Merge branch 'release/30.x'

* release/30.x:
  Update maven.yml
  No issue. Added GH actions file
  #4428 - Slow knowledge-base lookups on relation layers
  #4428 - Slow knowledge-base lookups on relation layers
  #4428 - Slow knowledge-base lookups on relation layers

% Conflicts:
%	.github/workflows/maven.yml

.github/workflows/maven.yml

@@ -28,7 +28,7 @@ jobs:
         distribution: 'temurin'
         cache: maven
     - name: Build with Maven
-      run: mvn --no-transfer-progress -B clean package -T2 --file pom.xml
+      run: mvn --no-transfer-progress -B clean package --file pom.xml
 
     # Fails with error message - no idea why...
     # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive

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

@@ -384,8 +384,7 @@ public List<KBHandle> disambiguate(KnowledgeBase aKB, String aConceptScope,
             ConceptFeatureValueType aValueType, String aQuery, String aMention,
             int aMentionBeginOffset, CAS aCas)
     {
-        Set<KBHandle> candidates = generateCandidates(aKB, aConceptScope, aValueType, aQuery,
-                aMention);
+        var candidates = generateCandidates(aKB, aConceptScope, aValueType, aQuery, aMention);
         return rankCandidates(aQuery, aMention, candidates, aCas, aMentionBeginOffset);
     }
 

inception/inception-kb/src/main/java/de/tudarmstadt/ukp/inception/kb/querybuilder/SPARQLQueryBuilder.java

@@ -1622,7 +1622,10 @@ private String asRegexp(String aValue)
         String value = aValue;
         // Escape metacharacters
         // value = value.replaceAll("[{}()\\[\\].+*?^$\\\\|]", "\\\\\\\\$0");
-        value = value.replaceAll("[{}()\\[\\].+*?^$\\\\|]+", ".+");
+        // Replace metacharacters with a match for any single char (.+ would be too slow)
+        value = value.replaceAll("[{}()\\[\\].+*?^$\\\\|]+", ".");
+        // Drop metacharacters
+        // value = value.replaceAll("[{}()\\[\\].+*?^$\\\\|]+", " ");
         // Replace consecutive whitespace or control chars with a whitespace matcher
         value = value.replaceAll("[\\p{Space}\\p{Cntrl}]+", "\\\\s+");
         return value;
@@ -1980,8 +1983,13 @@ public List<KBHandle> asHandles(RepositoryConnection aConnection, boolean aAll)
             results = evaluateListQuery(tupleQuery, aAll);
             results.sort(comparing(KBObject::getUiLabel, CASE_INSENSITIVE_ORDER));
 
-            LOG.debug("[{}] Query returned {} results in {}ms", queryId, results.size(),
-                    currentTimeMillis() - startTime);
+            long duration = currentTimeMillis() - startTime;
+            LOG.debug("[{}] Query returned {} results in {}ms {}", queryId, results.size(),
+                    duration, duration > 1000 ? "-- SLOW QUERY!" : "");
+
+            if (duration > 1000 && !LOG.isTraceEnabled()) {
+                LOG.debug("[{}] Slow query: {}", queryId, queryString);
+            }
 
             return results;
         }
@@ -2026,8 +2034,13 @@ public boolean exists(RepositoryConnection aConnection, boolean aAll)
             TupleQuery tupleQuery = aConnection.prepareTupleQuery(queryString);
             boolean result = !evaluateListQuery(tupleQuery, aAll).isEmpty();
 
-            LOG.debug("[{}] Query returned {} in {}ms", queryId, result,
-                    currentTimeMillis() - startTime);
+            long duration = currentTimeMillis() - startTime;
+            LOG.debug("[{}] Query returned {} in {}ms {}", queryId, result, duration,
+                    duration > 1000 ? "-- SLOW QUERY!" : "");
+
+            if (duration > 1000 && !LOG.isTraceEnabled()) {
+                LOG.debug("[{}] Slow query: {}", queryId, queryString);
+            }
 
             return result;
         }
@@ -2060,8 +2073,14 @@ public Optional<KBHandle> asHandle(RepositoryConnection aConnection, boolean aAl
             tupleQuery.setIncludeInferred(includeInferred);
             result = evaluateListQuery(tupleQuery, aAll).stream().findFirst();
 
