ch.epfl.bbp.uima.ae.relations

Class WriteCoocurrencesToLoadfile2

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

ch.epfl.bbp.uima.ae.relations.WriteCoocurrencesToLoadfile2

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

public class WriteCoocurrencesToLoadfile2
extends org.apache.uima.fit.component.JCasAnnotator_ImplBase

Extracts Cooccurrences. Snippet on same file. Format varies, but has the general structure:

• pmId
• confidence
• e1_id
• e1_start
• e1_end
• (e1_type)
• e2_id
• e2_start
• e2_end
• (e2_type)
• snippet_begin (= enclosing scope begin)
• snippet_end (= enclosing scope end)
• (snippet)

Output can be loaded into a db, e.g.:
cd to {outputFileDir}
cd . (if you ran it again...)
mysql -uroot --local-infile
use {outputFile}
LOAD DATA LOCAL INFILE '{outputFile}' INTO TABLE relations FIELDS TERMINATED BY ' ' LINES TERMINATED BY '\n' (`list`,`of`,`your`,`fields`, ...);

Author:

renaud.richardet@epfl.ch

Field Summary

Fields

Modifier and Type	Field and Description
protected String	annot1Type
protected String	annot2Type
protected int	cooccCnt
protected String	cooccurrenceType
protected static org.slf4j.Logger	LOG
protected String	outputFile
protected LoadDataFileWriter	writer
protected boolean	writeSnippet

Constructor Summary

Constructors

Constructor and Description
WriteCoocurrencesToLoadfile2()

Method Summary

Methods

Modifier and Type	Method and Description
void	collectionProcessComplete()
void	initialize(org.apache.uima.UimaContext context)
void	process(org.apache.uima.jcas.JCas jCas)
static String	snippet(org.apache.uima.jcas.JCas jCas, int snippetBegin, int snippetEnd, org.apache.uima.jcas.tcas.Annotation a1, org.apache.uima.jcas.tcas.Annotation a2)

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, 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

LOG

protected static org.slf4j.Logger LOG

outputFile

protected String outputFile

annot1Type

protected String annot1Type

annot2Type

protected String annot2Type

cooccurrenceType

protected String cooccurrenceType

writeSnippet

protected boolean writeSnippet

writer

protected LoadDataFileWriter writer

cooccCnt

protected int cooccCnt

Constructor Detail

WriteCoocurrencesToLoadfile2

public WriteCoocurrencesToLoadfile2()

Method Detail

initialize

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

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

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

snippet

public static String snippet(org.apache.uima.jcas.JCas jCas,
             int snippetBegin,
             int snippetEnd,
             org.apache.uima.jcas.tcas.Annotation a1,
             org.apache.uima.jcas.tcas.Annotation a2)

collectionProcessComplete

public void collectionProcessComplete()
                               throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Specified by:

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

Overrides:

collectionProcessComplete in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException