Merge branch 'main' into refactoring/Upgrade-to-Spring-Boot-3

* main:
  #4400 - Display recoomender name in log instead of RecommenderContext
  #4397 - Better error message when PMC document cannot be found
  #4395 - BioC export cannot be enabled
  #2696 - Document-level recommendations
  #2696 - Document-level recommendations
  #2696 - Document-level recommendations
  #2696 - Document-level recommendations
  No issue: Plugin complains on Jenkins that git is not found but it is there - try bumping plugin version

inception/inception-brat-editor/src/test/java/de/tudarmstadt/ukp/clarin/webanno/brat/render/BratSerializerImplTest.java

@@ -23,6 +23,8 @@
 import static java.util.Arrays.asList;
 import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine;
 import static org.apache.uima.fit.factory.CollectionReaderFactory.createReader;
+import static org.apache.uima.fit.util.CasUtil.getType;
+import static org.apache.uima.fit.util.CasUtil.select;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.assertj.core.api.Assertions.contentOf;
 import static org.mockito.ArgumentMatchers.any;
@@ -32,6 +34,7 @@
 
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.text.AnnotationFS;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.fit.factory.JCasFactory;
 import org.dkpro.core.io.tcf.TcfReader;
@@ -59,6 +62,7 @@
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
 import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
 import de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
 import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
 import de.tudarmstadt.ukp.inception.annotation.feature.bool.BooleanFeatureSupport;
 import de.tudarmstadt.ukp.inception.annotation.feature.link.LinkFeatureSupport;
@@ -76,7 +80,6 @@
 import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
 import de.tudarmstadt.ukp.inception.schema.service.FeatureSupportRegistryImpl;
 import de.tudarmstadt.ukp.inception.support.json.JSONUtil;
-import de.tudarmstadt.ukp.inception.support.uima.WebAnnoCasUtil;
 
 @ExtendWith(MockitoExtension.class)
 public class BratSerializerImplTest
@@ -180,7 +183,7 @@ public void thatSentenceOrientedStrategyRenderCorrectly() throws Exception
         state.setAllAnnotationLayers(schemaService.listAnnotationLayer(project));
         state.setPagingStrategy(new SentenceOrientedPagingStrategy());
         state.getPreferences().setWindowSize(10);
-        state.setFirstVisibleUnit(WebAnnoCasUtil.getFirstSentence(cas));
+        state.setFirstVisibleUnit(getFirstSentence(cas));
         state.setProject(project);
         state.setDocument(sourceDocument, asList(sourceDocument));
 
@@ -219,7 +222,7 @@ public void thatLineOrientedStrategyRenderCorrectly() throws Exception
         AnnotatorState state = new AnnotatorStateImpl(Mode.ANNOTATION);
         state.setPagingStrategy(new LineOrientedPagingStrategy());
         state.getPreferences().setWindowSize(10);
-        state.setFirstVisibleUnit(WebAnnoCasUtil.getFirstSentence(cas));
+        state.setFirstVisibleUnit(getFirstSentence(cas));
         state.setProject(project);
         state.setDocument(sourceDocument, asList(sourceDocument));
 
@@ -258,7 +261,7 @@ public void thatTokenWrappingStrategyRenderCorrectly() throws Exception
         AnnotatorState state = new AnnotatorStateImpl(Mode.ANNOTATION);
         state.setPagingStrategy(new TokenWrappingPagingStrategy(80));
         state.getPreferences().setWindowSize(10);
-        state.setFirstVisibleUnit(WebAnnoCasUtil.getFirstSentence(cas));
+        state.setFirstVisibleUnit(getFirstSentence(cas));
         state.setProject(project);
         state.setDocument(sourceDocument, asList(sourceDocument));
 
@@ -281,4 +284,22 @@ public void thatTokenWrappingStrategyRenderCorrectly() throws Exception
         assertThat(contentOf(new File("src/test/resources/longlines.json"), UTF_8))
                 .isEqualToNormalizingNewlines(contentOf(new File(jsonFilePath), UTF_8));
     }
+
+    /**
+     * Get the internal address of the first sentence annotation from CAS. This will be used as a
+     * reference for moving forward/backward sentences positions
+     *
+     * @param aCas
+     *            The CAS object assumed to contains some sentence annotations
+     * @return the sentence number or -1 if aCas don't have sentence annotation
+     */
+    private static AnnotationFS getFirstSentence(CAS aCas)
+    {
+        AnnotationFS firstSentence = null;
+        for (AnnotationFS s : select(aCas, getType(aCas, Sentence.class))) {
+            firstSentence = s;
+            break;
+        }
+        return firstSentence;
+    }
 }

