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Posted to commits@ctakes.apache.org by se...@apache.org on 2022/12/20 18:19:30 UTC
[ctakes] branch main updated: Add deprecation message and stub reminder for assertion. ListAnnotator Add catch for exception from TimSort
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 2eb5346 Add deprecation message and stub reminder for assertion. ListAnnotator Add catch for exception from TimSort
2eb5346 is described below
commit 2eb534696f5ab1badb37183726828ea9dd3f2331
Author: Sean Finan <se...@childrens.harvard.edu>
AuthorDate: Tue Dec 20 13:19:17 2022 -0500
Add deprecation message and stub reminder for assertion.
ListAnnotator Add catch for exception from TimSort
---
.../apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java | 5 +++++
.../ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java | 2 ++
.../src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java | 8 +++++++-
3 files changed, 14 insertions(+), 1 deletion(-)
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
index 45509af..49bae5d 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
@@ -48,12 +48,17 @@ import java.util.Set;
//import org.jfree.util.Log;
+/**
+ * Stub classes must be replaced. See https://issues.apache.org/jira/browse/CTAKES-76
+ * @deprecated Use AssertionAnalysisEngineFit.
+ */
@PipeBitInfo(
name = "Assertion Engine",
description = "Adds Negation, Uncertainty, Conditional and Subject to annotations.",
role = PipeBitInfo.Role.ANNOTATOR,
dependencies = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
)
+@Deprecated
public class AssertionAnalysisEngine extends JCasAnnotator_ImplBase
{
private static Logger logger = Logger.getLogger(AssertionAnalysisEngine.class.getName());
diff --git a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
index 1cdc876..f9ae740 100644
--- a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
+++ b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
@@ -26,6 +26,8 @@ import static org.apache.ctakes.typesystem.type.constants.CONST.ATTR_SUBJECT_PAT
/**
+ * Stub classes must be replaced. See https://issues.apache.org/jira/browse/CTAKES-76
+ *
* @author SPF , chip-nlp
* @version %I%
* @since 10/19/2016
diff --git a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java
index 562bf4b..61059ab 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java
@@ -238,7 +238,13 @@ final public class ListAnnotator extends JCasAnnotator_ImplBase {
}
final Collection<ListEntry> listEntries = new ArrayList<>( separators.size() + 1 );
final List<Pair<Integer>> boundsList = new ArrayList<>( separators );
- boundsList.sort( ( p1, p2 ) -> p1.getValue1() - p2.getValue2() );
+ try {
+ boundsList.sort( ( p1, p2 ) -> p1.getValue1() - p2.getValue2() );
+ } catch ( IllegalArgumentException iaE ) {
+ // TimSort sometimes throws an exception. Rare but unfortunate.
+ LOGGER.error( iaE.getMessage() + ", ignoring possible list entries." );
+ return Collections.emptyList();
+ }
Pair<Integer> leftBounds;
int previousEntryEnd = listBegin;
final int length = boundsList.size();