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Posted to commits@ctakes.apache.org by ja...@apache.org on 2012/10/31 06:26:55 UTC
svn commit: r1403989 [25/28] - in /incubator/ctakes/branches/SHARPn-cTAKES:
Constituency Parser/src/org/chboston/cnlp/ctakes/parser/ Constituency
Parser/src/org/chboston/cnlp/ctakes/parser/uima/ae/ Constituency
Parser/src/org/chboston/cnlp/ctakes/parse...
Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/DocumentMetaData.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/DocumentMetaData.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/DocumentMetaData.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/DocumentMetaData.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
/*
- * Copyright: (c) 2009 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
- * 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
- *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF 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. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
@@ -21,120 +14,120 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package edu.mayo.bmi.nlp.preprocessor;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-/**
- *
- * @author Mayo Clinic
- */
-public class DocumentMetaData
-{
- private String iv_text;
-
- private List iv_scAnnotationList = new ArrayList();
-
- // key = unique key, value = document meta data
- private Map iv_docMetaDataMap = new HashMap();
-
- // key = segment ID, value = SegmentMetaData object
- private Map<String, SegmentMetaData> iv_segMetaDataHash = new HashMap<String, SegmentMetaData>();
-
- /**
- * Adds a meta data entry for the document.
- * @param key
- * @param value
- */
- public void addMetaData(Object key, Object value)
- {
- iv_docMetaDataMap.put(key, value);
- }
-
- /**
- * Gets a map of meta data about the document.
- * @return
- */
- public Map getMetaData()
- {
- return iv_docMetaDataMap;
- }
-
- /**
- * Adds a segment.
- * @param smd
- */
- public void addSegment(SegmentMetaData smd)
- {
- iv_segMetaDataHash.put(smd.id, smd);
- }
-
- /**
- * Gets a set of segment identifiers. Each identifier is a String object.
- * @return Set of String objects, each String is a segment identifier.
- */
- public Set<String> getSegmentIdentifiers()
- {
- return (Set<String>)iv_segMetaDataHash.keySet();
- }
-
- /**
- * Gets meta data about the specified segment.
- * @param segmentID Identifier of segment.
- * @return SegmentMetaData object that contains meta data about the
- * specified segment.
- */
- public SegmentMetaData getSegment(String segmentID)
- {
- return (SegmentMetaData) iv_segMetaDataHash.get(segmentID);
- }
-
- /**
- * Adds a single annotation to the syntactic cue annotation list.
- * @param a
- */
- public void addAnnotation(Annotation a)
- {
- iv_scAnnotationList.add(a);
- }
-
- /**
- * Adds a list of annotations to the syntactic cue annotation list.
- * @param aList
- */
- public void addAnnotations(List aList)
- {
- iv_scAnnotationList.addAll(aList);
- }
-
- /**
- * Gets a list of Annotation objects that represent annotations based
- * off of document syntactic cues.
- * @return List of Annotation objects.
- */
- public List getAnnotations()
- {
- return iv_scAnnotationList;
- }
-
- /**
- * @return
- */
- public String getText()
- {
- return iv_text;
- }
-
- /**
- * @param string
- */
- public void setText(String string)
- {
- iv_text = string;
- }
-
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ *
+ * @author Mayo Clinic
+ */
+public class DocumentMetaData
+{
+ private String iv_text;
+
+ private List iv_scAnnotationList = new ArrayList();
+
+ // key = unique key, value = document meta data
+ private Map iv_docMetaDataMap = new HashMap();
+
+ // key = segment ID, value = SegmentMetaData object
+ private Map<String, SegmentMetaData> iv_segMetaDataHash = new HashMap<String, SegmentMetaData>();
+
+ /**
+ * Adds a meta data entry for the document.
+ * @param key
+ * @param value
+ */
+ public void addMetaData(Object key, Object value)
+ {
+ iv_docMetaDataMap.put(key, value);
+ }
+
+ /**
+ * Gets a map of meta data about the document.
+ * @return
+ */
+ public Map getMetaData()
+ {
+ return iv_docMetaDataMap;
+ }
+
+ /**
+ * Adds a segment.
+ * @param smd
+ */
+ public void addSegment(SegmentMetaData smd)
+ {
+ iv_segMetaDataHash.put(smd.id, smd);
+ }
+
+ /**
+ * Gets a set of segment identifiers. Each identifier is a String object.
+ * @return Set of String objects, each String is a segment identifier.
+ */
+ public Set<String> getSegmentIdentifiers()
+ {
+ return (Set<String>)iv_segMetaDataHash.keySet();
+ }
+
+ /**
+ * Gets meta data about the specified segment.
+ * @param segmentID Identifier of segment.
+ * @return SegmentMetaData object that contains meta data about the
+ * specified segment.
+ */
+ public SegmentMetaData getSegment(String segmentID)
+ {
+ return (SegmentMetaData) iv_segMetaDataHash.get(segmentID);
+ }
+
+ /**
+ * Adds a single annotation to the syntactic cue annotation list.
+ * @param a
+ */
+ public void addAnnotation(Annotation a)
+ {
+ iv_scAnnotationList.add(a);
+ }
+
+ /**
+ * Adds a list of annotations to the syntactic cue annotation list.
