Merge branch 'master' of https://www.github.com/TriNetX/MedTagger

� Conflicts:
�	src/main/java/org/ohnlp/medtagger/ae/AhoCorasickLookupAnnotator.java
�	src/main/java/org/ohnlp/medtagger/dict/DictWriter.java
�	src/main/java/org/ohnlp/medtagger/ie/ae/MedTaggerIEAnnotator.java

pom.xml

@@ -140,7 +140,7 @@
 
     <properties>
         <uimaj.version>2.10.0</uimaj.version>
-        <uimafit.version>2.4.0</uimafit.version>
+        <uimafit.version>2.5.0</uimafit.version>
     </properties>
 
     <dependencies>
@@ -170,9 +170,14 @@
             <version>1.3.3</version>
         </dependency>
         <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-            <version>1.2.17</version>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-api</artifactId>
+            <version>2.17.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-core</artifactId>
+            <version>2.17.1</version>
         </dependency>
         <dependency>
             <groupId>org.apache.opennlp</groupId>

src/main/java/org/ohnlp/medtagger/ae/AhoCorasickLookupAnnotator.java

@@ -1,67 +1,68 @@
 /*******************************************************************************
- * Copyright: (c)  2013  Mayo Foundation for Medical Education and
+ * Copyright: (c)  2013  Mayo Foundation for Medical Education and 
  *  Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
  *  triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- *  Except as contained in the copyright notice above, or as used to identify
+ *  
+ *  Except as contained in the copyright notice above, or as used to identify 
  *  MFMER as the author of this software, the trade names, trademarks, service
  *  marks, or product names of the copyright holder shall not be used in
  *  advertising, promotion or otherwise in connection with this software without
  *  prior written authorization of the copyright holder.
- *
+ *   
  *  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
- *
+ *   
+ *  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.
+ *  See the License for the specific language governing permissions and 
+ *  limitations under the License. 
  *******************************************************************************/
 
 package org.ohnlp.medtagger.ae;
 
-import java.io.*;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.file.Files;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Vector;
-
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.core.config.Configurator;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.resource.ResourceAccessException;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.ohnlp.typesystem.type.textspan.Segment;
-import org.ohnlp.typesystem.type.textspan.Sentence;
+import org.ohnlp.medtagger.dict.AhoCorasickDict;
+import org.ohnlp.medtagger.lvg.LvgLookup;
+import org.ohnlp.medtagger.type.ConceptMention;
 import org.ohnlp.typesystem.type.syntax.BaseToken;
 import org.ohnlp.typesystem.type.syntax.NumToken;
 import org.ohnlp.typesystem.type.syntax.PunctuationToken;
 import org.ohnlp.typesystem.type.syntax.WordToken;
-import org.ohnlp.medtagger.dict.AhoCorasickDict;
-import org.ohnlp.medtagger.lvg.LvgLookup;
-import org.ohnlp.medtagger.type.ConceptMention;
+import org.ohnlp.typesystem.type.textspan.Segment;
+import org.ohnlp.typesystem.type.textspan.Sentence;
+
+import java.io.*;
+import java.net.URI;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Vector;
 
 /**
  * @author Hongfang Liu
  */
 public class AhoCorasickLookupAnnotator extends JCasAnnotator_ImplBase {
 
-    // LOG4J logger based on class name
-    private Logger logger = Logger.getLogger(getClass().getName());
-    private boolean LONGEST = true;
+	// LOG4J logger based on class name
+	private Logger logger = LogManager.getLogger(getClass().getName());
+	private boolean LONGEST = true;
 
     // data structure that stores the TRIE
     AhoCorasickDict btac;
@@ -70,11 +71,11 @@ public class AhoCorasickLookupAnnotator extends JCasAnnotator_ImplBase {
     // add the path in resources
     LvgLookup lvg;
 
