Merge pull request #97 from dstl/v2.7

V2.7

.gitignore

@@ -63,3 +63,4 @@ target/
 
 # Baleen specific
 testing.log
+derby.log

BUILD.md

@@ -10,4 +10,4 @@
 2.  Run `mvn package` from the Baleen project directory
 3.  Optionally run `mvn javadoc:aggregate-jar` to build Javadoc
 4.  The Baleen JAR will be built and saved in the target directory under the top level project directory
-5.  Run Baleen by running `java -jar baleen-2.7.0-SNAPSHOT.jar` and then navigating to <http://localhost:6413>
+5.  Run Baleen by running `java -jar baleen-2.7.0.jar` and then navigating to <http://localhost:6413>

README.md

@@ -20,7 +20,7 @@ Baleen includes an in-built server, which hosts full documentation and guides on
 To get started, you will need to launch this server and read this documentation.
 To launch the server, run the following command.
 
-> java -jar baleen-2.7.0-SNAPSHOT.jar
+> java -jar baleen-2.7.0.jar
 
 Once running, the server can be accessed at [http://localhost:6413](http://localhost:6413).
 

baleen-activemq/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>uk.gov.dstl.baleen</groupId>
     <artifactId>baleen</artifactId>
-    <version>2.7.0-SNAPSHOT</version>
+    <version>2.7.0</version>
   </parent>
   <artifactId>baleen-activemq</artifactId>
   <name>Baleen ActiveMQ</name>

baleen-activemq/src/test/java/uk/gov/dstl/baleen/collectionreaders/ActiveMQReaderTest.java

@@ -40,11 +40,11 @@ public class ActiveMQReaderTest extends AbstractReaderTest {
         BROKERARGS_VALUE
       };
   final ExternalResourceDescription erd =
-      ExternalResourceFactory.createExternalResourceDescription(
+      ExternalResourceFactory.createNamedResourceDescription(
           ACTIVEMQ, SharedActiveMQResource.class, configArr);
 
   final ExternalResourceDescription cerd =
-      ExternalResourceFactory.createExternalResourceDescription(
+      ExternalResourceFactory.createNamedResourceDescription(
           KEY_CONTENT_EXTRACTOR, PlainTextContentExtractor.class);
 
   public ActiveMQReaderTest() {

baleen-activemq/src/test/java/uk/gov/dstl/baleen/consumers/ActiveMQTest.java

@@ -62,7 +62,7 @@ public static void setupClass() throws UIMAException, JMSException {
 
     // Create descriptors
     ExternalResourceDescription erd =
-        ExternalResourceFactory.createExternalResourceDescription(
+        ExternalResourceFactory.createNamedResourceDescription(
             ACTIVEMQ, SharedActiveMQResource.class, configArr);
     AnalysisEngineDescription aed =
         AnalysisEngineFactory.createEngineDescription(

baleen-activemq/src/test/java/uk/gov/dstl/baleen/transports/activemq/ActiveMQTransportsTest.java

@@ -26,7 +26,7 @@ public class ActiveMQTransportsTest {
   private static String BROKERARGS_VALUE = "broker.persistent=false";
 
   private final ExternalResourceDescription mqerd =
-      ExternalResourceFactory.createExternalResourceDescription(
+      ExternalResourceFactory.createNamedResourceDescription(
           SharedActiveMQResource.RESOURCE_KEY,
           SharedActiveMQResource.class,
           SharedActiveMQResource.PARAM_PROTOCOL,
@@ -35,7 +35,7 @@ public class ActiveMQTransportsTest {
           BROKERARGS_VALUE);
 
   private final ExternalResourceDescription ceerd =
-      ExternalResourceFactory.createExternalResourceDescription(
+      ExternalResourceFactory.createNamedResourceDescription(
           KEY_CONTENT_EXTRACTOR, FakeBaleenContentExtractor.class);
 
   @Test

baleen-annotators/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>uk.gov.dstl.baleen</groupId>
     <artifactId>baleen</artifactId>
-    <version>2.7.0-SNAPSHOT</version>
+    <version>2.7.0</version>
   </parent>
   <artifactId>baleen-annotators</artifactId>
   <name>Baleen Annotators</name>
@@ -81,6 +81,17 @@
       <artifactId>jsoup</artifactId>
       <version>${jsoup.version}</version>
     </dependency>
+    <dependency>
+      <groupId>org.opensextant</groupId>
+      <artifactId>geodesy</artifactId>
+      <version>${geodesy.version}</version>
+      <exclusions>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-simple</artifactId>
+        </exclusion>
+      </exclusions>
+    </dependency>
 
     <dependency>
       <groupId>uk.gov.dstl.baleen</groupId>

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/AbstractDiscardWithSameId.java

@@ -42,10 +42,7 @@ protected void doProcess(final JCas jCas) throws AnalysisEngineProcessException
 
     final List<T> toDelete = new LinkedList<>();
 
-    annotations
-        .asMap()
-        .entrySet()
-        .stream()
+    annotations.asMap().entrySet().stream()
         .map(Map.Entry::getValue)
         .filter(e -> e.size() > 1)
         // Convert to a list of all annotations, BUT skip (drop) one...

