From 633aa4a29840dcacae71d89e70ff3995b20b126d Mon Sep 17 00:00:00 2001
From: Chris Norman <cnorman@broadinstitute.org>
Date: Fri, 23 Dec 2022 15:18:45 -0500
Subject: [PATCH] Don't require python to just instantiate tool classes.
 (#8128)

* Don't require python to just instantiate tool classes.
---
 .../hellbender/tools/walkers/vqsr/CNNScoreVariants.java   | 8 +++++---
 .../hellbender/tools/walkers/vqsr/CNNVariantTrain.java    | 6 ++++--
 .../tools/walkers/vqsr/CNNVariantWriteTensors.java        | 7 +++++--
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariants.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariants.java
index c9741cc38dc..a17da13b0cf 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariants.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariants.java
@@ -205,9 +205,7 @@ public class CNNScoreVariants extends TwoPassVariantWalker {
     @Argument(fullName = "python-profile", shortName = "python-profile", doc = "Run the tool with the Python CProfiler on and write results to this file.", optional = true)
     private File pythonProfileResults;
 
-    // Create the Python executor. This doesn't actually start the Python process, but verifies that
-    // the requestedPython executable exists and can be located.
-    final StreamingPythonScriptExecutor<String> pythonExecutor = new StreamingPythonScriptExecutor<>(true);
+    private StreamingPythonScriptExecutor<String> pythonExecutor;
 
     private List<String> batchList = new ArrayList<>(inferenceBatchSize);
 
@@ -284,6 +282,10 @@ public void onTraversalStart() {
             }
         }
 
+        // Create the Python executor. This doesn't actually start the Python process, but verifies that
+        // the requestedPython executable exists and can be located.
+        pythonExecutor = new StreamingPythonScriptExecutor<>(true);
+
         final VCFHeader inputHeader = getHeaderForVariants();
         if (inputHeader.getGenotypeSamples().size() > 1) {
             logger.warn("CNNScoreVariants is a single sample tool but the input VCF has more than 1 sample.");
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantTrain.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantTrain.java
index 169bbe72096..7bb60d7477f 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantTrain.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantTrain.java
@@ -129,17 +129,19 @@ public class CNNVariantTrain extends CommandLineProgram {
     @Argument(fullName = "annotation-set", shortName = "annotation-set", doc = "Which set of annotations to use.", optional = true)
     private String annotationSet = "best_practices";
 
-    // Start the Python executor. This does not actually start the Python process, but fails if python can't be located
-    final PythonScriptExecutor pythonExecutor = new PythonScriptExecutor(true);
+    private PythonScriptExecutor pythonExecutor;
 
 
     @Override
     protected void onStartup() {
         PythonScriptExecutor.checkPythonEnvironmentForPackage("vqsr_cnn");
+        // Start the Python executor. This does not actually start the Python process, but fails if python can't be located
+        pythonExecutor = new PythonScriptExecutor(true);
     }
 
     @Override
     protected Object doWork() {
+
         final Resource pythonScriptResource = new Resource("training.py", CNNVariantTrain.class);
         List<String> arguments = new ArrayList<>(Arrays.asList(
                 "--data_dir", inputTensorDir,
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantWriteTensors.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantWriteTensors.java
index 58618b831f5..0fd0ec79e17 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantWriteTensors.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantWriteTensors.java
@@ -117,16 +117,19 @@ public class CNNVariantWriteTensors extends CommandLineProgram {
     @Argument(fullName = "max-tensors", shortName = "max-tensors", doc = "Maximum number of tensors to write.", optional = true, minValue = 0)
     private int maxTensors = 1000000;
 
-    // Start the Python executor. This does not actually start the Python process, but fails if python can't be located
-    final PythonScriptExecutor pythonExecutor = new PythonScriptExecutor(true);
+    private PythonScriptExecutor pythonExecutor;
 
     @Override
     protected void onStartup() {
         PythonScriptExecutor.checkPythonEnvironmentForPackage("vqsr_cnn");
+
+        // Start the Python executor. This does not actually start the Python process, but fails if python can't be located
+        pythonExecutor = new PythonScriptExecutor(true);
     }
 
     @Override
     protected Object doWork() {
+
         final Resource pythonScriptResource = new Resource("training.py", CNNVariantWriteTensors.class);
         List<String> arguments = new ArrayList<>(Arrays.asList(
                 "--reference_fasta", reference,