+ * @param aList
+ */
+ public void addAnnotations(List aList)
+ {
+ iv_scAnnotationList.addAll(aList);
+ }
+
+ /**
+ * Gets a list of Annotation objects that represent annotations based
+ * off of document syntactic cues.
+ * @return List of Annotation objects.
+ */
+ public List getAnnotations()
+ {
+ return iv_scAnnotationList;
+ }
+
+ /**
+ * @return
+ */
+ public String getText()
+ {
+ return iv_text;
+ }
+
+ /**
+ * @param string
+ */
+ public void setText(String string)
+ {
+ iv_text = string;
+ }
+
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/IntegerRange.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/IntegerRange.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/IntegerRange.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/IntegerRange.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
/*
- * Copyright: (c) 2009 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
- * 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
- *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF 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. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
@@ -21,14 +14,14 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package edu.mayo.bmi.nlp.preprocessor;
-
-/**
- * Defines a range of integers.
- * @author Mayo Clinic
- */
-public class IntegerRange
-{
- public int start;
- public int end;
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+/**
+ * Defines a range of integers.
+ * @author Mayo Clinic
+ */
+public class IntegerRange
+{
+ public int start;
+ public int end;
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/PreProcessor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/PreProcessor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/PreProcessor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/PreProcessor.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
/*
- * Copyright: (c) 2009 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
- * 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
- *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF 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. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
@@ -21,20 +14,20 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package edu.mayo.bmi.nlp.preprocessor;
-
-
-/**
- *
- * @author Mayo Clinic
- */
-public interface PreProcessor
-{
- /**
- * Process a document to retrieve meta data about the document.
- * @param document
- * @return
- * @throws Exception
- */
- public DocumentMetaData process(String document) throws Exception;
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+
+/**
+ *
+ * @author Mayo Clinic
+ */
+public interface PreProcessor
+{
+ /**
+ * Process a document to retrieve meta data about the document.
+ * @param document
+ * @return
+ * @throws Exception
+ */
+ public DocumentMetaData process(String document) throws Exception;
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/SegmentMetaData.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/SegmentMetaData.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/SegmentMetaData.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/SegmentMetaData.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
/*
- * Copyright: (c) 2009 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
- * 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
- *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF 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. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
@@ -21,17 +14,17 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package edu.mayo.bmi.nlp.preprocessor;
-
-import java.util.List;
-
-/**
- * MetaData about a segment.
- * @author Mayo Clinic
- */
-public class SegmentMetaData
-{
- public IntegerRange span;
- public String id;
- public List textSpans;
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+import java.util.List;
+
+/**
+ * MetaData about a segment.
+ * @author Mayo Clinic
+ */
+public class SegmentMetaData
+{
+ public IntegerRange span;
+ public String id;
+ public List textSpans;
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/Utility.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/preprocessor/Utility.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/Utility.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/preprocessor/Utility.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
/*
- * Copyright: (c) 2009 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
- * 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
- *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF 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. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
@@ -21,76 +14,76 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package edu.mayo.bmi.nlp.preprocessor;
-
-/**
- *
- * @author Mayo Clinic
- */
-public class Utility
-{
- /**
- * Replaces any non-ascii characters with the specified char.
- * @param sb
- */
- public static void replaceNonAsciiChars(StringBuffer sb, char replacementChar)
- {
- for (int i = 0; i < sb.length(); i++)
- {
- char c = sb.charAt(i);
- // Unicode range 0000-007f Basic Latin
- // equivalent to ASCII charset
- if (c > 0x007f)
- {
- // character is outside ASCII range of unicode char set
- sb.setCharAt(i, replacementChar);
- }
- }
- }
-
- /**
- * remove leading and trailing whitespace from each line
- * @param sb
- * @return
- */
- public static String compress(StringBuffer sb)
- {
- StringBuffer compressedSB = new StringBuffer();
- if (sb == null)
- {
- return compressedSB.toString();
- }
-
- int indexOfLastNewline = 0;
- // use for loop to handle through the last newline character
- for (int i = 0; i < sb.length(); i++)
- {
- char currentChar = sb.charAt(i);
- if (currentChar == '\n')
- {
- if ((i - indexOfLastNewline) > 1)
- {
- String lineText = sb.substring(indexOfLastNewline, i);
- String compressedText = lineText.trim();
- if (compressedText.length() > 0)
- {
- compressedSB.append(compressedText);
- compressedSB.append('\n');
- }
- }
- indexOfLastNewline = i;
- }
- }
-
- // handles text after last newline character, or text if
- // there were no newline characters
- if (indexOfLastNewline < sb.length())
- {
- String lineText = sb.substring(indexOfLastNewline, sb.length());
- String compressedText = lineText.trim();
- compressedSB.append(compressedText);
- }
-
- return compressedSB.toString();
- }
-}
+package edu.mayo.bmi.nlp.preprocessor;
+
+/**
+ *
+ * @author Mayo Clinic
+ */
+public class Utility
+{
+ /**
+ * Replaces any non-ascii characters with the specified char.
