Add a CNNSCoreVariants tests to force an exception during batch write.

broadinstitute · Aug 10, 2021 · 7a15b2f · 7a15b2f
1 parent a3b36b1
commit 7a15b2f
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diff --git a/...ava/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariantsIntegrationTest.java b/...ava/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariantsIntegrationTest.java
@@ -7,6 +7,7 @@
 import org.broadinstitute.hellbender.testutils.VariantContextTestUtils;
 import org.broadinstitute.hellbender.utils.Utils;
 
+import org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException;
 import org.testng.Assert;
 import org.testng.SkipException;
 import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
@@ -65,6 +66,22 @@ public void testAllDefaultArgs() {
         assertInfoFieldsAreClose(tempVcf, expectedVcf, GATKVCFConstants.CNN_1D_KEY);
     }
 
+    @Test(groups = {"python"}, expectedExceptions = PythonScriptExecutorException.class)
+    public void testExceptionDuringAsyncBatch() {
+        final ArgumentsBuilder argsBuilder = new ArgumentsBuilder();
+        final File tempVcf = createTempFile("tester", ".vcf");
+        // the last variant in this vcf has a  value of "." for the float attributes in the default CNN
+        // annotation set MQ, MQRankSum, ReadPosRankSum, SOR, VQSLOD, and QD
+        //TODO: move this into the large resources dir
+        final File malformedVCF = new File("src/test/resources/cnn_1d_chr20_subset_expected.badAnnotations.vcf");
+        argsBuilder.add(StandardArgumentDefinitions.VARIANT_LONG_NAME, malformedVCF)
+                .add(StandardArgumentDefinitions.OUTPUT_LONG_NAME, tempVcf.getPath())
+                .add(StandardArgumentDefinitions.REFERENCE_LONG_NAME, b37_reference_20_21)
+                .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false");
+
+        runCommandLine(argsBuilder);
+    }
+
     @Test(groups = {"python"})
     public void testInferenceArchitecture() {
         final boolean newExpectations = false;