[ctakes] branch main updated: PbjReceiverAE will disconnect on collectionProcessComplete() PythonRunner adds -u to command for unbuffered output

[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 6da4e78  PbjReceiverAE will disconnect on collectionProcessComplete() 
PythonRunner adds -u to command for unbuffered output
6da4e78 is described below

commit 6da4e7892a00031029a22691d46e1499a61aea8a
Author: Sean Finan <sean.fi...@childrens.harvard.edu>
AuthorDate: Tue May 16 15:43:31 2023 -0400

    PbjReceiverAE will disconnect on collectionProcessComplete()
    PythonRunner adds -u to command for unbuffered output
---
 .../src/main/java/org/apache/ctakes/core/ae/PythonRunner.java     | 4 ++--
 .../org/apache/ctakes/examples/pipeline/WordFinderInOne.piper     | 2 +-
 .../src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java     | 8 +++++++-
 .../src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java       | 2 +-
 4 files changed, 11 insertions(+), 5 deletions(-)

diff --git 
a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java 
b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java
index ad32683..37657f9 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java
@@ -113,8 +113,8 @@ public class PythonRunner extends AbstractCommandRunner {
       final String commandDir = getCommandDir();
       final String command = getCommand();
       return ( commandDir == null || commandDir.isEmpty() )
-             ? "python " + command
-             : commandDir + File.separator + "python " + command;
+             ? "python -u " + command
+             : commandDir + File.separator + "python -u " + command;
    }
 
    protected void runCommand() throws IOException {
diff --git 
a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/pipeline/WordFinderInOne.piper
 
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/pipeline/WordFinderInOne.piper
index 6539b03..516c3ec 100644
--- 
a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/pipeline/WordFinderInOne.piper
+++ 
b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/pipeline/WordFinderInOne.piper
@@ -34,7 +34,7 @@ set PbjSecondStep=ctakes_pbj.examples.word_finder_pipeline
 
 // There is a fixed order to queue specification in python pipelines.
 // The incoming (receiver) queue is named first, the outgoing (sender) queue 
is named second.
-add PythonRunner Command="-m $PbjSecondStep JavaToPy PyToJava" 
LogFile=word_finder_pipeline.log
+add PythonRunner Command="-m $PbjSecondStep JavaToPy PyToJava"
 
 
 //
diff --git 
a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java 
b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java
index c8f96ea..9716b2d 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java
@@ -78,7 +78,6 @@ public class PbjReceiverAE extends JCasAnnotator_ImplBase {
    )
    private String _acceptStop;
 
-
    private PbjReceiver _delegate;
 
 
@@ -117,5 +116,12 @@ public class PbjReceiverAE extends JCasAnnotator_ImplBase {
       }
    }
 
+   /**
+    * {@inheritDoc}
+    */
+   @Override
+   public void collectionProcessComplete() throws 
AnalysisEngineProcessException {
+      _delegate.disconnect();
+   }
 
 }
diff --git a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java 
b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java
index e974107..3f0480a 100644
--- a/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java
+++ b/ctakes-pbj/src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java
@@ -240,7 +240,7 @@ final public class PbjReceiver extends 
JCasCollectionReader_ImplBase {
    }
 
 
-   private void disconnect() {
+   public void disconnect() {
       try {
          _connection.stop();
          _connection.close();