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Merge pull request #663 from broadinstitute/pd_jexl_user_exception 

Recast the "Invalid JEXL expression detected" error in SelectVariants fr...
This commit is contained in:
Eric Banks 2014-06-20 17:17:54 -04:00
parent db7dc8ab5f 65eeb4a7ab
commit c191103326
2 changed files with 56 additions and 4 deletions
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14
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
View File

@ -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 &&

46
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java 100644
View File

@ -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);
}
}