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From seanfi...@apache.org
Subject svn commit: r1764816 - in /ctakes/trunk: ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/pipeline/ ctakes-clinical-pipeline-res/ ctakes-clinical-pipeline-res/src/ ctakes-clinical-pipeline-res/src/main/ ctakes-clinical-pipeline-res/src/m...
Date Fri, 14 Oct 2016 06:25:36 GMT
Author: seanfinan
Date: Fri Oct 14 06:25:36 2016
New Revision: 1764816

URL: http://svn.apache.org/viewvc?rev=1764816&view=rev
Log:
Adding Clinical-Pipeline-res
Adding getReader, getAeNames to PipelineBuilder
named simple pipeline configuration files ".piper"
Adding piper file runner for easy cli
refactoring

Added:
    ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/pipeline/
    ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/pipeline/DefaultChunkerSubPipe.piper
    ctakes/trunk/ctakes-clinical-pipeline-res/
    ctakes/trunk/ctakes-clinical-pipeline-res/pom.xml
    ctakes/trunk/ctakes-clinical-pipeline-res/src/
    ctakes/trunk/ctakes-clinical-pipeline-res/src/main/
    ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/
    ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/
    ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/
    ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/
    ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/
    ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/
    ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
    ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/pipeline/
    ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/pipeline/DefaultTokenizerPipeline.piper
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java
      - copied, changed from r1764579, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineReader.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java
      - copied, changed from r1764514, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PropertyAeFactory.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuilderRunner.java
      - copied, changed from r1764579, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuildPipeRunner.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java
      - copied, changed from r1764580, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiReadPipeRunner.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java
      - copied, changed from r1764579, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldReadPipeRunner.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java
      - copied, changed from r1764580, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsReadPipeRunner.java
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.piper
      - copied, changed from r1764580, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.txt
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper
      - copied unchanged from r1764580, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.txt
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
      - copied unchanged from r1764579, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.txt
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper
      - copied, changed from r1764580, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.txt
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper
      - copied, changed from r1764580, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.txt
Removed:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PropertyAeFactory.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineReader.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuildPipeRunner.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiReadPipeRunner.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsReadPipeRunner.java
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldReadPipeRunner.java
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.txt
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.txt
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.txt
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.txt
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.txt
Modified:
    ctakes/trunk/ctakes-clinical-pipeline/pom.xml
    ctakes/trunk/ctakes-core/pom.xml
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
    ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/AssertionDefaults.properties

Added: ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/pipeline/DefaultChunkerSubPipe.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/pipeline/DefaultChunkerSubPipe.piper?rev=1764816&view=auto
==============================================================================
--- ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/pipeline/DefaultChunkerSubPipe.piper
(added)
+++ ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/pipeline/DefaultChunkerSubPipe.piper
Fri Oct 14 06:25:36 2016
@@ -0,0 +1,5 @@
+// Commands and parameters to create a default chunker processing sub-pipeline.  This is
not a full pipeline.
+
+add Chunker
+addDescription adjuster.ChunkAdjuster NP,NP 1
+addDescription adjuster.ChunkAdjuster NP,PP,NP 2

Added: ctakes/trunk/ctakes-clinical-pipeline-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline-res/pom.xml?rev=1764816&view=auto
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline-res/pom.xml (added)
+++ ctakes/trunk/ctakes-clinical-pipeline-res/pom.xml Fri Oct 14 06:25:36 2016
@@ -0,0 +1,11 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+   <modelVersion>4.0.0</modelVersion>
+   <parent>
+      <groupId>org.apache.ctakes</groupId>
+      <artifactId>ctakes</artifactId>
+      <version>3.2.3-SNAPSHOT</version>
+   </parent>
+   <artifactId>ctakes-clinical-pipeline-res</artifactId>
+   <name>ctakes-clinical-pipeline-res</name>
+   <description>Resources for clinical pipeline</description>
+</project>
\ No newline at end of file

