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From chen...@apache.org
Subject svn commit: r1452577 [1/14] - in /incubator/ctakes/trunk/ctakes-regression-test: ./ desc/analysis_engine/ desc/collection_processing_engine/ src/test/java/org/apache/ctakes/regression/test/ testdata/expectedoutput/POSTaggerCPETest/ testdata/expectedout...
Date Mon, 04 Mar 2013 22:42:38 GMT
Author: chenpei
Date: Mon Mar  4 22:42:37 2013
New Revision: 1452577

URL: http://svn.apache.org/r1452577
Log:
CTAKES-84 - Use XMLUnit to compare xml output (Currently only compares skeletons because the xcas nodes could be not be in order.)
Modified the test to automatically run ALL CPE's in the desc/collection_processing_engine directory and compare the results.
That means that if there is a new test, all we need to do is add the CPE.xml into desc/collection_processing_engine 
and place the expected results into testdata/expectedoutput/{nameofcpe}/
and it will automatically run it in the future.  (No need for code changes.)

Added:
    incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/POSTaggerCPETest.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/SampleInputRadiologyNotes.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_current.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_past_smoker.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_unknown.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc2_07543210_sample_current.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc2_07543210_sample_past_smoker.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/sample_note.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/sample_note_plaintext.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/testfakenote.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/testpatient_plaintext_1.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/testpatient_plaintext_2.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/text1.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/SampleInputRadiologyNotes.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_current.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_past_smoker.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_unknown.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc2_07543210_sample_current.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc2_07543210_sample_past_smoker.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/sample_note.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/sample_note_plaintext.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testfakenote.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testpatient_plaintext_1.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testpatient_plaintext_2.txt.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/text1.txt.xml
Removed:
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/cda/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/plaintext/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/generatedoutput/cda/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/generatedoutput/plaintext/
Modified:
    incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml
    incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml
    incubator/ctakes/trunk/ctakes-regression-test/pom.xml
    incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java

Modified: incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml?rev=1452577&r1=1452576&r2=1452577&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml (original)
+++ incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml Mon Mar  4 22:42:37 2013
@@ -68,9 +68,11 @@
 <delegateAnalysisEngine key="AssertionAnnotator">
 <import location="../../../ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml"/>
 </delegateAnalysisEngine>
+<!-- 
 <delegateAnalysisEngine key="DependencyParser">
 <import location="../../../ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserAE.xml"/>
 </delegateAnalysisEngine>
+ -->
 </delegateAnalysisEngineSpecifiers>
 <analysisEngineMetaData>
 <name>AggregatePlaintextProcessor</name>
@@ -120,8 +122,10 @@ Includes adjusting NP chunks to include 
 <node>AdjustNounPhraseToIncludeFollowingPPNP</node>
 <node>LookupWindowAnnotator</node>
 <node>DictionaryLookupAnnotator</node>
+<!-- 
 <node>DependencyParser</node>
 <node>AssertionAnnotator</node>
+-->
 <!-- 
 	<node>StatusAnnotator</node>
 	<node>NegationAnnotator</node>

Added: incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/POSTaggerCPETest.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/POSTaggerCPETest.xml?rev=1452577&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/POSTaggerCPETest.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/POSTaggerCPETest.xml Mon Mar  4 22:42:37 2013
@@ -0,0 +1,98 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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 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.
+
+-->
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<collectionReader>
+<collectionIterator>
+<descriptor>
+<import location="../../../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
+</descriptor>
+<configurationParameterSettings>
+<nameValuePair>
+<name>InputDirectory</name>
+<value>
+<string>testdata/input/plaintext</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</collectionIterator>
+</collectionReader>
+<casProcessors casPoolSize="3" processingUnitThreadCount="1">
+<casProcessor deployment="integrated" name="POSTaggerCPETest">
+<descriptor>
+<import location="../../../ctakes-pos-tagger/desc/POSTaggerAggregate.xml"/>
+</descriptor>
+<configurationParameterSettings>
+<nameValuePair>
+<name>PosModelFile</name>
+<value>
+<string>org/apache/ctakes/postagger/models/mayo-pos.zip</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>CaseSensitive</name>
+<value>
+<boolean>true</boolean>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>TagDictionary</name>
+<value>
+<string>org/apache/ctakes/postagger/models/tag.dictionary.txt</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<deploymentParameters/>
+<errorHandling>
+<errorRateThreshold action="terminate" value="0/1000"/>
+<maxConsecutiveRestarts action="terminate" value="30"/>
+<timeout max="100000" default="-1"/>
+</errorHandling>
+<checkpoint batch="10000" time="1000ms"/>
+</casProcessor>
+<casProcessor deployment="integrated" name="Write CAS to XML file">
+<descriptor>
+<import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
+</descriptor>
+<deploymentParameters/>
+<errorHandling>
+<errorRateThreshold action="terminate" value="0/1000"/>
+<maxConsecutiveRestarts action="terminate" value="30"/>
+<timeout max="100000" default="-1"/>
+</errorHandling>
+<checkpoint batch="10000" time="1000ms"/>
+<configurationParameterSettings>
+<nameValuePair>
+<name>outputDir</name>
+<value>
+<string>testdata/generatedoutput/POSTaggerCPETest</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</casProcessor>
+</casProcessors>
+<cpeConfig>
+<numToProcess>-1</numToProcess>
+<deployAs>immediate</deployAs>
+<checkpoint batch="0" time="300000"/>
+<timerImpl></timerImpl>
+</cpeConfig>
+</cpeDescription>

Modified: incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml?rev=1452577&r1=1452576&r2=1452577&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml (original)
+++ incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml Mon Mar  4 22:42:37 2013
@@ -63,7 +63,7 @@
 <nameValuePair>
 <name>outputDir</name>
 <value>
-<string>testdata/generatedoutput/plaintext</string>
+<string>testdata/generatedoutput/RegressionPipelineCPETest</string>
 </value>
 </nameValuePair>
 </configurationParameterSettings>

Modified: incubator/ctakes/trunk/ctakes-regression-test/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/pom.xml?rev=1452577&r1=1452576&r2=1452577&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-regression-test/pom.xml Mon Mar  4 22:42:37 2013
@@ -89,6 +89,12 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-coreference</artifactId>
-		</dependency>				
+		</dependency>	
+		<dependency>
+			<groupId>xmlunit</groupId>
+			<artifactId>xmlunit</artifactId>
+			<version>1.4</version>
+			<scope>test</scope>			
+		</dependency>					
 	</dependencies>  
 </project>
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java?rev=1452577&r1=1452576&r2=1452577&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java (original)
+++ incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java Mon Mar  4 22:42:37 2013
@@ -20,73 +20,229 @@ package org.apache.ctakes.regression.tes
 
 import java.io.File;
 import java.io.IOException;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
 
-import org.apache.commons.io.FileUtils;
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAFramework;
+import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CollectionProcessingEngine;
+import org.apache.uima.collection.EntityProcessStatus;
+import org.apache.uima.collection.StatusCallbackListener;
 import org.apache.uima.collection.metadata.CpeDescription;
 import org.apache.uima.util.XMLInputSource;
+import org.custommonkey.xmlunit.Diff;
+import org.custommonkey.xmlunit.ElementNameAndTextQualifier;
+import org.custommonkey.xmlunit.IgnoreTextAndAttributeValuesDifferenceListener;
+import org.custommonkey.xmlunit.XMLTestCase;
 import org.junit.Assert;
-import org.junit.Before;
 import org.junit.Test;
-
+import org.w3c.dom.Document;
+import org.xml.sax.SAXException;
 
