|" + temp; } } else { //main disease is selected // selected_disease_main = main_disease; if (selected_disease_category.isEmpty()) { selected_disease_category = "rare_disease|" + main_disease + "|" + "Any"; } else { selected_disease_category = selected_disease_category + ";" + "rare_disease|" + main_disease + "|" + "Any"; } } } } main_disease = ""; for (Iterator i = otherDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (otherDisease.isSelected(iid)) { // System.out.println("Selected" + temp); if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "other_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + ";" + "other_disease|" + main_disease + "|" + temp; } } else { if (selected_disease_category.isEmpty()) { selected_disease_category = "other_disease|" + main_disease + "|" + "Any"; } else { selected_disease_category = selected_disease_category + ";" + "other_disease|" + main_disease + "|" + "Any"; } } } } int isCaseControl = 0; if (checkboxCaseControlYes.getValue() && !checkboxCaseControlNo.getValue()) { isCaseControl = 1; } int isTimeSeries = 0; if (checkboxTimeSeriesYes.getValue() && !checkboxTimeSeriesNo.getValue()) { isTimeSeries = 1; } int isTreatment = 0; if (checkboxTreatmentYes.getValue() && !checkboxTreatmentNo.getValue()) { isTreatment = 1; } int isTissue = 0; if (checkboxSampleTypeTissue.getValue()) { isTissue = 1; } int isCellLine = 0; if (checkboxSampleTypeCellLine.getValue()) { isCellLine = 1; } int isPrimaryCells = 0; if (checkboxSampleTypePrimaryCells.getValue()) { isPrimaryCells = 1; } int isWholeBlood = 0; if (checkboxSampleTypeWholeBlood.getValue()) { isWholeBlood = 1; } int isPlasma = 0; if (checkboxSampleTypePlasma.getValue()) { isPlasma = 1; } String selected_sequencing_platforms = ""; for (Iterator i = platformsListSelect.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (platformsListSelect.isSelected(iid)) { if (selected_sequencing_platforms.isEmpty()) { selected_sequencing_platforms = temp; } else { selected_sequencing_platforms = selected_sequencing_platforms + ";" + temp; } } } String annotation_status = "ongoing"; if (checkboxAnnotaionCompleted.getValue() && !checkboxAnnotaionOngoing.getValue()) { annotation_status = "completed"; } String custom_annotation_value = ""; for (int j = 1; j <= custom_annotation_counter; j++) { if (findById(rightTopAnnotationForm, "customAnnoName" + j) instanceof TextField) { TextField tempTFname = (TextField) findById(rightTopAnnotationForm, "customAnnoName" + j); custom_annotation_value = custom_annotation_value + tempTFname.getValue() + ":::"; // System.out.println(j + "custom name: " + tempTFname.getValue()); } if (findById(rightTopAnnotationForm, "customAnnoValue" + j) instanceof TextField) { TextField tempTFvalue = (TextField) findById(rightTopAnnotationForm, "customAnnoValue" + j); custom_annotation_value = custom_annotation_value + tempTFvalue.getValue() + "###"; // System.out.println(j + "custom value: " + tempTFvalue.getValue()); } } String annotator = "Anonymous"; boolean isLoggedIn = getSession().getAttribute("user") != null; if (isLoggedIn) { annotator = String.valueOf(getSession().getAttribute("user")); // System.out.println("annotator is " + annotator); } Boolean isInserted = true; try { // Insert new user details in the database SQLContainer insertContainer = createMySQLContainer("manual_annotation", "dummy"); Object id = insertContainer.addItem(); insertContainer.getContainerProperty(id, "studyId").setValue(selectedStudy); insertContainer.getContainerProperty(id, "isDisease").setValue(isDisease); insertContainer.getContainerProperty(id, "isTimeSeries").setValue(isTimeSeries); insertContainer.getContainerProperty(id, "isTreatment").setValue(isTreatment); insertContainer.getContainerProperty(id, "isCellLine").setValue(isCellLine); insertContainer.getContainerProperty(id, "isPrimaryCells").setValue(isPrimaryCells); insertContainer.getContainerProperty(id, "isCaseControl").setValue(isCaseControl); insertContainer.getContainerProperty(id, "isTissue").setValue(isTissue); insertContainer.getContainerProperty(id, "disease_category") .setValue(selected_disease_category); insertContainer.getContainerProperty(id, "sequencing_platform") .setValue(selected_sequencing_platforms); insertContainer.getContainerProperty(id, "replicate_type") .setValue(replicatTypesListComboBox.getValue()); insertContainer.getContainerProperty(id, "isWholeBlood").setValue(isWholeBlood); insertContainer.getContainerProperty(id, "isPlasma").setValue(isPlasma); insertContainer.getContainerProperty(id, "custom_annotation") .setValue(custom_annotation_value); insertContainer.getContainerProperty(id, "annotation_status") .setValue(annotation_status); insertContainer.getContainerProperty(id, "annotator").setValue(annotator); insertContainer.commit(); manualSubmitStatus.setCaption("Submitted Manual Annotation Successfully"); SQLContainer dummyStudyContainer = null; if (annotation_status.equalsIgnoreCase("ongoing")) { dummyStudyContainer = createMySQLContainer("study_summary_ongoing", selectedStudy); } else if (annotation_status.equalsIgnoreCase("completed")) { dummyStudyContainer = createMySQLContainer("study_summary_completed", selectedStudy); } // Object studyid = insertStudyContainer.getItem(new RowId(new Object[]{selectedStudy})); // System.out.println("selected study is " + selectedStudy); // System.out.println("selected study id is " + studyid.toString()); // insertStudyContainer.getContainerProperty(studyid, "annotation_status").setValue(annotation_status); // insertStudyContainer.commit(); if (submit_manual_count > 1) { manualSubmitStatus.setCaption("Submitted Manual Annotation Successfully " + submit_manual_count + " times"); } } catch (Exception e) { isInserted = false; manualSubmitStatus.setCaption( "Problem occured during submission of Manual Annotation to the database"); System.out.println("Problem in inserting manual annotation into the database"); // e.printStackTrace(); } } } }); rightTopAnnotationForm.addComponent(diseaseLayout); rightTopAnnotationForm.addComponent(studyTypesPanel); rightTopAnnotationForm.addComponent(diseaseCategoryPanel); rightTopAnnotationForm.addComponent(platformLayout); rightTopAnnotationForm.addComponent(sampleTypesPanel); rightTopAnnotationForm.addComponent(replicatTypesLayout); rightTopAnnotationForm.addComponent(addCustomAnnoButton); rightTopAnnotationForm.addComponent(annotationStatusPanel); rightTopAnnotationForm.addComponent(submitButton); rightTopAnnotationForm.addComponent(manualSubmitStatus); //</editor-fold> //</editor-fold> //<editor-fold