+ * @param sb
+ */
+ public static void replaceNonAsciiChars(StringBuffer sb, char replacementChar)
+ {
+ for (int i = 0; i < sb.length(); i++)
+ {
+ char c = sb.charAt(i);
+ // Unicode range 0000-007f Basic Latin
+ // equivalent to ASCII charset
+ if (c > 0x007f)
+ {
+ // character is outside ASCII range of unicode char set
+ sb.setCharAt(i, replacementChar);
+ }
+ }
+ }
+
+ /**
+ * remove leading and trailing whitespace from each line
+ * @param sb
+ * @return
+ */
+ public static String compress(StringBuffer sb)
+ {
+ StringBuffer compressedSB = new StringBuffer();
+ if (sb == null)
+ {
+ return compressedSB.toString();
+ }
+
+ int indexOfLastNewline = 0;
+ // use for loop to handle through the last newline character
+ for (int i = 0; i < sb.length(); i++)
+ {
+ char currentChar = sb.charAt(i);
+ if (currentChar == '\n')
+ {
+ if ((i - indexOfLastNewline) > 1)
+ {
+ String lineText = sb.substring(indexOfLastNewline, i);
+ String compressedText = lineText.trim();
+ if (compressedText.length() > 0)
+ {
+ compressedSB.append(compressedText);
+ compressedSB.append('\n');
+ }
+ }
+ indexOfLastNewline = i;
+ }
+ }
+
+ // handles text after last newline character, or text if
+ // there were no newline characters
+ if (indexOfLastNewline < sb.length())
+ {
+ String lineText = sb.substring(indexOfLastNewline, sb.length());
+ String compressedText = lineText.trim();
+ compressedSB.append(compressedText);
+ }
+
+ return compressedSB.toString();
+ }
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/test/TestDriver.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/nlp/test/TestDriver.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/test/TestDriver.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/nlp/test/TestDriver.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
/*
- * Copyright: (c) 2009 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
- * 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
- *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF 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. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
@@ -21,134 +14,134 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package edu.mayo.bmi.nlp.test;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Set;
-
-import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
-import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
-import edu.mayo.bmi.nlp.preprocessor.PreProcessor;
-import edu.mayo.bmi.nlp.preprocessor.SegmentMetaData;
-
-/**
- *
- * @author Mayo Clinic
- */
-public class TestDriver
-{
-
- public static void main(String[] args)
- {
- if (args.length < 1 || args.length > 2)
- {
- System.out.println("Usage: TestDriver <input file> [<dtd file>]");
- // example parameters: "test/data/testpatient_cn_1.xml"
- // example parameters: "test/data/testpatient_cn_1.xml" "resources/cda/NotesIIST_RTF.DTD"
- System.exit(1);
- }
- try
- {
- String hl7Text = load(args[0]);
- String dtdFilename = "resources/cda/NotesIIST_RTF.DTD";
- if (args.length > 1) {
- dtdFilename = args[1];
- }
-
-
- long timestamp, elapsedTime;
- Set sectionNames;
- Iterator snItr;
-
- File dtdFile = new File(dtdFilename);
- if (!exists(dtdFile)) {
- System.exit(-1);
- }
-
- PreProcessor pp = new ClinicalNotePreProcessor(dtdFile, false);
-
- timestamp = System.currentTimeMillis();
- DocumentMetaData dmd = pp.process(hl7Text);
- elapsedTime = System.currentTimeMillis() - timestamp;
- System.out.println("PreProcessor Took " + elapsedTime + "ms");
-
- System.out.println("Plain Text Start");
- System.out.println(dmd.getText());
- System.out.println("Plain Text End");
-
- sectionNames = dmd.getSegmentIdentifiers();
- snItr = sectionNames.iterator();
- while (snItr.hasNext())
- {
- String sectionId = (String) snItr.next();
- SegmentMetaData smd = dmd.getSegment(sectionId);
- System.out.println("SECTION="
- + sectionId
- + "\tSTART_OFFSET="
- + smd.span.start
- + "\tEND_OFFSET="
- + smd.span.end);
- //System.out.println(dmd.getText().substring(smd.span.start, smd.span.end));
- }
-
- Map metaDataMap = dmd.getMetaData();
- Iterator keyItr = metaDataMap.keySet().iterator();
- while (keyItr.hasNext())
- {
- Object key = keyItr.next();
- Object value = metaDataMap.get(key);
- System.out.println("MetaData KEY="
- + key.toString()
- + " VALUE="
- + value.toString());
- }
- }
- catch (Exception e)
- {
- e.printStackTrace();
- }
- }
-
- /**
- * Loads text from a file.