-    @Override
-    public void initialize(UimaContext aContext)
-            throws ResourceInitializationException {
-        super.initialize(aContext);
-        logger.setLevel(Level.DEBUG);
+	@Override
+	public void initialize(UimaContext aContext)
+			throws ResourceInitializationException {
+		super.initialize(aContext);
+		Configurator.setLevel(logger.getName(), Level.DEBUG);
 
         try {
             lvg = new LvgLookup(aContext);

src/main/java/org/ohnlp/medtagger/ae/LineSentenceDetector.java

@@ -27,7 +27,8 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
@@ -42,7 +43,7 @@
 
 public class LineSentenceDetector  extends JCasAnnotator_ImplBase {
 
-	private Logger logger = Logger.getLogger(getClass().getName());
+	private Logger logger = LogManager.getLogger(getClass().getName());
 
 	public static final byte CAPS_UNKNOWN = 0;
 	public static final byte CAPS_NONE = 1;

src/main/java/org/ohnlp/medtagger/ae/Open2OHTokenizer.java

@@ -27,7 +27,8 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
@@ -42,7 +43,7 @@
 
 public class Open2OHTokenizer  extends JCasAnnotator_ImplBase {
 
-	private Logger logger = Logger.getLogger(getClass().getName());
+	private Logger logger = LogManager.getLogger(getClass().getName());
 
 	public static final byte CAPS_UNKNOWN = 0;
 	public static final byte CAPS_NONE = 1;

src/main/java/org/ohnlp/medtagger/dict/AhoCorasickDict.java

@@ -39,13 +39,14 @@
 import java.util.Set;
 import java.util.Vector;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 
 
 public class AhoCorasickDict {
 
 	// LOG4J logger based on class name
-   private Logger iv_logger = Logger.getLogger(getClass().getName());
+   private Logger iv_logger = LogManager.getLogger(getClass().getName());
 
 	public static final String FAILLINK="_FAIL_";
 	public static final String SLDELIM="||";

src/main/java/org/ohnlp/medtagger/dict/DictWriter.java

@@ -29,10 +29,14 @@
 import java.util.HashSet;
 import java.util.Iterator;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.collection.CasConsumer_ImplBase;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.resource.ResourceInitializationException;
@@ -94,6 +98,7 @@ else if(token instanceof PunctuationToken){
 			pwr.flush();
 	}
 
+
 	@Override
 	public void destroy() {
 		super.destroy();

src/main/java/org/ohnlp/medtagger/ie/ae/LineSentenceDetector.java

@@ -27,7 +27,8 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
@@ -42,7 +43,7 @@
 
 public class LineSentenceDetector  extends JCasAnnotator_ImplBase {
 
-	private Logger logger = Logger.getLogger(getClass().getName());
+	private Logger logger = LogManager.getLogger(getClass().getName());
 
 	public static final byte CAPS_UNKNOWN = 0;
 	public static final byte CAPS_NONE = 1;

src/main/java/org/ohnlp/medtagger/ie/ae/MedTaggerDynamicIEAnnotator.java

@@ -24,7 +24,8 @@
 package org.ohnlp.medtagger.ie.ae;
 
 import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
 import org.apache.uima.cas.FSIterator;
@@ -60,7 +61,7 @@ public class MedTaggerDynamicIEAnnotator extends JCasAnnotator_ImplBase {
 	//private Boolean hyphen2space = false;
 	private Boolean punct2space = false;
 
-	private Logger iv_logger = Logger.getLogger(getClass().getName());
+	private Logger iv_logger = LogManager.getLogger(getClass().getName());
 
 	public void initialize(UimaContext aContext)
 			throws ResourceInitializationException {

src/main/java/org/ohnlp/medtagger/ie/ae/MedTaggerIEAnnotator.java

@@ -23,10 +23,11 @@
  *******************************************************************************/
 package org.ohnlp.medtagger.ie.ae;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
 import org.apache.uima.cas.FSIterator;
-import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
@@ -67,7 +68,7 @@ public class MedTaggerIEAnnotator extends JCasAnnotator_ImplBase {
 	//private Boolean hyphen2space = false;
 	private Boolean punct2space = false;
 