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

@@ -24,13 +24,13 @@
 import static de.tudarmstadt.ukp.inception.conceptlinking.model.CandidateEntity.KEY_QUERY;
 import static de.tudarmstadt.ukp.inception.conceptlinking.model.CandidateEntity.KEY_QUERY_BEST_MATCH_TERM_NC;
 import static de.tudarmstadt.ukp.inception.conceptlinking.model.CandidateEntity.KEY_QUERY_NC;
-import static de.tudarmstadt.ukp.inception.support.uima.WebAnnoCasUtil.selectSentenceCovering;
-import static de.tudarmstadt.ukp.inception.support.uima.WebAnnoCasUtil.selectTokensCovered;
 import static java.lang.System.currentTimeMillis;
 import static java.util.Arrays.asList;
 import static java.util.Collections.unmodifiableList;
 import static java.util.Comparator.comparingInt;
 import static java.util.stream.Collectors.toCollection;
+import static org.apache.uima.fit.util.CasUtil.getType;
+import static org.apache.uima.fit.util.CasUtil.select;
 
 import java.io.File;
 import java.net.URISyntaxException;
@@ -47,6 +47,7 @@
 import org.apache.commons.lang3.Validate;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.text.AnnotationFS;
+import org.apache.uima.fit.util.CasUtil;
 import org.eclipse.rdf4j.common.net.ParsedIRI;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -58,6 +59,8 @@
 import org.springframework.core.annotation.AnnotationAwareOrderComparator;
 
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
 import de.tudarmstadt.ukp.inception.conceptlinking.config.EntityLinkingProperties;
 import de.tudarmstadt.ukp.inception.conceptlinking.config.EntityLinkingPropertiesImpl;
 import de.tudarmstadt.ukp.inception.conceptlinking.config.EntityLinkingServiceAutoConfiguration;
@@ -513,4 +516,31 @@ public List<KBHandle> searchItems(KnowledgeBase aKB, String aQuery)
     {
         return disambiguate(aKB, null, ConceptFeatureValueType.ANY_OBJECT, aQuery, null, 0, null);
     }
+
+    /**
+     * Get the sentence based on the annotation begin offset
+     *
+     * @param aCas
+     *            the CAS.
+     * @param aBegin
+     *            the begin offset.
+     * @return the sentence.
+     */
+    private static AnnotationFS selectSentenceCovering(CAS aCas, int aBegin)
+    {
+        AnnotationFS currentSentence = null;
+        for (AnnotationFS sentence : select(aCas, getType(aCas, Sentence.class))) {
+            if (sentence.getBegin() <= aBegin && sentence.getEnd() > aBegin) {
+                currentSentence = sentence;
+                break;
+            }
+        }
+        return currentSentence;
+    }
+
+    private static Collection<AnnotationFS> selectTokensCovered(AnnotationFS aCover)
+    {
+        return CasUtil.selectCovered(aCover.getCAS(), getType(aCover.getCAS(), Token.class),
+                aCover);
+    }
 }

inception/inception-diag/src/main/java/de/tudarmstadt/ukp/clarin/webanno/diag/checks/UnreachableAnnotationsCheck.java

@@ -24,10 +24,13 @@
 import static org.apache.uima.cas.impl.Serialization.deserializeCASComplete;
 import static org.apache.uima.cas.impl.Serialization.serializeCASComplete;
 
+import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.FeatureStructure;
 import org.apache.uima.cas.impl.CASImpl;
 import org.apache.uima.resource.ResourceInitializationException;
 
@@ -93,8 +96,15 @@ public static CASImpl makeDummyCas()
 
     public static Map<String, Long> countFeatureStructures(CASImpl casImpl)
     {
-        return WebAnnoCasUtil.findAllFeatureStructures(casImpl).stream() //
+        return findAllFeatureStructures(casImpl).stream() //
                 .map(fs -> fs.getType().getName()) //
                 .collect(groupingBy(identity(), counting()));
     }
+
+    public static Set<FeatureStructure> findAllFeatureStructures(CAS aCas)
+    {
+        Set<FeatureStructure> allFSes = new LinkedHashSet<>();
+        ((CASImpl) aCas).walkReachablePlusFSsSorted(allFSes::add, null, null, null);
+        return allFSes;
+    }
 }

inception/inception-external-search-pubmed/pom.xml

@@ -86,6 +86,10 @@
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-annotations</artifactId>
     </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-databind</artifactId>
+    </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.dataformat</groupId>
       <artifactId>jackson-dataformat-xml</artifactId>

inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/pmcoa/PmcOaClient.java

@@ -17,10 +17,12 @@
  */
 package de.tudarmstadt.ukp.inception.externalsearch.pubmed.pmcoa;
 
+import java.io.IOException;
 import java.util.Map;
 
 import org.springframework.http.HttpMethod;
 import org.springframework.http.converter.xml.MappingJackson2XmlHttpMessageConverter;
+import org.springframework.web.client.HttpClientErrorException.NotFound;
 import org.springframework.web.client.RestTemplate;
 
 import de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits.PubMedProviderTraits;
@@ -40,14 +42,25 @@ public PmcOaClient()
         restTemplate.getMessageConverters().add(new MappingJackson2XmlHttpMessageConverter());
     }
 
-    public byte[] bioc(PubMedProviderTraits aTraits, String aID)
+    public byte[] bioc(PubMedProviderTraits aTraits, String aID) throws IOException
     {
-        var variables = Map.of( //
-                PARAM_ID, aID);
+        try {
+            var variables = Map.of( //
+                    PARAM_ID, aID);
 
-        var response = restTemplate.exchange(BIOC_URL, HttpMethod.GET, null, byte[].class,
-                variables);
+            var response = restTemplate.exchange(BIOC_URL, HttpMethod.GET, null, byte[].class,
+                    variables);
 
-        return response.getBody();
+            return response.getBody();
+        }
+        catch (NotFound e) {
+            throw new IOException("BioC version of document [" + aID + "] not found at ["
+                    + BIOC_URL.replace("{id}", aID)
+                    + "]. The Open Access files and BioC versions are not updated  as "
+                    + "quickly as the PMC website itself is updated. It may take a couple of days until "
+                    + "a particular file is available as BioC. Another reason could be that the document you "
+                    + "are looking for is not included in the Open Access set. Try adding "
+                    + "`\"open access\"[filter]` without \"`\" to your search to filter by Open Access files.");
+        }
     }
 }

inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraits.java

@@ -19,6 +19,13 @@
 
 import java.io.Serializable;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
+//The @JsonSerialize annotation avoid the "InvalidDefinitionException: No serializer found"
+//exception without having to set SerializationFeature.FAIL_ON_EMPTY_BEANS
+@JsonSerialize
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class PubMedProviderTraits
     implements Serializable
 {

inception/inception-imls-ollama/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/ollama/OllamaRecommender.java

@@ -49,6 +49,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.imls.ollama.response.ResponseAsLabelExtractor;
 import de.tudarmstadt.ukp.inception.recommendation.imls.ollama.response.ResponseExtractor;
 import de.tudarmstadt.ukp.inception.rendering.model.Range;
+import de.tudarmstadt.ukp.inception.support.logging.LogMessage;
 
 public class OllamaRecommender
     extends NonTrainableRecommenderEngineImplBase
@@ -103,8 +104,9 @@ public Range predict(PredictionContext aContext, CAS aCas, int aBegin, int aEnd)
                 responseExtractor.extract(this, aCas, promptContext, response);
             }
             catch (IOException e) {
-                aContext.error("Ollama [%s] failed to respond: %s", traits.getModel(),
-                        ExceptionUtils.getRootCauseMessage(e));
+                aContext.log(LogMessage.warn(getRecommender().getName(),
+                        "Ollama [%s] failed to respond: %s", traits.getModel(),
+                        ExceptionUtils.getRootCauseMessage(e)));
                 LOG.error("Ollama [{}] failed to respond: {}", traits.getModel(),
                         ExceptionUtils.getRootCauseMessage(e));
             }

inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/doccat/OpenNlpDoccatRecommender.java