- *
- * @param filename
- * @return
- * @throws FileNotFoundException
- * @throws IOException
- */
- public static String load(String filename)
- throws FileNotFoundException, IOException
- {
- String msg = "";
- File f = new File(filename);
- exists(f); // output error message if file does not exist
- BufferedReader br = new BufferedReader(new FileReader(f));
- String line = br.readLine();
- while (line != null)
- {
- msg += line + "\n";
- line = br.readLine();
- }
- br.close();
-
- return msg;
- }
-
- public static boolean exists(File f) {
-
- if (f.exists()) {
- return true;
- }
-
- System.out.println("cwd = " + new File(".").getAbsolutePath());
- System.out.println("File " + f + " does not exist.");
- return false;
- }
-}
+package edu.mayo.bmi.nlp.test;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Set;
+
+import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
+import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
+import edu.mayo.bmi.nlp.preprocessor.PreProcessor;
+import edu.mayo.bmi.nlp.preprocessor.SegmentMetaData;
+
+/**
+ *
+ * @author Mayo Clinic
+ */
+public class TestDriver
+{
+
+ public static void main(String[] args)
+ {
+ if (args.length < 1 || args.length > 2)
+ {
+ System.out.println("Usage: TestDriver <input file> [<dtd file>]");
+ // example parameters: "test/data/testpatient_cn_1.xml"
+ // example parameters: "test/data/testpatient_cn_1.xml" "resources/cda/NotesIIST_RTF.DTD"
+ System.exit(1);
+ }
+ try
+ {
+ String hl7Text = load(args[0]);
+ String dtdFilename = "resources/cda/NotesIIST_RTF.DTD";
+ if (args.length > 1) {
+ dtdFilename = args[1];
+ }
+
+
+ long timestamp, elapsedTime;
+ Set sectionNames;
+ Iterator snItr;
+
+ File dtdFile = new File(dtdFilename);
+ if (!exists(dtdFile)) {
+ System.exit(-1);
+ }
+
+ PreProcessor pp = new ClinicalNotePreProcessor(dtdFile, false);
+
+ timestamp = System.currentTimeMillis();
+ DocumentMetaData dmd = pp.process(hl7Text);
+ elapsedTime = System.currentTimeMillis() - timestamp;
+ System.out.println("PreProcessor Took " + elapsedTime + "ms");
+
+ System.out.println("Plain Text Start");
+ System.out.println(dmd.getText());
+ System.out.println("Plain Text End");
+
+ sectionNames = dmd.getSegmentIdentifiers();
+ snItr = sectionNames.iterator();
+ while (snItr.hasNext())
+ {
+ String sectionId = (String) snItr.next();
+ SegmentMetaData smd = dmd.getSegment(sectionId);
+ System.out.println("SECTION="
+ + sectionId
+ + "\tSTART_OFFSET="
+ + smd.span.start
+ + "\tEND_OFFSET="
+ + smd.span.end);
+ //System.out.println(dmd.getText().substring(smd.span.start, smd.span.end));
+ }
+
+ Map metaDataMap = dmd.getMetaData();
+ Iterator keyItr = metaDataMap.keySet().iterator();
+ while (keyItr.hasNext())
+ {
+ Object key = keyItr.next();
+ Object value = metaDataMap.get(key);
+ System.out.println("MetaData KEY="
+ + key.toString()
+ + " VALUE="
+ + value.toString());
+ }
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Loads text from a file.
+ *
+ * @param filename
+ * @return
+ * @throws FileNotFoundException
+ * @throws IOException
+ */
+ public static String load(String filename)
+ throws FileNotFoundException, IOException
+ {
+ String msg = "";
+ File f = new File(filename);
+ exists(f); // output error message if file does not exist
+ BufferedReader br = new BufferedReader(new FileReader(f));
+ String line = br.readLine();
+ while (line != null)
+ {
+ msg += line + "\n";
+ line = br.readLine();
+ }
+ br.close();
+
+ return msg;
+ }
+
+ public static boolean exists(File f) {
+
+ if (f.exists()) {
+ return true;
+ }
+
+ System.out.println("cwd = " + new File(".").getAbsolutePath());
+ System.out.println("File " + f + " does not exist.");
+ return false;
+ }
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/uima/ae/CdaCasInitializer.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/src/edu/mayo/bmi/uima/ae/CdaCasInitializer.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/uima/ae/CdaCasInitializer.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/src/edu/mayo/bmi/uima/ae/CdaCasInitializer.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
/*
- * Copyright: (c) 2009 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
- * 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
- *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF 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. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
@@ -21,8 +14,8 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package edu.mayo.bmi.uima.ae;
-
+package edu.mayo.bmi.uima.ae;
+
import java.io.File;
import java.util.HashSet;
import java.util.Iterator;
@@ -51,143 +44,143 @@ import edu.mayo.bmi.uima.core.type.struc
import edu.mayo.bmi.uima.core.type.textspan.Segment;
import edu.mayo.bmi.uima.core.type.util.Pair;
import edu.mayo.bmi.uima.core.type.util.Pairs;
-
-
-/**
- * Bootstraps the CAS by:
- * <ol>
- * <li>Transforms document's original CDA text into plain text,
- * inserting section (segment) markers into text .</li>
- * <li>Transformation also inserts hyphens into words that should be hyphenated</li>
