Feature/1856 support regex based recommendations

inception-app-webapp/hs_err_pid15048.log

@@ -0,0 +1,35 @@
+#
+# A fatal error has been detected by the Java Runtime Environment:
+#
+#  SIGSEGV (0xb) at pc=0x00007f92b74b8401, pid=15048, tid=15064
+#
+# JRE version: OpenJDK Runtime Environment (11.0.9.1+1) (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04)
+# Java VM: OpenJDK 64-Bit Server VM (11.0.9.1+1-Ubuntu-0ubuntu1.18.04, mixed mode, sharing, tiered, compressed oops, g1 gc, linux-amd64)
+# Problematic frame:
+# C  [libjimage.so+0x2401]
+#
+# Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport %p %s %c %d %P %E" (or dumping to /home/christoph/Desktop/Arbeit/inception/inception-app-webapp/core.15048)
+#
+# If you would like to submit a bug report, please visit:
+#   https://bugs.launchpad.net/ubuntu/+source/openjdk-lts
+#
+
+---------------  S U M M A R Y ------------
+
+Command Line: -agentlib:jdwp=transport=dt_socket,suspend=y,address=localhost:46701 -javaagent:/home/christoph/.eclipse/360744286_linux_gtk_x86_64/configuration/org.eclipse.osgi/222/0/.cp/lib/javaagent-shaded.jar -Dfile.encoding=UTF-8 de.tudarmstadt.ukp.inception.INCEpTION
+
+Host: Intel(R) Core(TM) i3-4005U CPU @ 1.70GHz, 4 cores, 3G, Ubuntu 18.04.5 LTS
+Time: Tue Jan 26 13:39:43 2021 CET elapsed time: 212.402363 seconds (0d 0h 3m 32s)
+
+---------------  T H R E A D  ---------------
+
+Current thread (0x00007f92b013c800):  JavaThread "Signal Dispatcher" daemon [_thread_in_vm, id=15064, stack(0x00007f9290bbe000,0x00007f9290cbf000)]
+
+Stack: [0x00007f9290bbe000,0x00007f9290cbf000],  sp=0x00007f9290cbc1e0,  free space=1016k
+Native frames: (J=compiled Java code, A=aot compiled Java code, j=interpreted, Vv=VM code, C=native code)
+C  [libjimage.so+0x2401]
+C  [libjimage.so+0x30ea]
+C  [libjimage.so+0x35c6]  JIMAGE_FindResource+0xd6
+V  [libjvm.so+0x5bf44e]
+V  [libjvm.so+0x5c21b0]
+V  [libjvm.so+0xe427d5]

inception-app-webapp/pom.xml

@@ -553,6 +553,10 @@
     	<groupId>de.tudarmstadt.ukp.inception.app</groupId>
     	<artifactId>inception-sharing</artifactId>
     </dependency>
+    <dependency>
+    	<groupId>de.tudarmstadt.ukp.inception.app</groupId>
+    	<artifactId>inception-regex-recommender</artifactId>
+    </dependency>
   </dependencies>
   <build>
     <plugins>
@@ -790,6 +794,7 @@
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-ui-curation</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-ui-monitoring</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-sharing</usedDependency>
+              <usedDependency>de.tudarmstadt.ukp.inception.app:inception-regex-recommender</usedDependency>
               <!-- INCEpTION annotation editor modules - used via Spring -->
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-brat-editor</usedDependency>
               <usedDependency>de.tudarmstadt.ukp.inception.app:inception-html-editor</usedDependency>
@@ -1097,4 +1102,4 @@
       </properties>
     </profile>
   </profiles>
-</project>
+</project>

inception-imls-stringmatch/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/stringmatch/StringMatchingRecommender.java

@@ -53,9 +53,9 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationException;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext.Key;
-import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.gazeteer.GazeteerService;
+import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.gazeteer.GazeteerServiceImpl;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model.Gazeteer;
-import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model.GazeteerEntry;
+import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model.GazeteerEntryImpl;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.trie.Trie;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.trie.WhitespaceNormalizingSanitizer;
 