 /**
- * Runs a full pipeline and compares the xml output 
- * to ensure all annotators work together in harmony.
+ * Runs a full pipeline and compares the xml output to ensure all annotators
+ * work together in harmony.
+ * 
+ * This is designed to run all CPE's inside the
+ * desc/collection_processing_engine Directory. So any new pipelines added there
+ * will automatically be run and tested as long as they put the generated output
+ * to expectedoutput/{nameofcpe}
  * 
- * The Apache cTAKES Release Manager should ensure that at a min
- * this test passes before releasing.
+ * The Apache cTAKES Release Manager should ensure that at a min this test
+ * passes before releasing.
  * 
- * If there are new modules, be sure to add the desc here.
- * If there are changes, after it's been manually reviewed, 
- * re-record the expected output and put them in output folder.
+ * If there are new modules, be sure to add the desc here. If there are changes,
+ * after it's been manually reviewed, re-record the expected output and put them
+ * in output folder.
+ * 
+ * This also tests the UMLS annotator(s) so be sure to download the UMLS
+ * Resources per README and add the jvm params -Dctakes.umlsuser=
+ * -Dctakes.umlspw= parameters before running
  * 
- * This also tests the UMLS annotator(s) so be sure to download
- * the UMLS Resources per README and add the jvm params
- * -Dctakes.umlsuser= -Dctakes.umlspw= parameters before running
- *
  */
-public class RegressionPipelineTest {
+public class RegressionPipelineTest extends XMLTestCase {
 
 	// LOG4J logger based on class name
-	private Logger logger = Logger.getLogger(getClass().getName());
-	private CollectionProcessingEngine mCPE;
-	private static final File dir = new File("testdata/generatedoutput");
-	private static final String CPEDESC = "desc/collection_processing_engine/RegressionPipelineCPETest.xml";
-	
+	Logger logger = Logger.getLogger(getClass().getName());
+	private static final File CPEDIR = new File(
+			"desc/collection_processing_engine");
+	int num_cpe = 0;
+
 	@Test
-	public void test() throws Exception {
-		// create the pipeline
-		setUp();
-		
-		// Start Processing
-		logger.info("Running CPE");
-		mCPE.process();
+	public void testCPE() throws Exception {
+
+		File[] listOfFiles = CPEDIR.listFiles();
+		for (File file : listOfFiles) {
+
+			if (file.isFile()) {
+				num_cpe++ ;
+				File generated = new File("testdata/generatedoutput/"
+						+ file.getName().substring(0,
+								file.getName().indexOf(".")));
+				File expected = new File("testdata/expectedoutput/"
+						+ file.getName().substring(0,
+								file.getName().indexOf(".")));
+
+				logger.info("Creating Dir" + generated);
+				
+				Assert.assertTrue(
+						"Unable to create " + generated.getAbsolutePath(),
+						generated.exists() || generated.mkdirs());
+
+				// Run all of the CPE's in the Dir
+				logger.info("Parsing CPE Descriptor:" + file.getName());
+				CpeDescription cpeDesc = UIMAFramework.getXMLParser()
+						.parseCpeDescription(new XMLInputSource(file));
+				CollectionProcessingEngine mCPE = UIMAFramework.produceCollectionProcessingEngine(cpeDesc);
+				// Create and register a Status Callback Listener
+				mCPE.addStatusCallbackListener(new StatusCallbackListenerImpl(expected, generated));
+				mCPE.process();
+			}
+		}
+		// Wait until all of the CPE's have been completed
+		// Before comparing.
+		while (num_cpe > 0) {
+			Thread.sleep(1000);
+		}
 	}
 
-	@Before
-	public void setUp() throws Exception {
+	public void compareXMLOutput(File expected_, File generated_) throws IOException,
+			ParserConfigurationException, SAXException {
 