defaultstate="collapsed" desc="fill tree in right bottom"> Iterator iterator = biosampleSet.iterator(); // check values int treeBiosampleCount = 0; while (iterator.hasNext()) { treeBiosampleCount = treeBiosampleCount + 1; // System.out.println("Value: "+ iterator.next() + " "); // if(treeBiosampleCount < 500){ String bsample = iterator.next().toString(); String[] biosample_parts = bsample.split("\\|"); String biosample_acc = biosample_parts[0]; tree.addItem(biosample_acc); tree.setParent(biosample_acc, selectedStudy); tree.setItemCaption(biosample_acc, "BioSample: " + biosample_acc); // } } Set expMap_entrset = expMap.entrySet(); Iterator it = expMap_entrset.iterator(); while (it.hasNext()) { Map.Entry me = (Map.Entry) it.next(); String[] expParts = expDetailMap.get(me.getKey()); String expTitle = ""; if (expParts.length > 3) { expTitle = expParts[3]; } tree.addItem(me.getKey()); tree.setParent(me.getKey(), me.getValue()); tree.setItemCaption(me.getKey(), "Experiment: " + me.getKey() + ": " + expTitle); } Set runMap_entrset = runMap.entrySet(); Iterator runit = runMap_entrset.iterator(); while (runit.hasNext()) { Map.Entry runEntry = (Map.Entry) runit.next(); tree.addItem(runEntry.getKey()); tree.setParent(runEntry.getKey(), runEntry.getValue()); tree.setItemCaption(runEntry.getKey(), "Run: " + runEntry.getKey()); } tree.expandItemsRecursively(selectedStudy); //</editor-fold> } }); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Events associated with the Tree (study/Biosample/Experiment/Runs"> tree.setSelectable(true); tree.setImmediate(true); tree.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { Object id = event.getProperty().getValue(); if (id != null) { String selectedTreeId = id.toString(); String selectedTreeItem = tree.getItemCaption(id).toString(); // System.out.println("Tree event is fired: " + selectedTreeItem); if (selectedTreeItem.startsWith("BioSample")) { myform.removeAllComponents(); SQLContainer tempContainer = createMySQLContainer("biosample", selectedTreeId); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { String accessType = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("AccessType").getValue().toString(); String publicationDate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("PublicationDate").getValue().toString(); String lastUpdate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("LastUpdate").getValue().toString(); String accession = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Accession").getValue().toString(); String title = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Title").getValue().toString(); String taxonomy_id = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("TaxonomyId").getValue().toString(); String taxonomy_name = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("TaxonomyName").getValue().toString(); String samplePackage = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Package").getValue().toString(); String status = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Status").getValue().toString(); String statusTime = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("StatusTime").getValue().toString(); String sampleIds = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Ids").getValue().toString(); String attributes = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Attributes").getValue().toString(); String models = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Models").getValue().toString(); String submissionDate = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("SubmissionDate").getValue().toString(); String owner = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Owner").getValue().toString(); String[] myfields = new String[] { accessType, publicationDate, lastUpdate, accession, title, taxonomy_id, taxonomy_name, samplePackage, status, statusTime, sampleIds, attributes, models, submissionDate, owner }; /* for (String fieldName : myfields) { Label tempLabl = new Label(""); } */ Label labelAccessType = new Label("Access Type: " + accessType); myform.addComponent(labelAccessType); Label labelPublicationDate = new Label("Publication Date: " + publicationDate); myform.addComponent(labelPublicationDate); Label labelLastUpdate = new Label("Last Update: " + lastUpdate); myform.addComponent(labelLastUpdate); Label labelAccession = new Label("Accession: " + accession); myform.addComponent(labelAccession); Label labelTitle = new Label("<b>Title: </b>" + title, ContentMode.HTML); myform.addComponent(labelTitle); Label labelTaxonomyId = new Label("Taxonomy Id: " + taxonomy_id); myform.addComponent(labelTaxonomyId); Label labelTaxonomyName = new Label("Taxonomy Name: " + taxonomy_name); myform.addComponent(labelTaxonomyName); Label labelPackage = new Label("Package: " + samplePackage); myform.addComponent(labelPackage); Label labelStatus = new Label("Status: " + status); myform.addComponent(labelStatus); Label labelStatusTime = new Label("Status Time: " + statusTime); myform.addComponent(labelStatusTime); Label labelOwner = new Label("Owner: " + owner); myform.addComponent(labelOwner); String[] id_parts = sampleIds.split("\\:\\-"); if (id_parts.length > 1) { String[] id_dbs = id_parts[0].split("\\|"); String[] id_values = id_parts[1].split("\\|"); for (int j = 0; j < id_dbs.length; j++) { Label tempLabel = new Label(id_dbs[j] + ": " + id_values[j]); myform.addComponent(tempLabel); } } String[] attribute_parts = attributes.split("\\:\\-"); if (attribute_parts.length > 1) { String[] attribute_names = attribute_parts[0].split("\\|"); String[] attribute_values = attribute_parts[1].split("\\|"); for (int j = 0; j < attribute_names.length; j++) { Label tempLabel = new Label( "<b>" + attribute_names[j] + ": </b>" + attribute_values[j], ContentMode.HTML); myform.addComponent(tempLabel); // System.out.println("inside attributes "); } } // TextField field = new TextField(lastDpdate); // myform.addComponent(field); //field.setWidth("100%"); } } if (selectedTreeItem.startsWith("Experiment")) { SQLContainer tempContainer = createMySQLContainer("sra_rnaseq_exp", selectedTreeId); myform.removeAllComponents(); Map expMap = new HashMap(); Map<String, String[]> expDetailMap = new HashMap<>(); Map<String, String[]> libraryDetailMap = new HashMap<>(); Map<String, String[]> platformMap = new HashMap<>(); Map runMap = new HashMap(); HashSet<String> biosampleSet = new HashSet<>(); for (int i = 0; i < tempContainer.getItemIds().size(); i++) { String docid = tempContainer.getIdByIndex(i).toString(); String biosample = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Biosample_Acc_Id_SampleId").getValue().toString(); biosampleSet.add(biosample); String[] b_parts = biosample.split("\\|"); String exp = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Experiment_Acc_Ver_Status_Name").getValue().toString(); String[] exp_parts = exp.split("\\|"); String exp_acc = exp_parts[0]; expMap.put(exp_acc, b_parts[0]); expDetailMap.put(exp_acc, exp_parts); String library_string = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Library_Name_Strategy_Source_Selection_Layout").getValue() .toString(); String[] library_parts = library_string.split("\\|"); String library_name = ""; String library_strategy = ""; String library_source = ""; String library_selection = ""; String library_layout = ""; if (library_parts.length > 0) { library_name = library_parts[0]; } if (library_parts.length > 1) { library_strategy = "<b> <i> Strategy </i> </b>" + library_parts[1]; } if (library_parts.length > 2) { library_source = "<b> <i> Source </i> </b>" + library_parts[2]; } if (library_parts.length > 3) { library_selection = "<b> <i> Selection </i> </b>" + library_parts[3]; } if (library_parts.length > 4) { String tempLayout = library_parts[4]; tempLayout = tempLayout.replaceAll("<", ""); tempLayout = tempLayout.replaceAll("/>", ""); library_layout = "<b> <i> Layout </i> </b>" + tempLayout; } String[] tempStringArray = new String[] { library_strategy, library_source, library_selection, library_layout }; if (library_name.length() > 1) { libraryDetailMap.put(library_name, tempStringArray); } String sra_plaforms = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Platform_InstrumentModel").getValue().toString(); String[] sra_plaforms_parts = sra_plaforms.split("\\|"); platformMap.put(exp_acc, sra_plaforms_parts); String run = tempContainer.getItem(tempContainer.getIdByIndex(i)) .getItemProperty("Runs").getValue().toString(); String[] run_parts = run.split("\\|"); if (run_parts.length > 0) { for (int j = 0; j < run_parts.length; j++) { String temprun = run_parts[j]; String[] temprun_parts = temprun.split("\\,"); runMap.put(temprun_parts[0], exp_acc); } } } // Label labelExperimentAcc = new Label("<b>Experiment Accession: </b>" + selectedTreeId, ContentMode.HTML); // myform.addComponent(labelExperimentAcc); String libraryDetails = "<b>Experiment Accession: </b>" + selectedTreeId + "<br><br>"; for (Map.Entry<String, String[]> entry : libraryDetailMap.entrySet()) { libraryDetails = libraryDetails + "<b>Library Details: </b>" + entry.getKey() + "<br><br>"; String[] temp_library_details = entry.getValue(); for (String dt : temp_library_details) { libraryDetails = libraryDetails + dt + "<br><br>"; } } Label labelLibraryDetails = new Label(libraryDetails, ContentMode.HTML); myform.addComponent(labelLibraryDetails); // myform.setComponentAlignment(labelExperimentAcc, Alignment.TOP_LEFT); myform.setComponentAlignment(labelLibraryDetails, Alignment.TOP_LEFT); } if (selectedTreeItem.startsWith("Run")) { myform.removeAllComponents(); SQLContainer tempContainer = createMySQLContainer("sra_rnaseq_run", selectedTreeId); if (tempContainer.size() > 0) { Item tempItem = tempContainer.getItem(tempContainer.firstItemId()); String runs = tempItem.getItemProperty("Runs").getValue().toString(); String[] runs_parts = runs.split("\\|"); for (String run : runs_parts) { if (run.contains(selectedTreeId)) { String[] run_details = run.split("\\,"); String stringRun = ""; if (run_details.length > 0) { stringRun = stringRun + "<b>Run Accession: </b>" + run_details[0] + "<br><br>"; } if (run_details.length > 1) { stringRun = stringRun + "<b>Number of spots or reads: </b>" + run_details[1] + "<br><br>"; } if (run_details.length > 1) { stringRun = stringRun + "<b>Number of bases: </b>" + run_details[2] + "<br><br>"; } Label labelRunDetails = new Label(stringRun, ContentMode.HTML); myform.addComponent(labelRunDetails); } } } } } else { System.out.println("id is null"); } } }); //</editor-fold> }
From source file:edu.cornell.qatarmed.planrnaseq.BrowseAndAnnotate.java
private void initSearch() { searchField.setInputPrompt("Search Project"); /*/*w ww .j a v a2s. co m*/ //Attempted to do autosuggestion but it require Indexcontainer for attached to vaadin table. Currently vaadin table is // attached to SqlContainer. It's possble to store fetch table data and use it for creating Indexcontainer and then attach it to vaadin table searchField.setTextChangeEventMode(AbstractTextField.TextChangeEventMode.LAZY); searchField.addTextChangeListener(new FieldEvents.TextChangeListener() { public void textChange(final FieldEvents.TextChangeEvent event) { rnaseqContainer.removeAllContainerFilters(); // rnaseqContainer.addContainerFilter(new AnnotateRNAseqSQL.ContactFilter(event // .getText())); } }); */ searchButton.setClickShortcut(KeyCode.ENTER); searchButton.addClickListener(new Button.ClickListener() { public void buttonClick(Button.ClickEvent event) { if (event.getButton() == searchButton) { Component cc = findById(leftLayout, "GuidedSearch"); if (cc != null) { leftLayout.removeComponent(cc); } String search_value = searchField.getValue(); rnaseqContainer = createMySQLContainer("study_filter", search_value); rnaseqContainer.removeAllContainerFilters(); bioprojectSummaryTable.setContainerDataSource(rnaseqContainer); // bioprojectSummaryTable.setVisibleColumns(new String[] { studyName }); bioprojectSummaryTable.setSelectable(true); bioprojectSummaryTable.setImmediate(true); bioprojectSummaryTable.setColumnReorderingAllowed(true); bioprojectSummaryTable.setSortEnabled(true); bioprojectSummaryTable.setVisibleColumns(new Object[] { "Study", "title", "Numsample", "Numexp", "Numrun", "Avgspots", "avgbases", "name" }); } } }); slowSearchButton.addClickListener(new Button.ClickListener() { public void buttonClick(Button.ClickEvent event) { if (event.getButton() == slowSearchButton) { Component cc = findById(leftLayout, "GuidedSearch"); if (cc != null) { leftLayout.removeComponent(cc); } String search_value = searchField.getValue(); rnaseqContainer = createMySQLContainer("study_filter_slow", search_value); rnaseqContainer.removeAllContainerFilters(); bioprojectSummaryTable.setContainerDataSource(rnaseqContainer); // bioprojectSummaryTable.setVisibleColumns(new