- * <li>Stores the resulting text in a new View (which has its own Sofa)</li>
- * <li>Detects sections and adds Segment (aka section) annotations </li>
- * <li>Extracts document level data and stores in CAS as Property annotations.</li>
- * </ol>
- *
- */
-public class CdaCasInitializer extends JCasAnnotator_ImplBase
-{
- // LOG4J logger based on class name
- private Logger logger = Logger.getLogger(getClass().getName());
-
- private File dtdFile;
- private Boolean includeSectionMarkers;
-
- private TextModifier tm;
-
-
- private UimaContext uimaContext;
-
- public void initialize(UimaContext aCtx) throws ResourceInitializationException {
-
- super.initialize(aCtx);
-
- uimaContext = aCtx;
- initialize();
-
- }
-
-
- public void initialize() throws ResourceInitializationException
- {
- // TODO Consider using a parameter for includeSectionMarkers
- //includeSectionMarkers = (Boolean) getConfigParameterValue("IncludeSectionMarkers");
- includeSectionMarkers = new Boolean(false);
-
- // TODO Consider using a parameter for hyphWindow/HyphenDetectionWindow
- //int hyphWindow = ((Integer) getConfigParameterValue("HyphenDetectionWindow")).intValue();
- int hyphWindow = 3;
-
- try {
- FileResource hyphResrc = (FileResource) uimaContext.getResourceObject("HyphenDictionary");
- File hyphFile = hyphResrc.getFile();
- logger.info("Hyphen dictionary: " + hyphFile.getAbsolutePath());
-
- tm = new HyphenTextModifierImpl(
- hyphFile.getAbsolutePath(),
- hyphWindow);
-
- FileResource dtdResrc = (FileResource) uimaContext.getResourceObject("DTD");
- dtdFile = dtdResrc.getFile();
- logger.info("DTD: " + dtdFile.getAbsolutePath());
- }
- catch (Exception e) {
- throw new ResourceInitializationException(e);
- }
- }
-
-
-
- /**
- * Apply text modifier to the text
- * TODO - move this to <code>TextModifier</code> and take a <code>Logger</code>
- * See <code>HyphenTextModifierImpl</code>
- * @param sb
- * @return
- */
- private void applyTextModifier(String text, StringBuffer sb) throws Exception {
- TextModification[] textModArr = tm.modify(text);
- for (int i = 0; i < textModArr.length; i++) {
-
- TextModification textMod = textModArr[i];
-
- if ((textMod.getOrigStartOffset() != textMod.getNewStartOffset())
- || (textMod.getOrigEndOffset() != textMod.getNewEndOffset())) {
- logger.warn("UNSUPPORTED: TextModification with offset changes.");
- }
- else {
- sb.replace(textMod.getOrigStartOffset(),
- textMod.getOrigEndOffset(),
- textMod.getNewText());
- }
- }
- }
-
-
- public void process(JCas jcas) throws AnalysisEngineProcessException {
-
- logger.info(" process(JCas)");
-
- String originalText = null;
- DocumentMetaData dmd;
-
+
+
+/**
+ * Bootstraps the CAS by:
+ * <ol>
+ * <li>Transforms document's original CDA text into plain text,
+ * inserting section (segment) markers into text .</li>
+ * <li>Transformation also inserts hyphens into words that should be hyphenated</li>
+ * <li>Stores the resulting text in a new View (which has its own Sofa)</li>
+ * <li>Detects sections and adds Segment (aka section) annotations </li>
+ * <li>Extracts document level data and stores in CAS as Property annotations.</li>
+ * </ol>
+ *
+ */
+public class CdaCasInitializer extends JCasAnnotator_ImplBase
+{
+ // LOG4J logger based on class name
+ private Logger logger = Logger.getLogger(getClass().getName());
+
+ private File dtdFile;
+ private Boolean includeSectionMarkers;
+
+ private TextModifier tm;
+
+
+ private UimaContext uimaContext;
+
+ public void initialize(UimaContext aCtx) throws ResourceInitializationException {
+
+ super.initialize(aCtx);
+
+ uimaContext = aCtx;
+ initialize();
+
+ }
+
+
+ public void initialize() throws ResourceInitializationException
+ {
+ // TODO Consider using a parameter for includeSectionMarkers
+ //includeSectionMarkers = (Boolean) getConfigParameterValue("IncludeSectionMarkers");
+ includeSectionMarkers = new Boolean(false);
+
+ // TODO Consider using a parameter for hyphWindow/HyphenDetectionWindow
+ //int hyphWindow = ((Integer) getConfigParameterValue("HyphenDetectionWindow")).intValue();
+ int hyphWindow = 3;
+
try {
-
- JCas originalView = jcas.getView("_InitialView");
- originalText = originalView.getSofaDataString();
-
- PreProcessor pp = new ClinicalNotePreProcessor(
- dtdFile,
- includeSectionMarkers.booleanValue());
- dmd = pp.process(originalText);
-
- String text = dmd.getText();
- StringBuffer sb = new StringBuffer(text);
-
- applyTextModifier(text, sb);
-
- // Create a view (and its Sofa) to hold the plain text version of
- // the CDA document
- JCas plaintextView = jcas.createView("plaintext");
- plaintextView.setDocumentText(sb.toString());
-
- // Add section (segment) annotations
- Iterator<String> segmentItr = (Iterator<String>)dmd.getSegmentIdentifiers().iterator();
+ FileResource hyphResrc = (FileResource) uimaContext.getResourceObject("HyphenDictionary");
+ File hyphFile = hyphResrc.getFile();
+ logger.info("Hyphen dictionary: " + hyphFile.getAbsolutePath());
+
+ tm = new HyphenTextModifierImpl(
+ hyphFile.getAbsolutePath(),
+ hyphWindow);
+
