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Posted to commits@ctakes.apache.org by se...@apache.org on 2019/11/30 18:30:30 UTC
svn commit: r1870633 - in
/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc:
FhirJsonFileWriter.java FhirJsonWriter.java
Author: seanfinan
Date: Sat Nov 30 18:30:30 2019
New Revision: 1870633
URL: http://svn.apache.org/viewvc?rev=1870633&view=rev
Log:
Add configuration parameter WriteNlpFhir, refactor
Modified:
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java?rev=1870633&r1=1870632&r2=1870633&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java Sat Nov 30 18:30:30 2019
@@ -1,18 +1,14 @@
package org.apache.ctakes.fhir.cc;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.parser.IParser;
import org.apache.ctakes.core.cc.AbstractJCasFileWriter;
import org.apache.ctakes.core.config.ConfigParameterConstants;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.fhir.resource.PractitionerCtakes;
import org.apache.log4j.Logger;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
-import org.hl7.fhir.dstu3.model.Bundle;
import java.io.*;
@@ -47,12 +43,7 @@ public class FhirJsonFileWriter extends
@Override
public void writeFile( final JCas jCas, final String outputDir,
final String documentId, final String fileName ) throws IOException {
- final Bundle bundle = FhirDocComposer.composeDocFhir( jCas, PractitionerCtakes.getInstance(), _writeNlpFhir );
-
- final FhirContext fhirContext = FhirContext.forDstu3();
- final IParser jsonParser = fhirContext.newJsonParser();
- jsonParser.setPrettyPrint( true );
- final String json = jsonParser.encodeResourceToString( bundle );
+ final String json = FhirJsonWriter.createJson( jCas, _writeNlpFhir );
final File file = new File( outputDir, fileName + ".json" );
try ( Writer writer = new BufferedWriter( new FileWriter( file ) ) ) {
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java?rev=1870633&r1=1870632&r2=1870633&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java Sat Nov 30 18:30:30 2019
@@ -8,6 +8,7 @@ import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
import org.hl7.fhir.dstu3.model.Bundle;
@@ -26,6 +27,14 @@ import org.hl7.fhir.dstu3.model.Bundle;
)
final public class FhirJsonWriter extends JCasAnnotator_ImplBase {
+ @ConfigurationParameter(
+ name = "WriteNlpFhir",
+ description = "Write all nlp information (paragraph, sentence, base annotations) to FHIR.",
+ mandatory = false,
+ defaultValue = "false"
+ )
+ private boolean _writeNlpFhir;
+
static private final Logger LOGGER = Logger.getLogger( "FhirJsonWriter" );
/**
@@ -47,12 +56,7 @@ final public class FhirJsonWriter extend
public void process( final JCas jCas ) throws AnalysisEngineProcessException {
LOGGER.info( "Processing ..." );
- final Bundle bundle = FhirDocComposer.composeDocFhir( jCas, PractitionerCtakes.getInstance(), false );
-
- final FhirContext fhirContext = FhirContext.forDstu3();
- final IParser jsonParser = fhirContext.newJsonParser();
- jsonParser.setPrettyPrint( true );
- final String json = jsonParser.encodeResourceToString( bundle );
+ final String json = createJson( jCas, _writeNlpFhir );
System.out.println( json );
System.out.println();
System.out.println();
@@ -60,5 +64,16 @@ final public class FhirJsonWriter extend
LOGGER.info( "Finished." );
}
+ static public String createJson( final JCas jCas ) {
+ return createJson( jCas, false );
+ }
+
+ static public String createJson( final JCas jCas, final boolean writeNlp ) {
+ final Bundle bundle = FhirDocComposer.composeDocFhir( jCas, PractitionerCtakes.getInstance(), writeNlp );
+ final FhirContext fhirContext = FhirContext.forDstu3();
+ final IParser jsonParser = fhirContext.newJsonParser();
+ jsonParser.setPrettyPrint( true );
+ return jsonParser.encodeResourceToString( bundle );
+ }
}