-		//Setup output dir
-	    Assert.assertTrue("Unable to create " + dir.getAbsolutePath(), dir.exists() || dir.mkdirs());
-	    
-		// parse CPE descriptor
-		logger.info("Parsing CPE Descriptor");
-		CpeDescription cpeDesc = UIMAFramework.getXMLParser()
-				.parseCpeDescription(new XMLInputSource(CPEDESC));
-		// instantiate CPE
-		logger.info("Instantiating CPE");
-		mCPE = UIMAFramework.produceCollectionProcessingEngine(cpeDesc);
+		File[] listOfFiles = expected_.listFiles();
+		for (File file : listOfFiles) {
+			if (file.isFile()) {
+				logger.info("Verifying Test Output: " + file.getAbsolutePath());
+				DocumentBuilderFactory dbf = DocumentBuilderFactory
+						.newInstance();
+				dbf.setNamespaceAware(true);
+				dbf.setCoalescing(true);
+				dbf.setIgnoringElementContentWhitespace(true);
+				dbf.setIgnoringComments(true);
+				DocumentBuilder db = dbf.newDocumentBuilder();
+				Document expected = db.parse(file);
+				File f = new File(generated_.getPath() + File.separator + file.getName() );
+				Document generated = db.parse(f);
+				generated.normalizeDocument();
+				expected.normalizeDocument();
+
+				Diff myDiff = new Diff(expected, generated);
+				// Only Testing the skeleton because the xml attributes in the
+				// xcas could be in different
+				// Ordering
+				myDiff.overrideElementQualifier(new ElementNameAndTextQualifier());
+				myDiff.overrideDifferenceListener(new IgnoreTextAndAttributeValuesDifferenceListener());
+				assertTrue("Verifying Test Output: " + file.getName() + myDiff,
+						myDiff.similar());
+				// assertXMLEqual("Verifying Test Output: " + file.getName(),
+				// myDiff, true);				
 
+			}
+		}
 	}
-	
-	@Test
-	public void testCompareXMLOutput() throws IOException {
-		//TODO: need to implement here.
-	    //final File expected = new File("xyz.txt");
-	    //final File output = new File(dir, "xyz.txt");
-	    //Assert.assertEquals(FileUtils.readLines(expected), FileUtils.readLines(output));
+
+	/**
+	 * Callback Listener. Receives event notifications from CPE.
+	 * 
+	 * 
+	 */
+	class StatusCallbackListenerImpl implements StatusCallbackListener {
+		int entityCount = 0;
+		long size = 0;
+		File expected = null;
+		File generated = null;
+
+		public StatusCallbackListenerImpl(File expected_, File generated_) {
+			this.expected = expected_;
+			this.generated = generated_;
+		}
+		/**
+		 * Called when the initialization is completed.
+		 * 
+		 * @see org.apache.uima.collection.processing.StatusCallbackListener#initializationComplete()
+		 */
+		public void initializationComplete() {
+			logger.info("CPM Initialization Complete");
+		}
+
+		/**
+		 * Called when the batchProcessing is completed.
+		 * 
+		 * @see org.apache.uima.collection.processing.StatusCallbackListener#batchProcessComplete()
+		 * 
+		 */
+		public void batchProcessComplete() {
+			logger.info("Completed " + entityCount + " documents");
+
+		}
+
+		/**
+		 * Called when the collection processing is completed.
+		 * 
+		 * @see org.apache.uima.collection.processing.StatusCallbackListener#collectionProcessComplete()
+		 */
+		public void collectionProcessComplete() {
+
+			logger.info("Completed " + entityCount + " documents");
+			// Only compare after the batch has been completed.
+			try {
+				compareXMLOutput(expected, generated);
+			} catch (Exception e) {
+				e.printStackTrace();
+			}
+			num_cpe--;
+		}
+
+		/**
+		 * Called when the CPM is paused.
+		 * 
+		 * @see org.apache.uima.collection.processing.StatusCallbackListener#paused()
+		 */
+		public void paused() {
+			logger.info("Paused");
+		}
+
+		/**
+		 * Called when the CPM is resumed after a pause.
+		 * 
+		 * @see org.apache.uima.collection.processing.StatusCallbackListener#resumed()
+		 */
+		public void resumed() {
+			logger.info("Resumed");
+		}
+
+		/**
+		 * Called when the CPM is stopped abruptly due to errors.
+		 * 
+		 * @see org.apache.uima.collection.processing.StatusCallbackListener#aborted()
+		 */
+		public void aborted() {
+			logger.info("Aborted");
+		}
+
+		/**
+		 * Called when the processing of a Document is completed. <br>
+		 * The process status can be looked at and corresponding actions taken.
+		 * 
+		 * @param aCas
+		 *            CAS corresponding to the completed processing
+		 * @param aStatus
+		 *            EntityProcessStatus that holds the status of all the
+		 *            events for aEntity
+		 */
+		public void entityProcessComplete(CAS aCas, EntityProcessStatus aStatus) {
+			if (aStatus.isException()) {
+				List<?> exceptions = aStatus.getExceptions();
+				for (int i = 0; i < exceptions.size(); i++) {
+					((Throwable) exceptions.get(i)).printStackTrace();
+				}
+				return;
+			}
+			entityCount++;
+		}
 	}
 }