@@ -70,7 +70,7 @@ public class StringMatchingRecommender
     private final Logger log = LoggerFactory.getLogger(getClass());
     private final StringMatchingRecommenderTraits traits;
 
-    private final GazeteerService gazeteerService;
+    private final GazeteerServiceImpl gazeteerService;
 
     public StringMatchingRecommender(Recommender aRecommender,
             StringMatchingRecommenderTraits aTraits)
@@ -79,10 +79,9 @@ public StringMatchingRecommender(Recommender aRecommender,
     }
 
     public StringMatchingRecommender(Recommender aRecommender,
-            StringMatchingRecommenderTraits aTraits, GazeteerService aGazeteerService)
+            StringMatchingRecommenderTraits aTraits, GazeteerServiceImpl aGazeteerService)
     {
         super(aRecommender);
-
         traits = aTraits;
         gazeteerService = aGazeteerService;
     }
@@ -92,13 +91,13 @@ public boolean isReadyForPrediction(RecommenderContext aContext)
     {
         return aContext.get(KEY_MODEL).map(Objects::nonNull).orElse(false);
     }
-
-    public void pretrain(List<GazeteerEntry> aData, RecommenderContext aContext)
+    
+    public void pretrain(List<GazeteerEntryImpl> aData, RecommenderContext aContext)
     {
         Trie<DictEntry> dict = aContext.get(KEY_MODEL).orElseGet(this::createTrie);
 
         if (aData != null) {
-            for (GazeteerEntry entry : aData) {
+            for (GazeteerEntryImpl entry : aData) {
                 learn(dict, entry.text, entry.label);
             }
         }

inception-imls-stringmatch/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/stringmatch/StringMatchingRecommenderFactory.java

@@ -32,7 +32,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationEngine;
 import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationEngineFactoryImplBase;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.config.StringMatchingRecommenderAutoConfiguration;
-import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.gazeteer.GazeteerService;
+import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.gazeteer.GazeteerServiceImpl;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.settings.StringMatchingRecommenderTraitsEditor;
 
 /**
@@ -48,9 +48,9 @@ public class StringMatchingRecommenderFactory
     // and without the database starting to refer to non-existing recommendation tools.
     public static final String ID = "de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.StringMatchingRecommender";
 
-    private final GazeteerService gazeteerService;
-
-    public StringMatchingRecommenderFactory(GazeteerService aGazeteerService)
+    private final GazeteerServiceImpl gazeteerService;
+    
+    public StringMatchingRecommenderFactory(GazeteerServiceImpl aGazeteerService)
     {
         gazeteerService = aGazeteerService;
     }

inception-imls-stringmatch/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/stringmatch/config/StringMatchingRecommenderAutoConfiguration.java

@@ -33,7 +33,6 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.StringMatchingRecommenderFactory;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.exporter.GazeteerExporter;
-import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.gazeteer.GazeteerService;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.gazeteer.GazeteerServiceImpl;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.ner.StringMatchingNerClassificationToolFactory;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.pos.StringMatchingPosClassificationToolFactory;
@@ -47,14 +46,14 @@ public class StringMatchingRecommenderAutoConfiguration
     @Bean
     @Autowired
     public GazeteerExporter gazeteerExporter(RecommendationService aRecommendationService,
-            GazeteerService aGazeteerService)
+            GazeteerServiceImpl aGazeteerService)
     {
         return new GazeteerExporter(aRecommendationService, aGazeteerService);
     }
 
     @Bean
     @Autowired
-    public GazeteerService gazeteerService(RepositoryProperties aRepositoryProperties)
+    public GazeteerServiceImpl gazeteerService(RepositoryProperties aRepositoryProperties)
     {
         return new GazeteerServiceImpl(aRepositoryProperties, entityManager);
     }
@@ -74,8 +73,8 @@ public StringMatchingPosClassificationToolFactory stringMatchingPosClassificatio
     @Bean
     @Autowired
     public StringMatchingRecommenderFactory stringMatchingRecommenderFactory(
-            GazeteerService aGazeteerService)
-    {
+            GazeteerServiceImpl aGazeteerService)
+    {   
         return new StringMatchingRecommenderFactory(aGazeteerService);
     }
 }

inception-imls-stringmatch/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/stringmatch/gazeteer/GazeteerService.java

