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

* main: #2696 - Document-level recommendations #2696 - Document-level recommendations #2696 - Document-level recommendations #2696 - Document-level recommendations #2696 - Document-level recommendations #2696 - Document-level recommendations #2696 - Document-level recommendations #2696 - Document-level recommendations #2696 - Document-level recommendations #4292 - ollama-based recommender #4292 - ollama-based recommender #4383 - Hide negative scores in annotation sidebar but still sort by it #4383 - Hide negative scores in annotation sidebar but still sort by it
inception-project · Dec 26, 2023 · b83e285 · b83e285
2 parents b1ca0fe + 5ec948d
commit b83e285
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diff --git a/.../main/java/de/tudarmstadt/ukp/inception/conceptlinking/recommender/NamedEntityLinker.java b/.../main/java/de/tudarmstadt/ukp/inception/conceptlinking/recommender/NamedEntityLinker.java
@@ -43,6 +43,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.DataSplitter;
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.EvaluationResult;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationEngine;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationException;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
@@ -90,7 +91,7 @@ public void train(RecommenderContext aContext, List<CAS> aCasList)
     }
 
     @Override
-    public Range predict(RecommenderContext aContext, CAS aCas, int aBegin, int aEnd)
+    public Range predict(PredictionContext aContext, CAS aCas, int aBegin, int aEnd)
         throws RecommendationException
     {
         Type predictedType = getPredictedType(aCas);

diff --git a/...king/src/test/java/de/tudarmstadt/ukp/inception/conceptlinking/NamedEntityLinkerTest.java b/...king/src/test/java/de/tudarmstadt/ukp/inception/conceptlinking/NamedEntityLinkerTest.java
@@ -65,6 +65,7 @@
 import de.tudarmstadt.ukp.inception.kb.graph.KBHandle;
 import de.tudarmstadt.ukp.inception.kb.model.KnowledgeBase;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
 import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureSupport;
 import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureSupportRegistry;
@@ -146,7 +147,7 @@ public void thatPredictionWorks() throws Exception
         sut.train(context, Collections.singletonList(cas));
         RecommenderTestHelper.addScoreFeature(cas, NamedEntity.class, "value");
 
-        sut.predict(context, cas);
+        sut.predict(new PredictionContext(context), cas);
 
         List<NamedEntity> predictions = getPredictions(cas, NamedEntity.class);
 

diff --git a/...n/java/de/tudarmstadt/ukp/inception/diam/model/compactv2/CompactAnnotationAttributes.java b/...n/java/de/tudarmstadt/ukp/inception/diam/model/compactv2/CompactAnnotationAttributes.java
@@ -20,6 +20,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import com.fasterxml.jackson.annotation.JsonFormat;
+import com.fasterxml.jackson.annotation.JsonFormat.Shape;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.annotation.JsonProperty;
@@ -32,11 +34,13 @@ public class CompactAnnotationAttributes
     public static final String ATTR_COLOR = "c";
     public static final String ATTR_COMMENTS = "cm";
     public static final String ATTR_SCORE = "s";
+    public static final String ATTR_HIDE_SCORE = "hs";
 
     private @JsonProperty(ATTR_LABEL) String labelText;
     private @JsonProperty(ATTR_COLOR) String color;
     private @JsonProperty(ATTR_COMMENTS) List<CompactComment> comments;
     private @JsonProperty(ATTR_SCORE) double score;
+    private @JsonProperty(ATTR_HIDE_SCORE) boolean hideScore;
 
     @JsonInclude(Include.NON_DEFAULT)
     @JsonSerialize(using = ScoreSerializer.class)
@@ -50,6 +54,18 @@ public void setScore(double aScore)
         score = aScore;
     }
 
+    @JsonFormat(shape = Shape.NUMBER)
+    @JsonInclude(Include.NON_DEFAULT)
+    public boolean isHideScore()
+    {
+        return hideScore;
+    }
+
+    public void setHideScore(boolean aHideScore)
+    {
+        hideScore = aHideScore;
+    }
+
     public void setLabelText(String aLabelText)
     {
         labelText = aLabelText;

diff --git a/.../main/java/de/tudarmstadt/ukp/inception/diam/model/compactv2/CompactSerializerV2Impl.java b/.../main/java/de/tudarmstadt/ukp/inception/diam/model/compactv2/CompactSerializerV2Impl.java
@@ -126,6 +126,7 @@ private CompactRelation renderRelation(VArc varc)
                 getArgument(varc.getSource(), varc.getTarget()), varc.getLabelHint(),
                 varc.getColorHint());
         carc.getAttributes().setScore(varc.getScore());
+        carc.getAttributes().setHideScore(varc.isHideScore());
         return carc;
     }
 