-            LOG.debug("[{}] Query returned a result in {}ms", queryId,
-                    currentTimeMillis() - startTime);
+            long duration = currentTimeMillis() - startTime;
+            LOG.debug("[{}] Query returned a result in {}ms {}", queryId, duration,
+                    duration > 1000 ? "-- SLOW QUERY!" : "");
+
+            if (duration > 1000 && !LOG.isTraceEnabled()) {
+                LOG.debug("[{}] Slow query: {}", queryId, queryString);
+            }
+
             return result;
         }
         catch (QueryEvaluationException e) {

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

@@ -32,7 +32,6 @@
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.uima.cas.CAS;
 import org.apache.wicket.MarkupContainer;
 import org.apache.wicket.core.request.handler.IPartialPageRequestHandler;
 import org.apache.wicket.feedback.IFeedback;
@@ -131,7 +130,7 @@ protected List<KBHandle> getCandidates(IModel<AnnotatorState> aStateModel,
             AnnotationFeature feat = getModelObject().feature;
 
             var traits = readFeatureTraits(feat);
-            String repoId = traits.getRepositoryId();
+            var repoId = traits.getRepositoryId();
             // Check if kb is actually enabled
             if (!(repoId == null || kbService.isKnowledgeBaseEnabled(feat.getProject(), repoId))) {
                 return Collections.emptyList();
@@ -140,12 +139,23 @@ protected List<KBHandle> getCandidates(IModel<AnnotatorState> aStateModel,
             // If there is a selection, we try obtaining its text from the CAS and use it as an
             // additional item in the query. Note that there is not always a mention, e.g. when the
             // feature is used in a document-level annotations.
-            CAS cas = aHandler != null ? aHandler.getEditorCas() : null;
-            String mention = aStateModel != null ? aStateModel.getObject().getSelection().getText()
-                    : null;
-            int mentionBegin = aStateModel != null
-                    ? aStateModel.getObject().getSelection().getBegin()
-                    : -1;
+            var cas = aHandler != null ? aHandler.getEditorCas() : null;
+
+            String mention = null;
+            int mentionBegin = -1;
+
+            if (aStateModel != null) {
+                var selection = aStateModel.getObject().getSelection();
+                if (selection.isSpan()) {
+                    mention = selection.getText();
+                    mentionBegin = selection.getBegin();
+                }
+
+                if (selection.isArc()) {
+                    mention = selection.getOriginText() + " " + selection.getTargetText();
+                    mentionBegin = selection.getBegin();
+                }
+            }
 
             choices = clService.getLinkingInstancesInKBScope(traits.getRepositoryId(),
                     traits.getScope(), traits.getAllowedValueType(), finalInput, mention,

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/feature/ConceptFeatureTraitsEditor.html

@@ -41,7 +41,7 @@
         <wicket:label key="scope"/>
       </label>
       <div class="col-sm-8">
-        <input wicket:id="scope" class="form-control w-100"/>
+        <input wicket:id="scope" class="w-100"/>
       </div>
     </div>
   </form>

inception/inception-ui-kb/src/main/resources/META-INF/asciidoc/user-guide/knowledge_base.adoc

@@ -41,6 +41,7 @@ The same is true for the object of a statement: After choosing the property for
 
 4. *KB Resource*: This is provided as an option when the property has a range as a particular concept from the knowledge base. In this option, the user is provided with an auto-complete field with a list of knowledge base entities. This includes the subclass and instances of the range specified for the property.
 
+[[sect_concept_features]]
 === Concept features
 
 Concept features are features that allow referencing concepts in the knowledge base during annotation.

inception/inception-ui-kb/src/main/resources/META-INF/asciidoc/user-guide/projects_knowledge-base.adoc

@@ -225,7 +225,14 @@ user can choose one of the pre-configured mapping or provide a custom mapping.
 
 === Root Concepts
 
-In the advanced settings, the user can leverage this feature of KB settings when one doesn't want the entire knowledge base to be used and rather choose to identify some specific root concepts. This feature specially helps in case of large knowledge bases such as Wikidata.
+The knowledge base browser displays a class tree. By default, it tries to automatically determine the root classes of
+this tree. However, for very large KBs this can be slow. Also you might not be interested in browsing the entire KB
+but would rather focus on specific subtrees. In such cases, you can define the root concepts explicitly here.
+
+NOTE: This setting currently affects **only class tree in the knowledge base browser**. You can still search for concepts
+      that are outside of the subtrees induced by the root concepts using the search field on the knowledge-base page and you
+      can also still link concept features. to concepts outside the subtrees. In order to limit a concept feature to a particular
+      subtree, use the **Scope** setting in the <<sect_concept_features,concept feature settings>>.
 
 
 === Additional Matching Properties