@@ -61,7 +61,7 @@ public interface GazeteerService
     /**
      * Loads the gazeteer.
      */
-    List<GazeteerEntry> readGazeteerFile(Gazeteer aGaz) throws IOException;
+    List<? extends GazeteerEntry> readGazeteerFile(Gazeteer aGaz) throws IOException;
 
     boolean existsGazeteer(Recommender aRecommender, String aName);
 }

inception-imls-stringmatch/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/stringmatch/gazeteer/GazeteerServiceImpl.java

@@ -49,14 +49,15 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.config.StringMatchingRecommenderAutoConfiguration;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model.Gazeteer;
-import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model.GazeteerEntry;
+import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model.GazeteerEntryImpl;
 
 /**
  * <p>
  * This class is exposed as a Spring Component via
  * {@link StringMatchingRecommenderAutoConfiguration#gazeteerService}.
  * </p>
  */
+
 public class GazeteerServiceImpl
     implements GazeteerService
 {
@@ -163,20 +164,22 @@ public void deleteGazeteers(Gazeteer aGazeteer) throws IOException
     }
 
     @Override
-    public List<GazeteerEntry> readGazeteerFile(Gazeteer aGaz) throws IOException
+    public List<GazeteerEntryImpl> readGazeteerFile(Gazeteer aGaz)
+        throws IOException
     {
         File file = getGazeteerFile(aGaz);
-
-        List<GazeteerEntry> data = new ArrayList<>();
-
+        
+        List<GazeteerEntryImpl> data = new ArrayList<>();
+        
         try (InputStream is = new FileInputStream(file)) {
             parseGazeteer(aGaz, is, data);
         }
-
+        
         return data;
     }
-
-    public void parseGazeteer(Gazeteer aGaz, InputStream aStream, List<GazeteerEntry> aTarget)
+
+
+    public void parseGazeteer(Gazeteer aGaz, InputStream aStream, List<GazeteerEntryImpl> aTarget)
         throws IOException
     {
         int lineNumber = 0;
@@ -195,7 +198,7 @@ public void parseGazeteer(Gazeteer aGaz, InputStream aStream, List<GazeteerEntry
                 String text = trimToNull(fields[0]);
                 String label = trimToNull(fields[1]);
                 if (label != null && text != null) {
-                    aTarget.add(new GazeteerEntry(text, label));
+                    aTarget.add(new GazeteerEntryImpl(text, label));
                 }
             }
             else {

inception-imls-stringmatch/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/stringmatch/model/GazeteerEntry.java

@@ -19,44 +19,16 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model;
 
-import org.apache.commons.lang3.builder.EqualsBuilder;
-import org.apache.commons.lang3.builder.HashCodeBuilder;
-import org.apache.commons.lang3.builder.ToStringBuilder;
+package de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model;
 
-public class GazeteerEntry
+public interface GazeteerEntry
 {
-    public final String text;
-    public final String label;
 
-    public GazeteerEntry(String aText, String aLabel)
-    {
-        super();
-        text = aText;
-        label = aLabel;
-    }
+    public boolean equals(final Object other);
 
-    @Override
-    public boolean equals(final Object other)
-    {
-        if (!(other instanceof GazeteerEntry)) {
-            return false;
-        }
-        GazeteerEntry castOther = (GazeteerEntry) other;
-        return new EqualsBuilder().append(text, castOther.text).append(label, castOther.label)
-                .isEquals();
-    }
+    public int hashCode();
 
-    @Override
-    public int hashCode()
-    {
-        return new HashCodeBuilder().append(text).append(label).toHashCode();
-    }
+    public String toString();
 
-    @Override
-    public String toString()
-    {
-        return new ToStringBuilder(this).append("text", text).append("label", label).toString();
-    }
 }

inception-imls-stringmatch/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/stringmatch/model/GazeteerEntryImpl.java

