Merge pull request #4462 from inception-project/feature/4461-Show-cla…

…ss-in-class-tree-when-selecting-a-class

#4461 - Show class in class tree when selecting a class

inception/inception-concept-linking/src/main/java/de/tudarmstadt/ukp/inception/conceptlinking/service/ConceptLinkingServiceImpl.java

@@ -434,10 +434,10 @@ private CandidateEntity initCandidate(CandidateEntity candidate, String aQuery,
     public List<KBHandle> rankCandidates(String aQuery, String aMention, Set<KBHandle> aCandidates,
             CAS aCas, int aBegin)
     {
-        long startTime = currentTimeMillis();
+        var startTime = currentTimeMillis();
 
         // Set the feature values
-        List<CandidateEntity> candidates = aCandidates.stream() //
+        var candidates = aCandidates.stream() //
                 .map(CandidateEntity::new) //
                 .map(candidate -> initCandidate(candidate, aQuery, aMention, aCas, aBegin))
                 .map(candidate -> {
@@ -452,7 +452,7 @@ public List<KBHandle> rankCandidates(String aQuery, String aMention, Set<KBHandl
         // Sort candidates by multiple keys.
         candidates.sort(BaselineRankingStrategy.getInstance());
 
-        List<KBHandle> results = candidates.stream() //
+        var results = candidates.stream() //
                 .map(candidate -> {
                     KBHandle handle = candidate.getHandle();
                     handle.setDebugInfo(String.valueOf(candidate.getFeatures()));
@@ -463,13 +463,13 @@ public List<KBHandle> rankCandidates(String aQuery, String aMention, Set<KBHandl
                 }) //
                 .collect(Collectors.toList());
 
-        int rank = 1;
-        for (KBHandle handle : results) {
+        var rank = 1;
+        for (var handle : results) {
             handle.setRank(rank);
             rank++;
         }
 
-        long duration = currentTimeMillis() - startTime;
+        var duration = currentTimeMillis() - startTime;
         log.debug("Ranked [{}] candidates for mention [{}] and query [{}] in [{}] ms",
                 results.size(), aMention, aQuery, duration);
 

inception/inception-kb/src/main/java/de/tudarmstadt/ukp/inception/kb/graph/KBHandle.java

@@ -242,7 +242,7 @@ public void setScore(double aScore)
 
     public static KBHandle of(KBObject aObject)
     {
-        return new KBHandle(aObject.getIdentifier(), aObject.getUiLabel());
+        return aObject.toKBHandle();
     }
 
     @SuppressWarnings("unchecked")

inception/inception-kb/src/main/java/de/tudarmstadt/ukp/inception/kb/graph/KBObject.java

@@ -122,6 +122,7 @@ default KBHandle toKBHandle()
         handle.setName(getName());
         handle.setLanguage(getLanguage());
         handle.setDescription(getDescription());
+        handle.setKB(getKB());
         return handle;
     }
 }

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/ConceptTreePanel.java

@@ -17,6 +17,7 @@
  */
 package de.tudarmstadt.ukp.inception.ui.kb;
 
+import java.lang.invoke.MethodHandles;
 import java.util.HashSet;
 import java.util.Objects;
 import java.util.Optional;
@@ -36,6 +37,9 @@
 import org.apache.wicket.model.Model;
 import org.apache.wicket.model.ResourceModel;
 import org.apache.wicket.spring.injection.annot.SpringBean;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.wicketstuff.event.annotation.OnEvent;
 
 import de.tudarmstadt.ukp.inception.kb.IriConstants;
 import de.tudarmstadt.ukp.inception.kb.KnowledgeBaseService;
@@ -51,11 +55,14 @@ public class ConceptTreePanel
 {
     private static final long serialVersionUID = -4032884234215283745L;
 
+    private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+
     private @SpringBean KnowledgeBaseService kbService;
 
     private IModel<KBObject> selectedConcept;
     private IModel<KnowledgeBase> kbModel;
     private IModel<ConceptTreeProviderOptions> options;
+    private AbstractTree<KBObject> tree;
 
     public ConceptTreePanel(String aId, IModel<KnowledgeBase> aKbModel,
             IModel<KBObject> selectedConceptModel)
@@ -68,7 +75,25 @@ public ConceptTreePanel(String aId, IModel<KnowledgeBase> aKbModel,
         kbModel = aKbModel;
         options = Model.of(new ConceptTreeProviderOptions());
 
