Merge branch 'release/28.x'

* release/28.x:
  #1496 - Some spans are missing begin offset field
  #1511 - External recommender fails when CAS contains control characters
  #1496 - Some spans are missing begin offset field

inception/inception-build/src/main/resources/inception/checkstyle.xml

@@ -38,6 +38,8 @@
   </module>
 
   <module name="TreeWalker">
+    <module name="SuppressionCommentFilter"/>
+
     <module name="OuterTypeFilename"/>
     <module name="IllegalTokenText">
       <property name="tokens" value="STRING_LITERAL, CHAR_LITERAL"/>

inception/inception-imls-external/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommender.java

@@ -72,6 +72,7 @@
 import de.tudarmstadt.ukp.inception.recommendation.imls.external.v1.model.Document;
 import de.tudarmstadt.ukp.inception.recommendation.imls.external.v1.model.Metadata;
 import de.tudarmstadt.ukp.inception.rendering.model.Range;
+import de.tudarmstadt.ukp.inception.support.xml.sanitizer.IllegalXmlCharacterSanitizingContentHandler;
 
 public class ExternalRecommender
     extends RecommendationEngine
@@ -194,7 +195,7 @@ public Range predict(RecommenderContext aContext, CAS aCas, int aBegin, int aEnd
             throw new RecommendationException("Error while deserializing CAS!", e);
         }
 
-        return new Range(aCas);
+        return Range.rangeCoveringDocument(aCas);
     }
 
     private String serializeTypeSystem(CAS aCas) throws RecommendationException
@@ -210,13 +211,13 @@ private String serializeTypeSystem(CAS aCas) throws RecommendationException
 
     private String serializeCas(CAS aCas) throws RecommendationException
     {
-        try (StringWriter out = new StringWriter()) {
+        try (var out = new StringWriter()) {
             // Passing "null" as the type system to the XmiCasSerializer means that we want
             // to serialize all types (i.e. no filtering for a specific target type system).
             XmiCasSerializer xmiCasSerializer = new XmiCasSerializer(null);
-            XMLSerializer sax2xml = new XMLSerializer(out, true);
-            xmiCasSerializer.serialize(getRealCas(aCas), sax2xml.getContentHandler(), null, null,
-                    null);
+            var contentHandler = new XMLSerializer(out, true).getContentHandler();
+            contentHandler = new IllegalXmlCharacterSanitizingContentHandler(contentHandler);
+            xmiCasSerializer.serialize(getRealCas(aCas), contentHandler, null, null, null);
             return out.toString();
         }
         catch (CASRuntimeException | SAXException | IOException e) {

inception/inception-io-json/pom.xml

@@ -50,6 +50,10 @@
       <groupId>org.springframework</groupId>
       <artifactId>spring-beans</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-autoconfigure</artifactId>

inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/LegacyUimaJsonFormatSupport.java

@@ -27,13 +27,21 @@
 
 import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.inception.io.jsoncas.config.LegacyUimaJsonCasFormatProperties;
 
 public class LegacyUimaJsonFormatSupport
     implements FormatSupport
 {
     public static final String ID = "json";
     public static final String NAME = "UIMA CAS JSON (legacy)";
 
+    private final LegacyUimaJsonCasFormatProperties properties;
+
+    public LegacyUimaJsonFormatSupport(LegacyUimaJsonCasFormatProperties aProps)
+    {
+        properties = aProps;
+    }
+
     @Override
     public String getId()
     {
@@ -57,6 +65,7 @@ public AnalysisEngineDescription getWriterDescription(Project aProject,
             TypeSystemDescription aTSD, CAS aCAS)
         throws ResourceInitializationException
     {
-        return createEngineDescription(JsonWriter.class, aTSD);
+        return createEngineDescription(JsonWriter.class, aTSD, //
+                JsonWriter.PARAM_OMIT_DEFAULT_VALUES, properties.isOmitDefaultValues());
     }
 }

inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/config/LegacyUimaJsonCasFormatProperties.java

@@ -0,0 +1,36 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The Technische Universität Darmstadt 
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *  
+ * 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.io.jsoncas.config;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+@ConfigurationProperties("format.json-cas-legacy")
+public class LegacyUimaJsonCasFormatProperties
+{
+    private boolean omitDefaultValues = false;
+
+    public void setOmitDefaultValues(boolean aOmitDefaultValues)
+    {
+        omitDefaultValues = aOmitDefaultValues;
+    }
+
+    public boolean isOmitDefaultValues()
+    {
+        return omitDefaultValues;
+    }
+}

inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/config/UimaJsonCasSupportAutoConfiguration.java

