Java tutorial
/******************************************************************************* * Copyright 2012 * Ubiquitous Knowledge Processing (UKP) Lab and FG Language Technology * Technische Universit?t Darmstadt * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. ******************************************************************************/ package de.tudarmstadt.ukp.clarin.webanno.monitoring.page; import static de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentStateTransition.ANNOTATION_FINISHED_TO_ANNOTATION_IN_PROGRESS; import static de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentStateTransition.ANNOTATION_IN_PROGRESS_TO_ANNOTATION_FINISHED; import static de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentStateTransition.IGNORE_TO_NEW; import static de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentStateTransition.NEW_TO_ANNOTATION_IN_PROGRESS; import static de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentStateTransition.NEW_TO_IGNORE; import static de.tudarmstadt.ukp.clarin.webanno.model.SourceDocumentStateTransition.CURATION_FINISHED_TO_CURATION_IN_PROGRESS; import static de.tudarmstadt.ukp.clarin.webanno.model.SourceDocumentStateTransition.CURATION_IN_PROGRESS_TO_CURATION_FINISHED; import static java.util.Arrays.asList; import java.awt.Color; import java.io.IOException; import java.io.Serializable; import java.text.DecimalFormat; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Collections; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.TreeMap; import org.apache.commons.lang.exception.ExceptionUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.uima.UIMAException; import org.apache.uima.jcas.JCas; import org.apache.wicket.AttributeModifier; import org.apache.wicket.Component; import org.apache.wicket.ajax.AjaxEventBehavior; import org.apache.wicket.ajax.AjaxRequestTarget; import org.apache.wicket.ajax.form.OnChangeAjaxBehavior; import org.apache.wicket.behavior.AttributeAppender; import org.apache.wicket.extensions.markup.html.repeater.data.grid.DataGridView; import org.apache.wicket.extensions.markup.html.repeater.data.grid.ICellPopulator; import org.apache.wicket.extensions.markup.html.repeater.data.table.AbstractColumn; import org.apache.wicket.extensions.markup.html.repeater.data.table.DefaultDataTable; import org.apache.wicket.extensions.markup.html.repeater.data.table.IColumn; import org.apache.wicket.markup.html.basic.Label; import org.apache.wicket.markup.html.form.CheckBox; import org.apache.wicket.markup.html.form.ChoiceRenderer; import org.apache.wicket.markup.html.form.DropDownChoice; import org.apache.wicket.markup.html.form.EnumChoiceRenderer; import org.apache.wicket.markup.html.form.Form; import org.apache.wicket.markup.html.form.ListChoice; import org.apache.wicket.markup.html.image.Image; import org.apache.wicket.markup.html.image.NonCachingImage; import org.apache.wicket.markup.html.panel.FeedbackPanel; import org.apache.wicket.markup.repeater.Item; import org.apache.wicket.model.AbstractReadOnlyModel; import org.apache.wicket.model.CompoundPropertyModel; import org.apache.wicket.model.IModel; import org.apache.wicket.model.LoadableDetachableModel; import org.apache.wicket.model.Model; import org.apache.wicket.request.resource.PackageResourceReference; import org.apache.wicket.request.resource.ResourceReference; import org.apache.wicket.spring.injection.annot.SpringBean; import org.jfree.chart.ChartFactory; import org.jfree.chart.JFreeChart; import org.jfree.chart.axis.NumberAxis; import org.jfree.chart.axis.NumberTickUnit; import org.jfree.chart.axis.TickUnits; import org.jfree.chart.plot.CategoryPlot; import org.jfree.chart.plot.PlotOrientation; import org.jfree.chart.renderer.category.BarRenderer; import org.jfree.chart.renderer.category.StandardBarPainter; import org.jfree.data.category.DefaultCategoryDataset; import org.jfree.ui.RectangleInsets; import org.jfree.util.UnitType; import org.springframework.dao.DataRetrievalFailureException; import org.springframework.security.core.context.SecurityContextHolder; import org.wicketstuff.annotation.mount.MountPath; import de.tudarmstadt.ukp.clarin.webanno.api.AnnotationService; import de.tudarmstadt.ukp.clarin.webanno.api.RepositoryService; import de.tudarmstadt.ukp.clarin.webanno.api.UserDao; import de.tudarmstadt.ukp.clarin.webanno.api.WebAnnoConst; import de.tudarmstadt.ukp.clarin.webanno.api.dao.SecurityUtil; import de.tudarmstadt.ukp.clarin.webanno.automation.AutomationService; import de.tudarmstadt.ukp.clarin.webanno.brat.curation.AgreementUtils; import de.tudarmstadt.ukp.clarin.webanno.brat.curation.AgreementUtils.AgreementReportExportFormat; import de.tudarmstadt.ukp.clarin.webanno.brat.curation.AgreementUtils.ConcreteAgreementMeasure; import de.tudarmstadt.ukp.clarin.webanno.brat.curation.CasDiff2; import de.tudarmstadt.ukp.clarin.webanno.brat.curation.CasDiff2.DiffAdapter; import de.tudarmstadt.ukp.clarin.webanno.brat.curation.CasDiff2.DiffResult; import de.tudarmstadt.ukp.clarin.webanno.brat.curation.CasDiff2.LinkCompareBehavior; import de.tudarmstadt.ukp.clarin.webanno.brat.curation.PairwiseAnnotationResult; import de.tudarmstadt.ukp.clarin.webanno.brat.curation.component.CurationPanel; import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument; import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentState; import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentStateTransition; import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature; import de.tudarmstadt.ukp.clarin.webanno.model.LinkMode; import de.tudarmstadt.ukp.clarin.webanno.model.MiraTemplate; import de.tudarmstadt.ukp.clarin.webanno.model.Mode; import de.tudarmstadt.ukp.clarin.webanno.model.PermissionLevel; import de.tudarmstadt.ukp.clarin.webanno.model.Project; import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument; import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocumentState; import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocumentStateTransition; import