-        AbstractTree<KBObject> tree = new DefaultNestedTree<KBObject>("tree",
+        tree = createConceptTree();
+        add(tree);
+
+        var addLink = new LambdaAjaxLink("add",
+                _target -> send(getPage(), Broadcast.BREADTH, new AjaxNewConceptEvent(_target)));
+        addLink.add(new Label("label", new ResourceModel("concept.list.add")));
+        addLink.add(new WriteProtectionBehavior(kbModel));
+        add(addLink);
+
+        var form = new Form<ConceptTreeProviderOptions>("form", CompoundPropertyModel.of(options));
+        form.add(new CheckBox("showAllConcepts").setOutputMarkupId(true) //
+                .add(new LambdaAjaxFormSubmittingBehavior("change",
+                        this::actionPreferenceChanged)));
+        add(form);
+    }
+
+    private DefaultNestedTree<KBObject> createConceptTree()
+    {
+        return new DefaultNestedTree<KBObject>("tree",
                 new ConceptTreeProvider(kbService, kbModel, options), Model.ofSet(new HashSet<>()))
         {
             private static final long serialVersionUID = -270550186750480253L;
@@ -112,27 +137,29 @@ protected boolean isSelected()
                 };
             }
         };
-        add(tree);
-
-        LambdaAjaxLink addLink = new LambdaAjaxLink("add",
-                target -> send(getPage(), Broadcast.BREADTH, new AjaxNewConceptEvent(target)));
-        addLink.add(new Label("label", new ResourceModel("concept.list.add")));
-        addLink.add(new WriteProtectionBehavior(kbModel));
-        add(addLink);
+    }
 
-        Form<ConceptTreeProviderOptions> form = new Form<>("form",
-                CompoundPropertyModel.of(options));
-        form.add(new CheckBox("showAllConcepts").setOutputMarkupId(true) //
-                .add(new LambdaAjaxFormSubmittingBehavior("change",
-                        this::actionPreferenceChanged)));
-        add(form);
+    @OnEvent
+    public void onConceptSelectionEvent(AjaxConceptSelectionEvent aEvent)
+    {
+        // Try expanding the path to the selected concept
+        if (selectedConcept.isPresent().getObject()) {
+            var c = (KBObject) selectedConcept.getObject();
+            var parents = kbService.getParentConceptList(c.getKB(), c.getIdentifier(), false);
+            LOG.debug("Trying to expand {}", parents);
+            for (var h : parents) {
+                tree.expand(h);
+            }
+            aEvent.getTarget().add(this);
+            aEvent.getTarget().appendJavaScript("document.querySelector('#" + getMarkupId()
+                    + " .selected')?.scrollIntoView({block: 'center'});");
+        }
     }
 
     private void actionSelectionChanged(AjaxRequestTarget aTarget)
     {
         // if the selection changes, publish an event denoting the change
-        AjaxConceptSelectionEvent e = new AjaxConceptSelectionEvent(aTarget,
-                selectedConcept.getObject().toKBHandle());
+        var e = new AjaxConceptSelectionEvent(aTarget, selectedConcept.getObject().toKBHandle());
         send(getPage(), Broadcast.BREADTH, e);
     }
 

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/ConceptTreeProvider.java

@@ -99,7 +99,7 @@ public boolean hasChildren(KBObject aNode)
                 // To avoid having to send a query to the KB for every child node, just assume
                 // that there might be child nodes and show the expander until we have actually
                 // loaded the children, cached them and can show the true information.
-                List<KBHandle> children = childrensCache.get(aNode);
+                var children = childrensCache.get(aNode);
                 if (children == null) {
                     return true;
                 }
@@ -135,7 +135,7 @@ public Iterator<? extends KBObject> getChildren(KBObject aNode)
         try {
             // If the KB is read-only, then we cache the values and re-use the cached values.
             if (kbModel.getObject().isReadOnly()) {
-                List<KBHandle> children = childrensCache.get(aNode);
+                var children = childrensCache.get(aNode);
                 if (children == null) {
                     children = kbService.listChildConcepts(kbModel.getObject(),
                             aNode.getIdentifier(), options.getObject().isShowAllConcepts());