@@ -18,6 +18,7 @@
 package de.tudarmstadt.ukp.inception.io.jsoncas.config;
 
 import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
@@ -26,14 +27,16 @@
 import de.tudarmstadt.ukp.inception.io.jsoncas.UimaJsonCasFormatSupport;
 
 @Configuration
+@EnableConfigurationProperties(LegacyUimaJsonCasFormatProperties.class)
 public class UimaJsonCasSupportAutoConfiguration
 {
     @ConditionalOnProperty(prefix = "format.json-cas-legacy", name = "enabled", //
             havingValue = "true", matchIfMissing = false)
     @Bean
-    public LegacyUimaJsonFormatSupport legacyUimaJsonFormatSupport()
+    public LegacyUimaJsonFormatSupport legacyUimaJsonFormatSupport(
+            LegacyUimaJsonCasFormatProperties aProps)
     {
-        return new LegacyUimaJsonFormatSupport();
+        return new LegacyUimaJsonFormatSupport(aProps);
     }
 
     @ConditionalOnProperty(prefix = "format.json-cas", name = "enabled", //

inception/inception-io-json/src/main/resources/META-INF/asciidoc/user-guide/formats-uimajson-legacy.adoc

@@ -23,14 +23,17 @@ CAUTION: Legacy feature. To use this functionality, you need to enable it first
 Support for this feature will be removed in a future version. The replacement is <<sect_formats_uimajson>>.
 ====
 
-
 This is an old and deprecated UIMA CAS JSON format which can be exported but not imported.
 It should no longer be used. Instead, one should turn to <<sect_formats_uimajson>>.
 
 The format does support custom layers.
 
 For more details on this format, please refer to the link:https://uima.apache.org/d/uimaj-current/references.html#ugr.ref.json[UIMA Reference Guide].
 
+By default, the format writes all values to the JSON output, even if the values are the default values
+in JSON (e.g. `0` for numbers or `false` for booleans). You can configure this behavior by setting
+`format.json-cas-legacy.omit-default-values` to `true` or `false` (default) respectively.
+
 [cols="2,1,1,1,3"]
 |====
 | Format | Read | Write | Custom Layers | Description
@@ -41,4 +44,3 @@ For more details on this format, please refer to the link:https://uima.apache.or
 | yes
 | UIMA CAS JSON (legacy)
 |====
-

inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/xml/ContentHandlerAdapter.java

@@ -37,6 +37,11 @@ public class ContentHandlerAdapter
 
     protected final ContentHandler delegate;
 
+    public ContentHandlerAdapter()
+    {
+        delegate = null;
+    }
+
     public ContentHandlerAdapter(ContentHandler aDelegate)
     {
         delegate = aDelegate;
@@ -45,30 +50,50 @@ public ContentHandlerAdapter(ContentHandler aDelegate)
     @Override
     public void setDocumentLocator(Locator aLocator)
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.setDocumentLocator(aLocator);
     }
 
     @Override
     public void startDocument() throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.startDocument();
     }
 
     @Override
     public void endDocument() throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.endDocument();
     }
 
     @Override
     public void startPrefixMapping(String aPrefix, String aUri) throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.startPrefixMapping(aPrefix, aUri);
     }
 
     @Override
     public void endPrefixMapping(String aPrefix) throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.endPrefixMapping(aPrefix);
     }
 
@@ -117,6 +142,10 @@ public void startElement(String aLocalName, Map<String, String> aAttributes) thr
     public void startElement(String aUri, String aLocalName, String aQName, Attributes aAtts)
         throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.startElement(aUri, aLocalName, aQName, aAtts);
     }
 
@@ -133,6 +162,10 @@ public void endElement(QName aElement) throws SAXException
     @Override
     public void endElement(String aUri, String aLocalName, String aQName) throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.endElement(aUri, aLocalName, aQName);
     }
 
@@ -144,24 +177,40 @@ public void characters(String aString) throws SAXException
     @Override
     public void characters(char[] aCh, int aStart, int aLength) throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.characters(aCh, aStart, aLength);
     }
 
     @Override
     public void ignorableWhitespace(char[] aCh, int aStart, int aLength) throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.ignorableWhitespace(aCh, aStart, aLength);
     }
 
     @Override
     public void processingInstruction(String aTarget, String aData) throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.processingInstruction(aTarget, aData);
     }
 
     @Override
     public void skippedEntity(String aName) throws SAXException
     {
+        if (delegate == null) {
+            return;
+        }
+
         delegate.skippedEntity(aName);
     }
 }