List of usage examples for com.vaadin.ui Window Window
public Window(String caption)
From source file:de.symeda.sormas.ui.utils.VaadinUiUtil.java
License:Open Source License
public static Window showPopupWindow(Component content) { Window window = new Window(null); window.setModal(true);/*from w ww.j av a2 s.c o m*/ window.setSizeUndefined(); window.setResizable(false); window.center(); window.setContent(content); UI.getCurrent().addWindow(window); return window; }
From source file:de.twenty11.skysail.MyVaadinApplication.java
License:Apache License
@Override public void init() { window = new Window("Skysail OSGi Monitor Vaadin Client"); setMainWindow(window);/*from w w w . j a v a2 s. c o m*/ // Needed because composites are full size window.getContent().setSizeFull(); MyComponent myComposite = new MyComponent(); window.addComponent(myComposite); Button button = new Button("Click Me"); button.addListener(new Button.ClickListener() { public void buttonClick(ClickEvent event) { window.addComponent(new Label("Thank you for clicking")); } }); window.addComponent(button); /* Create the table with a caption. */ Table table = new Table("This is my Table"); /* * Define the names and data types of columns. The "default value" parameter is meaningless here. */ table.addContainerProperty("First Name", String.class, null); table.addContainerProperty("Last Name", String.class, null); table.addContainerProperty("Year", Integer.class, null); /* Add a few items in the table. */ table.addItem(new Object[] { "Nicolaus", "Copernicus", new Integer(1473) }, new Integer(1)); table.addItem(new Object[] { "Tycho", "Brahe", new Integer(1546) }, new Integer(2)); table.addItem(new Object[] { "Giordano", "Bruno", new Integer(1548) }, new Integer(3)); table.addItem(new Object[] { "Galileo", "Galilei", new Integer(1564) }, new Integer(4)); table.addItem(new Object[] { "Johannes", "Kepler", new Integer(1571) }, new Integer(5)); table.addItem(new Object[] { "Isaac", "Newton", new Integer(1643) }, new Integer(6)); window.addComponent(table); setTheme("skysail.client.osgimonitor.vaadintheme"); }
From source file:de.uni_leipzig.informatik.pcai042.boa.gui.evaluation.EvaluationApp.java
License:Open Source License
@Override public void init() { rootFolder = new File(getContext().getBaseDirectory(), "WEB-INF/resources/"); cl = new ConfigLoader(rootFolder); sf = new SearcherFactory(cl); annotator = new Annotator(sf); tokenizer = new Tokenizer(); conWEIGHT = new ConverterWeight(cl); conLINEAR_MEASURE = new ConverterLinearMeasure(cl); conTEMPERATURE = new ConverterTemperature(cl); conDATE = new ConverterDate(cl); Window mainWindow = new Window("Boa"); setMainWindow(mainWindow);/* ww w. ja va 2 s .c o m*/ mainWindow.getContent().setSizeFull(); mainWindow.addComponent(view); view.getButtonAnnotate().addListener((ClickListener) this); view.getButtonNew().addListener((ClickListener) this); view.getButtonNext2().addListener((ClickListener) this); view.getTableEvaluation().addListener((Property.ValueChangeListener) this); view.getListSelectAnnotation().addListener((Property.ValueChangeListener) this); Scoring scoring = null; try { scoring = new Scoring(new File(rootFolder, "goldstandard.xml"), sf); sentences = scoring.getWorkSentences(); goldstandard = scoring.getGoldstandard(); ArrayList<double[]> result = scoring.score(); for (int i = 0; i < result.size(); i++) { // last "new Integer()" represents position of object in table! view.getTableEvaluation().addItem(new Object[] { new Integer(i), sentences.get(i).getSentence(), new Double(result.get(i)[0]), new Double(result.get(i)[1]), new Double(result.get(i)[2]) }, new Integer(i)); } } catch (ValidityException e) { } catch (ParsingException e) { } catch (IOException e) { } if (scoring == null) logger.error("Failed to load goldstandard"); }
From source file:de.uni_leipzig.informatik.pcai042.boa.gui.goldstandard.GoldstandardApp.java
License:Open Source License
@Override public void init() { if (!SentenceServer.isInitialized()) SentenceServer.init(getContext().getBaseDirectory()); Window mainWindow = new Window("Goldstandard"); setMainWindow(mainWindow);/* w w w . j a v a2s.c o m*/ mainWindow.getContent().setSizeFull(); mainWindow.addComponent(gui); }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.BiologicalSamplesComponent.java
License:Open Source License
/** * // ww w. jav a 2 s . c o m * @param id */ public void updateUI(String id) { currentID = id; sampleBioGrid = new Grid(); sampleEntityGrid = new Grid(); sampleEntityGrid.addSelectionListener(new SelectionListener() { @Override public void select(SelectionEvent event) { BeanItem<BiologicalEntitySampleBean> selectedBean = samplesEntity .getItem(sampleEntityGrid.getSelectedRow()); if (selectedBean == null) { TextField filterField = (TextField) sampleBioGrid.getHeaderRow(1).getCell("biologicalEntity") .getComponent(); filterField.setValue(""); } else { TextField filterField = (TextField) sampleBioGrid.getHeaderRow(1).getCell("biologicalEntity") .getComponent(); filterField.setValue(selectedBean.getBean().getCode()); // samplesBio.addContainerFilter("biologicalEntity", // selectedBean.getBean().getSecondaryName(), false, false); } } }); if (id == null) return; BeanItemContainer<BiologicalSampleBean> samplesBioContainer = new BeanItemContainer<BiologicalSampleBean>( BiologicalSampleBean.class); BeanItemContainer<BiologicalEntitySampleBean> samplesEntityContainer = new BeanItemContainer<BiologicalEntitySampleBean>( BiologicalEntitySampleBean.class); List<Sample> allSamples = datahandler.getOpenBisClient() .getSamplesWithParentsAndChildrenOfProjectBySearchService(id); List<VocabularyTerm> terms = null; Map<String, String> termsMap = new HashMap<String, String>(); for (Sample sample : allSamples) { if (sample.getSampleTypeCode().equals(sampleTypes.Q_BIOLOGICAL_ENTITY.toString())) { Map<String, String> sampleProperties = sample.getProperties(); BiologicalEntitySampleBean newEntityBean = new BiologicalEntitySampleBean(); newEntityBean.setCode(sample.getCode()); newEntityBean.setId(sample.getIdentifier()); newEntityBean.setType(sample.getSampleTypeCode()); newEntityBean.setAdditionalInfo(sampleProperties.get("Q_ADDITIONAL_INFO")); newEntityBean.setExternalDB(sampleProperties.get("Q_EXTERNALDB_ID")); newEntityBean.setSecondaryName(sampleProperties.get("Q_SECONDARY_NAME")); String organismID = sampleProperties.get("Q_NCBI_ORGANISM"); newEntityBean.setOrganism(organismID); if (terms != null) { if (termsMap.containsKey(organismID)) { newEntityBean.setOrganismName(termsMap.get(organismID)); } else { for (VocabularyTerm term : terms) { if (term.getCode().equals(organismID)) { newEntityBean.setOrganismName(term.getLabel()); break; } } } } else { for (Vocabulary vocab : datahandler.getOpenBisClient().getFacade().listVocabularies()) { if (vocab.getCode().equals("Q_NCBI_TAXONOMY")) { terms = vocab.getTerms(); for (VocabularyTerm term : vocab.getTerms()) { if (term.getCode().equals(organismID)) { newEntityBean.setOrganismName(term.getLabel()); termsMap.put(organismID, term.getLabel()); break; } } break; } } } newEntityBean.setProperties(sampleProperties); newEntityBean.setGender(sampleProperties.get("Q_GENDER")); samplesEntityContainer.addBean(newEntityBean); // for (Sample child : datahandler.getOpenBisClient().getChildrenSamples(sample)) { for (Sample realChild : sample.getChildren()) { if (realChild.getSampleTypeCode().equals(sampleTypes.Q_BIOLOGICAL_SAMPLE.toString())) { // Sample realChild = // datahandler.getOpenBisClient().getSampleByIdentifier(child.getIdentifier()); Map<String, String> sampleBioProperties = realChild.getProperties(); BiologicalSampleBean newBean = new BiologicalSampleBean(); newBean.setCode(realChild.getCode()); newBean.setId(realChild.getIdentifier()); newBean.setType(realChild.getSampleTypeCode()); newBean.setPrimaryTissue(sampleBioProperties.get("Q_PRIMARY_TISSUE")); newBean.setTissueDetailed(sampleBioProperties.get("Q_TISSUE_DETAILED")); newBean.setBiologicalEntity(sample.getCode()); newBean.setAdditionalInfo(sampleBioProperties.get("Q_ADDITIONAL_INFO")); newBean.setExternalDB(sampleBioProperties.get("Q_EXTERNALDB_ID")); newBean.setSecondaryName(sampleBioProperties.get("Q_SECONDARY_NAME")); newBean.setProperties(sampleBioProperties); samplesBioContainer.addBean(newBean); } } } } numberOfBioSamples = samplesBioContainer.size(); numberOfEntitySamples = samplesEntityContainer.size(); samplesBio = samplesBioContainer; samplesEntity = samplesEntityContainer; sampleEntityGrid.removeAllColumns(); final GeneratedPropertyContainer gpcEntity = new GeneratedPropertyContainer(samplesEntity); gpcEntity.removeContainerProperty("id"); gpcEntity.removeContainerProperty("type"); gpcEntity.removeContainerProperty("organismName"); gpcEntity.removeContainerProperty("organism"); sampleEntityGrid.setContainerDataSource(gpcEntity); sampleEntityGrid.setColumnReorderingAllowed(true); gpcEntity.addGeneratedProperty("Organism", new PropertyValueGenerator<String>() { @Override public Class<String> getType() { return String.class; } @Override public String getValue(Item item, Object itemId, Object propertyId) { String ncbi = String.format( "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=%s&lvl=0&srchmode=1&keep=1&unlock' target='_blank'>%s</a>", item.getItemProperty("organism").getValue(), item.getItemProperty("organismName").getValue()); String link = String.format("<a href='%s", ncbi); return link; } }); sampleEntityGrid.getColumn("Organism").setRenderer(new HtmlRenderer()); final GeneratedPropertyContainer gpcBio = new GeneratedPropertyContainer(samplesBio); gpcBio.removeContainerProperty("id"); gpcBio.removeContainerProperty("type"); sampleBioGrid.setContainerDataSource(gpcBio); sampleBioGrid.setColumnReorderingAllowed(true); sampleBioGrid.setColumnOrder("secondaryName", "code"); gpcEntity.addGeneratedProperty("edit", new PropertyValueGenerator<String>() { @Override public String getValue(Item item, Object itemId, Object propertyId) { return "Edit"; } @Override public Class<String> getType() { return String.class; } }); gpcBio.addGeneratedProperty("edit", new PropertyValueGenerator<String>() { @Override public String getValue(Item item, Object itemId, Object propertyId) { return "Edit"; } @Override public Class<String> getType() { return String.class; } }); sampleEntityGrid.addItemClickListener(new ItemClickListener() { @Override public void itemClick(ItemClickEvent event) { BeanItem selected = (BeanItem) samplesEntity.getItem(event.getItemId()); BiologicalEntitySampleBean selectedExp = (BiologicalEntitySampleBean) selected.getBean(); State state = (State) UI.getCurrent().getSession().getAttribute("state"); ArrayList<String> message = new ArrayList<String>(); message.add("clicked"); message.add(selectedExp.getId()); message.add("sample"); state.notifyObservers(message); } }); sampleEntityGrid.getColumn("edit").setRenderer(new ButtonRenderer(new RendererClickListener() { @Override public void click(RendererClickEvent event) { BeanItem selected = (BeanItem) samplesEntity.getItem(event.getItemId()); BiologicalEntitySampleBean selectedSample = (BiologicalEntitySampleBean) selected.getBean(); Window subWindow = new Window("Edit Metadata"); changeMetadata.updateUI(selectedSample.getId(), selectedSample.getType()); VerticalLayout subContent = new VerticalLayout(); subContent.setMargin(true); subContent.addComponent(changeMetadata); subWindow.setContent(subContent); // Center it in the browser window subWindow.center(); subWindow.setModal(true); subWindow.setIcon(FontAwesome.PENCIL); subWindow.setHeight("75%"); subWindow.addCloseListener(new CloseListener() { /** * */ private static final long serialVersionUID = -1329152609834711109L; @Override public void windowClose(CloseEvent e) { updateUI(currentID); } }); QbicmainportletUI ui = (QbicmainportletUI) UI.getCurrent(); ui.addWindow(subWindow); } })); sampleEntityGrid.getColumn("edit").setWidth(70); sampleEntityGrid.getColumn("edit").setHeaderCaption(""); sampleEntityGrid.setColumnOrder("edit", "secondaryName", "Organism", "properties", "code", "additionalInfo", "gender", "externalDB"); sampleBioGrid.addItemClickListener(new ItemClickListener() { @Override public void itemClick(ItemClickEvent event) { BeanItem selected = (BeanItem) samplesBio.getItem(event.getItemId()); BiologicalSampleBean selectedExp = (BiologicalSampleBean) selected.getBean(); State state = (State) UI.getCurrent().getSession().getAttribute("state"); ArrayList<String> message = new ArrayList<String>(); message.add("clicked"); message.add(selectedExp.getId()); message.add("sample"); state.notifyObservers(message); } }); sampleBioGrid.getColumn("edit").setRenderer(new ButtonRenderer(new RendererClickListener() { @Override public void click(RendererClickEvent event) { BeanItem selected = (BeanItem) samplesBio.getItem(event.getItemId()); try { BiologicalSampleBean selectedSample = (BiologicalSampleBean) selected.getBean(); Window subWindow = new Window(); changeMetadata.updateUI(selectedSample.getId(), selectedSample.getType()); VerticalLayout subContent = new VerticalLayout(); subContent.setMargin(true); subContent.addComponent(changeMetadata); subWindow.setContent(subContent); // Center