+ FileResource dtdResrc = (FileResource) uimaContext.getResourceObject("DTD");
+ dtdFile = dtdResrc.getFile();
+ logger.info("DTD: " + dtdFile.getAbsolutePath());
+ }
+ catch (Exception e) {
+ throw new ResourceInitializationException(e);
+ }
+ }
+
+
+
+ /**
+ * Apply text modifier to the text
+ * TODO - move this to <code>TextModifier</code> and take a <code>Logger</code>
+ * See <code>HyphenTextModifierImpl</code>
+ * @param sb
+ * @return
+ */
+ private void applyTextModifier(String text, StringBuffer sb) throws Exception {
+ TextModification[] textModArr = tm.modify(text);
+ for (int i = 0; i < textModArr.length; i++) {
+
+ TextModification textMod = textModArr[i];
+
+ if ((textMod.getOrigStartOffset() != textMod.getNewStartOffset())
+ || (textMod.getOrigEndOffset() != textMod.getNewEndOffset())) {
+ logger.warn("UNSUPPORTED: TextModification with offset changes.");
+ }
+ else {
+ sb.replace(textMod.getOrigStartOffset(),
+ textMod.getOrigEndOffset(),
+ textMod.getNewText());
+ }
+ }
+ }
+
+
+ public void process(JCas jcas) throws AnalysisEngineProcessException {
+
+ logger.info(" process(JCas)");
+
+ String originalText = null;
+ DocumentMetaData dmd;
+
+ try {
+
+ JCas originalView = jcas.getView("_InitialView");
+ originalText = originalView.getSofaDataString();
+
+ PreProcessor pp = new ClinicalNotePreProcessor(
+ dtdFile,
+ includeSectionMarkers.booleanValue());
+ dmd = pp.process(originalText);
+
+ String text = dmd.getText();
+ StringBuffer sb = new StringBuffer(text);
+
+ applyTextModifier(text, sb);
+
+ // Create a view (and its Sofa) to hold the plain text version of
+ // the CDA document
+ JCas plaintextView = jcas.createView("plaintext");
+ plaintextView.setDocumentText(sb.toString());
+
+ // Add section (segment) annotations
+ Iterator<String> segmentItr = (Iterator<String>)dmd.getSegmentIdentifiers().iterator();
while (segmentItr.hasNext())
- {
- String segmentID = (String) segmentItr.next();
- SegmentMetaData smd = dmd.getSegment(segmentID);
-
- Segment sa = new Segment(plaintextView);
- sa.setBegin(smd.span.start);
- sa.setEnd(smd.span.end);
- sa.setId(smd.id);
-
- sa.addToIndexes();
+ {
+ String segmentID = (String) segmentItr.next();
+ SegmentMetaData smd = dmd.getSegment(segmentID);
+
+ Segment sa = new Segment(plaintextView);
+ sa.setBegin(smd.span.start);
+ sa.setEnd(smd.span.end);
+ sa.setId(smd.id);
+
+ sa.addToIndexes();
}
- // Store meta data about the document
- Pairs propAnnot = new Pairs(plaintextView);
+ // Store meta data about the document
+ Pairs propAnnot = new Pairs(plaintextView);
Map metaDataMap = dmd.getMetaData();
String docID = (String)metaDataMap.get(ClinicalNotePreProcessor.MD_KEY_DOC_ID);
@@ -197,33 +190,33 @@ public class CdaCasInitializer extends J
newDocId.addToIndexes();
}
-
- FSArray fsArr = new FSArray(plaintextView, metaDataMap.size());
- Iterator keyItr = metaDataMap.keySet().iterator();
- int pos = 0;
- while (keyItr.hasNext()) {
-
- String key = (String) keyItr.next();
- Object value = metaDataMap.get(key);
-
- if (value instanceof String) {
- Pair prop = new Pair(plaintextView);
- prop.setAttribute(key);
- prop.setValue((String) value);
- fsArr.set(pos++, prop);
- }
- else if (value instanceof HashSet) {
- }
-
- }
-
- propAnnot.setPairs(fsArr);
- propAnnot.addToIndexes();
- }
- catch (Exception e) {
- throw new AnalysisEngineProcessException(e);
- }
-
- }
-
-}
+
+ FSArray fsArr = new FSArray(plaintextView, metaDataMap.size());
+ Iterator keyItr = metaDataMap.keySet().iterator();
+ int pos = 0;
+ while (keyItr.hasNext()) {
+
+ String key = (String) keyItr.next();
+ Object value = metaDataMap.get(key);
+
+ if (value instanceof String) {
+ Pair prop = new Pair(plaintextView);
+ prop.setAttribute(key);
+ prop.setValue((String) value);
+ fsArr.set(pos++, prop);
+ }
+ else if (value instanceof HashSet) {
+ }
+
+ }
+
+ propAnnot.setPairs(fsArr);
+ propAnnot.addToIndexes();
+ }
+ catch (Exception e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ }
+
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/document%20preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/document preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java Wed Oct 31 05:26:43 2012
@@ -1,18 +1,11 @@
/*
- * Copyright: (c) 2009 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
- * 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
- *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF 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. You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
@@ -21,125 +14,125 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package edu.mayo.bmi.test.preprocessor;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.net.URLDecoder;
-import java.util.Map;
-
-import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
-import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
-
-import junit.framework.TestCase;
-
-/**
- * Unit tests for the ClinicalNotePreProcessor class. These test the class
- * against clinical note XML data and determine whether the preprocessor
- * successfully parsed out the correct info.