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/KnowledgeBasePanel.java

@@ -22,7 +22,6 @@
 import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
-import java.util.stream.Collectors;
 
 import org.apache.wicket.AttributeModifier;
 import org.apache.wicket.Component;
@@ -151,16 +150,16 @@ public KnowledgeBasePanel(String id, IModel<Project> aProjectModel,
     private KnowledgeBaseItemAutoCompleteField createSearchField(String aId,
             IModel<KBHandle> aHandleModel, IModel<Project> aProjectModel)
     {
-        KnowledgeBaseItemAutoCompleteField field = new KnowledgeBaseItemAutoCompleteField(aId,
-                aHandleModel, _query -> listSearchResults(aProjectModel.getObject(), _query))
+        var field = new KnowledgeBaseItemAutoCompleteField(aId, aHandleModel,
+                _query -> listSearchResults(aProjectModel.getObject(), _query))
         {
             private static final long serialVersionUID = 3188821013226116770L;
 
             @Override
             protected void onSelected(AjaxRequestTarget aTarget)
             {
-                KBHandle selectedResource = this.getModelObject();
-                Optional<KBObject> optKbObject = kbService.readItem(kbModel.getObject(),
+                var selectedResource = this.getModelObject();
+                var optKbObject = kbService.readItem(kbModel.getObject(),
                         selectedResource.getIdentifier());
 
                 if (!optKbObject.isPresent()) {
@@ -186,12 +185,10 @@ protected void onSelected(AjaxRequestTarget aTarget)
      */
     private List<KBHandle> listSearchResults(Project aProject, String aTypedString)
     {
-        List<KBHandle> results;
-        KnowledgeBase kb = kbModel.getObject();
-        results = conceptLinkingService.searchItems(kb, aTypedString).stream()
-                .limit(entityLinkingProperties.getCandidateDisplayLimit())
-                .collect(Collectors.toList());
-        return results;
+        var kb = kbModel.getObject();
+        return conceptLinkingService.searchItems(kb, aTypedString).stream() //
+                .limit(entityLinkingProperties.getCandidateDisplayLimit()) //
+                .toList();
     }
 
     /**
@@ -204,8 +201,8 @@ private void sendSelectionChangedEvents(AjaxRequestTarget aTarget, KBObject aKbO
                     new AjaxConceptSelectionEvent(aTarget, KBHandle.of(aKbObject), true));
         }
         else if (aKbObject instanceof KBInstance) {
-            List<KBHandle> conceptsForInstance = kbService
-                    .getConceptForInstance(kbModel.getObject(), aKbObject.getIdentifier(), true);
+            var conceptsForInstance = kbService.getConceptForInstance(kbModel.getObject(),
+                    aKbObject.getIdentifier(), true);
 
             if (!conceptsForInstance.isEmpty()) {
                 send(getPage(), Broadcast.BREADTH,

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/project/KnowledgeBaseDetailsPanel.java

@@ -23,11 +23,8 @@
 import static java.util.Collections.emptyMap;
 import static org.apache.commons.lang3.exception.ExceptionUtils.getRootCauseMessage;
 
-import java.io.File;
 import java.io.FileInputStream;
-import java.io.InputStream;
 
-import org.apache.commons.lang3.tuple.Pair;
 import org.apache.wicket.ajax.AjaxRequestTarget;
 import org.apache.wicket.feedback.IFeedback;
 import org.apache.wicket.markup.html.form.Form;
@@ -147,7 +144,7 @@ private void actionSave(AjaxRequestTarget aTarget, Form<KnowledgeBaseWrapper> aF
         aTarget.add(this);
 
         try {
-            KnowledgeBaseWrapper kbw = kbwModel.getObject();
+            var kbw = kbwModel.getObject();
 
             // if dealing with a remote repository and a non-empty URL, get a new
             // RepositoryImplConfig for the new URL; otherwise keep using the existing config
@@ -167,8 +164,8 @@ private void actionSave(AjaxRequestTarget aTarget, Form<KnowledgeBaseWrapper> aF
 
             if (kb.getType() == LOCAL) {
                 kbService.defineBaseProperties(kb);
-                for (Pair<String, File> f : kbw.getFiles()) {
-                    try (InputStream is = new FileInputStream(f.getValue())) {
+                for (var f : kbw.getFiles()) {
+                    try (var is = new FileInputStream(f.getValue())) {
                         kbService.importData(kb, f.getValue().getName(), is);
                         success("Imported: " + f.getKey());
                     }

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/project/ProjectKnowledgeBasePanel.properties