it in the browser window subWindow.center(); subWindow.setModal(true); subWindow.setResizable(false); subWindow.addCloseListener(new CloseListener() { /** * */ private static final long serialVersionUID = -1329152609834711109L; @Override public void windowClose(CloseEvent e) { updateUI(currentID); } }); QbicmainportletUI ui = (QbicmainportletUI) UI.getCurrent(); ui.addWindow(subWindow); } catch (NullPointerException e) { System.err.println("NullPointerException while trying to set metadata: " + e.getMessage()); } } })); sampleBioGrid.getColumn("edit").setWidth(70); sampleBioGrid.getColumn("edit").setHeaderCaption(""); sampleBioGrid.setColumnOrder("edit", "secondaryName", "primaryTissue", "properties", "tissueDetailed", "code", "additionalInfo", "biologicalEntity", "externalDB"); sampleBioGrid.getColumn("biologicalEntity").setHeaderCaption("Source"); helpers.GridFunctions.addColumnFilters(sampleBioGrid, gpcBio); helpers.GridFunctions.addColumnFilters(sampleEntityGrid, gpcEntity); if (fileDownloaderSources != null) exportSources.removeExtension(fileDownloaderSources); StreamResource srSource = Utils.getTSVStream(Utils.containerToString(samplesEntityContainer), String.format("%s_%s_", id.substring(1).replace("/", "_"), "sample_sources")); fileDownloaderSources = new FileDownloader(srSource); fileDownloaderSources.extend(exportSources); if (fileDownloaderSamples != null) exportSamples.removeExtension(fileDownloaderSamples); StreamResource srSamples = Utils.getTSVStream(Utils.containerToString(samplesBioContainer), String.format("%s_%s_", id.substring(1).replace("/", "_"), "extracted_samples")); fileDownloaderSamples = new FileDownloader(srSamples); fileDownloaderSamples.extend(exportSamples); this.buildLayout(); }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.DatasetView.java
License:Open Source License
/** * Precondition: {DatasetView#table} has to be initialized. e.g. with * {DatasetView#buildFilterTable} If it is not, strange behaviour has to be expected. builds the * Layout of this view./* w ww . j ava 2s .com*/ */ private void buildLayout() { this.vert.removeAllComponents(); int browserWidth = UI.getCurrent().getPage().getBrowserWindowWidth(); int browserHeight = UI.getCurrent().getPage().getBrowserWindowHeight(); this.vert.setWidth("100%"); this.setWidth(String.format("%spx", (browserWidth * 0.6))); // this.setHeight(String.format("%spx", (browserHeight * 0.8))); VerticalLayout statistics = new VerticalLayout(); HorizontalLayout statContent = new HorizontalLayout(); statContent.setCaption("Statistics"); statContent.setIcon(FontAwesome.BAR_CHART_O); statContent.addComponent(new Label(String.format("%s registered dataset(s).", numberOfDatasets))); statContent.setMargin(true); statContent.setSpacing(true); statistics.addComponent(statContent); statistics.setMargin(true); this.vert.addComponent(statistics); // Table (containing datasets) section VerticalLayout tableSection = new VerticalLayout(); HorizontalLayout tableSectionContent = new HorizontalLayout(); tableSectionContent.setCaption("Registered Datasets"); tableSectionContent.setIcon(FontAwesome.FLASK); tableSectionContent.addComponent(this.table); tableSectionContent.setMargin(true); tableSection.setMargin(true); tableSection.addComponent(tableSectionContent); this.vert.addComponent(tableSection); table.setWidth("100%"); tableSection.setWidth("100%"); tableSectionContent.setWidth("100%"); // this.table.setSizeFull(); HorizontalLayout buttonLayout = new HorizontalLayout(); buttonLayout.setHeight(null); buttonLayout.setWidth("100%"); buttonLayout.setSpacing(false); final Button visualize = new Button(VISUALIZE_BUTTON_CAPTION); buttonLayout.addComponent(this.download); buttonLayout.addComponent(visualize); Button checkAll = new Button("Select all datasets"); checkAll.addClickListener(new ClickListener() { @Override public void buttonClick(ClickEvent event) { for (Object itemId : table.getItemIds()) { ((CheckBox) table.getItem(itemId).getItemProperty("Select").getValue()).setValue(true); } } }); Button uncheckAll = new Button("Unselect all datasets"); uncheckAll.addClickListener(new ClickListener() { @Override public void buttonClick(ClickEvent event) { for (Object itemId : table.getItemIds()) { ((CheckBox) table.getItem(itemId).getItemProperty("Select").getValue()).setValue(false); } } }); buttonLayout.addComponent(checkAll); buttonLayout.addComponent(uncheckAll); /** * prepare download. */ download.setResource(new ExternalResource("javascript:")); download.setEnabled(false); visualize.setEnabled(false); for (final Object itemId : this.table.getItemIds()) { setCheckedBox(itemId, (String) this.table.getItem(itemId).getItemProperty("CODE").getValue()); } /* * Update the visualize button. It is only enabled, if the files can be visualized. */ this.table.addValueChangeListener(new ValueChangeListener() { /** * */ private static final long serialVersionUID = -4875903343717437913L; /** * check for what selection can be visualized. If so, enable the button. TODO change to * checked. */ @Override public void valueChange(ValueChangeEvent event) { // Nothing selected or more than one selected. Set<Object> selectedValues = (Set<Object>) event.getProperty().getValue(); if (selectedValues == null || selectedValues.size() == 0 || selectedValues.size() > 1) { visualize.setEnabled(false); return; } // if one selected check whether its dataset type is either fastqc or qcml. // For now we only visulize these two file types. Iterator<Object> iterator = selectedValues.iterator(); Object next = iterator.next(); String datasetType = (String) table.getItem(next).getItemProperty("Dataset Type").getValue(); String fileName = (String) table.getItem(next).getItemProperty("File Name").getValue(); // TODO: No hardcoding!! // if (datasetType.equals("FASTQC") || datasetType.equals("QCML") || // datasetType.equals("BAM") // || datasetType.equals("VCF")) { if (datasetType.equals("Q_WF_MS_QUALITYCONTROL_RESULTS") && (fileName.endsWith(".html") || fileName.endsWith(".qcML"))) { visualize.setEnabled(true); } else if (datasetType.equals("Q_WF_MS_QUALITYCONTROL_LOGS") && (fileName.endsWith(".err") || fileName.endsWith(".out"))) { visualize.setEnabled(true); } else { visualize.setEnabled(false); } } }); // TODO Workflow Views should get those data and be happy /* * Send message that in datasetview the following was selected. WorkflowViews get those messages * and save them, if it is valid information for them. */ this.table.addValueChangeListener(new