-	private Logger iv_logger = Logger.getLogger(getClass().getName());
+	private Logger iv_logger = LogManager.getLogger(getClass().getName());
 
 	public ResourceUtilManager rum;
 

src/main/java/org/ohnlp/medtagger/ie/util/ResourceUtilManager.java

@@ -41,7 +41,8 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 
 
 /**
@@ -53,7 +54,7 @@ public class ResourceUtilManager implements Serializable {
     public transient static String RESOURCEDIR;
     private transient static ResourceUtilManager INSTANCE = null;
 
-    private transient Logger iv_logger = Logger.getLogger(getClass().getName());
+    private transient Logger iv_logger = LogManager.getLogger(getClass().getName());
 
     private Pattern regexpPattern = Pattern.compile("(.*)");
     private Pattern normPattern = Pattern.compile("^(.*?)\t(.*?)$");

src/main/java/org/ohnlp/medtagger/lvg/LvgLookup.java

@@ -32,7 +32,8 @@
 import java.util.Iterator;
 import java.util.Scanner;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -46,7 +47,7 @@
 public class LvgLookup extends JCasAnnotator_ImplBase {
 
 	// LOG4J logger based on class name
-	private Logger logger = Logger.getLogger("LvgLookup");
+	private Logger logger = LogManager.getLogger("LvgLookup");
      HashMap<String, String> lvgMap;
     HashSet<String> openclass; 
     //private static OpenClassWords pds = new OpenClassWords();

src/main/java/org/ohnlp/medtagger/ml/cr/transShareAnnotation.java

@@ -35,6 +35,8 @@
 import org.ohnlp.medtagger.ml.type.shareAnnotation;
 import org.ohnlp.medtagger.ml.type.shareSlot;
 
+import javax.xml.XMLConstants;
+import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.parsers.SAXParserFactory;
 import javax.xml.parsers.SAXParser;
 
@@ -52,27 +54,36 @@ public transShareAnnotation(JCas jcas) {
 	};
 
 	public transShareAnnotation(String str, JCas jcas) {
-		SAXParserFactory factory = SAXParserFactory.newInstance();
 		mjcas = jcas;
 		try {
-			SAXParser saxParser = factory.newSAXParser();
+			SAXParser saxParser = createSaxParser();
 			saxParser.parse(new ByteArrayInputStream(str.getBytes()), this);
 		} catch (Throwable t) {
 			t.printStackTrace();
 		}
 	}
 
 	public transShareAnnotation(File xmlfile, JCas jcas) {
-		SAXParserFactory factory = SAXParserFactory.newInstance();
 		mjcas=jcas;
 		try {
-			SAXParser saxParser = factory.newSAXParser();
+			SAXParser saxParser = createSaxParser();
 			saxParser.parse(xmlfile, this);
 		} catch (Throwable t) {
 			t.printStackTrace();
 		}
 	}
 
+	private SAXParser createSaxParser() throws ParserConfigurationException, SAXException {
+		SAXParserFactory factory = SAXParserFactory.newInstance();
+		factory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
+		factory.setFeature("http://xml.org/sax/features/external-general-entities", false);
+		factory.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
+		SAXParser saxParser = factory.newSAXParser(); // Noncompliant
+		saxParser.setProperty(XMLConstants.ACCESS_EXTERNAL_DTD, "");
+		saxParser.setProperty(XMLConstants.ACCESS_EXTERNAL_SCHEMA, "");
+		return saxParser;
+	}
+
 	// ===========================================================
 	// SAX DocumentHandler methods
 	// ===========================================================

src/main/java/org/ohnlp/medtagger/ml/crfsuite/CRFSuiteWrapper.java

@@ -39,14 +39,15 @@
 import java.util.List;
 import java.util.Set;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.ohnlp.medtagger.ml.feature.Feature;
 import org.ohnlp.medtagger.ml.util.Executer;
 import org.ohnlp.medtagger.ml.util.PlatformDetection;
 
 
 public class CRFSuiteWrapper {
-  private Logger iv_logger = Logger.getLogger(getClass().getName());
+  private Logger iv_logger = LogManager.getLogger(getClass().getName());
   private File executable;
 
   public CRFSuiteWrapper() throws Exception {