de.tudarmstadt.ukp.clarin.webanno.model.User; import de.tudarmstadt.ukp.clarin.webanno.monitoring.support.ChartImageResource; import de.tudarmstadt.ukp.clarin.webanno.monitoring.support.EmbeddableImage; import de.tudarmstadt.ukp.clarin.webanno.monitoring.support.TableDataProvider; import de.tudarmstadt.ukp.clarin.webanno.support.EntityModel; import de.tudarmstadt.ukp.clarin.webanno.webapp.home.page.ApplicationPageBase; import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData; import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token; /** * A Page To display different monitoring and statistics measurements tabularly and graphically. * * */ @MountPath("/monitoring.html") public class MonitoringPage extends ApplicationPageBase { private static final Log LOG = LogFactory.getLog(DocumentStatusColumnMetaData.class); private static final long serialVersionUID = -2102136855109258306L; private static final int CHART_WIDTH = 300; /** * The user column in the user-document status table */ public static final String USER = "user:"; /** * The document column in the user-document status table */ public static final String DOCUMENT = "document:"; public static final String CURATION = "curation"; public static final String LAST_ACCESS = "last access:"; public static final String LAST_ACCESS_ROW = "last access"; @SpringBean(name = "annotationService") private AnnotationService annotationService; @SpringBean(name = "automationService") private AutomationService automationService; @SpringBean(name = "documentRepository") private RepositoryService repository; @SpringBean(name = "userRepository") private UserDao userRepository; private final ProjectSelectionForm projectSelectionForm; private final MonitoringDetailForm monitoringDetailForm; private final Image annotatorsProgressImage; private final Image annotatorsProgressPercentageImage; private final Image overallProjectProgressImage; private TrainingResultForm trainingResultForm; private Label overview; private DefaultDataTable<?, ?> annotationDocumentStatusTable; private final Label projectName; private final AgreementForm agreementForm; private String result; private static final ResourceReference ICON_FINISHED = new PackageResourceReference(MonitoringPage.class, "accept.png"); private static final ResourceReference ICON_IGNORE = new PackageResourceReference(MonitoringPage.class, "lock.png"); private static final ResourceReference ICON_INPROGRESS = new PackageResourceReference(MonitoringPage.class, "resultset_next.png"); private static final ResourceReference ICON_NEW = new PackageResourceReference(MonitoringPage.class, "new.png"); private static final Map<Object, ResourceReference> ICONS; static { Map<Object, ResourceReference> icons = new HashMap<>(); icons.put(SourceDocumentState.ANNOTATION_FINISHED, ICON_FINISHED); icons.put(SourceDocumentState.CURATION_FINISHED, ICON_FINISHED); icons.put(SourceDocumentState.CURATION_IN_PROGRESS, ICON_INPROGRESS); icons.put(SourceDocumentState.ANNOTATION_IN_PROGRESS, ICON_INPROGRESS); icons.put(SourceDocumentState.NEW, ICON_NEW); icons.put(AnnotationDocumentState.FINISHED, ICON_FINISHED); icons.put(AnnotationDocumentState.IGNORE, ICON_IGNORE); icons.put(AnnotationDocumentState.IN_PROGRESS, ICON_INPROGRESS); icons.put(AnnotationDocumentState.NEW, ICON_NEW); ICONS = Collections.unmodifiableMap(icons); } @SuppressWarnings({ "unchecked", "rawtypes" }) public MonitoringPage() throws UIMAException, IOException, ClassNotFoundException { projectSelectionForm = new ProjectSelectionForm("projectSelectionForm"); monitoringDetailForm = new MonitoringDetailForm("monitoringDetailForm"); add(agreementForm = new AgreementForm("agreementForm")); trainingResultForm = new TrainingResultForm("trainingResultForm"); trainingResultForm.setVisible(false); add(trainingResultForm); annotatorsProgressImage = new NonCachingImage("annotator"); annotatorsProgressImage.setOutputMarkupPlaceholderTag(true); annotatorsProgressImage.setVisible(false); annotatorsProgressPercentageImage = new NonCachingImage("annotatorPercentage"); annotatorsProgressPercentageImage.setOutputMarkupPlaceholderTag(true); annotatorsProgressPercentageImage.setVisible(false); overallProjectProgressImage = new NonCachingImage("overallProjectProgressImage"); final Map<String, Integer> overallProjectProgress = getOverallProjectProgress(); overallProjectProgressImage.setImageResource(createProgressChart(overallProjectProgress, 100, true)); overallProjectProgressImage.setOutputMarkupPlaceholderTag(true); overallProjectProgressImage.setVisible(true); add(overallProjectProgressImage); add(overview = new Label("overview", "overview of projects")); add(projectSelectionForm); projectName = new Label("projectName", ""); Project project = repository.listProjects().get(0); List<List<String>> userAnnotationDocumentLists = new ArrayList<List<String>>(); List<SourceDocument> dc = repository.listSourceDocuments(project); List<SourceDocument> trainingDoc = new ArrayList<SourceDocument>(); for (SourceDocument sdc : dc) { if (sdc.isTrainingDocument()) { trainingDoc.add(sdc); } } dc.removeAll(trainingDoc); for (int j = 0; j < repository.listProjectUsersWithPermissions(project).size(); j++) { List<String> userAnnotationDocument = new ArrayList<String>(); userAnnotationDocument.add(""); for (int i = 0; i < dc.size(); i++) { userAnnotationDocument.add(""); } userAnnotationDocumentLists.add(userAnnotationDocument); } List<String> documentListAsColumnHeader = new ArrayList<String>(); documentListAsColumnHeader.add("Users"); for (SourceDocument d : dc) { documentListAsColumnHeader.add(d.getName()); } TableDataProvider prov = new TableDataProvider(documentListAsColumnHeader, userAnnotationDocumentLists); List<IColumn<?, ?>> cols = new ArrayList<IColumn<?, ?