Merge branch 'release/1.5.6'

* release/1.5.6:
  Updated travis config for deployment
  Updated changelog
  1.5.6
  fix #150

.travis.yml

@@ -1,3 +1,20 @@
+os: osx
+osx_image: xcode9.3
 language: java
 jdk:
 - oraclejdk8
+script: mvn package -Pquadrama -Pcreta -Drelease=release
+deploy:
+  skip_cleanup: true
+  provider: releases
+  api_key:
+    secure: iIB3NJmXlg0TIjqul5lpuRjF9YJf0syskDxgtdNrKTrFmRp/zXLvHBXzcYuHh+oS1DlueHChC+JRIIQx3NnP4LN9ErcgOAtQbpzl9EntCoGEtcMCd1bpwj1fLKirxxTBi9389g4dTutfIpK3nbhFU9vu6fOQVEKAle2x3g64zRIksUTWwCLTBn5UcctYEAgy+/Zi4uJwzzfEQUckDjCuaaFuIVuGfncK1n7hjtQA/omrgmHwGZ8910WHhgw4ErpKjyeooLvXcwzk/tbuvqFfbMhcqsscoaevkutfuygMCsVa4ux9y1F85QoE605zpSCYjwK4Pre/Y9rLPZ++SCuNS9gZ2wONqw69q5KJ8338hnNEGp+EXn1FwgbYvtYHxKVAFy7pF5MJaOCgWHEd8jC9miij0u21oRdcd1lc0eTATeNFXZ0BLWGmrm19Z0MrCu+7Pk1cku40tzA3cjRjLLMsZ3B8irNXIroj6AIVdkY8Md1OyDcAnxT3EGHawrPzl0+Q48FwPUCMptEBqMsgzjzN149ft3q/EAcfIO3ldFGz/4QXwfqodwHHvAWN1ctJFyH+kgrf3X5+DcH1Ce/9nZ635UYhyTrXem8c0v9yS0T5X5lsMy7As/I7r4Jr48C6278gcsmOh6ABFyaaK4fjOEXSkTpsGf+ITZPRU254/uV+/e4=
+  file_glob: true
+  file:
+  - target/CorefAnnotator-*-full.jar
+  - CorefAnnotator-*.dmg
+  on:
+    repo: nilsreiter/CorefAnnotator
+    tags: true
+  draft: true
+  name: $TRAVIS_TAG

CHANGELOG.md

@@ -3,6 +3,10 @@
 Issue numbers (e.g., #43) refer to GitHub issues:
 https://github.com/nilsreiter/CorefAnnotator/issues
 
+## 1.5.6
+
+- Fixed an issue that prevented merging compressed files #150
+
 ## 1.5.5
 
 - Fixed an issue that resulted in copied mentions #141

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>de.unistuttgart.ims</groupId>
 	<artifactId>coref.annotator</artifactId>
-	<version>1.5.5</version>
+	<version>1.5.6</version>
 	<packaging>jar</packaging>
 	<name>CorefAnnotator</name>
 	<url>https://github.com/nilsreiter/CorefAnnotator/</url>

src/main/java/de/unistuttgart/ims/coref/annotator/uima/MergeAnnotations.java

@@ -7,14 +7,13 @@
 import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
 import org.apache.uima.fit.descriptor.ConfigurationParameter;
 import org.apache.uima.fit.factory.AnnotationFactory;
-import org.apache.uima.fit.factory.JCasFactory;
-import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
 import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.StringArray;
 import org.eclipse.collections.api.map.MutableMap;
 import org.eclipse.collections.impl.factory.Maps;
+import org.xml.sax.SAXException;
 
 import de.unistuttgart.ims.coref.annotator.api.v1.DetachedMentionPart;
 import de.unistuttgart.ims.coref.annotator.api.v1.Entity;
@@ -32,7 +31,9 @@ public class MergeAnnotations extends JCasAnnotator_ImplBase {
 	public void process(JCas jcas) throws AnalysisEngineProcessException {
 		getLogger().debug("Processing file " + fileName);
 		try {
-			JCas jcas2 = JCasFactory.createJCas(fileName, TypeSystemDescriptionFactory.createTypeSystemDescription());
+
+			JCas jcas2 = UimaUtil.readJCas(fileName);// JCasFactory.createJCas(fileName,
+														// TypeSystemDescriptionFactory.createTypeSystemDescription());
 
 			MutableMap<Entity, Entity> entityMap = Maps.mutable.empty();
 
@@ -90,7 +91,7 @@ public void process(JCas jcas) throws AnalysisEngineProcessException {
 				}
 			}
 
-		} catch (UIMAException | IOException e) {
+		} catch (UIMAException | IOException | SAXException e) {
 			throw new AnalysisEngineProcessException(e);
 		}
 	}

src/main/java/de/unistuttgart/ims/coref/annotator/uima/UimaUtil.java

@@ -0,0 +1,39 @@
+package de.unistuttgart.ims.coref.annotator.uima;
+
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.zip.GZIPInputStream;
+
+import org.apache.commons.compress.archivers.zip.ZipArchiveInputStream;
+import org.apache.uima.UIMAException;
+import org.apache.uima.cas.impl.XmiCasDeserializer;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.jcas.JCas;
+import org.xml.sax.SAXException;
+
+public class UimaUtil {
+	public static JCas readJCas(String filename)
+			throws UIMAException, FileNotFoundException, SAXException, IOException {
+		if (filename.endsWith(".gz")) {
+			try (InputStream is = new GZIPInputStream(new FileInputStream(filename))) {
+				return readJCas(is);
+			}
+		} else if (filename.endsWith(".zip")) {
+			try (InputStream is = new ZipArchiveInputStream(new FileInputStream(filename))) {
+				return readJCas(is);
+			}
+		} else {
+			try (InputStream is = new FileInputStream(filename)) {
+				return readJCas(is);
+			}
+		}
+	}
+
+	public static JCas readJCas(InputStream is) throws UIMAException, SAXException, IOException {
+		JCas jcas = JCasFactory.createJCas();
+		XmiCasDeserializer.deserialize(is, jcas.getCas(), true);
+		return jcas;
+	}
+}