@@ -0,0 +1,59 @@
+/*
+ * Copyright 2019
+ * Ubiquitous Knowledge Processing (UKP) Lab
+ * Technische Universität 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.inception.recommendation.imls.stringmatch.model;
+
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.ToStringBuilder;
+
+public class GazeteerEntryImpl
+    implements GazeteerEntry
+{
+    public final String text;
+    public final String label;
+
+    public GazeteerEntryImpl(String aText, String aLabel)
+    {
+        super();
+        text = aText;
+        label = aLabel;
+    }
+
+    @Override
+    public boolean equals(final Object other)
+    {
+        if (!(other instanceof GazeteerEntryImpl)) {
+            return false;
+        }
+        GazeteerEntryImpl castOther = (GazeteerEntryImpl) other;
+        return new EqualsBuilder().append(text, castOther.text).append(label, castOther.label)
+                .isEquals();
+    }
+
+    @Override
+    public int hashCode()
+    {
+        return new HashCodeBuilder().append(text).append(label).toHashCode();
+    }
+
+    @Override
+    public String toString()
+    {
+        return new ToStringBuilder(this).append("text", text).append("label", label).toString();
+    }
+}

inception-imls-stringmatch/src/test/java/de/tudarmstadt/ukp/inception/recommendation/imls/stringmatch/StringMatchingRecommenderTest.java

@@ -65,7 +65,7 @@
 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.RecommenderContext;
-import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model.GazeteerEntry;
+import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.model.GazeteerEntryImpl;
 import de.tudarmstadt.ukp.inception.support.test.recommendation.RecommenderTestHelper;
 
 public class StringMatchingRecommenderTest
@@ -164,9 +164,9 @@ public void thatPredictionForCharacterLevelLayerWorks() throws Exception
 
         RecommenderTestHelper.addScoreFeature(cas, NamedEntity.class, "value");
 
-        List<GazeteerEntry> gazeteer = new ArrayList<>();
-        gazeteer.add(new GazeteerEntry("John Smith", "ORG"));
-        gazeteer.add(new GazeteerEntry("Peter John", "LOC"));
+        List<GazeteerEntryImpl> gazeteer = new ArrayList<>();
+        gazeteer.add(new GazeteerEntryImpl("John Smith", "ORG"));
+        gazeteer.add(new GazeteerEntryImpl("Peter John", "LOC"));
 
         sut.pretrain(gazeteer, context);
 
@@ -193,8 +193,8 @@ public void thatPredictionForCrossSentenceLayerWorks() throws Exception
 
         RecommenderTestHelper.addScoreFeature(cas, NamedEntity.class, "value");
 
-        List<GazeteerEntry> gazeteer = new ArrayList<>();
-        gazeteer.add(new GazeteerEntry("Smith . Peter", "ORG"));
+        List<GazeteerEntryImpl> gazeteer = new ArrayList<>();
+        gazeteer.add(new GazeteerEntryImpl("Smith . Peter", "ORG"));
 
         sut.pretrain(gazeteer, context);
 
@@ -233,10 +233,10 @@ public void thatPredictionWithPretrainigWorks() throws Exception
         CAS cas = casList.get(0);
         RecommenderTestHelper.addScoreFeature(cas, NamedEntity.class, "value");
 
-        List<GazeteerEntry> gazeteer = new ArrayList<>();
-        gazeteer.add(new GazeteerEntry("Toyota", "ORG"));
-        gazeteer.add(new GazeteerEntry("Deutschland", "LOC"));
-        gazeteer.add(new GazeteerEntry("Deutschland", "GPE"));
+        List<GazeteerEntryImpl> gazeteer = new ArrayList<>();
+        gazeteer.add(new GazeteerEntryImpl("Toyota", "ORG"));
+        gazeteer.add(new GazeteerEntryImpl("Deutschland", "LOC"));
+        gazeteer.add(new GazeteerEntryImpl("Deutschland", "GPE"));
 
         sut.pretrain(gazeteer, context);