- *
- * @author Mayo Clinic
- */
-public class ClinicalNotePreProcessorTest extends TestCase
-{
- private ClinicalNotePreProcessor iv_cnotePreProcessor;
- private String iv_cnoteXML;
-
- /**
- * Constructor for ClinicalNotePreProcessorTest.
- * @param arg0
- */
- public ClinicalNotePreProcessorTest(String arg0)
- {
- super(arg0);
- }
-
- /*
- * @see TestCase#setUp()
- */
- protected void setUp() throws Exception
- {
- super.setUp();
-
- String dtdLocation = "resources/cda/NotesIIST_RTF.DTD";
- File dtd = new File(dtdLocation);
- iv_cnotePreProcessor = new ClinicalNotePreProcessor(dtd, false);
-
- //String cnoteLocationOnCp = "/test/data/testpatient_cn_1.xml";
- String cnoteLocationOnCp = "../../../../../data/testpatient_cn_1.xml";
- String cnoteLocation =
- URLDecoder.decode(getClass().getResource(cnoteLocationOnCp).getPath());
-
- if (cnoteLocation == null) {
- throw new FileNotFoundException("Unable to find: " + cnoteLocationOnCp);
- }
- iv_cnoteXML = load(cnoteLocation);
- }
-
- /*
- * @see TestCase#tearDown()
- */
- protected void tearDown() throws Exception
- {
- super.tearDown();
- }
-
- /**
- * Tests the process method.
- */
- public void testProcess()
- {
- try
- {
- DocumentMetaData dmd = iv_cnotePreProcessor.process(iv_cnoteXML);
-
- // validate document properties
- String docID = "000000000";
- String serviceCode = "MNT";
- Map docProperties = dmd.getMetaData();
- String cnote_docID =
- (String) docProperties.get(
- ClinicalNotePreProcessor.MD_KEY_DOC_ID);
- String cnote_serviceCode =
- (String) docProperties.get(
- ClinicalNotePreProcessor.MD_KEY_SERVICE_CODE);
- assertEquals(docID, cnote_docID);
- assertEquals(serviceCode, cnote_serviceCode);
-
- // validate each section
- // TODO Consider validating each section
- }
- catch (Exception e)
- {
- e.printStackTrace(System.err);
- fail(e.getMessage());
- }
- }
-
- /**
- * Loads text from a file.
- * @param filename
- * @return
- * @throws FileNotFoundException
- * @throws IOException
- */
- private String load(String filename)
- throws FileNotFoundException, IOException
- {
- String msg = "";
- File f = new File(filename);
- BufferedReader br = new BufferedReader(new FileReader(f));
- String line = br.readLine();
- while (line != null)
- {
- msg += line + "\n";
- line = br.readLine();
- }
- br.close();
-
- return msg;
- }
-}
+package edu.mayo.bmi.test.preprocessor;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.net.URLDecoder;
+import java.util.Map;
+
+import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
+import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
+
+import junit.framework.TestCase;
+
+/**
+ * Unit tests for the ClinicalNotePreProcessor class. These test the class
+ * against clinical note XML data and determine whether the preprocessor
+ * successfully parsed out the correct info.
+ *
+ * @author Mayo Clinic
+ */
+public class ClinicalNotePreProcessorTest extends TestCase
+{
+ private ClinicalNotePreProcessor iv_cnotePreProcessor;
+ private String iv_cnoteXML;
+
+ /**
+ * Constructor for ClinicalNotePreProcessorTest.
+ * @param arg0
+ */
+ public ClinicalNotePreProcessorTest(String arg0)
+ {
+ super(arg0);
+ }
+
+ /*
+ * @see TestCase#setUp()
+ */
+ protected void setUp() throws Exception
+ {
+ super.setUp();
+
+ String dtdLocation = "resources/cda/NotesIIST_RTF.DTD";
+ File dtd = new File(dtdLocation);
+ iv_cnotePreProcessor = new ClinicalNotePreProcessor(dtd, false);
+
+ //String cnoteLocationOnCp = "/test/data/testpatient_cn_1.xml";
+ String cnoteLocationOnCp = "../../../../../data/testpatient_cn_1.xml";
+ String cnoteLocation =
+ URLDecoder.decode(getClass().getResource(cnoteLocationOnCp).getPath());
+
+ if (cnoteLocation == null) {
+ throw new FileNotFoundException("Unable to find: " + cnoteLocationOnCp);
+ }
+ iv_cnoteXML = load(cnoteLocation);
+ }
+
+ /*
+ * @see TestCase#tearDown()
+ */
+ protected void tearDown() throws Exception
+ {
+ super.tearDown();
+ }
+
+ /**
+ * Tests the process method.