@@ -56,6 +56,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext.Key;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.TrainingCapability;
 import de.tudarmstadt.ukp.inception.rendering.model.Range;
+import de.tudarmstadt.ukp.inception.support.logging.LogMessage;
 import opennlp.tools.doccat.DoccatFactory;
 import opennlp.tools.doccat.DoccatModel;
 import opennlp.tools.doccat.DocumentCategorizerME;
@@ -108,13 +109,14 @@ public void train(RecommenderContext aContext, List<CAS> aCasses) throws Recomme
         var docSamples = extractSamples(aCasses);
 
         if (docSamples.size() < 2) {
-            aContext.warn("Not enough training data: [%d] items", docSamples.size());
+            aContext.log(LogMessage.warn(getRecommender().getName(),
+                    "Not enough training data: [%d] items", docSamples.size()));
             return;
         }
 
         if (docSamples.stream().map(DocumentSample::getCategory).distinct().count() <= 1) {
-            aContext.warn("Training data requires at least two different labels",
-                    docSamples.size());
+            aContext.log(LogMessage.warn(getRecommender().getName(),
+                    "Training data requires at least two different labels", docSamples.size()));
             return;
         }
 

inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/ner/OpenNlpNerRecommender.java

@@ -50,6 +50,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext.Key;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.TrainingCapability;
 import de.tudarmstadt.ukp.inception.rendering.model.Range;
+import de.tudarmstadt.ukp.inception.support.logging.LogMessage;
 import it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap;
 import it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap;
 import opennlp.tools.ml.BeamSearch;
@@ -95,7 +96,8 @@ public void train(RecommenderContext aContext, List<CAS> aCasses) throws Recomme
         var nameSamples = extractNameSamples(aCasses);
 
         if (nameSamples.size() < 2) {
-            aContext.warn("Not enough training data: [%d] items", nameSamples.size());
+            aContext.log(LogMessage.warn(getRecommender().getName(),
+                    "Not enough training data: [%d] items", nameSamples.size()));
             return;
         }
 
@@ -104,10 +106,10 @@ public void train(RecommenderContext aContext, List<CAS> aCasses) throws Recomme
         // OpenNLP
         int beamSize = Math.max(maxRecommendations, NameFinderME.DEFAULT_BEAM_SIZE);
 
-        TrainingParameters params = traits.getParameters();
+        var params = traits.getParameters();
         params.put(BeamSearch.BEAM_SIZE_PARAMETER, Integer.toString(beamSize));
 
-        TokenNameFinderModel model = train(nameSamples, params);
+        var model = train(nameSamples, params);
 
         aContext.put(KEY_MODEL, model);
     }
@@ -304,7 +306,7 @@ private String determineLabel(Span aName, int aTokenIdx)
         return label;
     }
 
-    private List<NameSample> extractNameSamples(List<CAS> aCasses)
+    private List<NameSample> extractNameSamples(Iterable<CAS> aCasses)
     {
         var nameSamples = new ArrayList<NameSample>();
 
@@ -402,8 +404,8 @@ private TokenNameFinderModel train(List<NameSample> aNameSamples,
             TrainingParameters aParameters)
         throws RecommendationException
     {
-        try (NameSampleStream stream = new NameSampleStream(aNameSamples)) {
-            TokenNameFinderFactory finderFactory = new TokenNameFinderFactory();
+        try (var stream = new NameSampleStream(aNameSamples)) {
+            var finderFactory = new TokenNameFinderFactory();
             return NameFinderME.train("unknown", null, stream, aParameters, finderFactory);
         }
         catch (IOException e) {

inception/inception-imls-opennlp/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/opennlp/pos/OpenNlpPosRecommender.java

@@ -55,6 +55,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext.Key;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.TrainingCapability;
 import de.tudarmstadt.ukp.inception.rendering.model.Range;
+import de.tudarmstadt.ukp.inception.support.logging.LogMessage;
 import opennlp.tools.ml.BeamSearch;
 import opennlp.tools.postag.POSModel;
 import opennlp.tools.postag.POSSample;
@@ -97,7 +98,8 @@ public void train(RecommenderContext aContext, List<CAS> aCasses) throws Recomme
         var posSamples = extractPosSamples(aCasses);
 
         if (posSamples.size() < 2) {
-            aContext.warn("Not enough training data: [%d] items", posSamples.size());
+            aContext.log(LogMessage.warn(getRecommender().getName(),
+                    "Not enough training data: [%d] items", posSamples.size()));
             return;
         }