>>(); for (int i = 0; i < prov.getColumnCount(); i++) { cols.add(new DocumentStatusColumnMetaData(prov, i, new Project(), repository)); } annotationDocumentStatusTable = new DefaultDataTable("rsTable", cols, prov, 2); monitoringDetailForm.setVisible(false); add(monitoringDetailForm.add(annotatorsProgressImage).add(annotatorsProgressPercentageImage) .add(projectName).add(annotationDocumentStatusTable)); annotationDocumentStatusTable.setVisible(false); } private class ProjectSelectionForm extends Form<ProjectSelectionModel> { private static final long serialVersionUID = -1L; public ProjectSelectionForm(String id) { super(id, new CompoundPropertyModel<ProjectSelectionModel>(new ProjectSelectionModel())); add(new ListChoice<Project>("project") { private static final long serialVersionUID = 1L; { setChoices(new LoadableDetachableModel<List<Project>>() { private static final long serialVersionUID = 1L; @Override protected List<Project> load() { List<Project> allowedProject = new ArrayList<Project>(); String username = SecurityContextHolder.getContext().getAuthentication().getName(); User user = userRepository.get(username); List<Project> allProjects = repository.listProjects(); // if global admin, show all projects if (SecurityUtil.isSuperAdmin(repository, user)) { return allProjects; } // else only projects she is admin of for (Project project : allProjects) { if (SecurityUtil.isProjectAdmin(project, repository, user) || SecurityUtil.isCurator(project, repository, user)) { allowedProject.add(project); } } return allowedProject; } }); setChoiceRenderer(new ChoiceRenderer<Project>("name")); setNullValid(false); } @SuppressWarnings({ "unchecked", "rawtypes" }) @Override protected void onSelectionChanged(Project aNewSelection) { List<SourceDocument> sourceDocuments = repository.listSourceDocuments(aNewSelection); List<SourceDocument> trainingDoc = new ArrayList<SourceDocument>(); for (SourceDocument sdc : sourceDocuments) { if (sdc.isTrainingDocument()) { trainingDoc.add(sdc); } } sourceDocuments.removeAll(trainingDoc); if (aNewSelection == null) { return; } monitoringDetailForm.setModelObject(aNewSelection); monitoringDetailForm.setVisible(true); updateTrainingResultForm(aNewSelection); result = ""; agreementForm.setModelObject(new AgreementFormModel()); ProjectSelectionModel projectSelectionModel = ProjectSelectionForm.this.getModelObject(); projectSelectionModel.project = aNewSelection; projectSelectionModel.annotatorsProgress = new TreeMap<String, Integer>(); projectSelectionModel.annotatorsProgressInPercent = new TreeMap<String, Integer>(); projectSelectionModel.totalDocuments = sourceDocuments.size(); ProjectSelectionForm.this.setVisible(true); // Clear the cached CASes. When we switch to another project, we'll have to // reload them. updateAgreementTable(null, true); // Annotator's Progress if (projectSelectionModel.project != null) { projectSelectionModel.annotatorsProgressInPercent .putAll(getPercentageOfFinishedDocumentsPerUser(projectSelectionModel.project)); projectSelectionModel.annotatorsProgress .putAll(getFinishedDocumentsPerUser(projectSelectionModel.project)); } projectName.setDefaultModelObject(projectSelectionModel.project.getName()); overallProjectProgressImage.setVisible(false); overview.setVisible(false); annotatorsProgressImage.setImageResource(createProgressChart( projectSelectionModel.annotatorsProgress, projectSelectionModel.totalDocuments, false)); annotatorsProgressImage.setVisible(true); annotatorsProgressPercentageImage.setImageResource( createProgressChart(projectSelectionModel.annotatorsProgressInPercent, 100, true)); annotatorsProgressPercentageImage.setVisible(true); List<String> documentListAsColumnHeader = new ArrayList<String>(); documentListAsColumnHeader.add("Documents"); // A column for curation user annotation document status documentListAsColumnHeader.add(CURATION); // List of users with USER permission level List<User> users = repository.listProjectUsersWithPermissions(projectSelectionModel.project, PermissionLevel.USER); for (User user : users) { documentListAsColumnHeader.add(user.getUsername()); } List<List<String>> userAnnotationDocumentStatusList = new ArrayList<List<String>>(); // Add a timestamp row for every user. List<String> projectTimeStamp = new ArrayList<String>(); projectTimeStamp.add(LAST_ACCESS + LAST_ACCESS_ROW); // first // column if (repository.existsProjectTimeStamp(aNewSelection)) { projectTimeStamp.add(LAST_ACCESS + new SimpleDateFormat("dd/MM/yyyy HH:mm:ss") .format(repository.getProjectTimeStamp(aNewSelection))); } else { projectTimeStamp.add(LAST_ACCESS + "__"); } for (User user : users) { if (repository.existsProjectTimeStamp(projectSelectionModel.project, user.getUsername())) { projectTimeStamp.add(LAST_ACCESS + new SimpleDateFormat("dd/MM/yyyy HH:mm:ss") .format(repository.getProjectTimeStamp(projectSelectionModel.project, user.getUsername()))); } else { projectTimeStamp.add(LAST_ACCESS + "__"); } } userAnnotationDocumentStatusList.add(projectTimeStamp); for (SourceDocument document : sourceDocuments) { List<String> userAnnotationDocuments = new ArrayList<String>(); userAnnotationDocuments.add(DOCUMENT + document.getName()); // Curation Document status userAnnotationDocuments .add(CurationPanel.CURATION_USER + "-" + DOCUMENT + document.getName()); for (User user : users) { // annotation document status for this annotator userAnnotationDocuments.add(user.getUsername() + "-" + DOCUMENT + document.getName()); } userAnnotationDocumentStatusList.add(userAnnotationDocuments); } TableDataProvider provider = new TableDataProvider(documentListAsColumnHeader, userAnnotationDocumentStatusList); List<IColumn<?, ?>> columns = new ArrayList<IColumn<?, ?