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/SampleInputRadiologyNotes.txt.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/SampleInputRadiologyNotes.txt.xml?rev=1452577&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/SampleInputRadiologyNotes.txt.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/SampleInputRadiologyNotes.txt.xml Mon Mar  4 22:42:37 2013
@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<CAS version="2">
+    <uima.cas.Sofa _indexed="0" _id="3" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="CLINIC`rimsdate`rimstime`resultno`subtype`accesion`lastname`birth_dt`gender`status`secure`testcode`testdesc`doctor`COMMENTS&#13;&#10;54321`02/20/1999`13:21:00`14`GENRAD`987654-3`SMITH`04/03/1916`F`F`N`70955-RRIMS`CT ANGIO ABD W/WO CST ADD SECT`DAVIS, WILLIAM R`20Feb1999 1:21PM CT ABDOMEN w &amp; PELVIS w Indications: ct abd/pel - hernia ventral nos;USE IV CON ORIGINAL REPORT - 10 Aug 2009 3:15PM ROMAYO CT abdomen and pelvis with IV contrast. Comparison with prior MR angiography dated 4-2-04. Again seen is a large ventral hernia containing multiple nonobstructed loops of small bowel and ascending colon. No evidence of vascular compromise within this hernial sac. PO changes of aortobifemoral graft with occluded right limb of the graft just below the bifurcation. Patent femoral crossover graft. Possible diffuse fatty infiltration of the liver. Severe atrophy of the left kidney.
  The left renal artery is not well delineated and may be occluded. Small scarring in the lower right kidney. Low-lying urinary bladder with a possible small cystocele. Sigmoid diverticulosis. Vascular calcifications. Degenerative changes of the spine, symphysis pubis, and both SI and hip joints. Minimal atelectasis or fibrosis in the lung bases. Remainder of the study is unremarkable.. W. R. Davis MD 5-4321&#13;&#10;54321`02/20/1999`11:20:00`13`GENRAD`987654-4`SMITH`04/03/1916`F`F`N`07552-RRIMS`US Lower Extrem Art-Graft Cmpl`DAVIS, WILLIAM R`20Feb1999 11:20AM US Lower Extrem Art-Graft Cmpl ASO. Patent left femoral-popliteal  bypass. Diffuse tibial artery disease with posterior tibial occlusion. The anterior tibial is patent into the dorsalis pedis and the peroneal artery contributes to the plantar arch via a patent calcaneal branch. Right hypogastric artery stenosis. W. R. Davis MD 5-4321&#13;&#10;54321`02/20/2000`17:15:00`12`CT`876543-2`SMITH`04/03/1916`F`F`N`73200-RRIMS`CT
  EXT UPPER wo`DAVIS, WILLIAM R`20Feb2000 5:15PM Exam: CT RECONSTRUCTION 20Feb2000 3:17PM Exam: L CT EXT LOWER w Indications: le - L femur pain, r/o^osteomyelitis vs tumor ORIGINAL REPORT - 17 Apr 2006 2:31PM SMH CT left femur with IV contrast. No comparison exam. Along the mid left femoral diaphysis there is an aggressive, malignant appearing process involving the lateral cortex. Adjacent cortical scalloping is present. Codman's triangle's are seen at either end of the lesion consistent with aggressive periosteal reaction. The area of cortical scalloping measures 4.5 cm in length. There is some probable hazy mineral content within the peripheral lucent area suggesting that this is a malignant surface Osteogenic sarcoma. The other consideration is a periosteal Ewing's sarcoma. No associated soft tissue mass or fluid collections. Recommend further evaluation with MRI to evaluate for left femoral bone marrow involvement. Exam was discussed with Dr .W. R. Davis MD 5-4321&#13;&#1
