(ctakes) branch main updated: Fix for collection readers that don't init cas / type system.

[seanfinan]

This is an automated email from the ASF dual-hosted git repository.

seanfinan pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git


The following commit(s) were added to refs/heads/main by this push:
     new 7370cf5  Fix for collection readers that don't init cas / type system.
7370cf5 is described below

commit 7370cf54ccc6c479038b14ea93223be50e950222
Author: Sean Finan <sean.fi...@childrens.harvard.edu>
AuthorDate: Fri Aug 23 09:19:52 2024 -0400

    Fix for collection readers that don't init cas / type system.
---
 .../org/apache/ctakes/core/cr/AbstractFileTreeReader.java |  4 ++--
 .../org/apache/ctakes/core/pipeline/PiperFileRunner.java  | 15 +++++++++++++++
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git 
a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
 
b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
index f992ad8..75ed46a 100644
--- 
a/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
+++ 
b/ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
@@ -184,10 +184,10 @@ abstract public class AbstractFileTreeReader extends 
JCasCollectionReader_ImplBa
       // Workaround https://github.com/apache/uima-uimaj/issues/234
       // https://github.com/ClearTK/cleartk/issues/470
       try {
-         LOGGER.info( "Creating empty CAS to make certain that the typesystem 
is initialized ..." );
+         LOGGER.debug( "Creating empty CAS to make certain that the typesystem 
is initialized ..." );
          CasCreationUtils.createCas();
       } catch ( ResourceInitializationException riE ) {
-         LOGGER.error( "Could not create base CAS for initialization.\n" + 
riE.getMessage() );
+         LOGGER.error( "Could not create base CAS for initialization.\n{}", 
riE.getMessage() );
          LOGGER.error( Arrays.stream( riE.getStackTrace() )
                              .map( StackTraceElement::toString )
                              .collect( Collectors.joining("\n" ) ) );
diff --git 
a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
 
b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
index 95347d0..60abe2a 100644
--- 
a/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
+++ 
b/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
@@ -3,6 +3,8 @@ package org.apache.ctakes.core.pipeline;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import org.apache.ctakes.core.config.ConfigParameterConstants;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.util.CasCreationUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.apache.uima.UIMAException;
@@ -11,6 +13,8 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.PrintStream;
 import java.nio.file.Paths;
+import java.util.Arrays;
+import java.util.stream.Collectors;
 
 /**
  * @author SPF , chip-nlp
@@ -79,6 +83,17 @@ final public class PiperFileRunner {
                builder.writeHtml( htmlOutDir );
             }
          }
+         // Workaround https://github.com/apache/uima-uimaj/issues/234
+         // https://github.com/ClearTK/cleartk/issues/470
+         try {
+            LOGGER.debug( "Creating empty CAS to make certain that the 
typesystem is initialized ..." );
+            CasCreationUtils.createCas();
+         } catch ( ResourceInitializationException riE ) {
+            LOGGER.error( "Could not create base CAS for initialization.\n{}", 
riE.getMessage() );
+            LOGGER.error( Arrays.stream( riE.getStackTrace() )
+                                .map( StackTraceElement::toString )
+                                .collect( Collectors.joining("\n" ) ) );
+         }
          // run the pipeline
          builder.run();
       } catch ( UIMAException | IOException multE ) {