Fix for collection readers that don't init cas / type system.

apache · Aug 23, 2024 · 7370cf5 · 7370cf5
1 parent 5df171e
commit 7370cf5
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Showing 2 changed files with 17 additions and 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
@@ -184,10 +184,10 @@ public AbstractFileTreeReader() {
       // 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
@@ -3,6 +3,8 @@
 
 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.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 @@ public static boolean run( final String... args ) {
                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 ) {