 0;12345`02/20/1999`13:21:00`14`GENRAD`987654-3`SMITH`04/03/1916`F`F`N`07075-RRIMS`Tibia Fibula 2vw AP/Lat`DAVIS, WILLIAM R`20Feb1999 1:21PM Exam: R Tibia Fibula 2vw AP/Lat Indications: Exposed tibia;R/O osteo;S/p BKA ORIGINAL REPORT - 02 Feb 1999 1:21PM ROMAYO Amputation through the proximal shafts of the right tibia and fibula. Ulceration of soft tissues distally. No radiographic evidence of osteomyelitis. The right popliteal artery is largely obscured by metallic artifact from a right TKA. No radiographic evidence of loosening. Extensive arterial calcification. Cast obscures detail. W. R. Davis MD 5-4321&#13;&#10;12345`02/20/1999`11:20:00`13`GENRAD`987654-4`SMITH`04/03/1916`F`F`N`07552-RRIMS`US Lower Extrem Art-Graft Cmpl`DAVIS, WILLIAM R`20Feb1999 11:20AM Exam: Both popliteal arteries are patent with normal flow. W. R. Davis MD 5-4321&#13;&#10;12345`02/20/2000`17:15:00`12`CT`876543-2`SMITH`04/03/1916`F`F`N`73200-RRIMS`CT EXT UPPER wo`DAVIS, WILLIAM R`20Feb2000 5:15PM Exam
 : CT RECONSTRUCTION 20Feb2000 3:17PM Exam: CT EXT UPPER W/O CONTRAST Indications: Indications: Left shoulder fracture 02/20/2001 3:55PM SMH (2B-3495) CT of the left shoulder including oblique sagittal and oblique coronal reformats demonstrates a slightly comminuted fracture of the surgical neck of the proximal left humerus with anterior and proximal displacement and posterior angulation of the distal fragment. The fracture extends proximally into the greater humeral tuberosity and, to a lesser degree, the inferior aspect of the lesser tuberosity. The articular surface of the humeral head is intact and glenohumeral alignment maintained. W. R. Davis MD 5-4321"/>
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Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_current.txt.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_current.txt.xml?rev=1452577&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_current.txt.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_current.txt.xml Mon Mar  4 22:42:37 2013
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<CAS version="2">
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Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_past_smoker.txt.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_past_smoker.txt.xml?rev=1452577&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_past_smoker.txt.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_past_smoker.txt.xml Mon Mar  4 22:42:37 2013
@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<CAS version="2">
+    <uima.cas.Sofa _indexed="0" _id="3" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="REVIEW OF SYSTEMS:&#13;&#10;General: Has gained about 10 lb in the past 4 yr, no fatigue&#13;&#10;Skin: No rashes or other changes&#13;&#10;Head: See present illness.&#13;&#10;Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision&#13;&#10;Ears: Hearing good. No tinnitus, vertigo, infections&#13;&#10;Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble&#13;&#10;Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore&#13;&#10;Neck: No lumps, goiter, pain&#13;&#10;Breasts: No lumps, pain, discharge.&#13;&#10;Habits:&#13;&#10;Patient claims to have quit smoking about two years ago.&#13;&#10;FAMILY HISTORY&#13;&#10;- Mother died, 67, stroke; had varicose veins, headaches, hypertension&#13;&#10;- Father died, 43, train accident"/>
