From 65eeb4a7abeaeaa33de94ee7a2f74259ca32b2ad Mon Sep 17 00:00:00 2001
From: Phillip Dexheimer <phildex@broadinstitute.org>
Date: Thu, 19 Jun 2014 23:52:26 -0400
Subject: [PATCH] Recast the "Invalid JEXL expression detected" error in
 SelectVariants from a RuntimeException to a UserException  - PT 68931448

---
 .../walkers/variantutils/SelectVariants.java  | 14 ++++--
 .../SelectVariantsIntegrationTest.java        | 46 +++++++++++++++++++
 2 files changed, 56 insertions(+), 4 deletions(-)
 create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
index 206d6dc7a..d31a71fac 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
@@ -514,11 +514,17 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
             if ( (!EXCLUDE_NON_VARIANTS || sub.isPolymorphicInSamples()) && (!EXCLUDE_FILTERED || !sub.isFiltered()) ) {
                 boolean failedJexlMatch = false;
-                for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) {
-                    if ( !VariantContextUtils.match(sub, jexl) ) {
-                        failedJexlMatch = true;
-                        break;
+                try {
+                    for (VariantContextUtils.JexlVCMatchExp jexl : jexls) {
+                        if (!VariantContextUtils.match(sub, jexl)) {
+                            failedJexlMatch = true;
+                            break;
+                        }
                     }
+                } catch (IllegalArgumentException e) {
+                    /*The IAE thrown by htsjdk already includes an informative error message ("Invalid JEXL
+                      expression detected...")*/
+                    throw new UserException(e.getMessage());
                 }
                 if ( !failedJexlMatch &&
                         !justRead &&
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
new file mode 100644
index 000000000..d43147496
--- /dev/null
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -0,0 +1,46 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+*
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+*
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+*
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.variantutils;
+
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.testng.annotations.Test;
+
+public class SelectVariantsIntegrationTest extends WalkerTest {
+
+    @Test
+    public void testInvalidJexl() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants" +
+                        " -R "+b37KGReference +
+                        " -V "+privateTestDir+"ac0.vcf" +
+                        " -select 'vc.getGenotype(\"FAKE_SAMPLE\").isHomRef()'" +
+                        " -o %s",
+                1,
+                UserException.class);
+        executeTest("InvalidJexl", spec);
+    }
+}