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/Blacklist.java

@@ -46,9 +46,8 @@ public class Blacklist extends BaleenAnnotator {
   public static final String PARAM_BLACKLIST = "blacklist";
 
   @ConfigurationParameter(
-    name = PARAM_BLACKLIST,
-    defaultValue = {}
-  )
+      name = PARAM_BLACKLIST,
+      defaultValue = {})
   String[] terms;
 
   List<String> thingsToRemove = null;
@@ -72,9 +71,8 @@ public class Blacklist extends BaleenAnnotator {
   public static final String PARAM_TYPE = "type";
 
   @ConfigurationParameter(
-    name = PARAM_TYPE,
-    defaultValue = "uk.gov.dstl.baleen.types.semantic.Entity"
-  )
+      name = PARAM_TYPE,
+      defaultValue = "uk.gov.dstl.baleen.types.semantic.Entity")
   String type;
 
   Class<? extends Annotation> et = null;

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/CleanPunctuation.java

@@ -5,7 +5,7 @@
 import java.util.Collection;
 import java.util.Collections;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/CorefBrackets.java

@@ -62,9 +62,8 @@ public class CorefBrackets extends BaleenAnnotator {
   public static final String PARAM_TYPE = "excludedTypes";
 
   @ConfigurationParameter(
-    name = PARAM_TYPE,
-    defaultValue = {}
-  )
+      name = PARAM_TYPE,
+      defaultValue = {})
   String[] excludedTypes;
 
   List<Class<? extends Entity>> classTypes = new ArrayList<>();
@@ -104,9 +103,7 @@ public void doProcess(JCas jCas) throws AnalysisEngineProcessException {
       while (m.find()) {
         final Integer end = offset + m.end(1);
         matched.addAll(
-            entityMap
-                .get(offset + m.start(1))
-                .stream()
+            entityMap.get(offset + m.start(1)).stream()
                 .filter(
                     f ->
                         f.getClass().isAssignableFrom(e.getClass())

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/MergeAdjacent.java

@@ -63,9 +63,8 @@ public class MergeAdjacent extends BaleenAnnotator {
   public static final String PARAM_TYPE = "types";
 
   @ConfigurationParameter(
-    name = PARAM_TYPE,
-    defaultValue = {}
-  )
+      name = PARAM_TYPE,
+      defaultValue = {})
   String[] types;
 
   List<Class<? extends Entity>> classTypes = new ArrayList<>();
@@ -107,8 +106,7 @@ private void processType(JCas jCas, Class<? extends Entity> type) {
       int end = mergeable.get(mergeable.size() - 1).getEnd();
 
       Double lowestConfidence =
-          mergeable
-              .stream()
+          mergeable.stream()
               .min((e1, e2) -> Double.compare(e1.getConfidence(), e2.getConfidence()))
               .map(Entity::getConfidence)
               .orElse(Double.valueOf(0.0));

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/MergeAdjacentQuantities.java

@@ -7,7 +7,7 @@
 import java.util.Set;
 import java.util.regex.Pattern;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.uima.UimaContext;
 import org.apache.uima.resource.ResourceInitializationException;
 

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/MergeNationalityIntoEntity.java

@@ -28,9 +28,7 @@ protected void doProcessTextBlock(TextBlock block) throws AnalysisEngineProcessE
     if (nationalities.isEmpty()) return;
 
     List<Entity> entities =
-        block
-            .select(Entity.class)
-            .stream()
+        block.select(Entity.class).stream()
             .filter(e -> !e.getClass().equals(Nationality.class))
             .collect(Collectors.toList());
     for (Nationality n : nationalities) {

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/NormalizeTemporal.java

@@ -38,9 +38,8 @@ public class NormalizeTemporal extends AbstractNormalizeEntities {
   public static final String PARAM_DATE_FORMAT = "correctFormat";
 
   @ConfigurationParameter(
-    name = PARAM_DATE_FORMAT,
-    defaultValue = "yyyy'-'MM'-'dd'T'HH':'mm':'ss'Z'"
-  )
+      name = PARAM_DATE_FORMAT,
+      defaultValue = "yyyy'-'MM'-'dd'T'HH':'mm':'ss'Z'")
   String correctFormat;
 
   /**

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/RelationTypeFilter.java

@@ -1,13 +1,7 @@
 // Dstl (c) Crown Copyright 2017
 package uk.gov.dstl.baleen.annotators.cleaners;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -48,8 +42,9 @@
  *    }
  * </pre>
  *
- * See {@link UploadInteractionsToMongo} and {@link MongoInteractionWriter} for information how to
- * create this collection.
+ * See {@link uk.gov.dstl.baleen.jobs.interactions.UploadInteractionsToMongo} and {@link
+ * uk.gov.dstl.baleen.jobs.interactions.io.MongoInteractionWriter} for information how to create
+ * this collection.
  *
  * @baleen.javadoc
  */