Added: ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper?rev=1764816&view=auto
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
(added)
+++ ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
Fri Oct 14 06:25:36 2016
@@ -0,0 +1,24 @@
+// Commands and parameters to create a default plaintext document processing pipeline with
UMLS lookup
+
+// Load a simple token processing pipeline from another pipeline file
+load org/apache/ctakes/core/pipeline/DefaultTokenizerPipeline.piper
+
+// Add non-core annotators
+add ContextDependentTokenizerAnnotator
+addDescription POSTagger
+
+// Default fast dictionary lookup
+add DefaultJCasTermAnnotator
+
+// Add the Dependency parser for use by cleartk
+addDescription ClearNLPDependencyParserAE
+
+// Add the cleartk package for cleartk class lookups
+addPackage org.apache.ctakes.assertion.medfacts.cleartk
+// Add the cleartk attribute engines
+addDescription PolarityCleartkAnalysisEngine
+addDescription UncertaintyCleartkAnalysisEngine
+addDescription HistoryCleartkAnalysisEngine
+addDescription ConditionalCleartkAnalysisEngine
+addDescription GenericCleartkAnalysisEngine
+addDescription SubjectCleartkAnalysisEngine

Modified: ctakes/trunk/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/pom.xml?rev=1764816&r1=1764815&r2=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/pom.xml (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/pom.xml Fri Oct 14 06:25:36 2016
@@ -106,6 +106,10 @@
             <artifactId>cleartk-ml</artifactId>
             <version>2.0.0</version>
         </dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-clinical-pipeline-res</artifactId>
+		</dependency>
 	</dependencies>
 	<profiles>
 		<profile>

Added: ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/pipeline/DefaultTokenizerPipeline.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/pipeline/DefaultTokenizerPipeline.piper?rev=1764816&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/pipeline/DefaultTokenizerPipeline.piper
(added)
+++ ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/pipeline/DefaultTokenizerPipeline.piper
Fri Oct 14 06:25:36 2016
@@ -0,0 +1,5 @@
+// Commands and parameters to create a default token processing pipeline
+
+add SimpleSegmentAnnotator
+add SentenceDetector
+add TokenizerAnnotatorPTB

Modified: ctakes/trunk/ctakes-core/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/pom.xml?rev=1764816&r1=1764815&r2=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/pom.xml (original)
+++ ctakes/trunk/ctakes-core/pom.xml Fri Oct 14 06:25:36 2016
@@ -103,6 +103,10 @@
 			<groupId>org.apache.uima</groupId>
 			<artifactId>uimaj-examples</artifactId> <!--  for XCasWriterCasConsumer
-->
 		</dependency>
+      <dependency>
+         <groupId>com.lexicalscope.jewelcli</groupId>
+         <artifactId>jewelcli</artifactId>
+      </dependency>
 
 
 		<dependency>

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java?rev=1764816&r1=1764815&r2=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java
Fri Oct 14 06:25:36 2016
@@ -130,7 +130,7 @@ public class StartFinishLogger extends J
    public static AnalysisEngineDescription createLoggedDescription( final AnalysisEngineDescription
mainDescription )
          throws ResourceInitializationException {
       final String name = mainDescription.getAnnotatorImplementationName();
-      return org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription(
+      return AnalysisEngineFactory.createEngineDescription(
             createDescription( name, true ),
             mainDescription,
             createDescription( name, false ) );

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java?rev=1764816&r1=1764815&r2=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
Fri Oct 14 06:25:36 2016
@@ -1,9 +1,9 @@
 package org.apache.ctakes.core.pipeline;
 
 
-import org.apache.ctakes.core.ae.PropertyAeFactory;
 import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
 import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
+import org.apache.ctakes.core.util.PropertyAeFactory;
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_component.AnalysisComponent;
@@ -18,6 +18,7 @@ import org.apache.uima.resource.Resource
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 /**
@@ -34,11 +35,13 @@ final public class PipelineBuilder {
    static private final Logger LOGGER = Logger.getLogger( "PipelineBuilder" );
 
 
-   private final List<AnalysisEngineDescription> _aeList;
+   private final List<String> _aeNameList;
+   private final List<AnalysisEngineDescription> _descList;
    private CollectionReader _reader;
 
    public PipelineBuilder() {
-      _aeList = new ArrayList<>();
+      _aeNameList = new ArrayList<>();
+      _descList = new ArrayList<>();
    }
 