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Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_unknown.txt.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_unknown.txt.xml?rev=1452577&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_unknown.txt.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/POSTaggerCPETest/doc1_07543210_sample_unknown.txt.xml Mon Mar  4 22:42:37 2013
@@ -0,0 +1,252 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<CAS version="2">
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 eveloped a generalized rash.&#13;&#10;- Hypertension x 7 years, well controlled with home BPs normally 120-130/low 80s&#13;&#10;Patient Centered Medicine 2&#13;&#10;2 Revised: 7/27/99&#13;&#10;Psychiatric Illnesses/Hospitalizations&#13;&#10;None&#13;&#10;Operations&#13;&#10;Tonsillectomy, age 6,&#13;&#10;Appendectomy, age 13&#13;&#10;Injuries/Accidents&#13;&#10;1998 foot laceration, 4 stitches&#13;&#10;Obstetric History&#13;&#10;G3, P3, 3 living children. Menarche age 12. Last menses 2 weeks ago.&#13;&#10;Transfusions&#13;&#10;None&#13;&#10;CURRENT HEALTH STATUS&#13;&#10;Medications&#13;&#10;Aspirin for headaches&#13;&#10;Multivitamin 1 per day&#13;&#10;Hydrochlorothiazide 25 mg per day (x 7 years)&#13;&#10;No herbs or supplements&#13;&#10;Allergies/Drug Reactions&#13;&#10;Ampicillin causes rash&#13;&#10;Health Screening&#13;&#10;- Last pap smear 2000, normal.&#13;&#10;- Normal mammogram in 2000.&#13;&#10;- Does breast self-exams monthly&#13;&#10;- Cholesterol = 220 (in 2000
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 epression&#13;&#10;- Feels safe at work and home&#13;&#10;FAMILY HISTORY&#13;&#10;- Mother died, 67, stroke; had varicose veins, headaches, hypertension&#13;&#10;- Father died, 43, train accident&#13;&#10;- One brother, 56, has high blood pressure, otherwise well&#13;&#10;- One brother, 51, apparently well except for mild arthritis&#13;&#10;- Daughter, 23, �migraine headaches,� otherwise well&#13;&#10;- Son, 21, well&#13;&#10;- Son, 20, well&#13;&#10;REVIEW OF SYSTEMS:&#13;&#10;General: Has gained about 10 lb in the past 4 yr, no fatigue&#13;&#10;Skin: No rashes or other changes&#13;&#10;Head: See present illness.&#13;&#10;Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision&#13;&#10;Ears: Hearing good. No tinnitus, vertigo, infections&#13;&#10;Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble&#13;&#10;Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore&#13;&#10;Neck: No lumps, goiter, pain&#13;&#10;Breasts
 : No lumps, pain, discharge.&#13;&#10;Respiratory: No cough, wheezing, shortness of breath, pneumonia, tuberculosis.&#13;&#10;Cardiac: No known heart disease. No orthopnea, chest pain, palpitations.&#13;&#10;Gastrointestinal: Appetite good; no reflux. Bowel movement about once daily though&#13;&#10;sometimes has hard stools for 2-3 d when especially tense; no diarrhea or&#13;&#10;bleeding. No pain, jaundice, gallbladder or liver trouble&#13;&#10;Urinary: No frequency, dysuria, hematuria or flank pain&#13;&#10;Genitoreproductive: Regular menstrual periods. No vaginal discharge or itch&#13;&#10;Musculoskeletal: Mild aching low back pain often after a long day�s work; no radiation&#13;&#10;down legs; used to do back exercises, but not now. No other joint pain&#13;&#10;Patient Centered Medicine 2&#13;&#10;Peripheral Vascular: Varicose veins appeared in both legs during first pregnancy. Has had&#13;&#10;swollen ankles after prolonged standing for 10 yr; no history of&#13;&#1
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