Merge branch '0.17.x'

* 0.17.x:
  No issue: Avoid locally failing builds because of the rat plugin stumbling over the NPM cache
  #1828 - Error in importing projects
  #1825 duplicates in search
  #1825 duplicates in search
  #1825 Search results contains duplicates
  #1825 Search results contains duplicates

inception-html-editor/pom.xml

@@ -131,6 +131,7 @@
                   <exclude>src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/resources/annotator.*</exclude>
                   <exclude>src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/resources/annotator-full.*</exclude>
                   <exclude>src/main/js/annotatorjs/**/*</exclude>
+                  <exclude>cache/**/*</exclude>
                 </excludes>
               </configuration>
             </execution>

inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/FeatureIndexingSupport.java

@@ -47,12 +47,20 @@ public interface FeatureIndexingSupport
      *            features.
      * @param aFeature
      *            the feature from which to extract the values.
+     * @return key/value pairs as a map
      */
     MultiValuedMap<String, String> indexFeatureValue(String aFieldPrefix,
             AnnotationFS aAnnotation, String aFeaturePrefix, AnnotationFeature aFeature);
 
     /**
      * Get the name of the feature how it is used in the index
+     * @param aFieldPrefix 
+     *            the layer name
+     * @param aFeaturePrefix possible prefix to the feature name, 
+     *            currently for source and target of relation annotations
+     * @param aFeature 
+     *            the feature
+     * @return index feature name
      */
     String featureIndexName(String aFieldPrefix, String aFeaturePrefix, AnnotationFeature aFeature);
 }

inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchResult.java

@@ -149,6 +149,7 @@ public void setSelectedForAnnotation(boolean selectedForAnnotation)
     /**
      * Indicates whether the document to which this result applies cannot be modified by the user
      * who issued the query.
+     * @return whether the document is read-only
      */
     public boolean isReadOnly()
     {

inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchService.java

@@ -34,9 +34,19 @@ List<SearchResult> query(User aUser, Project aProject, String aQuery)
         throws IOException, ExecutionException;
 
     /**
-     * Receive the search results un-grouped as a list. See
-     * {@link #query(User, Project, String, SourceDocument, AnnotationLayer, AnnotationFeature, 
+     * Receive the search results un-grouped as a list. 
+     * See{@link #query(User, Project, String, SourceDocument, AnnotationLayer, AnnotationFeature, 
      * long, long)}
+     * @param aUser
+     *            the current user
+     * @param aProject
+     *            the project to search in
+     * @param aQuery
+     *            the search query
+     * @param aDocument
+     *            limit search to this document or search in the whole project if null
+     * @throws IOException
+     * @throws ExecutionException
      */
     List<SearchResult> query(User aUser, Project aProject, String aQuery, SourceDocument aDocument)
         throws IOException, ExecutionException;
@@ -50,6 +60,8 @@ List<SearchResult> query(User aUser, Project aProject, String aQuery, SourceDocu
      *            the current user
      * @param aProject
      *            the project to search in
+     * @param aQuery
+     *            the search query
      * @param aDocument
      *            limit search to this document or search in the whole project if null
      * @param aAnnotationLayer
@@ -75,7 +87,10 @@ Map<String, List<SearchResult>> query(User aUser, Project aProject, String aQuer
 
     /**
      * This method is only for testing. It allows waiting until the indexing process has completed
-     * before issueing a query.
+     * before issuing a query.
+     * @param aProject
+     *           the project
+     * @return whether the index is flagged as valid
      */
     boolean isIndexValid(Project aProject);
 

inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchServiceImpl.java

@@ -25,7 +25,6 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
 
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
@@ -167,6 +166,7 @@ private Index loadIndex(long aProjectId)
      * 
      * @param aEvent
      *            The BeforeProjectRemovedEvent event
+     * @throws IOException
      */
     @EventListener
     public void beforeProjectRemove(BeforeProjectRemovedEvent aEvent) throws IOException
@@ -311,7 +311,6 @@ public void indexDocument(SourceDocument aSourceDocument, byte[] aBinaryCas)
             // threads to update the index concurrently. The underlying index code should hopefully
             // be thread-safe...
             try {
-                index.getPhysicalIndex().deindexDocument(aSourceDocument);
                 index.getPhysicalIndex().indexDocument(aSourceDocument, aBinaryCas);
             }
             catch (IOException e) {
@@ -355,34 +354,12 @@ public void indexDocument(AnnotationDocument aAnnotationDocument, byte[] aBinary
             // threads to update the index concurrently. The underlying index code should hopefully
             // be thread-safe...
             try {
-                // NOTE: Deleting and then re-indexing the annotation document could lead to
-                // no results for this annotation document being returned while the
-                // re-indexing is still in process. Therefore, we check if there is already
-                // a version of the annotation document index, we obtain the timestamp of this
-                // version, then we add the new version, and finally we remove the old version
-                // as identified by the timestamp.
-
-                // Retrieve the timestamp for the current indexed annotation document
-                Optional<String> oldVersionTimestamp = index.getPhysicalIndex()
-                        .getTimestamp(aAnnotationDocument);
-
                 // Add annotation document to the index again
                 log.trace(
                         "Indexing new version of annotation document [{}]({}) in project [{}]({})",
                         aAnnotationDocument.getName(), aAnnotationDocument.getId(),
                         project.getName(), project.getId());
                 index.getPhysicalIndex().indexDocument(aAnnotationDocument, aBinaryCas);
-
-                // If there was a previous timestamped indexed annotation document, remove it from
-                // index
-                if (oldVersionTimestamp.isPresent()) {
-                    log.trace(
-                            "Removing old version of annotation document [{}]({}) in project [{}]({}) with timestamp [{}]",
-                            aAnnotationDocument.getName(), aAnnotationDocument.getId(),
-                            project.getName(), project.getId(), oldVersionTimestamp.get());
-                    index.getPhysicalIndex().deindexDocument(aAnnotationDocument,
-                            oldVersionTimestamp.get());
-                }
             }
             catch (IOException e) {
                 log.error("Error indexing annotation document [{}]({}) in project [{}]({})",

inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/event/SearchQueryEvent.java

@@ -79,6 +79,7 @@ public String getQuery()
 
     /**
      * Query is limited to the given document.
+     * @return the source document if it exists or empty optional
      */
     public Optional<SourceDocument> getSourceDocument()
     {

inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/index/PhysicalIndex.java

@@ -38,6 +38,7 @@ public interface PhysicalIndex
     /**
      * Deletes the index data, e.g. by removing the index files from disk. If necessary, the index
      * is closed before.
+     * @throws IOException
      */
     void delete() throws IOException;
 
@@ -50,26 +51,29 @@ Map<String, List<SearchResult>> executeQuery(SearchQueryRequest aRequest)
 
     long numberOfQueryResults(SearchQueryRequest aSearchQueryRequest)
         throws IOException, ExecutionException;
-
-    void indexDocument(SourceDocument aDocument, byte[] aBinaryCas) throws IOException;
-
-    void indexDocument(AnnotationDocument aDocument, byte[] aBinaryCas) throws IOException;
 
     void deindexDocument(SourceDocument aDocument) throws IOException;
 
     void deindexDocument(AnnotationDocument aDocument) throws IOException;
 
     void deindexDocument(AnnotationDocument aDocument, String aTimestamp) throws IOException;
+
+    void indexDocument(AnnotationDocument aDocument, byte[] aBinaryCas) throws IOException;
 
     void clear() throws IOException;
 
     /**
      * Retrieve the timestamp of this annotation document
-     * @param aDocument
-     *          The annotation document
-     * @return
-     *          The document timestamp field value. Empty string if document is not found.
+     * 
+     * @param aSrcDocId
+     *            the source document's ID
+     * @param aAnnoDocId
+     *            the annotation document's ID
+     * @return The first found document timestamp field value. Empty string if document is not
+     *         found.
      * @throws IOException
      */
-    public Optional<String> getTimestamp(AnnotationDocument aDocument) throws IOException;
+    public Optional<String> getTimestamp(long aSrcDocId, long aAnnoDocId) throws IOException;
+
+    void indexDocument(SourceDocument aSourceDocument, byte[] aBinaryCas) throws IOException;
 }

inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/scheduling/tasks/Task.java

@@ -121,6 +121,10 @@ public String toString()
     /**
      * Used to avoid scheduling duplicate tasks. Returns true if the current task is a duplicate of
      * the given task.
+     * 
+     * @param aTask
+     *            the given scheduling task
+     * @return whether the given task matches this one
      */
     public abstract boolean matches(Task aTask);