    /**
@@ -103,6 +106,14 @@ final public class PipelineBuilder {
    }
 
    /**
+    *
+    * @return the CollectionReader for the pipeline or null if none has been specified
+    */
+   public CollectionReader getReader() {
+      return _reader;
+   }
+
+   /**
     * Use of this method is order-specific.
     *
     * @param component  ae or cc component class to add to the pipeline
@@ -112,7 +123,8 @@ final public class PipelineBuilder {
     */
    public PipelineBuilder add( final Class<? extends AnalysisComponent> component,
                                final Object... parameters ) throws ResourceInitializationException
{
-      _aeList.add( PropertyAeFactory.getInstance().createDescription( component, parameters
) );
+      _aeNameList.add( component.getName() );
+      _descList.add( PropertyAeFactory.getInstance().createDescription( component, parameters
) );
       return this;
    }
 
@@ -127,7 +139,8 @@ final public class PipelineBuilder {
     */
    public PipelineBuilder addLogged( final Class<? extends AnalysisComponent> component,
                                      final Object... parameters ) throws ResourceInitializationException
{
-      _aeList.add( PropertyAeFactory.getInstance().createLoggedDescription( component, parameters
) );
+      _aeNameList.add( component.getName() );
+      _descList.add( PropertyAeFactory.getInstance().createLoggedDescription( component,
parameters ) );
       return this;
    }
 
@@ -138,11 +151,20 @@ final public class PipelineBuilder {
     * @return this PipelineBuilder
     */
    public PipelineBuilder addDescription( final AnalysisEngineDescription description ) {
-      _aeList.add( description );
+      _aeNameList.add( description.getAnnotatorImplementationName() );
+      _descList.add( description );
       return this;
    }
 
    /**
+    *
+    * @return an ordered list of the annotation engines in the pipeline
+    */
+   public List<String> getAeNames() {
+      return Collections.unmodifiableList( _aeNameList );
+   }
+
+   /**
     * Adds ae that maintains CUI information throughout the run.
     * CUI information can later be accessed using the {@link CuiCollector} singleton
     * Use of this method is order-specific.
@@ -204,7 +226,7 @@ final public class PipelineBuilder {
          return this;
       }
       final AggregateBuilder builder = new AggregateBuilder();
-      _aeList.forEach( builder::add );
+      _descList.forEach( builder::add );
       final AnalysisEngineDescription desc = builder.createAggregateDescription();
       SimplePipeline.runPipeline( _reader, desc );
       return this;
@@ -227,7 +249,7 @@ final public class PipelineBuilder {
       final JCas jcas = JCasFactory.createJCas();
       jcas.setDocumentText( text );
       final AggregateBuilder builder = new AggregateBuilder();
-      _aeList.forEach( builder::add );
+      _descList.forEach( builder::add );
       final AnalysisEngineDescription desc = builder.createAggregateDescription();
       SimplePipeline.runPipeline( jcas, desc );
       return this;

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java
(from r1764579, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineReader.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineReader.java&r1=1764579&r2=1764816&rev=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineReader.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java
Fri Oct 14 06:25:36 2016
@@ -50,9 +50,9 @@ import java.util.regex.Pattern;
  * @version %I%
  * @since 10/10/2016
  */
-final public class PipelineReader {
+final public class PiperFileReader {
 
-   static private final Logger LOGGER = Logger.getLogger( "PipelineReader" );
+   static private final Logger LOGGER = Logger.getLogger( "PiperFileReader" );
 
    static private final String[] CTAKES_PACKAGES
          = { "core",
@@ -90,7 +90,7 @@ final public class PipelineReader {
    /**
     * Create and empty PipelineReader
     */
-   public PipelineReader() {
+   public PiperFileReader() {
       _builder = new PipelineBuilder();
       _userPackages = new ArrayList<>();
    }
@@ -101,7 +101,7 @@ final public class PipelineReader {
     * @param filePath path to the pipeline command file
     * @throws UIMAException if the pipeline cannot be loaded
     */
-   public PipelineReader( final String filePath ) throws UIMAException {
+   public PiperFileReader( final String filePath ) throws UIMAException {
       _builder = new PipelineBuilder();
       _userPackages = new ArrayList<>();
       loadPipelineFile( filePath );
@@ -114,7 +114,8 @@ final public class PipelineReader {
     */
    public void loadPipelineFile( final String filePath ) throws UIMAException {
       try ( final BufferedReader reader
-                  = new BufferedReader( new InputStreamReader( FileLocator.getAsStream( filePath
) ) ) ) {
+                  = new BufferedReader( new InputStreamReader(
+            FileLocator.getAsStream( FileLocator.getFullPath( filePath ) ) ) ) ) {
          String line = reader.readLine();
          while ( line != null ) {
             line = line.trim();
@@ -131,7 +132,7 @@ final public class PipelineReader {
             line = reader.readLine();
          }
       } catch ( IOException ioE ) {
-         LOGGER.error( "Property File not found: " + filePath );
+         LOGGER.error( "Piper File not found: " + filePath );
       }
    }
 

Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java?rev=1764816&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
(added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
Fri Oct 14 06:25:36 2016
@@ -0,0 +1,120 @@
+package org.apache.ctakes.core.pipeline;
+
+
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+import org.apache.log4j.Logger;
+import org.apache.uima.UIMAException;
+
+import java.io.IOException;
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 10/13/2016
+ */
+public class PiperFileRunner {
+
+   static private final Logger LOGGER = Logger.getLogger( "PiperFileRunner" );
+
+   interface RunOptions {
+      @Option(
+            shortName = "p",
+            longName = "piper",
+            description = "path to the piper file containing commands and parameters for
pipeline configuration." )
+      String getPiperPath();
+
+      @Option(
+            shortName = "i",
+            longName = "inputDir",
+            description = "path to the directory containing the clinical notes to be processed.",
+            defaultValue = "" )
+      String getInputDirectory();
+
+      @Option(
+            shortName = "o",
+            longName = "outputDir",
+            description = "path to the directory where the output files are to be written.",
+            defaultValue = "" )
+      String getOutputDirectory();
+
+      @Option(
+            longName = "xmiOut",
+            description = "path to the directory where xmi files are to be written.  Adds
XmiWriter to pipeline.",
+            defaultValue = "" )
+      String getXmiOutDirectory();
+
+      @Option(
+            longName = "user",
+            description = "UMLS username.",
+            defaultValue = "" )
+      String getUmlsUserName();
+
+      @Option(
+            longName = "pass",
+            description = "UMLS user password.",
+            defaultValue = "" )
+      String getUmlsPassword();
+
+      @Option(
+            shortName = { "?", "h" },
+            longName = "help",
+            description = "print usage",
+            helpRequest = true )
+      boolean isHelpWanted();
+
+   }
+
+   /**
+    * @param args general run options
+    */
+   public static void main( final String... args ) {
+      final RunOptions options = CliFactory.parseArguments( RunOptions.class, args );
+      try {
+         final PiperFileReader reader = new PiperFileReader();
+         final PipelineBuilder builder = reader.getBuilder();
+         // set the input directory parameter if needed
+         final String inputDir = options.getInputDirectory();
+         if ( !inputDir.isEmpty() ) {
+            builder.addParameters( "InputDirectory", inputDir );
+         }
+         // set the output directory parameter if needed
+         final String outputDir = options.getOutputDirectory();
+         final String xmiOutDir = options.getXmiOutDirectory();
+         if ( !outputDir.isEmpty() ) {
+            builder.addParameters( "OutputDirectory", outputDir );
+         } else if ( !xmiOutDir.isEmpty() ) {
+            builder.addParameters( "OutputDirectory", xmiOutDir );
+         }
+         // set the umls user and password parameters if needed
+         final String umlsUser = options.getUmlsUserName();
+         if ( !umlsUser.isEmpty() ) {
+            builder.addParameters( "umlsUser", umlsUser );
+         }
+         final String umlsPass = options.getUmlsPassword();
+         if ( !umlsPass.isEmpty() ) {
+            builder.addParameters( "umlsPass", umlsPass );
+         }
+         // load the piper file
+         reader.loadPipelineFile( options.getPiperPath() );
+         // if an input directory was specified but the piper didn't add a collection reader,
add the default reader
+         if ( !inputDir.isEmpty() && builder.getReader() == null ) {
+            builder.readFiles( inputDir );
+         }
+         // if an xmi output directory was specified but the piper didn't add the xmi writer,
add the
+         if ( !xmiOutDir.isEmpty() ) {
+            if ( !builder.getAeNames().stream().map( String::toLowerCase )
+                  .anyMatch( n -> n.contains( "xmiwriter" ) ) ) {
+               builder.writeXMIs( xmiOutDir );
+            }
+         }
+         // run the pipeline
+         builder.run();
+      } catch ( UIMAException | IOException multE ) {
+         LOGGER.error( multE.getMessage() );
+         System.exit( 1 );
+      }
+   }
+
+
+}