String[] { studyName }); bioprojectSummaryTable.setSelectable(true); bioprojectSummaryTable.setImmediate(true); bioprojectSummaryTable.setColumnReorderingAllowed(true); bioprojectSummaryTable.setSortEnabled(true); bioprojectSummaryTable.setVisibleColumns(new Object[] { "Study", "title", "Numsample", "Numexp", "Numrun", "Avgspots", "avgbases", "name" }); } } }); guidedSearchButton.addClickListener(new Button.ClickListener() { public void buttonClick(Button.ClickEvent event) { if (event.getButton() == guidedSearchButton) { VerticalLayout guidedSearchLayout = new VerticalLayout(); guidedSearchLayout.setId("GuidedSearch"); //<editor-fold defaultstate="collapsed" desc="Guided search layout"> HorizontalLayout diseaseLayout = new HorizontalLayout(); CheckBox checkboxDiseaseYes = new CheckBox("Yes"); CheckBox checkboxDiseaseNo = new CheckBox("No"); Label diseaseTitle = new Label("<b>Disease: </b>", ContentMode.HTML); diseaseLayout.addComponent(diseaseTitle); diseaseLayout.addComponent(checkboxDiseaseNo); diseaseLayout.addComponent(checkboxDiseaseYes); //<editor-fold defaultstate="collapsed" desc="Study types panel (guided search)"> Panel studyTypesPanel = new Panel("Sample Types"); HorizontalLayout studyTypesLayout = new HorizontalLayout(); HorizontalLayout caseControlLayout = new HorizontalLayout(); CheckBox checkboxCaseControlYes = new CheckBox("Yes"); CheckBox checkboxCaseControlNo = new CheckBox("No"); Label caseControlTitle = new Label("<b>Case-Control: </b>", ContentMode.HTML); caseControlLayout.addComponent(caseControlTitle); caseControlLayout.addComponent(checkboxCaseControlYes); caseControlLayout.addComponent(checkboxCaseControlNo); HorizontalLayout timeSeriesLayout = new HorizontalLayout(); CheckBox checkboxTimeSeriesYes = new CheckBox("Yes"); CheckBox checkboxTimeSeriesNo = new CheckBox("No"); Label timeSeriesTitle = new Label("<b>Time Series: </b>", ContentMode.HTML); timeSeriesLayout.addComponent(timeSeriesTitle); timeSeriesLayout.addComponent(checkboxTimeSeriesYes); timeSeriesLayout.addComponent(checkboxTimeSeriesNo); HorizontalLayout treatementLayout = new HorizontalLayout(); CheckBox checkboxTreatmentYes = new CheckBox("Yes"); CheckBox checkboxTreatmentNo = new CheckBox("No"); // checkboxTreatmentYes.setValue(true); Label treatmentTitle = new Label("<b>Treatment: </b>", ContentMode.HTML); treatementLayout.addComponent(treatmentTitle); treatementLayout.addComponent(checkboxTreatmentYes); treatementLayout.addComponent(checkboxTreatmentNo); studyTypesLayout.addComponent(caseControlLayout); Label emptyLabel = new Label(" ", ContentMode.HTML); studyTypesLayout.addComponent(emptyLabel); studyTypesLayout.addComponent(timeSeriesLayout); Label emptyLabel_2 = new Label(" ", ContentMode.HTML); studyTypesLayout.addComponent(emptyLabel_2); studyTypesLayout.addComponent(treatementLayout); studyTypesLayout.setSizeFull(); studyTypesPanel.setContent(studyTypesLayout); studyTypesPanel.setWidth(Sizeable.SIZE_UNDEFINED, Unit.PERCENTAGE); studyTypesPanel.addStyleName("panelborder"); //</editor-fold>` //<editor-fold defaultstate="collapsed" desc="Disease Category Panel (guided search)"> Panel diseaseCategoryPanel = new Panel("Disease Category"); HorizontalLayout diseaseCategoriesLayout = new HorizontalLayout(); //Complex Disease ListSelect complexDisease = new ListSelect("Complex Disease"); complexDisease.setMultiSelect(true); for (String disease : complexDiseaseArray) { complexDisease.addItem(disease); } diseaseCategoriesLayout.addComponent(complexDisease); Label emptyLabel2 = new Label(" ", ContentMode.HTML); diseaseCategoriesLayout.addComponent(emptyLabel2); // Rare disease ListSelect rareDisease = new ListSelect("Rare Diseases"); rareDisease.setMultiSelect(true); for (String disease : rareDiseaseArray) { rareDisease.addItem(disease); } diseaseCategoriesLayout.addComponent(rareDisease); Label emptyLabel3 = new Label(" ", ContentMode.HTML); diseaseCategoriesLayout.addComponent(emptyLabel3); // Other diseases ListSelect otherDisease = new ListSelect("Other Diseases"); otherDisease.setMultiSelect(true); for (String disease : otherDiseaseArray) { otherDisease.addItem(disease); } diseaseCategoriesLayout.addComponent(otherDisease); // Label emptyLabel4 = new Label(" ", ContentMode.HTML); // diseaseCategoriesLayout.addComponent(emptyLabel4); diseaseCategoryPanel.setContent(diseaseCategoriesLayout); diseaseCategoryPanel.setWidth(Sizeable.SIZE_UNDEFINED, Unit.PERCENTAGE); diseaseCategoryPanel.addStyleName("panelborder"); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Platform (guided search)"> ListSelect platformsListSelect = new ListSelect("Sequencing Platform"); platformsListSelect.setMultiSelect(true); for (String platform : platforms) { platformsListSelect.addItem(platform); } HorizontalLayout platformLayout = new HorizontalLayout(); platformsListSelect.setHeight(platformsListSelect.size() + 2, Unit.EM); platformLayout.addComponent(platformsListSelect); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Sample types panel (guided search)"> Panel sampleTypesPanel = new Panel("Sample Types"); HorizontalLayout sampleTypesLayout = new HorizontalLayout(); CheckBox checkboxSampleTypeCellLine = new CheckBox("Cell Line"); CheckBox checkboxSampleTypeTissue = new CheckBox("Tissue"); CheckBox checkboxSampleTypePrimaryCells = new CheckBox("Primary Cells"); CheckBox checkboxSampleTypeWholeBlood = new CheckBox("Whole Blood"); CheckBox checkboxSampleTypePlasma = new CheckBox("Plasma"); HorizontalLayout CellLineLayout = new HorizontalLayout(); CellLineLayout.addComponent(checkboxSampleTypeCellLine); HorizontalLayout PrimaryCellsLayout = new HorizontalLayout(); PrimaryCellsLayout.addComponent(checkboxSampleTypePrimaryCells); HorizontalLayout TissueLayout = new HorizontalLayout(); TissueLayout.addComponent(checkboxSampleTypeTissue); HorizontalLayout WholeBloodLayout = new HorizontalLayout(); WholeBloodLayout.addComponent(checkboxSampleTypeWholeBlood); HorizontalLayout PlasmaLayout = new HorizontalLayout(); PlasmaLayout.addComponent(checkboxSampleTypePlasma); sampleTypesLayout.addComponent(CellLineLayout); Label emptyLabel8 = new Label(" ", ContentMode.HTML); sampleTypesLayout.addComponent(emptyLabel8); sampleTypesLayout.addComponent(PrimaryCellsLayout); Label emptyLabel5 = new