ValueChangeListener() { /** * */ private static final long serialVersionUID = -3554627008191389648L; @Override public void valueChange(ValueChangeEvent event) { // Nothing selected or more than one selected. Set<Object> selectedValues = (Set<Object>) event.getProperty().getValue(); State state = (State) UI.getCurrent().getSession().getAttribute("state"); ArrayList<String> message = new ArrayList<String>(); message.add("DataSetView"); if (selectedValues != null && selectedValues.size() == 1) { Iterator<Object> iterator = selectedValues.iterator(); Object next = iterator.next(); String datasetType = (String) table.getItem(next).getItemProperty("Dataset Type").getValue(); message.add(datasetType); String project = (String) table.getItem(next).getItemProperty("Project").getValue(); String space = datahandler.getOpenBisClient().getProjectByCode(project).getSpaceCode();// .getIdentifier().split("/")[1]; message.add(project); message.add((String) table.getItem(next).getItemProperty("Sample").getValue()); // message.add((String) table.getItem(next).getItemProperty("Sample Type").getValue()); message.add((String) table.getItem(next).getItemProperty("dl_link").getValue()); message.add((String) table.getItem(next).getItemProperty("File Name").getValue()); message.add(space); // state.notifyObservers(message); } else { message.add("null"); } // TODO // state.notifyObservers(message); } }); // TODO get the GV to work here. Together with reverse proxy // Assumes that table Value Change listner is enabling or disabling the button if preconditions // are not fullfilled visualize.addClickListener(new ClickListener() { /** * */ private static final long serialVersionUID = 9015273307461506369L; @Override public void buttonClick(ClickEvent event) { Set<Object> selectedValues = (Set<Object>) table.getValue(); Iterator<Object> iterator = selectedValues.iterator(); Object next = iterator.next(); String datasetCode = (String) table.getItem(next).getItemProperty("CODE").getValue(); String datasetFileName = (String) table.getItem(next).getItemProperty("File Name").getValue(); URL url; try { Object parent = table.getParent(next); if (parent != null) { String parentDatasetFileName = (String) table.getItem(parent).getItemProperty("File Name") .getValue(); url = datahandler.getOpenBisClient().getUrlForDataset(datasetCode, parentDatasetFileName + "/" + datasetFileName); } else { url = datahandler.getOpenBisClient().getUrlForDataset(datasetCode, datasetFileName); } Window subWindow = new Window( "QC of Sample: " + (String) table.getItem(next).getItemProperty("Sample").getValue()); VerticalLayout subContent = new VerticalLayout(); subContent.setMargin(true); subWindow.setContent(subContent); QbicmainportletUI ui = (QbicmainportletUI) UI.getCurrent(); // Put some components in it Resource res = null; String datasetType = (String) table.getItem(next).getItemProperty("Dataset Type").getValue(); final RequestHandler rh = new ProxyForGenomeViewerRestApi(); boolean rhAttached = false; if (datasetType.equals("Q_WF_MS_QUALITYCONTROL_RESULTS") && datasetFileName.endsWith(".qcML")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("application/xml"); res = streamres; } else if (datasetType.equals("Q_WF_MS_QUALITYCONTROL_RESULTS") && datasetFileName.endsWith(".html")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("text/html"); res = streamres; } else if (datasetType.equals("Q_WF_MS_QUALITYCONTROL_LOGS") && (datasetFileName.endsWith(".err") || datasetFileName.endsWith(".out"))) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("text/plain"); res = streamres; } else if (datasetType.equals("FASTQC")) { res = new ExternalResource(url); } else if (datasetType.equals("BAM") || datasetType.equals("VCF")) { String filePath = (String) table.getItem(next).getItemProperty("dl_link").getValue(); filePath = String.format("/store%s", filePath.split("store")[1]); String fileId = (String) table.getItem(next).getItemProperty("File Name").getValue(); // fileId = "control.1kg.panel.samples.vcf.gz"; // UI.getCurrent().getSession().addRequestHandler(rh); rhAttached = true; ThemeDisplay themedisplay = (ThemeDisplay) VaadinService.getCurrentRequest() .getAttribute(WebKeys.THEME_DISPLAY); String hostTmp = "http://localhost:7778/vizrest/rest";// "http://localhost:8080/web/guest/mainportlet?p_p_id=QbicmainportletApplicationPortlet_WAR_QBiCMainPortlet_INSTANCE_5pPd5JQ8uGOt&p_p_lifecycle=2&p_p_state=normal&p_p_mode=view&p_p_cacheability=cacheLevelPage&p_p_col_id=column-1&p_p_col_count=1"; // hostTmp += // "&qbicsession=" + UI.getCurrent().getSession().getAttribute("gv-restapi-session") // + "&someblabla="; // String hostTmp = themedisplay.getURLPortal() + // UI.getCurrent().getPage().getLocation().getPath() + "?qbicsession=" + // UI.getCurrent().getSession().getAttribute("gv-restapi-session") + "&someblabla=" ; // String host = Base64.encode(hostTmp.getBytes()); String title = (String) table.getItem(next).getItemProperty("Sample").getValue(); // res = // new ExternalResource( // String // .format( // "http://localhost:7778/genomeviewer/?host=%s&title=%s&fileid=%s&featuretype=alignments&filepath=%s&removeZeroGenotypes=false", // host, title, fileId, filePath)); } BrowserFrame frame = new BrowserFrame("", res); if (rhAttached) { frame.addDetachListener(new DetachListener() { /** * */ private static final long serialVersionUID = 1534523447730906543L; @Override public void detach(DetachEvent event) { UI.getCurrent().getSession().removeRequestHandler(rh); } }); } frame.setSizeFull(); subContent.addComponent(frame); // Center it in the browser window subWindow.center(); subWindow.setModal(true); subWindow.setSizeFull(); frame.setHeight((int) (ui.getPage().getBrowserWindowHeight() * 0.8), Unit.PIXELS); // Open it in the UI ui.addWindow(subWindow); } catch (MalformedURLException e) { LOGGER.error(String.format("Visualization failed because of malformedURL for dataset: %s", datasetCode)); Notification.show( "Given dataset has no file attached to it!! Please Contact your project manager. Or check whether it already has some data", Notification.Type.ERROR_MESSAGE); } } }); this.vert.addComponent(buttonLayout); }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.ExperimentComponent.java
License:Open Source License