Copied: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java
(from r1764514, ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PropertyAeFactory.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java?p2=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java&p1=ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PropertyAeFactory.java&r1=1764514&r2=1764816&rev=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PropertyAeFactory.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java
Fri Oct 14 06:25:36 2016
@@ -1,5 +1,6 @@
-package org.apache.ctakes.core.ae;
+package org.apache.ctakes.core.util;
 
+import org.apache.ctakes.core.ae.StartFinishLogger;
 import org.apache.ctakes.core.resource.FileLocator;
 import org.apache.log4j.Logger;
 import org.apache.uima.analysis_component.AnalysisComponent;

Modified: ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java?rev=1764816&r1=1764815&r2=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java
(original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java
Fri Oct 14 06:25:36 2016
@@ -27,7 +27,7 @@ import java.util.*;
  */
 public class SemanticCleanupTermConsumer extends AbstractTermConsumer {
 
-   static private final Logger LOGGER = Logger.getLogger( "MetaWsdTermConsumer" );
+   static private final Logger LOGGER = Logger.getLogger( "SemanticCleanupTermConsumer" );
 
    private final TermConsumer _idHitConsumer;
 

Copied: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuilderRunner.java
(from r1764579, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuildPipeRunner.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuilderRunner.java?p2=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuilderRunner.java&p1=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuildPipeRunner.java&r1=1764579&r2=1764816&rev=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuildPipeRunner.java
(original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldBuilderRunner.java
Fri Oct 14 06:25:36 2016
@@ -23,13 +23,13 @@ import java.io.IOException;
  * @version %I%
  * @since 10/10/2016
  */
-final public class HelloWorldBuildPipeRunner {
+final public class HelloWorldBuilderRunner {
 
-   static private final Logger LOGGER = Logger.getLogger( "HelloWorldBuildPipeRunner" );
+   static private final Logger LOGGER = Logger.getLogger( "HelloWorldBuilderRunner" );
 
    static private final String DOC_TEXT = "Hello World!";
 
-   private HelloWorldBuildPipeRunner() {
+   private HelloWorldBuilderRunner() {
    }
 
    /**

Copied: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java
(from r1764580, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiReadPipeRunner.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java?p2=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java&p1=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiReadPipeRunner.java&r1=1764580&r2=1764816&rev=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiReadPipeRunner.java
(original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java
Fri Oct 14 06:25:36 2016
@@ -3,14 +3,14 @@ package org.apache.ctakes.examples.pipel
 
 import org.apache.ctakes.core.pipeline.CuiCollector;
 import org.apache.ctakes.core.pipeline.PipelineBuilder;
-import org.apache.ctakes.core.pipeline.PipelineReader;
+import org.apache.ctakes.core.pipeline.PiperFileReader;
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 
 import java.io.IOException;
 
 /**
- * Build and run a pipeline using a {@link PipelineReader} and a {@link PipelineBuilder}.
+ * Build and run a pipeline using a {@link PiperFileReader} and a {@link PipelineBuilder}.
  * <p>
  * Example of a running a pipeline programatically w/o uima xml descriptor xml files
  * Adds the default Tokenization pipeline and adding the Example HelloWorld Annotator
@@ -19,15 +19,15 @@ import java.io.IOException;
  * @version %I%
  * @since 10/10/2016
  */
-final public class HelloWorldCuiReadPipeRunner {
+final public class HelloWorldCuiPiperRunner {
 
-   static private final Logger LOGGER = Logger.getLogger( "HelloWorldReadPipeRunner" );
+   static private final Logger LOGGER = Logger.getLogger( "HelloWorldCuiPiperRunner" );
 
-   static private final String PIPELINE_FILE_PATH = "org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.txt";
+   static private final String PIPELINE_FILE_PATH = "org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper";
 
    static private final String DOC_TEXT = "Hello World!  I have allergies to nuts, bee stings,
and shark bites.";
 