Label(" ", ContentMode.HTML); sampleTypesLayout.addComponent(emptyLabel5); sampleTypesLayout.addComponent(TissueLayout); Label emptyLabel6 = new Label(" ", ContentMode.HTML); sampleTypesLayout.addComponent(emptyLabel6); sampleTypesLayout.addComponent(WholeBloodLayout); Label emptyLabel7 = new Label(" ", ContentMode.HTML); sampleTypesLayout.addComponent(emptyLabel7); sampleTypesLayout.addComponent(PlasmaLayout); sampleTypesPanel.setContent(sampleTypesLayout); sampleTypesPanel.setWidth(Sizeable.SIZE_UNDEFINED, Unit.PERCENTAGE); sampleTypesPanel.addStyleName("panelborder"); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Replicate Type"> HorizontalLayout replicatTypesLayout = new HorizontalLayout(); String replicateType_from_sra = ""; String replicateType_confidence = ""; Label suggestedreplicatTypeLabel = new Label("<b><i>Suggestion: </i></b>" + replicateType_from_sra + " <b> <i> Confidence: <i></b> " + replicateType_confidence, ContentMode.HTML); String[] replicatTypes = new String[] { "Biological -- different individuals", "Biological -- same individual but severe treatment to RNA", "Semi Biological/Technical -- mild treatment", "Technical -- machine parameter or buffer (very mild)" }; List<String> replicatTypesList = Arrays.asList(replicatTypes); ComboBox replicatTypesListComboBox = new ComboBox("Replicates Type ", replicatTypesList); replicatTypesLayout.addComponent(replicatTypesListComboBox); replicatTypesLayout.addComponent(suggestedreplicatTypeLabel); //</editor-fold> checkboxCaseControlYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxCaseControlYes.getValue()) { checkboxCaseControlNo.setValue(!checkboxCaseControlYes.getValue()); } } }); checkboxCaseControlNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxCaseControlNo.getValue()) { checkboxCaseControlYes.setValue(!checkboxCaseControlNo.getValue()); } } }); checkboxTimeSeriesYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxTimeSeriesYes.getValue()) { checkboxTimeSeriesNo.setValue(!checkboxTimeSeriesYes.getValue()); } } }); checkboxTimeSeriesNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxTimeSeriesNo.getValue()) { checkboxTimeSeriesYes.setValue(!checkboxTimeSeriesNo.getValue()); } } }); checkboxTreatmentYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxTreatmentYes.getValue()) { checkboxTreatmentNo.setValue(!checkboxTreatmentYes.getValue()); } } }); checkboxTreatmentNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxTreatmentNo.getValue()) { checkboxTreatmentYes.setValue(!checkboxTreatmentNo.getValue()); } } }); checkboxDiseaseYes.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxDiseaseYes.getValue()) { checkboxDiseaseNo.setValue(!checkboxDiseaseYes.getValue()); diseaseCategoryPanel.setVisible(true); } } }); checkboxDiseaseNo.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxDiseaseNo.getValue()) { checkboxDiseaseYes.setValue(!checkboxDiseaseNo.getValue()); diseaseCategoryPanel.setVisible(false); } } }); //<editor-fold defaultstate="collapsed" desc="CheckBox Annotation Ongoing or Completed "> CheckBox checkboxAnnotaionCompleted = new CheckBox("Annotaion Completed"); CheckBox checkboxAnnotaionOngoing = new CheckBox("Annotaion Ongoing"); // checkboxAnnotaionOngoing.setValue(true); checkboxAnnotaionCompleted.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxAnnotaionCompleted.getValue()) { checkboxAnnotaionOngoing.setValue(!checkboxAnnotaionCompleted.getValue()); } } }); checkboxAnnotaionOngoing.addValueChangeListener(new Property.ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { if (checkboxAnnotaionOngoing.getValue()) { checkboxAnnotaionCompleted.setValue(!checkboxAnnotaionOngoing.getValue()); } } }); //</editor-fold> HorizontalLayout annotationStatusLayout = new HorizontalLayout(); annotationStatusLayout.addComponent(checkboxAnnotaionOngoing); annotationStatusLayout.addComponent(checkboxAnnotaionCompleted); Button guidedSearchSubmitButton = new Button("Search Meeting ALL Criteria"); guidedSearchSubmitButton.addClickListener(new Button.ClickListener() { public void buttonClick(Button.ClickEvent event) { if (event.getButton() == guidedSearchSubmitButton) { String query_part3 = ""; if (checkboxDiseaseYes.getValue() && !checkboxDiseaseNo.getValue()) { query_part3 = query_part3 + " AND ( isDisease = 1) "; } else if (!checkboxDiseaseYes.getValue() && checkboxDiseaseNo.getValue()) { query_part3 = query_part3 + " AND (isDisease = null or isDisease = 0 ) "; } String selected_disease_category = ""; String main_disease = ""; for (Iterator i = complexDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (complexDisease.isSelected(iid)) { // System.out.println("Selected" + temp); if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "complex_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + ";" + "complex_disease|" + main_disease + "|" + temp; } } else { //main disease is selected // selected_disease_main = main_disease; if (selected_disease_category.isEmpty()) { selected_disease_category = "complex_disease|" + main_disease + "|" + "Any"; } else { selected_disease_category = selected_disease_category + ";" + "complex_disease|" + main_disease + "|" + "Any"; } } } } main_disease = ""; for (Iterator i = rareDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (rareDisease.isSelected(iid)) { // System.out.println("Selected" + temp); if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "rare_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + ";" + "rare_disease|" + main_disease + "|" + temp; } } else { if (selected_disease_category.isEmpty()) { selected_disease_category = "rare_disease|" + main_disease + "|" + "Any"; } else { selected_disease_category = selected_disease_category + ";" + "rare_disease|" + main_disease + "|" + "Any"; } } } } main_disease = ""; for (Iterator i = otherDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (otherDisease.isSelected(iid)) { // System.out.println("Selected" + temp); if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "other_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + ";" + "other_disease|" + main_disease + "|" + temp; } } else { if (selected_disease_category.isEmpty()) { selected_disease_category = "other_disease|" + main_disease + "|" + "Any"; } else { selected_disease_category = selected_disease_category + ";" + "other_disease|" + main_disease + "|" + "Any"; } } } } if (checkboxCaseControlYes.getValue() && !checkboxCaseControlNo.getValue()) { query_part3 = query_part3 + " AND ( isCaseControl = 1) "; } else if (!checkboxCaseControlYes.getValue() && checkboxCaseControlNo.getValue()) { query_part3 = query_part3 + " AND (isCaseControl = null or isCaseControl = 0 ) "; } if (checkboxTimeSeriesYes.getValue() && !checkboxTimeSeriesNo.getValue()) { query_part3 = query_part3 + " AND ( isTimeSeries = 1) "; } else if (!checkboxTimeSeriesYes.getValue() && checkboxTimeSeriesNo.getValue()) { query_part3 = query_part3 + " AND (isTimeSeries = null or isTimeSeries = 0 ) "; } if (checkboxTreatmentYes.getValue() && !checkboxTreatmentNo.getValue()) { query_part3 = query_part3 + " AND ( isTreatment = 1) "; } else if (!checkboxTreatmentYes.getValue() && checkboxTreatmentNo.getValue()) { query_part3 = query_part3 + " AND (isTreatment = null or isTreatment = 0 ) "; } if (checkboxSampleTypeTissue.getValue()) { query_part3 = query_part3 + " AND ( isTissue = 1) "; } else { // query_part3 = query_part3 + " AND (isTissue = null or isTissue = 0 ) " ; } if (checkboxSampleTypeCellLine.getValue()) { query_part3 = query_part3 + " AND ( isCellLine = 1) "; } else { // query_part3 = query_part3 + " AND (isCellLine = null or isCellLine = 0 ) " ; } if (checkboxSampleTypePrimaryCells.getValue()) { query_part3 = query_part3 + " AND ( isPrimaryCells = 1) "; } else { // query_part3 = query_part3 + " AND (isPrimaryCells = null or isPrimaryCells = 0 ) " ; } if (checkboxSampleTypeWholeBlood.getValue()) { query_part3 = query_part3 + " AND ( isWholeBlood = 1) "; } else { // query_part3 = query_part3 + " AND (isWholeBlood = null or isWholeBlood = 0 ) " ; } if (checkboxSampleTypePlasma.getValue()) { query_part3 = query_part3 + " AND ( isPlasma = 1) "; } else { // query_part3 = query_part3 + " AND (isPlasma = null or isPlasma = 0 ) " ; } String selected_sequencing_platforms = ""; for (Iterator i = platformsListSelect.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (platformsListSelect.isSelected(iid)) { if (selected_sequencing_platforms.isEmpty()) { selected_sequencing_platforms = temp; } else { selected_sequencing_platforms = selected_sequencing_platforms + ";" + temp; } } } String replicate_type = ""; if (!(replicatTypesListComboBox.getValue() == null)) { replicate_type = replicatTypesListComboBox.getValue().toString(); } String annotation_status = ""; if (checkboxAnnotaionCompleted.getValue() && !checkboxAnnotaionOngoing.getValue()) { annotation_status = "completed"; } else if (!checkboxAnnotaionCompleted.getValue() && checkboxAnnotaionOngoing.getValue()) { annotation_status = "completed"; } try { String query_part1 = "SELECT * FROM study_summary "; String query_part2 = " SELECT studyid FROM manual_annotation "; if (replicate_type.length() > 1) { query_part3 = query_part3 + " AND ( replicate_type = '" + replicate_type + "' ) "; } if (annotation_status.length() > 1) { query_part3 = query_part3 + " AND ( annotation_status = '" + annotation_status + "' ) "; } if (selected_disease_category.length() > 1) { query_part3 = query_part3 + " AND disease_category like " + "'%" + selected_disease_category + "%'"; } if (selected_sequencing_platforms.length() > 1) { query_part3 = query_part3 + " AND sequencing_platform like " + "'%" + selected_sequencing_platforms + "%'"; } query_part3 = query_part3.trim(); if (query_part3.startsWith("AND")) { query_part3 = query_part3.substring(3); } String search_query = query_part1 + " where Study in (" + query_part2 + " WHERE " + query_part3 + ")"; rnaseqContainer = createMySQLContainer("search_manual_annotation", search_query); rnaseqContainer.removeAllContainerFilters(); bioprojectSummaryTable.setContainerDataSource(rnaseqContainer); // bioprojectSummaryTable.setVisibleColumns(new String[] { studyName }); bioprojectSummaryTable.setSelectable(true); bioprojectSummaryTable.setImmediate(true); bioprojectSummaryTable.setColumnReorderingAllowed(true); bioprojectSummaryTable.setSortEnabled(true); bioprojectSummaryTable.setVisibleColumns(new Object[] { "Study", "title", "Numsample", "Numexp", "Numrun", "Avgspots", "avgbases", "name" }); } catch (Exception e) { } } } }); Button guidedSearchANYSubmitButton = new Button("Search Meeting ANY Criteria"); guidedSearchANYSubmitButton.addClickListener(new Button.ClickListener() { public void buttonClick(Button.ClickEvent event) { if (event.getButton() == guidedSearchANYSubmitButton) { String query_part3 = ""; if (checkboxDiseaseYes.getValue() && !checkboxDiseaseNo.getValue()) { query_part3 = query_part3 + " OR ( isDisease = 1) "; } else if (!checkboxDiseaseYes.getValue() && checkboxDiseaseNo.getValue()) { query_part3 = query_part3 + " OR (isDisease = null or isDisease = 0 ) "; } String selected_disease_category = ""; String main_disease = ""; for (Iterator i = complexDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (complexDisease.isSelected(iid)) { //System.out.println("Selected" + temp); if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "complex_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + ";" + "complex_disease|" + main_disease + "|" + temp; } } else { //main disease is selected // selected_disease_main = main_disease; if (selected_disease_category.isEmpty()) { selected_disease_category = "complex_disease|" + main_disease + "|" + "Any"; } else { selected_disease_category = selected_disease_category + ";" + "complex_disease|" + main_disease + "|" + "Any"; } } } } main_disease = ""; for (Iterator i = rareDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (rareDisease.isSelected(iid)) { // System.out.println("Selected" + temp); if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "rare_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + ";" + "rare_disease|" + main_disease + "|" + temp; } } else { if (selected_disease_category.isEmpty()) { selected_disease_category = "rare_disease|" + main_disease + "|" + "Any"; } else { selected_disease_category = selected_disease_category + ";" + "rare_disease|" + main_disease + "|" + "Any"; } } } } main_disease = ""; for (Iterator i = otherDisease.