public void updateUI(ProjectBean currentBean) { projectBean = currentBean;//from w w w . j av a 2s .c o m experiments.removeAllColumns(); // experiments.setContainerDataSource(projectBean.getExperiments()); // BeanItemContainer<ExperimentBean> experimentBeans = // loadMoreExperimentInformation(projectBean.getExperiments()); // GeneratedPropertyContainer gpc = new GeneratedPropertyContainer(experimentBeans); GeneratedPropertyContainer gpc = new GeneratedPropertyContainer(projectBean.getExperiments()); gpc.removeContainerProperty("containsData"); gpc.removeContainerProperty("controlledVocabularies"); gpc.removeContainerProperty("id"); gpc.removeContainerProperty("lastChangedDataset"); gpc.removeContainerProperty("lastChangedSample"); gpc.removeContainerProperty("properties"); gpc.removeContainerProperty("type"); gpc.removeContainerProperty("samples"); gpc.removeContainerProperty("status"); gpc.removeContainerProperty("typeLabels"); gpc.removeContainerProperty("registrationDate"); experiments.addItemClickListener(new ItemClickListener() { /** * */ private static final long serialVersionUID = -43367719647620455L; @Override public void itemClick(ItemClickEvent event) { BeanItem selected = (BeanItem) projectBean.getExperiments().getItem(event.getItemId()); ExperimentBean selectedExp = (ExperimentBean) selected.getBean(); State state = (State) UI.getCurrent().getSession().getAttribute("state"); ArrayList<String> message = new ArrayList<String>(); message.add("clicked"); message.add(selectedExp.getId()); message.add("experiment"); state.notifyObservers(message); } }); gpc.addGeneratedProperty("edit", new PropertyValueGenerator<String>() { /** * */ private static final long serialVersionUID = 7558511163500976236L; @Override public String getValue(Item item, Object itemId, Object propertyId) { return "Edit"; } @Override public Class<String> getType() { return String.class; } }); gpc.addGeneratedProperty("registrationDate", new PropertyValueGenerator<String>() { @Override public Class<String> getType() { return String.class; } @Override public String getValue(Item item, Object itemId, Object propertyId) { BeanItem selected = (BeanItem) projectBean.getExperiments().getItem(itemId); ExperimentBean expBean = (ExperimentBean) selected.getBean(); Date date = expBean.getRegistrationDate(); SimpleDateFormat sd = new SimpleDateFormat("yyyy-MM-dd hh:mm a"); String dateString = sd.format(date); return dateString; } }); experiments.setContainerDataSource(gpc); experiments.getColumn("prettyType").setHeaderCaption("Type"); experiments.getColumn("edit").setRenderer(new ButtonRenderer(new RendererClickListener() { @Override public void click(RendererClickEvent event) { BeanItem selected = (BeanItem) projectBean.getExperiments().getItem(event.getItemId()); ExperimentBean selectedSample = (ExperimentBean) selected.getBean(); Window subWindow = new Window("Edit Metadata"); changeMetadata.updateUI(selectedSample.getId(), selectedSample.getType()); VerticalLayout subContent = new VerticalLayout(); subContent.setMargin(true); subContent.addComponent(changeMetadata); subWindow.setContent(subContent); // Center it in the browser window subWindow.center(); subWindow.setModal(true); subWindow.setSizeUndefined(); subWindow.setIcon(FontAwesome.PENCIL); subWindow.setHeight("75%"); subWindow.setResizable(false); QbicmainportletUI ui = (QbicmainportletUI) UI.getCurrent(); ui.addWindow(subWindow); } })); experiments.getColumn("edit").setWidth(70); experiments.setColumnOrder("edit", "prettyType"); experiments.getColumn("edit").setHeaderCaption(""); // experiments.setHeightMode(HeightMode.ROW); // experiments.setHeightByRows(gpc.size()); if (fileDownloader != null) this.export.removeExtension(fileDownloader); StreamResource sr = Utils.getTSVStream(Utils.containerToString(projectBean.getExperiments()), String.format("%s_%s_", projectBean.getId().substring(1).replace("/", "_"), "experimental_steps")); fileDownloader = new FileDownloader(sr); fileDownloader.extend(export); }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.HomeView.java
License:Open Source License
/** * sets the ContainerDataSource of this view. Should usually contain project information. Caption * is caption.//from w w w. j av a 2s . c o m * * @param homeViewInformation * @param caption */ public void setContainerDataSource(SpaceBean spaceBean, String newCaption) { caption = newCaption; currentBean = spaceBean; numberOfProjects = currentBean.getProjects().size(); projectGrid = new Grid(); GeneratedPropertyContainer gpcProjects = new GeneratedPropertyContainer(spaceBean.getProjects()); gpcProjects.removeContainerProperty("members"); gpcProjects.removeContainerProperty("id"); gpcProjects.removeContainerProperty("experiments"); gpcProjects.removeContainerProperty("contact"); gpcProjects.removeContainerProperty("contactPerson"); gpcProjects.removeContainerProperty("projectManager"); gpcProjects.removeContainerProperty("containsData"); gpcProjects.removeContainerProperty("containsResults"); gpcProjects.removeContainerProperty("containsAttachments"); gpcProjects.removeContainerProperty("description"); gpcProjects.removeContainerProperty("progress"); gpcProjects.removeContainerProperty("registrationDate"); gpcProjects.removeContainerProperty("registrator"); gpcProjects.removeContainerProperty("longDescription"); projectGrid.setContainerDataSource(gpcProjects); projectGrid.setHeightMode(HeightMode.ROW); projectGrid.setHeightByRows(20); // projectGrid.getColumn("space").setWidthUndefined(); // projectGrid.getColumn("code").setWidthUndefined(); // projectGrid.getColumn("secondaryName").setWidthUndefined(); // projectGrid.getColumn("principalInvestigator").setWidthUndefined(); projectGrid.getColumn("code").setHeaderCaption("Sub-Project").setWidth(150); // projectGrid.getColumn("space").setWidth(200); Column nameCol = projectGrid.getColumn("secondaryName"); nameCol.setHeaderCaption("Short Name"); nameCol.setMaximumWidth(450); projectGrid.getColumn("space").setMaximumWidth(350); projectGrid.getColumn("space").setHeaderCaption("Project"); projectGrid.getColumn("principalInvestigator").setHeaderCaption("Investigator"); projectGrid.setColumnOrder("code", "space", "secondaryName", "principalInvestigator"); projectGrid.setResponsive(true); helpers.GridFunctions.addColumnFilters(projectGrid, gpcProjects); gpcProjects.addGeneratedProperty("Summary", new PropertyValueGenerator<String>() { @Override public String getValue(Item item, Object itemId, Object propertyId) { return "show"; } @Override public Class<String> getType() { return String.class; } }); projectGrid.getColumn("Summary").setWidthUndefined(); projectGrid.getColumn("Summary").setRenderer(new ButtonRenderer(new RendererClickListener() { @Override public void click(RendererClickEvent event) { // Show loading window ProgressBar bar = new ProgressBar(); bar.setIndeterminate(true); VerticalLayout