-   private HelloWorldCuiReadPipeRunner() {
+   private HelloWorldCuiPiperRunner() {
    }
 
    /**
@@ -36,7 +36,7 @@ final public class HelloWorldCuiReadPipe
    public static void main( final String... args ) {
       try {
          // Add a simple pre-defined existing pipeline for Tokenization from file
-         final PipelineReader reader = new PipelineReader( PIPELINE_FILE_PATH );
+         final PiperFileReader reader = new PiperFileReader( PIPELINE_FILE_PATH );
          PipelineBuilder builder = reader.getBuilder();
          if ( args.length > 0 ) {
             // Example to save the Aggregate descriptor to an xml file for external use such
as the UIMA CVD

Copied: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java
(from r1764579, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldReadPipeRunner.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java?p2=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java&p1=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldReadPipeRunner.java&r1=1764579&r2=1764816&rev=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldReadPipeRunner.java
(original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java
Fri Oct 14 06:25:36 2016
@@ -2,14 +2,14 @@ package org.apache.ctakes.examples.pipel
 
 
 import org.apache.ctakes.core.pipeline.PipelineBuilder;
-import org.apache.ctakes.core.pipeline.PipelineReader;
+import org.apache.ctakes.core.pipeline.PiperFileReader;
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 
 import java.io.IOException;
 
 /**
- * Build and run a pipeline using a {@link PipelineReader} and a {@link PipelineBuilder}.
+ * Build and run a pipeline using a {@link PiperFileReader} and a {@link PipelineBuilder}.
  * <p>
  * Example of a running a pipeline programatically w/o uima xml descriptor xml files
  * Adds the default Tokenization pipeline and adding the Example HelloWorld Annotator
@@ -18,15 +18,15 @@ import java.io.IOException;
  * @version %I%
  * @since 10/10/2016
  */
-final public class HelloWorldReadPipeRunner {
+final public class HelloWorldPiperRunner {
 
-   static private final Logger LOGGER = Logger.getLogger( "HelloWorldReadPipeRunner" );
+   static private final Logger LOGGER = Logger.getLogger( "HelloWorldPiperRunner" );
 
-   static private final String PIPELINE_FILE_PATH = "org/apache/ctakes/examples/pipeline/HelloWorldPipeline.txt";
+   static private final String PIPELINE_FILE_PATH = "org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper";
 
    static private final String DOC_TEXT = "Hello World!";
 
-   private HelloWorldReadPipeRunner() {
+   private HelloWorldPiperRunner() {
    }
 
    /**
@@ -35,7 +35,7 @@ final public class HelloWorldReadPipeRun
    public static void main( final String... args ) {
       try {
          // Add a simple pre-defined existing pipeline for Tokenization from file
-         final PipelineReader reader = new PipelineReader( PIPELINE_FILE_PATH );
+         final PiperFileReader reader = new PiperFileReader( PIPELINE_FILE_PATH );
          PipelineBuilder builder = reader.getBuilder();
          if ( args.length > 0 ) {
             // Example to save the Aggregate descriptor to an xml file for external use such
as the UIMA CVD

Copied: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java
(from r1764580, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsReadPipeRunner.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java?p2=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java&p1=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsReadPipeRunner.java&r1=1764580&r2=1764816&rev=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsReadPipeRunner.java
(original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java
Fri Oct 14 06:25:36 2016
@@ -3,14 +3,14 @@ package org.apache.ctakes.examples.pipel
 
 import org.apache.ctakes.core.pipeline.EntityCollector;
 import org.apache.ctakes.core.pipeline.PipelineBuilder;
-import org.apache.ctakes.core.pipeline.PipelineReader;
+import org.apache.ctakes.core.pipeline.PiperFileReader;
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 
 import java.io.IOException;
 
 /**
- * Build and run a pipeline using a {@link PipelineReader} and a {@link PipelineBuilder}.
+ * Build and run a pipeline using a {@link PiperFileReader} and a {@link PipelineBuilder}.
  * <p>
  * Example of a running a pipeline programatically w/o uima xml descriptor xml files
  * Adds the default Tokenization pipeline and adding the Example HelloWorld Annotator
@@ -19,17 +19,17 @@ import java.io.IOException;
  * @version %I%
  * @since 10/10/2016
  */
-final public class HelloWorldPropsReadPipeRunner {
+final public class HelloWorldPropsPiperRunner {
 