@@ -152,6 +153,7 @@ private CompactSpan renderSpan(RenderRequest aRequest, VSpan vspan)
                     vspan.getColorHint());
         }
         cspan.getAttributes().setScore(vspan.getScore());
+        cspan.getAttributes().setHideScore(vspan.isHideScore());
         return cspan;
     }
 

diff --git a/inception/inception-diam-editor/src/main/ts/src/LabelBadge.svelte b/inception/inception-diam-editor/src/main/ts/src/LabelBadge.svelte
@@ -61,7 +61,8 @@
             {#if showText}
                 <span class="label">{renderLabel(annotation)}</span>
             {/if}
-            {#if annotation.score}
+            <!-- Negative scores used only for sorting/ranking but not shown -->
+            {#if annotation.score && !annotation.hideScore}
                 <span class="small font-monospace score"
                     >{annotation.score.toFixed(2)}</span
                 >
@@ -88,7 +89,8 @@
         {#if showText}
             <span class="label">{renderLabel(annotation)}</span>
         {/if}
-        {#if annotation.score}
+        <!-- Negative scores used only for sorting/ranking but not shown -->
+        {#if annotation.score && !annotation.hideScore}
             <span class="small font-monospace score"
                 >{annotation.score.toFixed(2)}</span
             >

diff --git a/...udarmstadt/ukp/inception/recommendation/imls/datamajority/DataMajorityNerRecommender.java b/...udarmstadt/ukp/inception/recommendation/imls/datamajority/DataMajorityNerRecommender.java
@@ -42,6 +42,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.EvaluationResult;
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.LabelPair;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationEngine;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationException;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
@@ -133,7 +134,7 @@ private DataMajorityModel trainModel(List<Annotation> aAnnotations)
 
     // tag::predict1[]
     @Override
-    public Range predict(RecommenderContext aContext, CAS aCas, int aBegin, int aEnd)
+    public Range predict(PredictionContext aContext, CAS aCas, int aBegin, int aEnd)
         throws RecommendationException
     {
         DataMajorityModel model = aContext.get(KEY_MODEL).orElseThrow(

diff --git a/...mstadt/ukp/inception/recommendation/imls/datamajority/DataMajorityNerRecommenderTest.java b/...mstadt/ukp/inception/recommendation/imls/datamajority/DataMajorityNerRecommenderTest.java
@@ -59,6 +59,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.IncrementalSplitter;
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.PercentageBasedSplitter;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
 import de.tudarmstadt.ukp.inception.support.test.recommendation.DkproTestHelper;
 import de.tudarmstadt.ukp.inception.support.test.recommendation.RecommenderTestHelper;
@@ -104,7 +105,7 @@ public void thatPredictionWorks() throws Exception
 
         sut.train(context, asList(cas));
 
-        sut.predict(context, cas);
+        sut.predict(new PredictionContext(context), cas);
 
         Collection<NamedEntity> predictions = getPredictions(cas, NamedEntity.class);
 

diff --git a/...lg/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/elg/ElgRecommender.java b/...lg/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/elg/ElgRecommender.java
@@ -34,8 +34,8 @@
 
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.NonTrainableRecommenderEngineImplBase;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationException;
-import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
 import de.tudarmstadt.ukp.inception.recommendation.imls.elg.model.ElgAnnotation;
 import de.tudarmstadt.ukp.inception.recommendation.imls.elg.model.ElgAnnotationsResponse;
 import de.tudarmstadt.ukp.inception.recommendation.imls.elg.model.ElgServiceResponse;
@@ -67,7 +67,7 @@ public ElgRecommender(Recommender aRecommender, ElgRecommenderTraits aTraits,
     }
 
     @Override
-    public Range predict(RecommenderContext aContext, CAS aCas, int aBegin, int aEnd)
+    public Range predict(PredictionContext aContext, CAS aCas, int aBegin, int aEnd)
         throws RecommendationException
     {
         ElgServiceResponse response;

diff --git a/...ava/de/tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommender.java b/...ava/de/tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommender.java
@@ -64,6 +64,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.DataSplitter;
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.EvaluationResult;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationEngine;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationException;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
@@ -216,7 +217,7 @@ else if (response.statusCode() >= HTTP_BAD_REQUEST) {
     }
 
