List of usage examples for com.vaadin.ui VerticalLayout setMargin
@Override
public void setMargin(boolean enabled)
From source file:de.uni_tuebingen.qbic.qbicmainportlet.ExperimentView.java
License:Open Source License
/** * // w w w .j av a 2s . c om * @return * */ VerticalLayout initStatistics() { VerticalLayout statistics = new VerticalLayout(); HorizontalLayout statContent = new HorizontalLayout(); // statContent.setCaption("Statistics"); // statContent.setIcon(FontAwesome.BAR_CHART_O); // int numberOfDatasets = dh.datasetMap.get(experimentBean.getId()).size(); statContentLabel = new Label(""); statContent.addComponent(statContentLabel); statContent.setMargin(new MarginInfo(true, false, true, true)); // statContent.addComponent(new Label(String.format("%s dataset(s).",numberOfDatasets ))); // statContent.setMargin(true); // statContent.setMargin(new MarginInfo(false, false, false, true)); // statContent.setSpacing(true); /* * if (numberOfDatasets > 0) { * * String lastSample = "No samples available"; if (experimentBean.getLastChangedSample() != * null) { lastSample = experimentBean.getLastChangedSample();// .split("/")[2]; } * statContent.addComponent(new Label(String.format( "Last change %s", String.format( * "occurred in sample %s (%s)", lastSample, * experimentBean.getLastChangedDataset().toString())))); } */ statistics.addComponent(statContent); // statistics.setMargin(true); // Properties of experiment // VerticalLayout properties = new VerticalLayout(); // VerticalLayout propertiesContent = new VerticalLayout(); // propertiesContent.setCaption("Properties"); // propertiesContent.setIcon(FontAwesome.LIST_UL); // propertiesContentLabel = new Label("", ContentMode.HTML); // propertiesContent.addComponent(propertiesContentLabel); // properties.addComponent(propertiesContent); // propertiesContent.setMargin(new MarginInfo(true, false, false, true)); // properties.setMargin(true); // statistics.addComponent(properties); statistics.setMargin(new MarginInfo(true, false, true, true)); statistics.setSpacing(true); return statistics; }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.ExperimentView.java
License:Open Source License
VerticalLayout initProperties() {
// Properties of experiment
VerticalLayout properties = new VerticalLayout();
VerticalLayout propertiesContent = new VerticalLayout();
// propertiesContent.setCaption("Properties");
// propertiesContent.setIcon(FontAwesome.LIST_UL);
propertiesContentLabel = new Label("", ContentMode.HTML);
propertiesContentLabel.setCaption("Properties");
experimentalFactorLabel = new Label("", ContentMode.HTML);
experimentalFactorLabel.setCaption("Workflow Settings");
propertiesContent.addComponent(propertiesContentLabel);
propertiesContent.addComponent(experimentalFactorLabel);
properties.addComponent(propertiesContent);
propertiesContent.setMargin(new MarginInfo(true, false, true, true));
return properties;
}
From source file:de.uni_tuebingen.qbic.qbicmainportlet.ExperimentView.java
License:Open Source License
VerticalLayout initTable() {
this.table = this.buildFilterTable();
this.tableClickChangeTreeView();
VerticalLayout tableSection = new VerticalLayout();
HorizontalLayout tableSectionContent = new HorizontalLayout();
// tableSectionContent.setCaption("Registered Samples");
// tableSectionContent.setIcon(FontAwesome.FLASK);
tableSectionContent.addComponent(this.table);
tableSectionContent.setMargin(new MarginInfo(true, true, false, true));
// tableSectionContent.setMargin(true);
// tableSection.setMargin(true);
tableSection.setMargin(new MarginInfo(true, false, false, true));
// this.table.setWidth("100%");
tableSection.setWidth("100%");
tableSectionContent.setWidth("100%");
tableSection.addComponent(tableSectionContent);
this.export = new Button("Export as TSV");
buttonLayoutSection = new VerticalLayout();
HorizontalLayout buttonLayout = new HorizontalLayout();
buttonLayout.setMargin(new MarginInfo(false, false, false, true));
buttonLayout.setHeight(null);/* ww w . j a v a 2s .c o m*/
buttonLayout.setWidth("100%");
buttonLayoutSection.setSpacing(true);
buttonLayoutSection.addComponent(buttonLayout);
buttonLayoutSection.setMargin(new MarginInfo(true, false, true, false));
buttonLayout.addComponent(this.export);
tableSection.addComponent(buttonLayoutSection);
return tableSection;
}
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 ava 2 s .co 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;/*from www .j av a 2 s. c om*/ 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.LevelComponent.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.// www . j av a 2s . c o m */ private void buildLayout() { this.vert.removeAllComponents(); this.vert.setWidth("100%"); // Table (containing datasets) section VerticalLayout tableSectionDatasets = new VerticalLayout(); VerticalLayout tableSectionSamples = new VerticalLayout(); HorizontalLayout tableSectionContent = new HorizontalLayout(); HorizontalLayout sampletableSectionContent = new HorizontalLayout(); tableSectionContent.setMargin(new MarginInfo(false, false, false, false)); sampletableSectionContent.setMargin(new MarginInfo(false, false, false, false)); // tableSectionContent.setCaption("Datasets"); // tableSectionContent.setIcon(FontAwesome.FLASK); descriptionLabel.setWidth("100%"); tableSectionDatasets.addComponent(descriptionLabel); sampletableSectionContent.addComponent(sampleGrid); tableSectionContent.addComponent(this.datasetTable); tableSectionDatasets.setMargin(new MarginInfo(true, false, false, true)); tableSectionDatasets.setSpacing(true); tableSectionSamples.setMargin(new MarginInfo(true, false, true, true)); tableSectionSamples.setSpacing(true); tableSectionDatasets.addComponent(tableSectionContent); tableSectionSamples.addComponent(sampletableSectionContent); tableSectionSamples.addComponent(exportSamples); this.vert.addComponent(tableSectionDatasets); sampleGrid.setWidth("100%"); datasetTable.setWidth("100%"); tableSectionDatasets.setWidth("100%"); tableSectionSamples.setWidth("100%"); sampletableSectionContent.setWidth("100%"); tableSectionContent.setWidth("100%"); HorizontalLayout buttonLayout = new HorizontalLayout(); buttonLayout.setMargin(new MarginInfo(false, false, false, true)); buttonLayout.setHeight(null); buttonLayout.setSpacing(true); this.download.setEnabled(false); buttonLayout.setSpacing(true); Button checkAll = new Button("Select all datasets"); checkAll.addClickListener(new ClickListener() { @Override public void buttonClick(ClickEvent event) { for (Object itemId : datasetTable.getItemIds()) { ((CheckBox) datasetTable.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 : datasetTable.getItemIds()) { ((CheckBox) datasetTable.getItem(itemId).getItemProperty("Select").getValue()).setValue(false); } } }); buttonLayout.addComponent(exportData); buttonLayout.addComponent(checkAll); buttonLayout.addComponent(uncheckAll); // buttonLayout.addComponent(visualize); buttonLayout.addComponent(this.download); String content = "<p> In case of multiple file selections, Project Browser will create a tar archive.</p>" + "<hr>" + "<p> If you need help on extracting a tar archive file, follow the tips below: </p>" + "<p>" + FontAwesome.WINDOWS.getHtml() + " Windows </p>" + "<p> To open/extract TAR file on Windows, you can use 7-Zip, Easy 7-Zip, PeaZip.</p>" + "<hr>" + "<p>" + FontAwesome.APPLE.getHtml() + " MacOS </p>" + "<p> To open/extract TAR file on Mac, you can use Mac OS built-in utility Archive Utility,<br> or third-part freeware. </p>" + "<hr>" + "<p>" + FontAwesome.LINUX.getHtml() + " Linux </p>" + "<p> You need to use command tar. The tar is the GNU version of tar archiving utility. <br> " + "To extract/unpack a tar file, type: $ tar -xvf file.tar</p>"; PopupView tooltip = new PopupView(new helpers.ToolTip(content)); tooltip.setHeight("44px"); HorizontalLayout help = new HorizontalLayout(); help.setSizeFull(); HorizontalLayout helpContent = new HorizontalLayout(); // helpContent.setSizeFull(); help.setMargin(new MarginInfo(false, false, false, true)); Label helpText = new Label("Attention: Click here before Download!"); helpContent.addComponent(new Label(FontAwesome.QUESTION_CIRCLE.getHtml(), ContentMode.HTML)); helpContent.addComponent(helpText); helpContent.addComponent(tooltip); helpContent.setSpacing(true); help.addComponent(helpContent); help.setComponentAlignment(helpContent, Alignment.TOP_CENTER); /** * prepare download. */ download.setResource(new ExternalResource("javascript:")); download.setEnabled(false); for (final Object itemId : this.datasetTable.getItemIds()) { setCheckedBox(itemId, (String) this.datasetTable.getItem(itemId).getItemProperty("CODE").getValue()); } this.datasetTable.addItemClickListener(new ItemClickListener() { @Override public void itemClick(ItemClickEvent event) { if (!event.isDoubleClick() & !