+ */
+ public void testProcess()
+ {
+ try
+ {
+ DocumentMetaData dmd = iv_cnotePreProcessor.process(iv_cnoteXML);
+
+ // validate document properties
+ String docID = "000000000";
+ String serviceCode = "MNT";
+ Map docProperties = dmd.getMetaData();
+ String cnote_docID =
+ (String) docProperties.get(
+ ClinicalNotePreProcessor.MD_KEY_DOC_ID);
+ String cnote_serviceCode =
+ (String) docProperties.get(
+ ClinicalNotePreProcessor.MD_KEY_SERVICE_CODE);
+ assertEquals(docID, cnote_docID);
+ assertEquals(serviceCode, cnote_serviceCode);
+
+ // validate each section
+ // TODO Consider validating each section
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace(System.err);
+ fail(e.getMessage());
+ }
+ }
+
+ /**
+ * Loads text from a file.
+ * @param filename
+ * @return
+ * @throws FileNotFoundException
+ * @throws IOException
+ */
+ private String load(String filename)
+ throws FileNotFoundException, IOException
+ {
+ String msg = "";
+ File f = new File(filename);
+ BufferedReader br = new BufferedReader(new FileReader(f));
+ String line = br.readLine();
+ while (line != null)
+ {
+ msg += line + "\n";
+ line = br.readLine();
+ }
+ br.close();
+
+ return msg;
+ }
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/RelationExtractorAnnotator.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyParseUtils.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
@@ -76,9 +70,9 @@ public class DependencyParseUtils {
* @return
*/
public static ConllDependencyNode findAnnotationHead(JCas jcas, Annotation annotation) {
-
+
for (ConllDependencyNode depNode : JCasUtil.selectCovered(jcas, ConllDependencyNode.class, annotation)) {
-
+
ConllDependencyNode head = depNode.getHead();
if (head == null || head.getEnd() <= annotation.getBegin() || head.getBegin() > annotation.getEnd()) {
// The head is outside the bounds of the annotation, so this node must be the annotation's head
@@ -115,9 +109,9 @@ public class DependencyParseUtils {
return path;
}
- // Join the two paths
+ // Join the two paths
if (!srcToAncestorPath.isEmpty()) {
- srcToAncestorPath.removeLast();
+ srcToAncestorPath.removeLast();
}
path = srcToAncestorPath;
while (!tgtToAncestorPath.isEmpty()) {
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
@@ -45,8 +39,8 @@ public class DependencyPathFeaturesExtra
List<Feature> features = new ArrayList<Feature>();
ConllDependencyNode node1 = DependencyParseUtils.findAnnotationHead(jCas, arg1);
- ConllDependencyNode node2 = DependencyParseUtils.findAnnotationHead(jCas, arg2);
- if (node1 == null || node2 == null) { return features; }
+ ConllDependencyNode node2 = DependencyParseUtils.findAnnotationHead(jCas, arg2);
+ if (node1 == null || node2 == null) { return features; }
List<LinkedList<ConllDependencyNode>> paths = DependencyParseUtils.getPathsToCommonAncestor(node1, node2);
LinkedList<ConllDependencyNode> path1 = paths.get(0);
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
@@ -49,7 +43,7 @@ public class DependencyTreeFeaturesExtra
public List<Feature> extractForNode(JCas jCas, IdentifiedAnnotation mention, String ftrPrefix) {
List<Feature> features = new ArrayList<Feature>();
ConllDependencyNode mentionHeadNode = DependencyParseUtils.findAnnotationHead(jCas, mention);
-
+
if (mentionHeadNode != null) {
ConllDependencyNode dependsOn = mentionHeadNode.getHead();
if (dependsOn != null) {
@@ -62,7 +56,7 @@ public class DependencyTreeFeaturesExtra
features.add(new Feature(ftrPrefix + "_HEAD_WORD-GOVERNING_WORD", String.format("%s-%s", mentionHeadNode.getCoveredText(), dependsOn.getCoveredText())));
features.add(new Feature(ftrPrefix + "_TYPE-GOVERNING_POS", String.format("%d-%s", mention.getTypeID(), dependsOn.getPostag())));
features.add(new Feature(ftrPrefix + "_HEAD_POS-GOVERNING_POS", String.format("%s-%s", mentionHeadNode.getPostag(), dependsOn.getPostag())));
- }
+ }
}
return features;
}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
@@ -50,4 +44,4 @@ public interface RelationFeaturesExtract
*/
public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1, IdentifiedAnnotation arg2)
throws AnalysisEngineProcessException;
-}
\ No newline at end of file
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Constants.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Constants.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Constants.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Constants.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityAndRelationReader.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/GoldEntityReader.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
@@ -109,4 +103,4 @@ public class GoldEntityReader extends JC
entityMention.addToIndexes();
}
}
-}
\ No newline at end of file
+}
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/cr/Mapper.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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
Modified: incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/data/CategoricalDistribution.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/data/CategoricalDistribution.java?rev=1403989&r1=1403988&r2=1403989&view=diff
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/data/CategoricalDistribution.java (original)
+++ incubator/ctakes/branches/SHARPn-cTAKES/relation-extractor/src/org/chboston/cnlp/ctakes/relationextractor/data/CategoricalDistribution.java Wed Oct 31 05:26:43 2012
@@ -1,12 +1,6 @@
/*
* Copyright: (c) 2012 Children's Hospital Boston, Regents of the University of Colorado
*
- * 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