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Posted to commits@ctakes.apache.org by se...@apache.org on 2016/10/15 01:14:27 UTC
svn commit: r1765003 - in /ctakes/trunk/ctakes-examples/src/main:
java/org/apache/ctakes/examples/pipeline/
resources/org/apache/ctakes/examples/pipeline/
Author: seanfinan
Date: Sat Oct 15 01:14:26 2016
New Revision: 1765003
URL: http://svn.apache.org/viewvc?rev=1765003&view=rev
Log:
Adding ProcessDir.piper
Refactoring
Added:
ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java
- copied, changed from r1765001, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java
ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorld.piper
- copied unchanged from r1764965, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertProps.piper
- copied unchanged from r1764816, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.piper
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCui.piper
- copied unchanged from r1764965, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldProps.piper
- copied unchanged from r1764816, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkProps.piper
- copied unchanged from r1764965, ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/ProcessDir.piper
Removed:
ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.piper
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper
ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper
Modified:
ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java
ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java
ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java
Modified: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java?rev=1765003&r1=1765002&r2=1765003&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java (original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java Sat Oct 15 01:14:26 2016
@@ -23,7 +23,7 @@ final public class HelloWorldCuiPiperRun
static private final Logger LOGGER = Logger.getLogger( "HelloWorldCuiPiperRunner" );
- static private final String PIPELINE_FILE_PATH = "org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper";
+ static private final String PIPER_FILE_PATH = "org/apache/ctakes/examples/pipeline/HelloWorldCui.piper";
static private final String DOC_TEXT = "Hello World! I have allergies to nuts, bee stings, and shark bites.";
@@ -36,7 +36,7 @@ final public class HelloWorldCuiPiperRun
public static void main( final String... args ) {
try {
// Add a simple pre-defined existing pipeline for Tokenization from file
- final PiperFileReader reader = new PiperFileReader( PIPELINE_FILE_PATH );
+ final PiperFileReader reader = new PiperFileReader( PIPER_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
@@ -44,11 +44,11 @@ final public class HelloWorldCuiPiperRun
}
// Run the pipeline with specified text
builder.run( DOC_TEXT );
+ // Log the IdentifiedAnnotation objects
+ LOGGER.info( "\n" + CuiCollector.getInstance().toString() );
} catch ( IOException | UIMAException multE ) {
LOGGER.error( multE.getMessage() );
}
- // Log the IdentifiedAnnotation objects
- LOGGER.info( "\n" + CuiCollector.getInstance().toString() );
}
Modified: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java?rev=1765003&r1=1765002&r2=1765003&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java (original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java Sat Oct 15 01:14:26 2016
@@ -22,7 +22,7 @@ final public class HelloWorldPiperRunner
static private final Logger LOGGER = Logger.getLogger( "HelloWorldPiperRunner" );
- static private final String PIPELINE_FILE_PATH = "org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper";
+ static private final String PIPER_FILE_PATH = "org/apache/ctakes/examples/pipeline/HelloWorld.piper";
static private final String DOC_TEXT = "Hello World!";
@@ -35,7 +35,7 @@ final public class HelloWorldPiperRunner
public static void main( final String... args ) {
try {
// Add a simple pre-defined existing pipeline for Tokenization from file
- final PiperFileReader reader = new PiperFileReader( PIPELINE_FILE_PATH );
+ final PiperFileReader reader = new PiperFileReader( PIPER_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
Modified: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java?rev=1765003&r1=1765002&r2=1765003&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java (original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java Sat Oct 15 01:14:26 2016
@@ -23,8 +23,8 @@ final public class HelloWorldPropsPiperR
static private final Logger LOGGER = Logger.getLogger( "HelloWorldPropsPiperRunner" );
- static private final String PROPS_PIPELINE_FILE_PATH
- = "org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper";
+ static private final String PIPER_FILE_PATH
+ = "org/apache/ctakes/examples/pipeline/HelloWorldProps.piper";
static private final String DOC_TEXT
= "Hello World! I feel no pain. My father takes aspirin. My sister might have a headache.";