>>(); for (int i = 0; i < provider.getColumnCount(); i++) { columns.add(new DocumentStatusColumnMetaData(provider, i, projectSelectionModel.project, repository)); } annotationDocumentStatusTable.remove(); annotationDocumentStatusTable = new DefaultDataTable("rsTable", columns, provider, 20); annotationDocumentStatusTable.setOutputMarkupId(true); monitoringDetailForm.add(annotationDocumentStatusTable); } @Override protected boolean wantOnSelectionChangedNotifications() { return true; } @Override protected CharSequence getDefaultChoice(String aSelectedValue) { return ""; } }); } } Model<Project> projectModel = new Model<Project>() { private static final long serialVersionUID = -6394439155356911110L; @Override public Project getObject() { return projectSelectionForm.getModelObject().project; } }; private Map<String, Integer> getFinishedDocumentsPerUser(Project aProject) { Map<String, Integer> annotatorsProgress = new HashMap<String, Integer>(); if (aProject != null) { for (User user : repository.listProjectUsersWithPermissions(aProject, PermissionLevel.USER)) { for (SourceDocument document : repository.listSourceDocuments(aProject)) { if (repository.isAnnotationFinished(document, user)) { if (annotatorsProgress.get(user.getUsername()) == null) { annotatorsProgress.put(user.getUsername(), 1); } else { int previousValue = annotatorsProgress.get(user.getUsername()); annotatorsProgress.put(user.getUsername(), previousValue + 1); } } } if (annotatorsProgress.get(user.getUsername()) == null) { annotatorsProgress.put(user.getUsername(), 0); } } } return annotatorsProgress; } private Map<String, Integer> getPercentageOfFinishedDocumentsPerUser(Project aProject) { Map<String, Integer> annotatorsProgress = new HashMap<String, Integer>(); if (aProject != null) { for (User user : repository.listProjectUsersWithPermissions(aProject, PermissionLevel.USER)) { int finished = 0; int ignored = 0; int totalDocs = 0; List<SourceDocument> documents = repository.listSourceDocuments(aProject); List<SourceDocument> trainingDoc = new ArrayList<SourceDocument>(); for (SourceDocument sdc : documents) { if (sdc.isTrainingDocument()) { trainingDoc.add(sdc); } } documents.removeAll(trainingDoc); for (SourceDocument document : documents) { totalDocs++; if (repository.isAnnotationFinished(document, user)) { finished++; } else if (repository.existsAnnotationDocument(document, user)) { AnnotationDocument annotationDocument = repository.getAnnotationDocument(document, user); if (annotationDocument.getState().equals(AnnotationDocumentState.IGNORE)) { ignored++; } } } annotatorsProgress.put(user.getUsername(), (int) Math.round((double) (finished * 100) / (totalDocs - ignored))); } } return annotatorsProgress; } private Map<String, Integer> getOverallProjectProgress() { Map<String, Integer> overallProjectProgress = new LinkedHashMap<String, Integer>(); String username = SecurityContextHolder.getContext().getAuthentication().getName(); User user = userRepository.get(username); for (Project project : repository.listProjects()) { if (SecurityUtil.isCurator(project, repository, user) || SecurityUtil.isProjectAdmin(project, repository, user)) { int annoFinished = repository.listFinishedAnnotationDocuments(project).size(); int allAnno = repository.numberOfExpectedAnnotationDocuments(project); int progress = (int) Math.round((double) (annoFinished * 100) / (allAnno)); overallProjectProgress.put(project.getName(), progress); } } return overallProjectProgress; } static public class ProjectSelectionModel implements Serializable { protected int totalDocuments; private static final long serialVersionUID = -1L; public Project project; public Map<String, Integer> annotatorsProgress = new TreeMap<String, Integer>(); public Map<String, Integer> annotatorsProgressInPercent = new TreeMap<String, Integer>(); } private class MonitoringDetailForm extends Form<Project> { private static final long serialVersionUID = -1L; public MonitoringDetailForm(String id) { super(id, new CompoundPropertyModel<Project>(new EntityModel<Project>(new Project()))); } } private class AgreementForm extends Form<AgreementFormModel> { private static final long serialVersionUID = -1L; private ListChoice<AnnotationFeature> featureList; private AgreementTable agreementTable2; private DropDownChoice<ConcreteAgreementMeasure> measureDropDown; private DropDownChoice<LinkCompareBehavior> linkCompareBehaviorDropDown; private DropDownChoice<AgreementReportExportFormat> exportFormat; private CheckBox excludeIncomplete; public AgreementForm(String id) { super(id, new CompoundPropertyModel<AgreementFormModel>(new AgreementFormModel())); setOutputMarkupId(true); setOutputMarkupPlaceholderTag(true); add(measureDropDown = new DropDownChoice<ConcreteAgreementMeasure>("measure", asList(ConcreteAgreementMeasure.values()), new EnumChoiceRenderer<ConcreteAgreementMeasure>(MonitoringPage.this))); addUpdateAgreementTableBehavior(measureDropDown); add(linkCompareBehaviorDropDown = new DropDownChoice<LinkCompareBehavior>("linkCompareBehavior", asList(LinkCompareBehavior.values()), new EnumChoiceRenderer<LinkCompareBehavior>(MonitoringPage.this)) { private static final long serialVersionUID = 1L; @Override protected void onConfigure() { AgreementFormModel model = AgreementForm.this.getModelObject(); if (model != null && model.feature != null) { setVisible(!LinkMode.NONE.equals(model.feature.getLinkMode())); } else { setVisible(false); } } }); linkCompareBehaviorDropDown.setOutputMarkupId(true); linkCompareBehaviorDropDown.setOutputMarkupPlaceholderTag(true); addUpdateAgreementTableBehavior(linkCompareBehaviorDropDown); add(exportFormat = new DropDownChoice<AgreementReportExportFormat>("exportFormat", asList(AgreementReportExportFormat.values()), new EnumChoiceRenderer<AgreementReportExportFormat>(MonitoringPage.this))); exportFormat.add(new OnChangeAjaxBehavior() { private static final long serialVersionUID = -1L; @Override protected void onUpdate(AjaxRequestTarget aTarget) { // Actually nothing to do, we just want the Ajax behavior to update the model // object. } }); add(excludeIncomplete = new CheckBox("excludeIncomplete") { private static final long serialVersionUID = 1L; @Override protected void onConfigure() { super.onConfigure(); setEnabled(AgreementForm.this.getModelObject().measure.isNullValueSupported()); } }); addUpdateAgreementTableBehavior(excludeIncomplete); add(featureList = new ListChoice<AnnotationFeature>("feature") { private static final long serialVersionUID = 1L; { setOutputMarkupId(true); setChoices(new LoadableDetachableModel<List<AnnotationFeature>>() { private static final long serialVersionUID = 1L; @Override protected List<AnnotationFeature> load() { List<AnnotationFeature> features = annotationService .listAnnotationFeature((projectSelectionForm.getModelObject().project)); List<AnnotationFeature> unusedFeatures = new ArrayList<AnnotationFeature>(); for (AnnotationFeature feature : features) { if (feature.getLayer().getName().equals(Token.class.getName()) || feature.getLayer().getName().equals(WebAnnoConst.COREFERENCE_LAYER)) { unusedFeatures.add(feature); } } features.removeAll(unusedFeatures); return features; } }); setChoiceRenderer(new ChoiceRenderer<AnnotationFeature>() { private static final long serialVersionUID = -3370671999669664776L; @Override public Object getDisplayValue(AnnotationFeature aObject) { return aObject.getLayer().getUiName() + " : " + aObject.getUiName(); } }); setNullValid(false); } @Override protected CharSequence getDefaultChoice(String aSelectedValue) { return ""; } }); addUpdateAgreementTableBehavior(featureList); add(agreementTable2 = new AgreementTable("agreementTable", getModel(), new LoadableDetachableModel<PairwiseAnnotationResult>() { private static final long serialVersionUID = 1L; @Override protected PairwiseAnnotationResult load() { AnnotationFeature feature = featureList.getModelObject(); // Do not do any agreement if no feature has been selected yet. if (feature == null) { return null; } Map<String, List<JCas>> casMap = getJCases(); Project project = projectSelectionForm.getModelObject().project; List<DiffAdapter> adapters = CasDiff2.getAdapters(annotationService, project); AgreementFormModel pref = AgreementForm.this.getModelObject(); DiffResult diff = CasDiff2.doDiff(asList(feature.getLayer().getName()), adapters, pref.linkCompareBehavior, casMap); return AgreementUtils.getPairwiseAgreement(AgreementForm.this.getModelObject().measure, pref.excludeIncomplete, diff, feature.getLayer().getName(), feature.getName(), casMap); } })); } @Override protected void onConfigure() { ProjectSelectionModel model = projectSelectionForm.getModelObject(); setVisible(model != null && model.project != null); } private void addUpdateAgreementTableBehavior(Component aComponent) { aComponent.add(new OnChangeAjaxBehavior() { private static final long serialVersionUID = 1L; @Override protected void onUpdate(AjaxRequestTarget aTarget) { updateAgreementTable(aTarget, false); // // Adding this as well because when choosing a different measure, it may affect // // the ability to exclude incomplete configurations. // aTarget.add(excludeIncomplete); // aTarget.add(linkCompareBehaviorDropDown); // #1791 - for some reason the updateAgreementTableBehavior does not work // anymore on the linkCompareBehaviorDropDown if we add it explicitly here/ // control its visibility in onConfigure() // as a workaround, we currently just re-render the whole form aTarget.add(agreementForm); } }); } } static public class AgreementFormModel implements Serializable { private static final long serialVersionUID = -1L; public AnnotationFeature feature; public LinkCompareBehavior linkCompareBehavior = LinkCompareBehavior.LINK_TARGET_AS_LABEL; public boolean excludeIncomplete = false; public ConcreteAgreementMeasure measure = ConcreteAgreementMeasure.KRIPPENDORFF_ALPHA_NOMINAL_AGREEMENT; private boolean savedExcludeIncomplete = excludeIncomplete; private boolean savedNullSupported = measure.isNullValueSupported(); public AgreementReportExportFormat exportFormat = AgreementReportExportFormat.CSV; public void setMeasure(ConcreteAgreementMeasure aMeasure) { measure = aMeasure; // Did the null-support status change? if (savedNullSupported != measure.isNullValueSupported()) { savedNullSupported = measure.isNullValueSupported(); // If it changed, is null support locked or not? if (!measure.isNullValueSupported()) { // Is locked, so save what we had before and lock it savedExcludeIncomplete = excludeIncomplete; excludeIncomplete = true; } else { // Is not locked, so restore what we had before excludeIncomplete = savedExcludeIncomplete; } } } // This method must be here so Wicket sets the "measure" value through the setter instead // of using field injection public ConcreteAgreementMeasure getMeasure() { return measure; } } private void updateTrainingResultForm(Project aProject) { trainingResultForm.remove(); trainingResultForm = new TrainingResultForm("trainingResultForm"); add(trainingResultForm); trainingResultForm.setVisible(aProject.getMode().equals(Mode.AUTOMATION)); } private class TrainingResultForm extends Form<ResultModel> { private static final long serialVersionUID = 1037668483966897381L; ListChoice<MiraTemplate> selectedTemplate; public TrainingResultForm(String id) { super(id, new CompoundPropertyModel<ResultModel>(new ResultModel())); add(new Label("resultLabel", new LoadableDetachableModel<String>() { private static final long serialVersionUID = 891566759811286173L; @Override protected String load() { return result; } }).setOutputMarkupId(true)); add(new Label("annoDocs", new LoadableDetachableModel<String>() { private static final long serialVersionUID = 891566759811286173L; @Override protected String load() { MiraTemplate template = selectedTemplate.getModelObject(); if (template != null && automationService.existsAutomationStatus(template)) { return automationService.getAutomationStatus(template).getAnnoDocs() + ""; } else { return ""; } } }).setOutputMarkupId(true)); add(new Label("trainDocs", new LoadableDetachableModel<String>() { private static final long serialVersionUID = 891566759811286173L; @Override protected String load() { MiraTemplate template = selectedTemplate.getModelObject(); if (template != null && automationService.existsAutomationStatus(template)) { return automationService.getAutomationStatus(template).getTrainDocs() + ""; } else { return ""; } } }).setOutputMarkupId(true)); add(new Label("totalDocs", new LoadableDetachableModel<String>() { private static final long serialVersionUID = 891566759811286173L; @Override protected String load() { MiraTemplate template = selectedTemplate.getModelObject(); if (template != null && automationService.existsAutomationStatus(template)) { return