org.apache.ctakes.lvg.ae

Class LvgAnnotator

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.lvg.ae.LvgAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

@PipeBitInfo(name="LVG Annotator",
             description="Adds cononical form of words.",
             dependencies={SECTION,BASE_TOKEN})
public class LvgAnnotator
extends org.apache.uima.fit.component.JCasAnnotator_ImplBase

UIMA annotator that uses the UMLS LVG package to find the canonical form of WordTokens. The package is also used to find one or more lemmas for a given WordToken along with its associated part of speech.

Author:

Mayo Clinic to do: what effect does using the cache have on words that may be misspelled. It seems that if you automatically normalize a word from the cache, this may be bad if it is misspelled in the case where the misspelling is a word in the lexicon.

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	defaultExclusionWords
static String[]	defaultTreebankMap
static String	PARAM_CMD_CACHE_FILE
static String	PARAM_EXCLUSION_WORDS
static String	PARAM_LEMMA_CACHE_FILE_LOCATION Value is "LemmaCacheFileLocation".
static String	PARAM_LEMMA_CACHE_FREQUENCY_CUTOFF Value is "LemmaCacheFrequencyCutoff".
static String	PARAM_LEMMA_FREQ_CUTOFF
static String	PARAM_LVGCMDAPI_RESRC_KEY
static String	PARAM_POST_LEMMAS Value is "PostLemmas".
static String	PARAM_SKIP_SEGMENTS
static String	PARAM_USE_CMD_CACHE
static String	PARAM_USE_LEMMA_CACHE Value is "UseLemmaCache".
static String	PARAM_USE_SEGMENTS
static String	PARAM_XT_MAP

Constructor Summary

Constructors

Constructor and Description
LvgAnnotator()

Method Summary

Modifier and Type	Method and Description
protected void	annotateRange(org.apache.uima.jcas.JCas jcas, String text, int rangeBegin, int rangeEnd) A utility method that annotates a given range.
static String	copyLvgFiles(String absolutePath) Copy to under /tmp/ (or some other specified directory) the files needed for EventAnnotatorTest and anyone else using UIMAfit to create a pipeline.
static org.apache.uima.analysis_engine.AnalysisEngineDescription	createAnnotatorDescription()
void	initialize(org.apache.uima.UimaContext aContext) Performs initialization logic.
void	process(org.apache.uima.jcas.JCas jcas) Invokes this annotator's analysis logic.

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

getLogger

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

defaultExclusionWords

public static final String[] defaultExclusionWords

defaultTreebankMap

public static final String[] defaultTreebankMap

PARAM_POST_LEMMAS

public static final String PARAM_POST_LEMMAS

Value is "PostLemmas". This parameter determines whether the feature lemmaEntries will be populated for word annotations.

See Also:

Constant Field Values

PARAM_USE_LEMMA_CACHE

public static final String PARAM_USE_LEMMA_CACHE

Value is "UseLemmaCache". This parameter determines whether a cache will be used to improve performance of setting lemma entries.

See Also:

Constant Field Values

PARAM_LEMMA_CACHE_FILE_LOCATION

public static final String PARAM_LEMMA_CACHE_FILE_LOCATION

Value is "LemmaCacheFileLocation". This parameter determines where the lemma cache is located.

See Also:

Constant Field Values

PARAM_LEMMA_CACHE_FREQUENCY_CUTOFF

public static final String PARAM_LEMMA_CACHE_FREQUENCY_CUTOFF

Value is "LemmaCacheFrequencyCutoff". This parameter sets a threshold for the frequency of a lemma to be loaded into the cache.

See Also:

Constant Field Values

PARAM_USE_SEGMENTS

public static final String PARAM_USE_SEGMENTS

See Also:

Constant Field Values

PARAM_SKIP_SEGMENTS

public static final String PARAM_SKIP_SEGMENTS

See Also:

Constant Field Values

PARAM_XT_MAP

public static final String PARAM_XT_MAP

See Also:

Constant Field Values

PARAM_USE_CMD_CACHE

public static final String PARAM_USE_CMD_CACHE

See Also:

Constant Field Values

PARAM_CMD_CACHE_FILE

public static final String PARAM_CMD_CACHE_FILE

See Also:

Constant Field Values

PARAM_LEMMA_FREQ_CUTOFF

public static final String PARAM_LEMMA_FREQ_CUTOFF

See Also:

Constant Field Values

PARAM_EXCLUSION_WORDS

public static final String PARAM_EXCLUSION_WORDS

See Also:

Constant Field Values

PARAM_LVGCMDAPI_RESRC_KEY

public static final String PARAM_LVGCMDAPI_RESRC_KEY

See Also:

Constant Field Values

Constructor Detail

LvgAnnotator

public LvgAnnotator()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext aContext)
                throws org.apache.uima.resource.ResourceInitializationException

Performs initialization logic. This implementation just reads values for the configuration parameters.

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

initialize in class org.apache.uima.fit.component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

See Also:

BaseAnnotator.initialize(AnnotatorContext)

process

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

Invokes this annotator's analysis logic.

Specified by:

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

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

annotateRange

protected void annotateRange(org.apache.uima.jcas.JCas jcas,
                             String text,
                             int rangeBegin,
                             int rangeEnd)
                      throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

A utility method that annotates a given range.

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

copyLvgFiles

public static String copyLvgFiles(String absolutePath)

Copy to under /tmp/ (or some other specified directory) the files needed for EventAnnotatorTest and anyone else using UIMAfit to create a pipeline. Localize to this method all hardcoded file names and subdirs related to copying files to under /tmp (or C:\tmp).

Parameters:

absolutePath - - Where to copy the LVG data/config subtree. Typically "/tmp/".

Returns:

The full path to the copy of lvg.properties file

createAnnotatorDescription

public static org.apache.uima.analysis_engine.AnalysisEngineDescription createAnnotatorDescription()
                                                                                            throws org.apache.uima.resource.ResourceInitializationException,
                                                                                                   MalformedURLException

Throws:

org.apache.uima.resource.ResourceInitializationException

MalformedURLException