@@ -60,6 +60,7 @@ kb.wizard.steps.accessSpecific.description=Description
 kb.wizard.steps.accessSpecific.hostInstitutionName=Host Institution
 kb.wizard.steps.accessSpecific.authorName=Author(s)
 kb.wizard.steps.accessSpecific.homepage=Homepage
+kb.wizard.steps.accessSpecific.license=License
 kb.wizard.title=New Knowledge Base
 
 kb.settings.general = General Settings
@@ -102,7 +103,7 @@ kb.export.nt=N-Triples
 RepositoryType.LOCAL=Local
 RepositoryType.REMOTE=Remote (SPARQL)
 
-kb.reification = Reification        
+kb.reification = Reification
 
 SchemaProfile.RDFSCHEMA=RDF
 SchemaProfile.OWLSCHEMA=OWL

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/project/local/LocalRepositorySettingsPanel.java

@@ -389,25 +389,25 @@ private void actionDownloadKbAndSetIRIs(AjaxRequestTarget aTarget)
     {
         try {
             if (selectedKnowledgeBaseProfile != null) {
-                String accessUrl = selectedKnowledgeBaseProfile.getAccess().getAccessUrl();
+                var accessUrl = selectedKnowledgeBaseProfile.getAccess().getAccessUrl();
 
-                FileUploadDownloadHelper fileUploadDownloadHelper = new FileUploadDownloadHelper(
-                        getApplication());
+                var fileUploadDownloadHelper = new FileUploadDownloadHelper(getApplication());
 
-                if (!accessUrl.startsWith(CLASSPATH_PREFIX)) {
-                    File tmpFile = fileUploadDownloadHelper
-                            .writeFileDownloadToTemporaryFile(accessUrl, getModel());
-                    getModel().getObject().putFile(selectedKnowledgeBaseProfile.getName(), tmpFile);
-                }
-                else {
+                if (accessUrl.startsWith(CLASSPATH_PREFIX)) {
                     // import from classpath
-                    File kbFile = fileUploadDownloadHelper
+                    var kbFile = fileUploadDownloadHelper
                             .writeClasspathResourceToTemporaryFile(accessUrl, getModel());
                     getModel().getObject().putFile(selectedKnowledgeBaseProfile.getName(), kbFile);
                 }
+                else if (accessUrl != null) {
+                    var tmpFile = fileUploadDownloadHelper
+                            .writeFileDownloadToTemporaryFile(accessUrl, getModel());
+                    getModel().getObject().putFile(selectedKnowledgeBaseProfile.getName(), tmpFile);
+                }
 
-                KnowledgeBase kb = getModel().getObject().getKb();
+                var kb = getModel().getObject().getKb();
                 kb.applyRootConcepts(selectedKnowledgeBaseProfile);
+                kb.applyAdditionalMatchingProperties(selectedKnowledgeBaseProfile);
                 kb.applyMapping(selectedKnowledgeBaseProfile.getMapping());
                 kb.setFullTextSearchIri(
                         selectedKnowledgeBaseProfile.getAccess().getFullTextSearchIri());

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/project/remote/RemoteRepositorySettingsPanel.java

@@ -42,7 +42,6 @@
 import org.apache.wicket.model.IModel;
 import org.apache.wicket.model.Model;
 
-import de.tudarmstadt.ukp.inception.kb.model.KnowledgeBase;
 import de.tudarmstadt.ukp.inception.kb.yaml.KnowledgeBaseInfo;
 import de.tudarmstadt.ukp.inception.kb.yaml.KnowledgeBaseProfile;
 import de.tudarmstadt.ukp.inception.security.client.auth.AuthenticationTraitsEditor;
@@ -219,11 +218,11 @@ protected void populateItem(ListItem<KnowledgeBaseProfile> item)
     private void actionPopulate(AjaxRequestTarget aTarget, KnowledgeBaseProfile aProfile)
     {
         // set all the fields according to the chosen profile
-        KnowledgeBaseWrapper kbw = getModel().getObject();
+        var kbw = getModel().getObject();
         kbw.setUrl(aProfile.getAccess().getAccessUrl());
         // sets root concepts list - if null then an empty list otherwise change the
         // values to IRI and populate the list
-        KnowledgeBase kb = kbw.getKb();
+        var kb = kbw.getKb();
         kb.applyRootConcepts(aProfile);
         kb.applyAdditionalMatchingProperties(aProfile);
         kb.applyMapping(aProfile.getMapping());