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/RemoveNestedEntities.java

@@ -47,9 +47,8 @@ public class RemoveNestedEntities extends AbstractNestedEntities<Entity> {
   public static final String PARAM_EXCLUDED_TYPES = "excludedTypes";
 
   @ConfigurationParameter(
-    name = PARAM_EXCLUDED_TYPES,
-    defaultValue = {}
-  )
+      name = PARAM_EXCLUDED_TYPES,
+      defaultValue = {})
   private Set<String> excluded;
 
   Set<Class<? extends Annotation>> classTypes = new HashSet<>();

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/cleaners/RemoveOverlappingEntities.java

@@ -50,9 +50,8 @@ public class RemoveOverlappingEntities extends AbstractNestedEntities<Entity> {
   public static final String PARAM_EXCLUDED_TYPES = "excludedTypes";
 
   @ConfigurationParameter(
-    name = PARAM_EXCLUDED_TYPES,
-    defaultValue = {}
-  )
+      name = PARAM_EXCLUDED_TYPES,
+      defaultValue = {})
   private Set<String> excluded;
 
   Set<Class<? extends Annotation>> classTypes = new HashSet<>();

baleen-annotators/src/main/java/uk/gov/dstl/baleen/annotators/coreference/SieveCoreference.java

@@ -1,12 +1,7 @@
 // Dstl (c) Crown Copyright 2017
 package uk.gov.dstl.baleen.annotators.coreference;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Objects;
+import java.util.*;
 
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -21,35 +16,13 @@
 import uk.gov.dstl.baleen.annotators.coreference.impl.MentionDetector;
 import uk.gov.dstl.baleen.annotators.coreference.impl.data.Cluster;
 import uk.gov.dstl.baleen.annotators.coreference.impl.data.Mention;
-import uk.gov.dstl.baleen.annotators.coreference.impl.enhancers.AcronymEnhancer;
-import uk.gov.dstl.baleen.annotators.coreference.impl.enhancers.AnimacyEnhancer;
-import uk.gov.dstl.baleen.annotators.coreference.impl.enhancers.GenderEnhancer;
-import uk.gov.dstl.baleen.annotators.coreference.impl.enhancers.MentionEnhancer;
-import uk.gov.dstl.baleen.annotators.coreference.impl.enhancers.MultiplicityEnhancer;
-import uk.gov.dstl.baleen.annotators.coreference.impl.enhancers.PersonEnhancer;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.CoreferenceSieve;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.ExactStringMatchSieve;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.ExtractReferenceTargets;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.InSentencePronounSieve;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.PreciseConstructsSieve;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.PronounResolutionSieve;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.ProperHeadMatchSieve;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.RelaxedHeadMatchSieve;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.RelaxedStringMatchSieve;
-import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.StrictHeadMatchSieve;
+import uk.gov.dstl.baleen.annotators.coreference.impl.enhancers.*;
+import uk.gov.dstl.baleen.annotators.coreference.impl.sieves.*;
 import uk.gov.dstl.baleen.core.pipelines.orderers.AnalysisEngineAction;
 import uk.gov.dstl.baleen.resources.SharedGenderMultiplicityResource;
 import uk.gov.dstl.baleen.resources.SharedStopwordResource;
 import uk.gov.dstl.baleen.types.Base;
-import uk.gov.dstl.baleen.types.common.CommsIdentifier;
-import uk.gov.dstl.baleen.types.common.DocumentReference;
-import uk.gov.dstl.baleen.types.common.Frequency;
-import uk.gov.dstl.baleen.types.common.Money;
-import uk.gov.dstl.baleen.types.common.Nationality;
-import uk.gov.dstl.baleen.types.common.Organisation;
-import uk.gov.dstl.baleen.types.common.Person;
-import uk.gov.dstl.baleen.types.common.Url;
-import uk.gov.dstl.baleen.types.common.Vehicle;
+import uk.gov.dstl.baleen.types.common.*;
 import uk.gov.dstl.baleen.types.geo.Coordinate;
 import uk.gov.dstl.baleen.types.language.PhraseChunk;
 import uk.gov.dstl.baleen.types.language.Sentence;
@@ -150,7 +123,7 @@ public class SieveCoreference extends BaleenAnnotator {
 
   /**
    * The stoplist to use. If the stoplist matches one of the enum's provided in {@link
-   * uk.gov.dstl.baleen.resources.SharedStopwordResource#StopwordList}, then that list will be
+   * uk.gov.dstl.baleen.resources.SharedStopwordResource.StopwordList}, then that list will be
    * loaded.
    *
    * <p>Otherwise, the string is taken to be a file path and that file is used. The format of the