svn commit: r1814739 - /ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java

[se...@apache.org]

Author: seanfinan
Date: Thu Nov  9 15:29:49 2017
New Revision: 1814739

URL: http://svn.apache.org/viewvc?rev=1814739&view=rev
Log:
FileTreeReader : Allow specification of a single file

Modified:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java?rev=1814739&r1=1814738&r2=1814739&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java Thu Nov  9 15:29:49 2017
@@ -83,9 +83,12 @@ final public class FileTreeReader extend
    private String[] _explicitExtensions;
 
    /**
-    * Name of optional configuration parameter that specifies the extensions
-    * of the files that the collection reader will read.  Values for this
-    * parameter should not begin with a dot <code>'.'</code>.
+    * The patient id for each note is set using a directory name.
+    * By default this is the directory directly under the root directory (PatientLevel=1).
+    * This is appropriate for files such as in rootDir=data/, file in data/patientA/Text1.txt
+    * It can be set to use directory names at any level below.
+    * For instance, using PatientLevel=2 for rootDir=data/, file in data/hospitalX/patientA/Text1.txt
+    * In this manner the notes for the same patient from several sites can be properly collated.
     */
    public static final String PATIENT_LEVEL = "PatientLevel";
    @ConfigurationParameter(
@@ -115,8 +118,16 @@ final public class FileTreeReader extend
       }
       _validExtensions = createValidExtensions( _explicitExtensions );
       _currentIndex = 0;
-      _files = getDescendentFiles( _rootDir, _validExtensions, 0 );
-      _patientDocCounts.forEach( ( k, v ) -> PatientNoteStore.getInstance().setDocCount( k, v ) );
+      if ( _rootDir.isFile() ) {
+         // does not check for valid extensions.  With one file just trust the user.
+         _files = Collections.singletonList( _rootDir );
+         final String patient = _rootDir.getParentFile().getName();
+         PatientNoteStore.getInstance().setDocCount( patient, 1 );
+      } else {
+         // gather all of the files and set the document counts per patient.
+         _files = getDescendentFiles( _rootDir, _validExtensions, 0 );
+         _patientDocCounts.forEach( ( k, v ) -> PatientNoteStore.getInstance().setDocCount( k, v ) );
+      }
    }
 
    /**