ch.epfl.bbp.uima.ae.relations

Class WriteCoocurrencesToLoadfile

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.WriteCoocurrencesToLoadfile

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

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

Extracts cooccurences Format:
`pubmed_id`,`annot_1_id`,`annot_1_start`,`annot_1_end`,` annot_2_id`,` annot_2_start`,`annot_2_end` Import:
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' (`pubmed_id`,`sentence_id`,`region_1_name`,`region_1_start`,`region_1_end`,`region_2_name`,`region_2_start`,`region_2_end`, `snippet`);

Author:

renaud.richardet@epfl.ch

Field Summary

Fields

Modifier and Type	Field and Description
protected int	cooccCnt
protected int	docCnt
static String[]	FIELDS
protected static org.slf4j.Logger	LOG
protected String	outputFile
static String	PARAM_WRITE_SNIPPETS
protected LoadDataFileWriter	snippetWriter
protected LoadDataFileWriter	writer
protected boolean	writeSnippets

Constructor Summary

Constructors

Constructor and Description
WriteCoocurrencesToLoadfile()

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)

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

FIELDS

public static final String[] FIELDS

outputFile

protected String outputFile

PARAM_WRITE_SNIPPETS

public static final String PARAM_WRITE_SNIPPETS

See Also:

Constant Field Values

writeSnippets

protected boolean writeSnippets

writer

protected LoadDataFileWriter writer

snippetWriter

protected LoadDataFileWriter snippetWriter

docCnt

protected int docCnt

cooccCnt

protected int cooccCnt

Constructor Detail

WriteCoocurrencesToLoadfile

public WriteCoocurrencesToLoadfile()

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

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