automationService.getAutomationStatus(template).getTotalDocs() + ""; } else { return ""; } } }).setOutputMarkupId(true)); add(new Label("startTime", new LoadableDetachableModel<String>() { private static final long serialVersionUID = 891566759811286173L; @Override protected String load() { MiraTemplate template = selectedTemplate.getModelObject(); if (template != null && automationService.existsAutomationStatus(template)) { return automationService.getAutomationStatus(template).getStartime().toString(); } else { return ""; } } }).setOutputMarkupId(true)); add(new Label("endTime", new LoadableDetachableModel<String>() { private static final long serialVersionUID = 891566759811286173L; @Override protected String load() { MiraTemplate template = selectedTemplate.getModelObject(); if (template != null && automationService.existsAutomationStatus(template)) { if (automationService.getAutomationStatus(template).getEndTime() .equals(automationService.getAutomationStatus(template).getStartime())) { return "---"; } return automationService.getAutomationStatus(template).getEndTime().toString(); } else { return ""; } } }).setOutputMarkupId(true)); add(new Label("status", new LoadableDetachableModel<String>() { private static final long serialVersionUID = 891566759811286173L; @Override protected String load() { MiraTemplate template = selectedTemplate.getModelObject(); if (template != null && automationService.existsAutomationStatus(template)) { return automationService.getAutomationStatus(template).getStatus().getName(); } else { return ""; } } }).setOutputMarkupId(true)); add(selectedTemplate = new ListChoice<MiraTemplate>("layerResult") { private static final long serialVersionUID = 1L; { setChoices(new LoadableDetachableModel<List<MiraTemplate>>() { private static final long serialVersionUID = 1L; @Override protected List<MiraTemplate> load() { return automationService .listMiraTemplates(projectSelectionForm.getModelObject().project); } }); setChoiceRenderer(new ChoiceRenderer<MiraTemplate>() { private static final long serialVersionUID = -2000622431037285685L; @Override public Object getDisplayValue(MiraTemplate aObject) { return "[" + aObject.getTrainFeature().getLayer().getUiName() + "] " + (aObject.getTrainFeature().getTagset() == null ? aObject.getTrainFeature().getUiName() : aObject.getTrainFeature().getTagset().getName()); } }); setNullValid(false); } @Override protected CharSequence getDefaultChoice(String aSelectedValue) { return ""; } }); selectedTemplate.add(new OnChangeAjaxBehavior() { private static final long serialVersionUID = 7492425689121761943L; @Override protected void onUpdate(AjaxRequestTarget aTarget) { result = getModelObject().layerResult.getResult(); aTarget.add(TrainingResultForm.this); } }).setOutputMarkupId(true); } } public class ResultModel implements Serializable { private static final long serialVersionUID = 3611186385198494181L; public MiraTemplate layerResult; public String annoDocs; public String trainDocs; public String totalDocs; public String startTime; public String endTime; public String status; } // The CASes cannot be serialized, so we make them transient here. However, it does not matter // as we do not access the field directly but via getJCases() which will re-load them if // necessary, e.g. if the transient field is empty after a session is restored from a // persisted state. private transient Map<String, List<JCas>> cachedCASes; /** * Get the finished CASes used to compute agreement. */ private Map<String, List<JCas>> getJCases() { // Avoid reloading the CASes when switching features. if (cachedCASes != null) { return cachedCASes; } Project project = projectSelectionForm.getModelObject().project; List<User> users = repository.listProjectUsersWithPermissions(project, PermissionLevel.USER); List<SourceDocument> sourceDocuments = repository.listSourceDocuments(project); // Filter training documents out from the source documents. Training documents are not // being annotated // FIXME actually, listSourceDocuments() shouldn return training documents in the first // place. Cf. https://github.com/webanno/webanno/issues/23 List<SourceDocument> trainingDoc = new ArrayList<SourceDocument>(); for (SourceDocument sdc : sourceDocuments) { if (sdc.isTrainingDocument()) { trainingDoc.add(sdc); } } sourceDocuments.removeAll(trainingDoc); cachedCASes = new LinkedHashMap<>(); for (User user : users) { List<JCas> cases = new ArrayList<>(); for (SourceDocument document : sourceDocuments) { JCas jCas = null; // Load the CAS if there is a finished one. if (repository.existsAnnotationDocument(document, user)) { AnnotationDocument annotationDocument = repository.getAnnotationDocument(document, user); if (annotationDocument.getState().equals(AnnotationDocumentState.FINISHED)) { try { jCas = repository.readAnnotationCas(annotationDocument); repository.upgradeCas(jCas.getCas(), annotationDocument); // REC: I think there is no need to write the CASes here. We would not // want to interfere with currently active annotator users // Set the CAS name in the DocumentMetaData so that we can pick it // up in the Diff position for the purpose of debugging / transparency. DocumentMetaData documentMetadata = DocumentMetaData.get(jCas); documentMetadata.setDocumentId(annotationDocument.getDocument().getName()); documentMetadata.setCollectionId(annotationDocument.getProject().getName()); } catch (DataRetrievalFailureException e) { error(e.getCause().getMessage()); } catch (UIMAException e) { error(ExceptionUtils.getRootCause(e)); } catch (IOException e) { error(ExceptionUtils.getRootCause(e)); } } } // The next line can enter null values into the list if a user didn't work on this // source document yet. cases.add(jCas); } cachedCASes.put(user.getUsername(), cases); } return cachedCASes; } private void updateAgreementTable(AjaxRequestTarget aTarget, boolean aClearCache) { try { if (aClearCache) { cachedCASes = null; } agreementForm.agreementTable2.getDefaultModel().detach(); if (aTarget != null) { aTarget.add(agreementForm.agreementTable2); } } catch (Throwable e) { error(ExceptionUtils.getRootCauseMessage(e)); if (aTarget != null) { aTarget.addChildren(getPage(), FeedbackPanel.class); } } } private ChartImageResource createProgressChart(Map<String, Integer> chartValues, int aMaxValue, boolean aIsPercentage) { // fill dataset DefaultCategoryDataset dataset = new DefaultCategoryDataset(); for (String chartValue : chartValues.keySet()) { dataset.setValue(chartValues.get(chartValue), "Completion", chartValue); } // create chart JFreeChart chart = ChartFactory.createBarChart(null, null, null, dataset, PlotOrientation.HORIZONTAL, false, false, false); CategoryPlot plot = chart.getCategoryPlot(); plot.setInsets(new RectangleInsets(UnitType.ABSOLUTE, 0, 20, 0, 20)); plot.getRangeAxis().setRange(0.0, aMaxValue); ((NumberAxis) plot.getRangeAxis()).setNumberFormatOverride(new DecimalFormat("0")); // For documents lessan 10, avoid repeating the number of documents such // as 0 0 1 1 1 // NumberTickUnit automatically determin the range if (!aIsPercentage && aMaxValue <= 10) { TickUnits standardUnits = new TickUnits(); NumberAxis tick = new NumberAxis(); tick.setTickUnit(new NumberTickUnit(1)); standardUnits.add(tick.getTickUnit()); plot.getRangeAxis().setStandardTickUnits(standardUnits); } plot.setOutlineVisible(false); plot.setBackgroundPaint(null); BarRenderer renderer = new BarRenderer(); renderer.setBarPainter(new StandardBarPainter()); renderer.setShadowVisible(false); // renderer.setGradientPaintTransformer(new // StandardGradientPaintTransformer( // GradientPaintTransformType.HORIZONTAL)); renderer.setSeriesPaint(0, Color.BLUE); chart.getCategoryPlot().setRenderer(renderer); return new ChartImageResource(chart, CHART_WIDTH, 30 + (chartValues.size() * 18)); } /** * Build dynamic columns for the user's annotation documents status {@link DataGridView} */ public class DocumentStatusColumnMetaData extends AbstractColumn<List<String>, Object> { // private RepositoryService projectRepositoryService; private static final long serialVersionUID = 1L; private int columnNumber; private Project project; public DocumentStatusColumnMetaData(final TableDataProvider prov, final int colNumber, Project aProject, RepositoryService aProjectreRepositoryService) { super(new AbstractReadOnlyModel<String>() { private static final long serialVersionUID = 1L; @Override public String getObject() { return prov.getColNames().get(colNumber); } }); columnNumber = colNumber; project = aProject; // projectRepositoryService = aProjectreRepositoryService; } @Override public void populateItem(final Item<ICellPopulator<List<String>>> aCellItem, final String componentId, final IModel<List<String>> rowModel) { String username = SecurityContextHolder.getContext().getAuthentication().getName(); final User user = userRepository.get(username); int rowNumber = aCellItem.getIndex(); aCellItem.setOutputMarkupId(true); final String value = getCellValue(rowModel.getObject().get(columnNumber)).trim(); if (rowNumber == 0) { aCellItem.add(new Label(componentId, value.substring(value.indexOf(":") + 1))); } else if (value.startsWith(MonitoringPage.LAST_ACCESS)) { aCellItem.add(new Label(componentId, value.substring(value.indexOf(":") + 1))); aCellItem.add(AttributeModifier.append("class", "centering")); } else if (value.substring(0, value.indexOf(":")).equals(CurationPanel.CURATION_USER)) { SourceDocument document = repository.getSourceDocument(project, value.substring(value.indexOf(":") + 1)); SourceDocumentState state = document.getState(); // #770 - Disable per-document progress on account of slowing down monitoring page // if (iconNameForState.equals(AnnotationDocumentState.IN_PROGRESS.toString()) // && document.getSentenceAccessed() != 0) { // JCas jCas = null; // try { // jCas = projectRepositoryService.readJCas(document, document.getProject(), user); // } // catch (UIMAException e) { // LOG.info(ExceptionUtils.getRootCauseMessage(e)); // } // catch (ClassNotFoundException e) { // LOG.info(e.getMessage()); // } // catch (IOException e) { // LOG.info(e.getMessage()); // } // int totalSN = BratAjaxCasUtil.getNumberOfPages(jCas); // aCellItem.add(new Label(componentId, document.getSentenceAccessed() + "/"+totalSN)); // } // else { EmbeddableImage icon = new EmbeddableImage(componentId, ICONS.get(state)); icon.add(new AttributeAppender("style", "cursor: pointer", ";")); aCellItem.add(icon); // } aCellItem.add(AttributeModifier.append("class", "centering")); aCellItem.add(new AjaxEventBehavior("onclick") { private static final long serialVersionUID = -4213621740511947285L; @Override protected void onEvent(AjaxRequestTarget aTarget) { SourceDocument document = repository.getSourceDocument(project, value.substring(value.indexOf(":") + 1)); SourceDocumentState state = document.getState(); if (state.toString().equals(SourceDocumentState.CURATION_FINISHED.toString())) { try { changeSourceDocumentState(document, user, CURATION_FINISHED_TO_CURATION_IN_PROGRESS); } catch (IOException e) { LOG.info(e.getMessage()); } } else if (state.toString().equals(SourceDocumentState.CURATION_IN_PROGRESS.toString())) { try { changeSourceDocumentState(document, user, CURATION_IN_PROGRESS_TO_CURATION_FINISHED); } catch (IOException e) { LOG.info(e.getMessage()); } } else { aTarget.appendJavaScript( "alert('the state can only be changed explicitly by the curator')"); } updateAgreementTable(aTarget, true); aTarget.add(aCellItem); updateStats(aTarget, projectSelectionForm.getModelObject()); } }); } else { SourceDocument document = repository.getSourceDocument(project, value.substring(value.indexOf(":") + 1)); User annotator = userRepository.get(value.substring(0, value.indexOf(":"))); AnnotationDocumentState state; AnnotationDocument annoDoc = null; if (repository.existsAnnotationDocument(document, annotator)) { annoDoc = repository.getAnnotationDocument(document, annotator); state = annoDoc.getState(); } // user didn't even start working on it else { state = AnnotationDocumentState.NEW; AnnotationDocument annotationDocument = new