((boolean) datasetTable.getItem(event.getItemId()) .getItemProperty("isDirectory").getValue())) { String datasetCode = (String) datasetTable.getItem(event.getItemId()).getItemProperty("CODE") .getValue(); String datasetFileName = (String) datasetTable.getItem(event.getItemId()) .getItemProperty("File Name").getValue(); URL url = null; try { Resource res = null; Object parent = datasetTable.getParent(event.getItemId()); if (parent != null) { String parentDatasetFileName = (String) datasetTable.getItem(parent) .getItemProperty("File Name").getValue(); try { url = datahandler.getOpenBisClient().getUrlForDataset(datasetCode, parentDatasetFileName + "/" + URLEncoder.encode(datasetFileName, "UTF-8")); } catch (UnsupportedEncodingException e) { // TODO Auto-generated catch block e.printStackTrace(); } } else { try { url = datahandler.getOpenBisClient().getUrlForDataset(datasetCode, URLEncoder.encode(datasetFileName, "UTF-8")); } catch (UnsupportedEncodingException e) { // TODO Auto-generated catch block e.printStackTrace(); } } Window subWindow = new Window(); VerticalLayout subContent = new VerticalLayout(); subContent.setMargin(true); subContent.setSizeFull(); subWindow.setContent(subContent); QbicmainportletUI ui = (QbicmainportletUI) UI.getCurrent(); Boolean visualize = false; if (datasetFileName.endsWith(".pdf")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("application/pdf"); res = streamres; visualize = true; } if (datasetFileName.endsWith(".png")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("application/png"); res = streamres; visualize = true; } if (datasetFileName.endsWith(".qcML")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("text/xml"); res = streamres; visualize = true; } if (datasetFileName.endsWith(".alleles")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("text/plain"); res = streamres; visualize = true; } if (datasetFileName.endsWith(".tsv")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("text/plain"); res = streamres; visualize = true; } if (datasetFileName.endsWith(".log")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("text/plain"); res = streamres; visualize = true; } if (datasetFileName.endsWith(".html")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("text/html"); res = streamres; visualize = true; } if (datasetFileName.endsWith(".GSvar")) { QcMlOpenbisSource re = new QcMlOpenbisSource(url); StreamResource streamres = new StreamResource(re, datasetFileName); streamres.setMIMEType("text/plain"); res = streamres; visualize = true; } if (visualize) { BrowserFrame frame = new BrowserFrame("", res); frame.setSizeFull(); subContent.addComponent(frame); // Center it in the browser window subWindow.center(); subWindow.setModal(true); subWindow.setSizeUndefined(); subWindow.setHeight("75%"); subWindow.setWidth("75%"); subWindow.setResizable(false); frame.setSizeFull(); frame.setHeight("100%"); // frame.setHeight((int) (ui.getPage().getBrowserWindowHeight() * 0.9), 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)); helpers.Utils.Notification("No file attached.", "Given dataset has no file attached to it!! Please Contact your project manager. Or check whether it already has some data", "error"); // 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(help); this.vert.addComponent(buttonLayout); this.vert.addComponent(tableSectionSamples); }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.MultiscaleComponent.java
License:Open Source License
void buildEmptyComments() { // add comments VerticalLayout addComment = new VerticalLayout(); addComment.setMargin(true); addComment.setWidth(100, Unit.PERCENTAGE); final TextArea comments = new TextArea(); comments.setInputPrompt("Write your comment here..."); comments.setWidth(100, Unit.PERCENTAGE); comments.setRows(2);//from ww w. j a va2 s .c o m Button commentsOk = new Button("Add Comment"); commentsOk.addStyleName(ValoTheme.BUTTON_FRIENDLY); commentsOk.addClickListener(new ClickListener() { /** * */ private static final long serialVersionUID = -5369241494545155677L; public void buttonClick(ClickEvent event) { if ("".equals(comments.getValue())) return; String newComment = comments.getValue(); // reset comments comments.setValue(""); // use some date format Date dNow = new Date(); SimpleDateFormat ft = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS'Z'"); Note note = new Note(); note.setComment(newComment); note.setUsername(controller.getUser()); note.setTime(ft.format(dNow)); // show