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (!temp.startsWith("--")) { main_disease = temp; } if (otherDisease.isSelected(iid)) { // System.out.println("Selected" + temp); if (iid.toString().startsWith("--")) { // sub disease is selected if (selected_disease_category.isEmpty()) { selected_disease_category = "other_disease|" + main_disease + "|" + temp; } else { selected_disease_category = selected_disease_category + ";" + "other_disease|" + main_disease + "|" + temp; } } else { if (selected_disease_category.isEmpty()) { selected_disease_category = "other_disease|" + main_disease + "|" + "Any"; } else { selected_disease_category = selected_disease_category + ";" + "other_disease|" + main_disease + "|" + "Any"; } } } } if (checkboxCaseControlYes.getValue() && !checkboxCaseControlNo.getValue()) { query_part3 = query_part3 + " OR ( isCaseControl = 1) "; } else if (!checkboxCaseControlYes.getValue() && checkboxCaseControlNo.getValue()) { query_part3 = query_part3 + " OR (isCaseControl = null or isCaseControl = 0 ) "; } if (checkboxTimeSeriesYes.getValue() && !checkboxTimeSeriesNo.getValue()) { query_part3 = query_part3 + " OR ( isTimeSeries = 1) "; } else if (!checkboxTimeSeriesYes.getValue() && checkboxTimeSeriesNo.getValue()) { query_part3 = query_part3 + " OR (isTimeSeries = null or isTimeSeries = 0 ) "; } if (checkboxTreatmentYes.getValue() && !checkboxTreatmentNo.getValue()) { query_part3 = query_part3 + " OR ( isTreatment = 1) "; } else if (!checkboxTreatmentYes.getValue() && checkboxTreatmentNo.getValue()) { query_part3 = query_part3 + " OR (isTreatment = null or isTreatment = 0 ) "; } if (checkboxSampleTypeTissue.getValue()) { query_part3 = query_part3 + " OR ( isTissue = 1) "; } else { // query_part3 = query_part3 + " AND (isTissue = null or isTissue = 0 ) " ; } if (checkboxSampleTypeCellLine.getValue()) { query_part3 = query_part3 + " OR ( isCellLine = 1) "; } else { // query_part3 = query_part3 + " AND (isCellLine = null or isCellLine = 0 ) " ; } if (checkboxSampleTypePrimaryCells.getValue()) { query_part3 = query_part3 + " OR ( isPrimaryCells = 1) "; } else { // query_part3 = query_part3 + " AND (isPrimaryCells = null or isPrimaryCells = 0 ) " ; } if (checkboxSampleTypeWholeBlood.getValue()) { query_part3 = query_part3 + " OR ( isWholeBlood = 1) "; } else { // query_part3 = query_part3 + " AND (isWholeBlood = null or isWholeBlood = 0 ) " ; } if (checkboxSampleTypePlasma.getValue()) { query_part3 = query_part3 + " OR ( isPlasma = 1) "; } else { // query_part3 = query_part3 + " AND (isPlasma = null or isPlasma = 0 ) " ; } String selected_sequencing_platforms = ""; for (Iterator i = platformsListSelect.getItemIds().iterator(); i.hasNext();) { Object iid = (Object) i.next(); String temp = iid.toString(); if (platformsListSelect.isSelected(iid)) { if (selected_sequencing_platforms.isEmpty()) { selected_sequencing_platforms = temp; } else { selected_sequencing_platforms = selected_sequencing_platforms + ";" + temp; } } } String replicate_type = ""; if (!(replicatTypesListComboBox.getValue() == null)) { replicate_type = replicatTypesListComboBox.getValue().toString(); } String annotation_status = ""; if (checkboxAnnotaionCompleted.getValue() && !checkboxAnnotaionOngoing.getValue()) { annotation_status = "completed"; } else if (!checkboxAnnotaionCompleted.getValue() && checkboxAnnotaionOngoing.getValue()) { annotation_status = "completed"; } try { String query_part1 = "SELECT * FROM study_summary "; String query_part2 = " SELECT studyid FROM manual_annotation "; if (replicate_type.length() > 1) { query_part3 = query_part3 + " OR ( replicate_type = '" + replicate_type + "' ) "; } if (annotation_status.length() > 1) { query_part3 = query_part3 + " OR ( annotation_status = '" + annotation_status + "' ) "; } if (selected_disease_category.length() > 1) { query_part3 = query_part3 + " OR disease_category like " + "'%" + selected_disease_category + "%'"; } if (selected_sequencing_platforms.length() > 1) { query_part3 = query_part3 + " AND sequencing_platform like " + "'%" + selected_sequencing_platforms + "%'"; } query_part3 = query_part3.trim(); if (query_part3.startsWith("OR")) { query_part3 = query_part3.substring(2); } String search_query = query_part1 + " where Study in (" + query_part2 + " WHERE " + query_part3 + ")"; rnaseqContainer = createMySQLContainer("search_manual_annotation", search_query); rnaseqContainer.removeAllContainerFilters(); bioprojectSummaryTable.setContainerDataSource(rnaseqContainer); // bioprojectSummaryTable.setVisibleColumns(new String[] { studyName }); bioprojectSummaryTable.setSelectable(true); bioprojectSummaryTable.setImmediate(true); bioprojectSummaryTable.setColumnReorderingAllowed(true); bioprojectSummaryTable.setSortEnabled(true); bioprojectSummaryTable.setVisibleColumns(new Object[] { "Study", "title", "Numsample", "Numexp", "Numrun", "Avgspots", "avgbases", "name" }); } catch (Exception e) { } } } }); HorizontalLayout guidedSearchButtonLayout = new HorizontalLayout(); guidedSearchButtonLayout.addComponent(guidedSearchSubmitButton); guidedSearchButtonLayout.addComponent(guidedSearchANYSubmitButton); guidedSearchLayout.addComponent(diseaseLayout); // guidedSearchLayout.addComponent(caseControlLayout); // guidedSearchLayout.addComponent(timeSeriesLayout); guidedSearchLayout.addComponent(studyTypesPanel); guidedSearchLayout.addComponent(diseaseCategoryPanel); guidedSearchLayout.addComponent(platformLayout); guidedSearchLayout.addComponent(sampleTypesPanel); guidedSearchLayout.addComponent(replicatTypesLayout); guidedSearchLayout.addComponent(annotationStatusLayout); guidedSearchLayout.addComponent(guidedSearchButtonLayout); guidedSearchLayout.setComponentAlignment(guidedSearchButtonLayout, Alignment.MIDDLE_CENTER); int leftTopLayoutIndex = leftLayout.getComponentIndex(leftTopLayout); leftLayout.addComponent(guidedSearchLayout, leftTopLayoutIndex + 1); //</editor-fold> } } }); }
From source file:edu.nps.moves.mmowgli.AbstractMmowgliController.java
License:Open Source License
@SuppressWarnings("serial") private void handleAdminMessage(Game g) { final Window dialog = new Window("Important!"); VerticalLayout vl = new VerticalLayout(); dialog.setContent(vl);/* w ww . ja v a 2s . co m*/ vl.setSizeUndefined(); vl.setMargin(true); vl.setSpacing(true); vl.addComponent(new HtmlLabel(g.getAdminLoginMessage())); HorizontalLayout buttHL = new HorizontalLayout(); buttHL.setSpacing(true); final CheckBox cb; buttHL.addComponent(cb = new CheckBox("Show this message again on the next administrator login")); cb.setValue(true); Button closeButt; buttHL.addComponent(closeButt = new Button("Close")); closeButt.addClickListener(new ClickListener() { @Override @MmowgliCodeEntry @HibernateOpened @HibernateClosed public void buttonClick(ClickEvent event) { if (Boolean.parseBoolean(cb.getValue().toString())) ; // do nothing else { HSess.init(); Game.getTL().setAdminLoginMessage(null); Game.updateTL(); HSess.close(); } UI.getCurrent().removeWindow(dialog); } }); vl.addComponent(buttHL); vl.setComponentAlignment(buttHL, Alignment.MIDDLE_RIGHT); UI.getCurrent().addWindow(dialog); dialog.center(); }