AnnotationDocument(); annotationDocument.setDocument(document); annotationDocument.setName(document.getName()); annotationDocument.setProject(project); annotationDocument.setUser(annotator.getUsername()); annotationDocument.setState(state); try { repository.createAnnotationDocument(annotationDocument); } catch (IOException e) { LOG.info("Unable to get the LOG file"); } } // if state is in progress, add the last sentence number accessed // #770 - Disable per-document progress on account of slowing down monitoring page // if (annoDoc != null && (annoDoc.getSentenceAccessed() != 0) // && annoDoc.getState().equals(AnnotationDocumentState.IN_PROGRESS)) { // JCas jCas = null; // try { // jCas = projectRepositoryService.readJCas(document, document.getProject(), annotator); // } // catch (UIMAException e) { // LOG.info(ExceptionUtils.getRootCauseMessage(e)); // } // catch (ClassNotFoundException e) { // LOG.info(e.getMessage()); // } // catch (IOException e) { // LOG.info(e.getMessage()); // } // int totalSN = BratAjaxCasUtil.getNumberOfPages(jCas); // aCellItem.add(new Label(componentId, annoDoc.getSentenceAccessed() + "/"+totalSN)); // } // else { EmbeddableImage icon = new EmbeddableImage(componentId, ICONS.get(state)); icon.add(new AttributeAppender("style", "cursor: pointer", ";")); aCellItem.add(icon); // } aCellItem.add(AttributeModifier.append("class", "centering")); aCellItem.add(new AjaxEventBehavior("onclick") { private static final long serialVersionUID = -5089819284917455111L; @Override protected void onEvent(AjaxRequestTarget aTarget) { SourceDocument document = repository.getSourceDocument(project, value.substring(value.indexOf(":") + 1)); User user = userRepository.get(value.substring(0, value.indexOf(":"))); AnnotationDocumentState state; if (repository.existsAnnotationDocument(document, user)) { AnnotationDocument annoDoc = repository.getAnnotationDocument(document, user); state = annoDoc.getState(); if (state.toString().equals(AnnotationDocumentState.FINISHED.toString())) { changeAnnotationDocumentState(document, user, ANNOTATION_FINISHED_TO_ANNOTATION_IN_PROGRESS); } else if (state.toString().equals(AnnotationDocumentState.IN_PROGRESS.toString())) { changeAnnotationDocumentState(document, user, ANNOTATION_IN_PROGRESS_TO_ANNOTATION_FINISHED); } if (state.toString().equals(AnnotationDocumentState.NEW.toString())) { changeAnnotationDocumentState(document, user, NEW_TO_IGNORE); } if (state.toString().equals(AnnotationDocumentState.IGNORE.toString())) { changeAnnotationDocumentState(document, user, IGNORE_TO_NEW); } } // user didn't even start working on it else { AnnotationDocument annotationDocument = new AnnotationDocument(); annotationDocument.setDocument(document); annotationDocument.setName(document.getName()); annotationDocument.setProject(project); annotationDocument.setUser(user.getUsername()); annotationDocument.setState( AnnotationDocumentStateTransition.transition(NEW_TO_ANNOTATION_IN_PROGRESS)); try { repository.createAnnotationDocument(annotationDocument); } catch (IOException e) { LOG.info("Unable to get the LOG file"); } } updateAgreementTable(aTarget, true); aTarget.add(aCellItem); updateStats(aTarget, projectSelectionForm.getModelObject()); } }); } } private void updateStats(AjaxRequestTarget aTarget, ProjectSelectionModel aModel) { aModel.annotatorsProgress.clear(); aModel.annotatorsProgress.putAll(getFinishedDocumentsPerUser(project)); annotatorsProgressImage .setImageResource(createProgressChart(aModel.annotatorsProgress, aModel.totalDocuments, false)); aTarget.add(annotatorsProgressImage.setOutputMarkupId(true)); aModel.annotatorsProgressInPercent.clear(); aModel.annotatorsProgressInPercent.putAll(getPercentageOfFinishedDocumentsPerUser(project)); annotatorsProgressPercentageImage .setImageResource(createProgressChart(aModel.annotatorsProgressInPercent, 100, true)); aTarget.add(annotatorsProgressPercentageImage.setOutputMarkupId(true)); aTarget.add(monitoringDetailForm.setOutputMarkupId(true)); aTarget.add(agreementForm); } /** * Helper method to get the cell value for the user-annotation document status as * <b>username:documentName</b> * * @param aValue * @return */ private String getCellValue(String aValue) { // It is the user column, return user name if (aValue.startsWith(MonitoringPage.DOCUMENT)) { return aValue.substring(aValue.indexOf(MonitoringPage.DOCUMENT)); } // return as it is else if (aValue.startsWith(MonitoringPage.LAST_ACCESS)) { return aValue; } // Initialization of the appliaction, no project selected else if (project.getId() == 0) { return ""; } // It is document column, get the status from the database else { String username = aValue.substring(0, aValue.indexOf(MonitoringPage.DOCUMENT) - 1); String documentName = aValue .substring(aValue.indexOf(MonitoringPage.DOCUMENT) + MonitoringPage.DOCUMENT.length()); return username + ":" + documentName; } } /** * change the state of an annotation document. used to re-open closed documents * * @param aSourceDocument * @param aUser * @param aAnnotationDocumentStateTransition */ private void changeAnnotationDocumentState(SourceDocument aSourceDocument, User aUser, AnnotationDocumentStateTransition aAnnotationDocumentStateTransition) { AnnotationDocument annotationDocument = repository.getAnnotationDocument(aSourceDocument, aUser); annotationDocument .setState(AnnotationDocumentStateTransition.transition(aAnnotationDocumentStateTransition)); try { repository.createAnnotationDocument(annotationDocument); } catch (IOException e) { LOG.info("Unable to get the LOG file"); } } /** * change source document state when curation document state is changed. * * @param aSourceDocument * @param aUser * @param aSourceDocumentStateTransition * @throws IOException */ private void changeSourceDocumentState(SourceDocument aSourceDocument, User aUser, SourceDocumentStateTransition aSourceDocumentStateTransition) throws IOException { aSourceDocument.setState(SourceDocumentStateTransition.transition(aSourceDocumentStateTransition)); repository.createSourceDocument(aSourceDocument, aUser); } } }