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From seanfi...@apache.org
Subject svn commit: r1823103 - in /ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core: patient/PatientNoteStore.java util/SourceMetadataUtil.java
Date Sun, 04 Feb 2018 19:12:04 GMT
Author: seanfinan
Date: Sun Feb  4 19:12:03 2018
New Revision: 1823103

URL: http://svn.apache.org/viewvc?rev=1823103&view=rev
Log:
Set patientId in patient cas

Modified:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java?rev=1823103&r1=1823102&r2=1823103&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
Sun Feb  4 19:12:03 2018
@@ -3,6 +3,8 @@ package org.apache.ctakes.core.patient;
 
 import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.ctakes.core.util.SourceMetadataUtil;
+import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;
+import org.apache.ctakes.typesystem.type.structured.Metadata;
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.cas.CASException;
@@ -239,6 +241,7 @@ public enum PatientNoteStore {
       if ( patientCas == null ) {
          try {
             patientCas = JCasFactory.createJCas();
+            setPatientId( patientCas, patientId );
             _patientMap.put( patientId, patientCas );
          } catch ( UIMAException uE ) {
             LOGGER.error( uE.getMessage() );
@@ -260,6 +263,20 @@ public enum PatientNoteStore {
       }
    }
 
+   /**
+    * Make sure the patient cas contains its patient id
+    *
+    * @param jCas      -
+    * @param patientId -
+    */
+   static private void setPatientId( final JCas jCas, final String patientId ) {
+      final DocumentIdPrefix documentIdPrefix = new DocumentIdPrefix( jCas );
+      documentIdPrefix.setDocumentIdPrefix( patientId );
+      documentIdPrefix.addToIndexes();
+      final Metadata metadata = SourceMetadataUtil.getOrCreateMetadata( jCas );
+      metadata.setPatientIdentifier( patientId );
+   }
+
    /////////////////    view fetchers   ///////////////
 
    /**

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java?rev=1823103&r1=1823102&r2=1823103&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java
Sun Feb  4 19:12:03 2018
@@ -56,7 +56,7 @@ final public class SourceMetadataUtil {
     * @param jcas ye olde jay-cas
     * @return the Metadata for the given jcas or null if one is not found
     */
-   static private Metadata getMetadata( final JCas jcas ) {
+   static public Metadata getMetadata( final JCas jcas ) {
       final Collection<Metadata> metadatas = JCasUtil.select( jcas, Metadata.class
);
       if ( metadatas == null || metadatas.isEmpty() ) {
          return null;
@@ -65,6 +65,20 @@ final public class SourceMetadataUtil {
    }
 
    /**
+    * @param jCas ye olde jay-cas
+    * @return the Metadata for the given jcas
+    */
+   static public Metadata getOrCreateMetadata( final JCas jCas ) {
+      final Metadata metadata = getMetadata( jCas );
+      if ( metadata != null ) {
+         return metadata;
+      }
+      final Metadata newMetadata = new Metadata( jCas );
+      newMetadata.addToIndexes();
+      return newMetadata;
+   }
+
+   /**
     * The first step in utilizing SourceData is getting it!
     *
     * @param jcas ye olde jay-cas
@@ -79,6 +93,21 @@ final public class SourceMetadataUtil {
    }
 
    /**
+    * @param jCas ye olde jay-cas
+    * @return the metadata for the source associated with the jcas
+    */
+   static public SourceData getOrCreateSourceData( final JCas jCas ) {
+      final SourceData sourceData = getSourceData( jCas );
+      if ( sourceData != null ) {
+         return sourceData;
+      }
+      final Metadata metadata = getOrCreateMetadata( jCas );
+      final SourceData newSourceData = new SourceData( jCas );
+      metadata.setSourceData( newSourceData );
+      return newSourceData;
+   }
+
+   /**
     * @param sourcedata -
     * @return the instance id or -1 if there isn't one
     * @throws ResourceProcessException if the internal value is not parseable as long



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