     @Override
-    public Range predict(RecommenderContext aContext, CAS aCas, int aBegin, int aEnd)
+    public Range predict(PredictionContext aContext, CAS aCas, int aBegin, int aEnd)
         throws RecommendationException
     {
         var client = getClient();

diff --git a/...tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderFactory.java b/...tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderFactory.java
@@ -97,4 +97,11 @@ public boolean isEvaluable()
     {
         return false;
     }
+
+    @Override
+    public boolean isRanker(Recommender aRecommender)
+    {
+        var traits = readTraits(aRecommender);
+        return traits.isRanker();
+    }
 }
diff --git a/.../tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderTraits.java b/.../tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderTraits.java
@@ -30,6 +30,7 @@ public class ExternalRecommenderTraits
     private String remoteUrl;
     private boolean trainable;
     private boolean verifyCertificates = true;
+    private boolean ranker;
 
     public String getRemoteUrl()
     {
@@ -60,4 +61,14 @@ public boolean isVerifyCertificates()
     {
         return verifyCertificates;
     }
+
+    public void setRanker(boolean aRanker)
+    {
+        ranker = aRanker;
+    }
+
+    public boolean isRanker()
+    {
+        return ranker;
+    }
 }
diff --git a/...mstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderTraitsEditor.html b/...mstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderTraitsEditor.html
@@ -47,6 +47,16 @@
         </div>
       </div>
     </div>
+    <div class="row form-row" wicket:enclosure="ranker">
+      <div class="offset-sm-3 col-sm-9">
+        <div class="form-check">
+          <input wicket:id="ranker" class="form-check-input" type="checkbox"/>
+          <label wicket:for="ranker" class="form-check-label">
+            <wicket:label key="ranker"/>
+          </label>
+        </div>
+      </div>
+    </div>
   </form>
 </wicket:extend>
 </html>
diff --git a/...mstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderTraitsEditor.java b/...mstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderTraitsEditor.java
@@ -80,6 +80,10 @@ protected void onSubmit()
 
         getTrainingStatesChoice().add(visibleWhen(() -> trainable.getModelObject() == true));
 
+        var ranker = new CheckBox("ranker");
+        ranker.setOutputMarkupId(true);
+        form.add(ranker);
+
         add(form);
     }
 }
diff --git a/.../ukp/inception/recommendation/imls/external/v1/ExternalRecommenderTraitsEditor.properties b/.../ukp/inception/recommendation/imls/external/v1/ExternalRecommenderTraitsEditor.properties
@@ -16,4 +16,5 @@
 
 remoteUrl=Remote URL
 trainable=Trainable
+ranker=Ranker
 verifyCertificates=Verify certificates
diff --git a/...adt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderIntegrationTest.java b/...adt/ukp/inception/recommendation/imls/external/v1/ExternalRecommenderIntegrationTest.java
@@ -57,6 +57,7 @@
 import de.tudarmstadt.ukp.inception.annotation.storage.CasMetadataUtils;
 import de.tudarmstadt.ukp.inception.annotation.storage.CasStorageSession;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
 import de.tudarmstadt.ukp.inception.recommendation.imls.external.v1.config.ExternalRecommenderPropertiesImpl;
 import de.tudarmstadt.ukp.inception.recommendation.imls.external.v1.messages.PredictionRequest;
@@ -133,7 +134,7 @@ public void thatPredictingWorks() throws Exception
 
         var cas = casses.get(0);
         RecommenderTestHelper.addScoreFeature(cas, NamedEntity.class, "value");
-        sut.predict(context, cas);
+        sut.predict(new PredictionContext(context), cas);
 
         var predictions = getPredictions(cas, NamedEntity.class);
 
@@ -180,7 +181,7 @@ public void thatPredictingSendsCorrectRequest() throws Exception
 
         var cas = casses.get(0);
         RecommenderTestHelper.addScoreFeature(cas, NamedEntity.class, "value");
-        sut.predict(context, cas);
+        sut.predict(new PredictionContext(context), cas);
 
         var request = fromJsonString(PredictionRequest.class, requestBodies.get(1));
 

diff --git a/...ukp/inception/recommendation/imls/external/v1/MockRemoteStringMatchingNerRecommender.java b/...ukp/inception/recommendation/imls/external/v1/MockRemoteStringMatchingNerRecommender.java
@@ -40,6 +40,7 @@
 import org.xml.sax.SAXException;
 
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationException;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
 import de.tudarmstadt.ukp.inception.recommendation.imls.external.v1.messages.PredictionRequest;
@@ -93,7 +94,7 @@ public String predict(String aPredictionRequestJson)
             }
         }
 
-        recommendationEngine.predict(context, cas);
+        recommendationEngine.predict(new PredictionContext(context), cas);
 
         return buildPredictionResponse(cas);
     }

diff --git a/...s-hf/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/hf/HfRecommender.java b/...s-hf/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/hf/HfRecommender.java
@@ -29,8 +29,8 @@
 
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.NonTrainableRecommenderEngineImplBase;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationException;
-import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
 import de.tudarmstadt.ukp.inception.recommendation.imls.hf.client.HfInferenceClient;
 import de.tudarmstadt.ukp.inception.recommendation.imls.hf.model.HfEntityGroup;
 import de.tudarmstadt.ukp.inception.rendering.model.Range;
@@ -53,7 +53,7 @@ public HfRecommender(Recommender aRecommender, HfRecommenderTraits aTraits,
     }
 
     @Override
-    public Range predict(RecommenderContext aContext, CAS aCas, int aBegin, int aEnd)
+    public Range predict(PredictionContext aContext, CAS aCas, int aBegin, int aEnd)
         throws RecommendationException
     {
         List<HfEntityGroup> response;

diff --git a/...ain/java/de/tudarmstadt/ukp/inception/recommendation/imls/lapps/LappsGridRecommender.java b/...ain/java/de/tudarmstadt/ukp/inception/recommendation/imls/lapps/LappsGridRecommender.java
@@ -39,6 +39,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.DataSplitter;
 import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.EvaluationResult;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationEngine;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationException;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
@@ -67,7 +68,7 @@ public void train(RecommenderContext aContext, List<CAS> aCasses)
     }
 
     @Override
-    public Range predict(RecommenderContext aContext, CAS aCas, int aBegin, int aEnd)
+    public Range predict(PredictionContext aContext, CAS aCas, int aBegin, int aEnd)
         throws RecommendationException
     {
         // FIXME: Ignores begin/end - always fetches predictions for the entire CAS

diff --git a/.../tudarmstadt/ukp/inception/recommendation/imls/lapps/LappsRecommenderIntegrationTest.java b/.../tudarmstadt/ukp/inception/recommendation/imls/lapps/LappsRecommenderIntegrationTest.java
@@ -42,6 +42,7 @@
 import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
 import de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.recommender.PredictionContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
 import de.tudarmstadt.ukp.inception.recommendation.imls.lapps.traits.LappsGridRecommenderTraits;
 import okhttp3.mockwebserver.MockResponse;
@@ -83,7 +84,7 @@ public void thatPredictingPosWorks() throws Exception
         RecommenderContext context = new RecommenderContext();
         CAS cas = loadData();
 
-        sut.predict(context, cas);
+        sut.predict(new PredictionContext(context), cas);
 
         Collection<POS> predictions = JCasUtil.select(cas.getJCas(), POS.class);
 

diff --git a/inception/inception-imls-ollama/pom.xml b/inception/inception-imls-ollama/pom.xml
@@ -46,6 +46,14 @@
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-api-render</artifactId>
     </dependency>
+    <dependency>
+      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
+      <artifactId>inception-api-annotation</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
+      <artifactId>inception-layer-docmetadata</artifactId>
+    </dependency>
     <dependency>
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-support</artifactId>
@@ -96,6 +104,10 @@
       <groupId>org.apache.wicket</groupId>
       <artifactId>wicket-spring</artifactId>
     </dependency>
+    <dependency>
+      <groupId>com.googlecode.wicket-jquery-ui</groupId>
+      <artifactId>wicket-kendo-ui</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.danekja</groupId>
       <artifactId>jdk-serializable-functional</artifactId>

diff --git a/...src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/ollama/ExtractionMode.java b/...src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/ollama/ExtractionMode.java
@@ -19,11 +19,24 @@
 
 import com.fasterxml.jackson.annotation.JsonProperty;
 
+import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
+import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanLayerSupport;
+
 public enum ExtractionMode
 {
     @JsonProperty("response-as-label")
     RESPONSE_AS_LABEL, //
 
     @JsonProperty("mentions-from-json")
-    MENTIONS_FROM_JSON
+    MENTIONS_FROM_JSON;
+
+    public boolean accepts(AnnotationLayer aLayer)
+    {
+        if (this == MENTIONS_FROM_JSON) {
+            // Mention extraction only makes sense for span layers
+            return SpanLayerSupport.TYPE.equals(aLayer.getType());
+        }
+
+        return true;
+    }
 }