org.apache.ctakes.assertion.cr

Class MiPACQKnowtatorXMLReader

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

org.apache.uima.fit.component.JCasAnnotator_ImplBase

org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

@PipeBitInfo(name="Knowtator XML Reader (MiPACQ)",
             description="Reads annotations from MiPACQ schema Knowtator XML files in a directory.",
             role=SPECIAL,
             products={IDENTIFIED_ANNOTATION,GENERIC_RELATION})
public class MiPACQKnowtatorXMLReader
extends org.apache.uima.fit.component.JCasAnnotator_ImplBase

assumes knowtator xml files are in "exported-xml" subdirectory w/ train/dev/test subsubdirs and the original plaintext files are in "text" subdirectory w/ train/dev/test subsubdirs

Field Summary

Fields

Modifier and Type	Field and Description
static String	PARAM_SET_DEFAULTS
static String	PARAM_TEXT_DIRECTORY

Constructor Summary

Constructors

Constructor and Description
MiPACQKnowtatorXMLReader()

Method Summary

Modifier and Type	Method and Description
protected static String[]	getAnnotatorNames() Returns the names of the annotators in the Knowtator files that represent the gold standard
protected URI	getKnowtatorURI(org.apache.uima.jcas.JCas jCas) Get the URI for the Knowtator XML file that should be loaded
protected URI	getTextURI(org.apache.uima.jcas.JCas jCas) Get the URI that the text in this class was loaded from
static void	main(String[] args) This main method is only for testing purposes.
void	process(org.apache.uima.jcas.JCas jCas)

Methods inherited from class org.apache.uima.fit.component.JCasAnnotator_ImplBase

getLogger, initialize

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, collectionProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PARAM_TEXT_DIRECTORY

public static final String PARAM_TEXT_DIRECTORY

See Also:

Constant Field Values

PARAM_SET_DEFAULTS

public static final String PARAM_SET_DEFAULTS

See Also:

Constant Field Values

Constructor Detail

MiPACQKnowtatorXMLReader

public MiPACQKnowtatorXMLReader()

Method Detail

getTextURI

protected URI getTextURI(org.apache.uima.jcas.JCas jCas)
                  throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Get the URI that the text in this class was loaded from

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

getKnowtatorURI

protected URI getKnowtatorURI(org.apache.uima.jcas.JCas jCas)
                       throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Get the URI for the Knowtator XML file that should be loaded

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

getAnnotatorNames

protected static String[] getAnnotatorNames()

Returns the names of the annotators in the Knowtator files that represent the gold standard

process

public void process(org.apache.uima.jcas.JCas jCas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Specified by:

process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

main

public static void main(String[] args)
                 throws Exception

This main method is only for testing purposes. It runs the reader on Knowtator directories. args[0] = "/usr/data/MiPACQ/copies-of-just-clinical-knowtator-xml-and-text/"; should have a child directory called "text" should have a child directory called "exported-xml" files in knowtator xml directory should have files that end with .xml

Throws:

Exception