@@ -38,7 +38,7 @@ final public class HelloWorldPropsPiperR
public static void main( final String... args ) {
try {
// Add a simple pre-defined existing pipeline for Tokenization from file
- final PiperFileReader reader = new PiperFileReader( PROPS_PIPELINE_FILE_PATH );
+ final PiperFileReader reader = new PiperFileReader( PIPER_FILE_PATH );
// Add the property extraction pipeline
PipelineBuilder builder = reader.getBuilder();
if ( args.length > 0 ) {
@@ -47,11 +47,11 @@ final public class HelloWorldPropsPiperR
}
// Run the pipeline with specified text
builder.run( DOC_TEXT );
+ // Log the IdentifiedAnnotation objects
+ LOGGER.info( "\n" + EntityCollector.getInstance().toString() );
} catch ( IOException | UIMAException multE ) {
LOGGER.error( multE.getMessage() );
}
- // Log the IdentifiedAnnotation objects
- LOGGER.info( "\n" + EntityCollector.getInstance().toString() );
}
Copied: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java (from r1765001, ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java)
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java?p2=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java&p1=ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java&r1=1765001&r2=1765003&rev=1765003&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java (original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java Sat Oct 15 01:14:26 2016
@@ -19,13 +19,13 @@ import java.io.IOException;
* @version %I%
* @since 10/12/2016
*/
-final public class DirNotesBuildPipeRunner {
+final public class ProcessDirBuilderRunner {
- static private final Logger LOGGER = Logger.getLogger( "DirNotesBuildPipeRunner" );
+ static private final Logger LOGGER = Logger.getLogger( "ProcessDirBuilderRunner" );
static private final String INPUT_DIR = "org/apache/ctakes/examples/notes";
- private DirNotesBuildPipeRunner() {
+ private ProcessDirBuilderRunner() {
}
/**
Added: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java?rev=1765003&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java (added)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java Sat Oct 15 01:14:26 2016
@@ -0,0 +1,54 @@
+package org.apache.ctakes.examples.pipeline;
+
+
+import org.apache.ctakes.core.pipeline.EntityCollector;
+import org.apache.ctakes.core.pipeline.PipelineBuilder;
+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 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
+ *
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 10/10/2016
+ */
+final public class ProcessDirPiperRunner {
+
+ static private final Logger LOGGER = Logger.getLogger( "ProcessDirPiperRunner" );
+
+ static private final String PIPER_FILE_PATH = "org/apache/ctakes/examples/pipeline/ProcessDir.piper";
+
+ private ProcessDirPiperRunner() {
+ }
+
+ /**
+ * @param args an output directory for xmi files or none if xmi files are not wanted
+ */
+ public static void main( final String... args ) {
+ try {
+ // Add a simple pre-defined existing pipeline for Tokenization from file
+ final PiperFileReader reader = new PiperFileReader( PIPER_FILE_PATH );
+ // Add the property extraction pipeline
+ 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
+ builder.writeXMIs( args[ 0 ] );
+ }
+ // Run the pipeline with specified text
+ builder.run();
+ // Log the IdentifiedAnnotation objects
+ LOGGER.info( "\n" + EntityCollector.getInstance().toString() );
+ } catch ( IOException | UIMAException multE ) {
+ LOGGER.error( multE.getMessage() );
+ }
+ }
+
+
+}
Added: ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/ProcessDir.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/ProcessDir.piper?rev=1765003&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/ProcessDir.piper (added)
+++ ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/ProcessDir.piper Sat Oct 15 01:14:26 2016
@@ -0,0 +1,21 @@
+// This file contains commands and parameters to run the ctakes-examples "Hello World" pipeline
+// with Entity Property output
+
+readFiles org/apache/ctakes/examples/notes
+
+// Load a simple token processing pipeline from another pipeline file
+load org/apache/ctakes/core/pipeline/DefaultTokenizerPipeline.piper
+
+// Add non-core annotators
+add ContextDependentTokenizerAnnotator
+// The POSTagger has a -complex- startup, but it can create its own description to handle it
+addDescription POSTagger
+
+// Add the context annotator for simple annotation properties
+// The default call sets it to detect negation
+add ContextAnnotator
+// It can also detect Status if you change some parameters from the defaults
+add ContextAnnotator ContextAnalyzerClass=org.apache.ctakes.necontexts.status.StatusContextAnalyzer ContextHitConsumerClass=org.apache.ctakes.necontexts.status.StatusContextHitConsumer MaxLeftScopeSize=10 MaxRightScopeSize=10
+
+// Collect discovered Entity information for post-run access
+collectEntities