-   static private final Logger LOGGER = Logger.getLogger( "HelloWorldReadPipeRunner" );
+   static private final Logger LOGGER = Logger.getLogger( "HelloWorldPropsPiperRunner" );
 
    static private final String PROPS_PIPELINE_FILE_PATH
-         = "org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.txt";
+         = "org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper";
 
    static private final String DOC_TEXT
          = "Hello World!  I feel no pain.  My father takes aspirin.  My sister might have
a headache.";
 
-   private HelloWorldPropsReadPipeRunner() {
+   private HelloWorldPropsPiperRunner() {
    }
 
    /**
@@ -38,7 +38,7 @@ final public class HelloWorldPropsReadPi
    public static void main( final String... args ) {
       try {
          // Add a simple pre-defined existing pipeline for Tokenization from file
-         final PipelineReader reader = new PipelineReader( PROPS_PIPELINE_FILE_PATH );
+         final PiperFileReader reader = new PiperFileReader( PROPS_PIPELINE_FILE_PATH );
          // Add the property extraction pipeline
          PipelineBuilder builder = reader.getBuilder();
          if ( args.length > 0 ) {

Modified: ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/AssertionDefaults.properties
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/AssertionDefaults.properties?rev=1764816&r1=1764815&r2=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/AssertionDefaults.properties
(original)
+++ ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/AssertionDefaults.properties
Fri Oct 14 06:25:36 2016
@@ -1,6 +1,6 @@
 # Parameters for AssertionAnalysisEngine and ConceptConverterAnalysisEngine
-assertionModelResourceImpl=file:org/apache/ctakes/assertion/models/i2b2.model
-scopeModelResourceImpl=file:org/apache/ctakes/assertion/models/scope.model
-cueModelResourceImpl=file:org/apache/ctakes/assertion/models/cue.model
-enabledFeaturesResourceImpl=file:org/apache/ctakes/assertion/models/featureFile11b
-posModelResourceImpl=file:org/apache/ctakes/assertion/models/pos.model
+assertionModelResource=file:org/apache/ctakes/assertion/models/i2b2.model
+scopeModelResource=file:org/apache/ctakes/assertion/models/scope.model
+cueModelResource=file:org/apache/ctakes/assertion/models/cue.model
+enabledFeaturesResource=file:org/apache/ctakes/assertion/models/featureFile11b
+posModelResource=file:org/apache/ctakes/assertion/models/pos.model

Copied: ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.piper
(from r1764580, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.txt)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.piper?p2=ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.piper&p1=ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.txt&r1=1764580&r2=1764816&rev=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.txt
(original)
+++ ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.piper
Fri Oct 14 06:25:36 2016
@@ -2,7 +2,7 @@
 // with Entity Property output
 
 // Load a simple token processing pipeline from another file
-load org/apache/ctakes/examples/pipeline/HelloWorldPipeline.txt
+load org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
 
 // Assertion engines require dependencies
 addDescription ClearNLPDependencyParserAE

Copied: ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper
(from r1764580, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.txt)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper?p2=ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper&p1=ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.txt&r1=1764580&r2=1764816&rev=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.txt
(original)
+++ ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper
Fri Oct 14 06:25:36 2016
@@ -2,7 +2,7 @@
 // with Entity Property output
 
 // Load a simple token processing pipeline from another file
-load org/apache/ctakes/examples/pipeline/HelloWorldPipeline.txt
+load org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
 
 // Add the context annotator for simple annotation properties
 // The default call sets it to detect negation

Copied: ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper
(from r1764580, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.txt)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper?p2=ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper&p1=ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.txt&r1=1764580&r2=1764816&rev=1764816&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.txt
(original)
+++ ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper
Fri Oct 14 06:25:36 2016
@@ -2,7 +2,7 @@
 // with Entity Property output
 
 // Load a simple token processing pipeline from another file
-load org/apache/ctakes/examples/pipeline/HelloWorldPipeline.txt
+load org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
 
 // I don't think that the chunker is strictly necessary, but here it is ...
 add Chunker




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