it now // pastcomments.getContainerDataSource().addItem(note); notes.add(note); // TODO write back Label commentsLabel = new Label(translateComments(notes), ContentMode.HTML); commentsPanel.setContent(commentsLabel); // write back to openbis if (!controller.addNote(note)) { Notification.show("Could not add comment to sample. How did you do that?"); } } }); HorizontalLayout inputPrompt = new HorizontalLayout(); inputPrompt.addComponent(comments); inputPrompt.addComponent(commentsOk); inputPrompt.setWidth(50, Unit.PERCENTAGE); inputPrompt.setComponentAlignment(commentsOk, Alignment.TOP_RIGHT); inputPrompt.setExpandRatio(comments, 1.0f); // addComment.addComponent(comments); // addComment.addComponent(commentsOk); addComment.addComponent(commentsPanel); addComment.addComponent(inputPrompt); // addComment.setComponentAlignment(comments, Alignment.TOP_CENTER); // addComment.setComponentAlignment(commentsOk, Alignment.MIDDLE_CENTER); addComment.setComponentAlignment(commentsPanel, Alignment.TOP_CENTER); addComment.setComponentAlignment(inputPrompt, Alignment.MIDDLE_CENTER); mainlayout.addComponent(addComment); // mainlayout.addComponent(pastcomments); Label commentsLabel = new Label("No comments added so far.", ContentMode.HTML); commentsPanel.setContent(commentsLabel); // mainlayout.addComponent(commentsPanel); // mainlayout.setComponentAlignment(commentsPanel, // Alignment.TOP_CENTER); }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.PatientStatusComponent.java
License:Open Source License
private void initUI() { status = new VerticalLayout(); status.setWidth(100.0f, Unit.PERCENTAGE); status.setMargin(new MarginInfo(true, false, false, true)); status.setSpacing(true);// w w w . j a v a 2s.c om // status.setSizeFull(); VerticalLayout projectStatus = new VerticalLayout(); projectStatus.setMargin(new MarginInfo(true, false, true, true)); projectStatus.setSpacing(true); experiments = new Grid(); experiments.setReadOnly(true); experiments.setWidth(100.0f, Unit.PERCENTAGE); // experiments.setHeightMode(HeightMode.ROW); status.addComponent(experiments); ProgressBar progressBar = new ProgressBar(); progressBar.setValue(0f); status.addComponent(progressBar); projectStatus.addComponent(status); this.setWidth(Page.getCurrent().getBrowserWindowWidth() * 0.85f, Unit.PIXELS); this.setCompositionRoot(projectStatus); }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.PatientView.java
License:Open Source License
/** * initializes the description layout//from w ww . j av a2 s. co m * * @return */ VerticalLayout initDescription() { VerticalLayout projDescription = new VerticalLayout(); VerticalLayout projDescriptionContent = new VerticalLayout(); projDescription.setCaption(""); projDescription.setIcon(FontAwesome.FILE_TEXT_O); descContent = new Label(""); contact = new Label("", ContentMode.HTML); patientInformation = new Label("No patient information provided.", ContentMode.HTML); projDescriptionContent.addComponent(patientInformation); projDescriptionContent.addComponent(descContent); projDescriptionContent.addComponent(contact); projDescriptionContent.setMargin(new MarginInfo(true, false, true, true)); projDescriptionContent.setSpacing(true); projDescription.addComponent(projDescriptionContent); descContent.setStyleName("patientview"); contact.setStyleName("patientview"); patientInformation.setStyleName("patientview"); projDescription.setMargin(new MarginInfo(true, false, true, true)); projDescription.setSpacing(true); projDescription.setWidth("100%"); return projDescription; }
From source file:de.uni_tuebingen.qbic.qbicmainportlet.PatientView.java
License:Open Source License
VerticalLayout initMemberSection() {
VerticalLayout projMembers = new VerticalLayout();
projMembers.setCaption("Members");
membersSection = new VerticalLayout();
Component membersContent = new VerticalLayout();
// membersContent.setIcon(FontAwesome.USERS);
// membersContent.setCaption("Members");
membersSection.addComponent(membersContent);
// membersSection.setMargin(new MarginInfo(false, false, false, true));
membersSection.setWidth("100%");
membersSection.setSpacing(true);//from w w w. j ava2s . c o m
membersSection.setMargin(new MarginInfo(true, false, true, true));
projMembers.addComponent(membersSection);
projMembers.setMargin(new MarginInfo(true, false, true, true));
projMembers.setWidth("100%");
projMembers.setSpacing(true);
return projMembers;
}