From source file:edu.nps.moves.mmowgli.modules.actionplans.ActionPlanPage2.java
License:Open Source License
@SuppressWarnings("serial") private void maybeAddHiddenCheckBoxTL(HorizontalLayout hl, ActionPlan ap) { User me = Mmowgli2UI.getGlobals().getUserTL(); if (me.isAdministrator() || me.isGameMaster()) { Label sp;//ww w . ja va2 s . c o m hl.addComponent(sp = new Label()); sp.setWidth("80px"); final CheckBox hidCb = new CheckBox("hidden"); hidCb.setValue(ap.isHidden()); hidCb.setDescription("Only game masters see this"); hidCb.setImmediate(true); hl.addComponent(hidCb); hl.setComponentAlignment(hidCb, Alignment.BOTTOM_RIGHT); hidCb.addValueChangeListener(new ValueChangeListener() { @Override @MmowgliCodeEntry @HibernateOpened @HibernateClosed public void valueChange(ValueChangeEvent event) { HSess.init(); ActionPlan acntp = ActionPlan.getTL(getApId()); boolean nowHidden = acntp.isHidden(); boolean tobeHidden = hidCb.getValue(); if (nowHidden != tobeHidden) { acntp.setHidden(tobeHidden); ActionPlan.updateTL(acntp); } HSess.close(); } }); final CheckBox supIntCb = new CheckBox("super interesting"); supIntCb.setValue(ap.isSuperInteresting()); supIntCb.setDescription("Mark plan super-interesting (only game masters see this)"); supIntCb.setImmediate(true); hl.addComponent(supIntCb); hl.setComponentAlignment(supIntCb, Alignment.BOTTOM_RIGHT); supIntCb.addValueChangeListener(new ValueChangeListener() { @Override @MmowgliCodeEntry @HibernateOpened @HibernateClosed public void valueChange(ValueChangeEvent event) { HSess.init(); ActionPlan acntp = ActionPlan.getTL(getApId()); boolean nowSupInt = acntp.isSuperInteresting(); boolean tobeSupInt = supIntCb.getValue(); if (nowSupInt != tobeSupInt) { acntp.setSuperInteresting(tobeSupInt); ActionPlan.updateTL(acntp); } HSess.close(); } }); } }
From source file:edu.nps.moves.mmowgli.modules.userprofile.ManageAwardsDialog.java
License:Open Source License
@HibernateUserRead private void fillPanelTL(User u) { @SuppressWarnings("unchecked") List<AwardType> typs = (List<AwardType>) HSess.get().createCriteria(AwardType.class).list(); gridList = new ArrayList<AwardType>(typs.size()); gridList.addAll(typs);/*from w w w. ja v a 2 s . c om*/ gridLayout.removeAllComponents(); gridLayout.setRows(typs.size()); gridLayout.setColumns(4); gridLayout.setSpacing(true); gridLayout.setColumnExpandRatio(2, 0.5f); gridLayout.setColumnExpandRatio(3, 0.5f); Set<Award> uAwards = u.getAwards(); MediaLocator mediaLoc = Mmowgli2UI.getGlobals().getMediaLocator(); for (AwardType at : typs) { CheckBox cb; boolean checked = hasBeenAwarded(uAwards, at); gridLayout.addComponent(cb = new CheckBox()); cb.setValue(checked); gridLayout.setComponentAlignment(cb, Alignment.MIDDLE_CENTER); Embedded emb = new Embedded(null, mediaLoc.locate(at.getIcon55x55())); emb.addStyleName("m-greyborder3"); gridLayout.addComponent(emb); Label lab; gridLayout.addComponent(lab = new Label(at.getName())); gridLayout.setComponentAlignment(lab, Alignment.MIDDLE_LEFT); gridLayout.addComponent(lab = new Label(at.getDescription())); gridLayout.setComponentAlignment(lab, Alignment.MIDDLE_LEFT); } }
From source file:eu.maxschuster.vaadin.buttonlink.demo.DemoUI.java
License:Apache License
@Override protected void init(VaadinRequest request) { final VerticalLayout wrapper = new VerticalLayout(); wrapper.setSizeFull();// w w w .j ava2 s .c o m setContent(wrapper); // Show it in the middle of the screen final VerticalLayout layout = new VerticalLayout(); layout.setSpacing(true); layout.setSizeUndefined(); wrapper.addComponent(layout); wrapper.setComponentAlignment(layout, Alignment.MIDDLE_CENTER); final Label themeName = new Label(); themeName.setCaption("Current Theme:"); themeName.addStyleName("h1"); layout.addComponent(themeName); Label waring = new Label("<strong>Attention:</strong><br />\nChanging the theme may take a few seconds!"); waring.setContentMode(ContentMode.HTML); layout.addComponent(waring); getPage().addUriFragmentChangedListener(new UriFragmentChangedListener() { @Override public void uriFragmentChanged(UriFragmentChangedEvent event) { String fragment = event.getUriFragment().replace("!", ""); if (fragment.isEmpty()) { fragment = defaultTheme; } loadTheme(fragment); } }); themeSelect.setSizeFull(); themeSelect.setNullSelectionAllowed(false); themeSelect.addValueChangeListener(new ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { String fragment = "!" + themeSelect.getValue(); getPage().setUriFragment(fragment); } }); layout.addComponent(themeSelect); layout.setComponentAlignment(themeSelect, Alignment.BOTTOM_CENTER); final CheckBox useIcon = new CheckBox("Use icons"); useIcon.setValue(false); layout.addComponent(useIcon); final HorizontalLayout comparsionLayout = new HorizontalLayout(); comparsionLayout.setSpacing(true); layout.addComponent(comparsionLayout); layout.setComponentAlignment(comparsionLayout, Alignment.TOP_CENTER); final Button button = new Button("This is a \"normal\" Button", new Button.ClickListener() { @Override public void buttonClick(ClickEvent event) { Notification.show("Hello World!"); } }); comparsionLayout.addComponent(button); comparsionLayout.setComponentAlignment(button, Alignment.MIDDLE_RIGHT); // Initialize our new UI component final ButtonLink buttonLink = new ButtonLink("This is a ButtonLink", new ExternalResource("https://vaadin.com")); buttonLink.setTargetName("_blank"); buttonLink.setDescription("Visit vaadin.com in a new tab or window."); buttonLink.addStyleName("test-stylename"); comparsionLayout.addComponent(buttonLink); comparsionLayout.setComponentAlignment(buttonLink, Alignment.MIDDLE_LEFT); themeName.setPropertyDataSource(themeSelect); useIcon.addValueChangeListener(new ValueChangeListener() { @Override public void valueChange(ValueChangeEvent event) { boolean b = (Boolean) event.getProperty().getValue(); if (b) { button.setIcon(vaadinIcon, "Vaadin Logo"); buttonLink.setIcon(vaadinIcon, "Vaadin Logo"); } else { button.setIcon(null); buttonLink.setIcon(null); } } }); String fragment = getPage().getUriFragment(); loadTheme( fragment == null || fragment.replace("!", "").isEmpty() ? defaultTheme : fragment.replace("!", "")); }