vl = new VerticalLayout(bar); vl.setComponentAlignment(bar, Alignment.MIDDLE_CENTER); vl.setWidth("50%"); vl.setSpacing(true); vl.setMargin(true); Window loadingWindow = new Window("Loading project summary..."); loadingWindow.setWidth("50%"); loadingWindow.setContent(vl); loadingWindow.center(); loadingWindow.setModal(true); loadingWindow.setResizable(false); QbicmainportletUI ui = (QbicmainportletUI) UI.getCurrent(); ui.addWindow(loadingWindow); // fetch summary and create docx in tmp folder ProjectBean proj = (ProjectBean) event.getItemId(); summaryFetcher.fetchSummaryComponent(proj.getCode(), proj.getSecondaryName(), proj.getDescription(), new ProjectSummaryReadyRunnable(summaryFetcher, loadingWindow, proj.getCode())); } })); projectGrid.getColumn("Summary").setWidth(100); projectGrid.addSelectionListener(new SelectionListener() { @Override public void select(SelectionEvent event) { Set<Object> selectedElements = event.getSelected(); if (selectedElements == null) { return; } ProjectBean selectedProject = (ProjectBean) selectedElements.iterator().next(); if (selectedProject == null) { return; } String entity = selectedProject.getId(); State state = (State) UI.getCurrent().getSession().getAttribute("state"); ArrayList<String> message = new ArrayList<String>(); message.add("clicked"); message.add(entity); message.add(ProjectView.navigateToLabel); state.notifyObservers(message); } }); }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.LevelComponent.java
License:Open Source License
public void updateUI(String type, String id, String filterFor) { sampleGrid = new Grid(); typeString = type;/* w ww. j a v a 2 s . com*/ idString = id; filterString = filterFor; if (id == null) return; try { HierarchicalContainer datasetContainer = new HierarchicalContainer(); datasetContainer.addContainerProperty("Select", CheckBox.class, null); datasetContainer.addContainerProperty("Project", String.class, null); datasetContainer.addContainerProperty("Sample", String.class, null); datasetContainer.addContainerProperty("Description", String.class, null); // datasetContainer.addContainerProperty("Sample Type", String.class, null); datasetContainer.addContainerProperty("File Name", String.class, null); datasetContainer.addContainerProperty("File Type", String.class, null); datasetContainer.addContainerProperty("Dataset Type", String.class, null); datasetContainer.addContainerProperty("Registration Date", String.class, null); datasetContainer.addContainerProperty("Validated", Boolean.class, null); datasetContainer.addContainerProperty("File Size", String.class, null); datasetContainer.addContainerProperty("file_size_bytes", Long.class, null); datasetContainer.addContainerProperty("dl_link", String.class, null); datasetContainer.addContainerProperty("isDirectory", Boolean.class, null); datasetContainer.addContainerProperty("CODE", String.class, null); List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet> retrievedDatasetsAll = null; List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet> retrievedDatasets = new ArrayList<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet>(); Map<String, ArrayList<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet>> datasetFilter = new HashMap<String, ArrayList<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet>>(); // clear download queue for new view PortletSession portletSession = ((QbicmainportletUI) UI.getCurrent()).getPortletSession(); portletSession.setAttribute("qbic_download", new HashMap<String, AbstractMap.SimpleEntry<String, Long>>(), PortletSession.APPLICATION_SCOPE); Map<String, Sample> checkedTestSamples = new HashMap<String, Sample>(); switch (type) { case "project": String projectIdentifier = id; retrievedDatasetsAll = datahandler.getOpenBisClient() .getDataSetsOfProjectByIdentifierWithSearchCriteria(projectIdentifier); for (ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet ds : retrievedDatasetsAll) { ArrayList<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet> values = datasetFilter .get(ds.getSampleIdentifierOrNull()); if (values == null) { values = new ArrayList<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet>(); datasetFilter.put(ds.getSampleIdentifierOrNull(), values); } values.add(ds); } if (filterFor.equals("measured")) { BeanItemContainer<TestSampleBean> samplesContainer = new BeanItemContainer<TestSampleBean>( TestSampleBean.class); // List<Sample> allSamples = // datahandler.getOpenBisClient() // .getSamplesOfProjectBySearchService(projectIdentifier); List<Sample> allSamples = datahandler.getOpenBisClient() .getSamplesWithParentsAndChildrenOfProjectBySearchService(id); for (Sample sample : allSamples) { checkedTestSamples.put(sample.getCode(), sample); if (sample.getSampleTypeCode().equals("Q_TEST_SAMPLE")) { // samplesContainer.addBean(new SampleBean(sample.getIdentifier(), sample.getCode(), // sample.getSampleTypeCode(), null, null, null, sample.getProperties(), null, // null)); Map<String, String> sampleProperties = sample.getProperties(); TestSampleBean newBean = new TestSampleBean(); newBean.setCode(sample.getCode()); newBean.setId(sample.getIdentifier()); newBean.setType(sample.getSampleTypeCode()); newBean.setSampleType(sampleProperties.get("Q_SAMPLE_TYPE")); newBean.setAdditionalInfo(sampleProperties.get("Q_ADDITIONAL_INFO")); newBean.setExternalDB(sampleProperties.get("Q_EXTERNALDB_ID")); newBean.setSecondaryName(sampleProperties.get("Q_SECONDARY_NAME")); newBean.setProperties(sampleProperties); samplesContainer.addBean(newBean); ArrayList<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet> foundDataset = datasetFilter .get(sample.getIdentifier()); if (foundDataset != null) { retrievedDatasets.addAll(foundDataset); } for (Sample child : sample.getChildren()) { foundDataset = datasetFilter.get(child.getIdentifier()); if (foundDataset != null) { retrievedDatasets.addAll(foundDataset); } } } else if (sample.getSampleTypeCode().equals("Q_MHC_LIGAND_EXTRACT")) { // samplesContainer.addBean(new SampleBean(sample.getIdentifier(), sample.getCode(), // sample.getSampleTypeCode(), null, null, null, sample.getProperties(), null, // null)); Map<String, String> sampleProperties = sample.getProperties(); TestSampleBean newBean = new TestSampleBean(); newBean.setCode(sample.getCode()); newBean.setId(sample.getIdentifier()); newBean.setType(sample.getSampleTypeCode()); newBean.setSampleType(sampleProperties.get("Q_MHC_CLASS")); newBean.setAdditionalInfo(sampleProperties.get("Q_ANTIBODY")); newBean.setExternalDB(sampleProperties.get("Q_EXTERNALDB_ID")); newBean.setSecondaryName(sampleProperties.get("Q_SECONDARY_NAME")); newBean.setProperties(sampleProperties); samplesContainer.addBean(newBean); ArrayList<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet> foundDataset = datasetFilter .get(sample.getIdentifier()); if (foundDataset != null) { retrievedDatasets.addAll(foundDataset); } for (Sample child : sample.getChildren()) { foundDataset = datasetFilter.get(child.getIdentifier()); if (foundDataset != null) { retrievedDatasets.addAll(foundDataset); } } } } numberOfSamples = samplesContainer.size(); samples = samplesContainer; final GeneratedPropertyContainer gpc = new GeneratedPropertyContainer(samples); gpc.removeContainerProperty("id"); gpc.removeContainerProperty("type"); sampleGrid.setContainerDataSource(gpc); sampleGrid.setColumnReorderingAllowed(true); gpc.addGeneratedProperty("edit", new PropertyValueGenerator<String>() { @Override public String getValue(Item item, Object itemId, Object propertyId) { return "Edit"; } @Override public Class<String> getType() { return String.class; } }); sampleGrid.addItemClickListener(new ItemClickListener() { @Override public void itemClick(ItemClickEvent event) { BeanItem selected = (BeanItem) samples.getItem(event.getItemId()); TestSampleBean selectedExp = (TestSampleBean) selected.getBean(); State state = (State) UI.getCurrent().getSession().getAttribute("state"); ArrayList<String> message = new ArrayList<String>(); message.add("clicked"); message.add(selectedExp.getId()); message.add("sample"); state.notifyObservers(message); } }); sampleGrid.getColumn("edit").setRenderer(new ButtonRenderer(new RendererClickListener() { @Override public void click(RendererClickEvent event) { BeanItem selected = (BeanItem) samples.getItem(event.getItemId()); TestSampleBean selectedSample = (TestSampleBean) selected.getBean(); Window subWindow = new Window("Edit Metadata"); changeMetadata.updateUI(selectedSample.getId(), selectedSample.getType()); VerticalLayout subContent = new VerticalLayout(); subContent.setMargin(true); subContent.addComponent(changeMetadata); subWindow.setContent(subContent); // Center it in the browser window subWindow.center(); subWindow.setModal(true); subWindow.setIcon(FontAwesome.PENCIL); subWindow.setHeight("75%"); subWindow.setResizable(false); subWindow.addCloseListener(new CloseListener() { /** * */ private static final long serialVersionUID = -1329152609834711109L; @Override public void windowClose(CloseEvent e) { updateUI(typeString, idString, filterString); } }); QbicmainportletUI ui = (QbicmainportletUI) UI.getCurrent(); ui.addWindow(subWindow); } })); sampleGrid.getColumn("edit").setHeaderCaption(""); sampleGrid.getColumn("edit").setWidth(70); sampleGrid.setColumnOrder("edit", "secondaryName", "sampleType", "code", "properties", "additionalInfo", "externalDB"); helpers.GridFunctions.addColumnFilters(sampleGrid, gpc); numberOfSamples = samplesContainer.size(); sampleGrid.setCaption("Measured Samples"); this.datasetTable.setCaption("Raw Data"); numberOfDatasets = retrievedDatasets.size(); this.datasetTable.setPageLength(Math.max(3, Math.min(numberOfDatasets, 10))); // sampleGrid.setHeightMode(HeightMode.ROW); // sampleGrid.setHeightByRows(numberOfSamples); } else if (filterFor.equals("results")) { BeanItemContainer<TestSampleBean> samplesContainer = new BeanItemContainer<TestSampleBean>( TestSampleBean.class); List<Sample> allSamples = datahandler.getOpenBisClient() .getSamplesWithParentsAndChildrenOfProjectBySearchService(projectIdentifier); for (Sample sample : allSamples) { checkedTestSamples.put(sample.getCode(), sample); if (!sample.getSampleTypeCode().equals("Q_TEST_SAMPLE") && !sample.getSampleTypeCode().equals("Q_MICROARRAY_RUN") && !sample.getSampleTypeCode().equals("Q_MS_RUN") && !sample.getSampleTypeCode().equals("Q_BIOLOGICAL_SAMPLE") && !sample.getSampleTypeCode().equals("Q_BIOLOGICAL_ENTITY") && !sample.getSampleTypeCode().equals("Q_NGS_SINGLE_SAMPLE_RUN")) { Map<String, String> sampleProperties = sample.getProperties(); TestSampleBean newBean = new TestSampleBean(); newBean.setCode(sample.getCode()); newBean.setId(sample.getIdentifier()); newBean.setType(prettyNameMapper.getPrettyName(sample.getSampleTypeCode())); newBean.setAdditionalInfo(sampleProperties.get("Q_ADDITIONAL_INFO")); newBean.setSecondaryName(sampleProperties.get("Q_SECONDARY_NAME")); newBean.setProperties(sampleProperties); samplesContainer.addBean(newBean); ArrayList<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet> foundDataset = datasetFilter .get(sample.getIdentifier()); if (foundDataset != null) { for (ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet ds : foundDataset) { // we don't want to show project data or log files in the results tab if (ds.getDataSetTypeCode().equals("Q_PROJECT_DATA")) { if (ds.getProperties().get("Q_ATTACHMENT_TYPE").equals("INFORMATION")) { continue; } else { retrievedDatasets.add(ds); } } else if (ds.getDataSetTypeCode().contains("LOGS")) { continue; } else { retrievedDatasets.add(ds); } } // retrievedDatasets.addAll(foundDataset); } } } // numberOfSamples = samplesContainer.size(); samples = samplesContainer; final GeneratedPropertyContainer gpc = new GeneratedPropertyContainer(samples); gpc.removeContainerProperty("id"); gpc.removeContainerProperty("sampleType"); sampleGrid.setContainerDataSource(gpc); sampleGrid.setColumnReorderingAllowed(true); sampleGrid.setColumnOrder("secondaryName", "type", "code", "properties"); numberOfSamples = samplesContainer.size(); // sampleGrid.setHeightMode(HeightMode.ROW); // sampleGrid.setHeightByRows(numberOfSamples); sampleGrid.setCaption("Workflow Runs"); helpers.GridFunctions.addColumnFilters(sampleGrid, gpc); this.datasetTable.setCaption("Result Files"); datasetTable.setColumnHeader("Sample", "Workflow Run"); sampleGrid.addItemClickListener(new ItemClickListener() { @Override public void itemClick(ItemClickEvent event) { BeanItem selected = (BeanItem) samples.getItem(event.getItemId()); TestSampleBean selectedExp = (TestSampleBean) selected.getBean(); State state = (State) UI.getCurrent().getSession().getAttribute("state"); ArrayList<String> message = new ArrayList<String>(); message.add("clicked"); message.add(selectedExp.getId()); message.add("sample"); state.notifyObservers(message); } }); numberOfDatasets = retrievedDatasets.size(); this.datasetTable.setPageLength(Math.max(3, Math.min(numberOfDatasets, 10))); } break; case "experiment": String experimentIdentifier = id; retrievedDatasets = datahandler.getOpenBisClient() .getDataSetsOfExperimentByCodeWithSearchCriteria(experimentIdentifier); break; case "sample": String sampleIdentifier = id; String sampleCode = sampleIdentifier.split("/")[2]; retrievedDatasets = datahandler.getOpenBisClient().getDataSetsOfSample(sampleCode); break; default: retrievedDatasets = new ArrayList<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet>(); break; } BeanItemContainer<DatasetBean> forExport = new BeanItemContainer(DatasetBean.class); numberOfDatasets = retrievedDatasets.size(); if (numberOfDatasets == 0 & filterFor.equals("measured")) { descriptionLabel = new Label(String.format( "This project contains %s measured samples for which %s raw data dataset(s) have been registered.", numberOfSamples, 0), ContentMode.HTML); helpers.Utils.Notification("No raw data available.", "No raw data is available for this project. Please contact the project manager if this is not expected.", "warning"); } else if (numberOfDatasets == 0 & filterFor.equals("results")) { descriptionLabel = new Label(String.format("This project contains %s result datasets.", 0), ContentMode.HTML); helpers.Utils.Notification("No results available.", "No result data is available for this project. Please contact the project manager if this is not expected.", "warning"); } else { Map<String, String> samples = new HashMap<String, String>(); // project same for all datasets String projectCode = retrievedDatasets.get(0).getExperimentIdentifier().split("/")[2]; for (ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet dataset : retrievedDatasets) { samples.put(dataset.getCode(), dataset.getSampleIdentifierOrNull().split("/")[2]); } List<DatasetBean> dsBeans = datahandler.queryDatasetsForFolderStructure(retrievedDatasets); for (DatasetBean d : dsBeans) { Date date = d.getRegistrationDate(); SimpleDateFormat sd = new SimpleDateFormat("yyyy-MM-dd hh:mm a"); String dateString = sd.format(date); // Timestamp ts = Timestamp.valueOf(dateString); String sampleID = samples.get(d.getCode()); forExport.addBean(d); Sample dsSample = checkedTestSamples.get(sampleID); String secNameDS = d.getProperties().get("Q_SECONDARY_NAME"); String secName = datahandler.getSecondaryName(dsSample, secNameDS); registerDatasetInTable(d, datasetContainer, projectCode, sampleID, dateString, null, secName); } if (filterFor.equals("measured")) { descriptionLabel = new Label(String.format( "This project contains %s measured samples for which %s raw data dataset(s) have been registered.", numberOfSamples, dsBeans.size()), ContentMode.HTML); } else if (filterFor.equals("results")) { descriptionLabel = new Label( String.format("This project contains %s result datasets.", dsBeans.size()), ContentMode.HTML); } } this.setContainerDataSource(datasetContainer); if (fileDownloaderData != null) this.exportData.removeExtension(fileDownloaderData); StreamResource srData = Utils.getTSVStream(Utils.containerToString(forExport), String.format("%s_%s_", id.substring(1).replace("/", "_"), datasetTable.getCaption().replace(" ", "_"))); fileDownloaderData = new FileDownloader(srData); fileDownloaderData.extend(exportData); if (fileDownloaderSamples != null) this.exportSamples.removeExtension(fileDownloaderSamples); StreamResource srSamples = Utils.getTSVStream(Utils.containerToString(samples), String.format("%s_%s_", id.substring(1).replace("/", "_"), sampleGrid.getCaption().replaceAll(" ", "_"))); fileDownloaderSamples = new FileDownloader(srSamples); fileDownloaderSamples.extend(exportSamples); } catch (Exception e) { e.printStackTrace(); LOGGER.error(String.format("getting dataset failed for dataset %s %s", type, id), e.getStackTrace()); } }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.ProjInformationComponent.java
License:Open Source License
private void initUI() { vert = new VerticalLayout(); descHorz = new HorizontalLayout(); // horz = new HorizontalLayout(); statusPanel = new Panel(); descriptionPanel = new Panel(); datasetTable = buildFilterTable();//from ww w. jav a 2s . c o m peopleInCharge = new Accordion(); setResponsive(true); vert.setResponsive(true); descHorz.setResponsive(true); statusPanel.setResponsive(true); descriptionPanel.setResponsive(true); vert.setMargin(new MarginInfo(true, true, false, false)); setSizeFull(); vert.setSizeFull(); descHorz.setSizeFull(); statusPanel.setSizeFull(); descriptionPanel.setSizeFull(); investigator = new Label("", ContentMode.HTML); contactPerson = new Label("", ContentMode.HTML); projectManager = new Label("", ContentMode.HTML); final VerticalLayout layoutI = new VerticalLayout(investigator); final VerticalLayout layoutC = new VerticalLayout(contactPerson); final VerticalLayout layoutP = new VerticalLayout(projectManager); layoutI.setMargin(true); layoutC.setMargin(true); layoutP.setMargin(true); peopleInCharge.addTab(layoutI, "Investigator"); peopleInCharge.addTab(layoutC, "Contact Person"); peopleInCharge.addTab(layoutP, "Project Manager"); descEdit = new Button("Edit"); descEdit.setIcon(FontAwesome.PENCIL); descEdit.setStyleName(ValoTheme.BUTTON_BORDERLESS_COLORED); descEdit.setResponsive(true); descEdit.addClickListener(new ClickListener() { @Override public void buttonClick(ClickEvent event) { changeMetadata.updateUI(projectBean); VerticalLayout subContent = new VerticalLayout(); subContent.setMargin(true); subContent.addComponent(changeMetadata); Window subWindow = new Window("Edit Metadata"); subWindow.setContent(subContent); // Center it in the browser window subWindow.center(); subWindow.setModal(true); subWindow.setIcon(FontAwesome.PENCIL); subWindow.setHeight("75%"); subWindow.setResizable(false); // subWindow.setSizeFull(); subWindow.addCloseListener(new CloseListener() { /** * */ private static final long serialVersionUID = -1329152609834711109L; @Override public void windowClose(CloseEvent e) { ProjectBean updatedBean = datahandler.getProjectFromDB(projectBean.getId()); updateUI(updatedBean, projectType); } }); QbicmainportletUI ui = (QbicmainportletUI) UI.getCurrent(); ui.addWindow(subWindow); } }); // horz.addComponent(descEdit); // horz.setComponentAlignment(descEdit, Alignment.TOP_RIGHT); // horz.setExpandRatio(investigator, 0.4f); // horz.setExpandRatio(contactPerson, 0.4f); // horz.setExpandRatio(descEdit, 0.2f); contact = new Label("", ContentMode.HTML); patientInformation = new Label("No patient information provided.", ContentMode.HTML); experimentLabel = new Label(""); statusContent = new VerticalLayout(); hlaTypeLabel = new Label("Not available.", ContentMode.HTML); hlaTypeLabel.setStyleName("patientview"); this.setCompositionRoot(vert); // this.setCompositionRoot(mainLayout); }