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Various fixes for package tests. 

Explicitly including gatk/queue test-jar artifacts in package test classpaths.
SelectVariantsIntegrationTest#testInvalidJexl now resets the JexlEngine silent flag that VariantFiltration.initialize() toggles.
External example no longer tries to unpack nonexistent gatk artifact jars during package tests.
This commit is contained in:
Khalid Shakir 2014-08-31 12:35:53 -04:00
parent 9705df2f7a
commit 376592f423
3 changed files with 11 additions and 2 deletions
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4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -359,6 +359,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testInvalidJexl() {
// NOTE: JexlEngine singleton construction in VariantContextUtils sets silent to false.
// However VariantFiltration.initialize() sets setSilent(true) on the shared instance.
// Just in case this test runs after a VariantFiltration in the same VM, always set silent back to false.
htsjdk.variant.variantcontext.VariantContextUtils.engine.get().setSilent(false);
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants" +
" -R "+b37KGReference +

5
public/external-example/pom.xml
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@ -28,6 +28,7 @@
<gatk.integrationtests.skipped>${gatk.committests.skipped}</gatk.integrationtests.skipped>
<!-- This flag is used by the package tests to disable re-shading -->
<gatk.unpack.phase>process-resources</gatk.unpack.phase>
<gatk.shade.phase>package</gatk.shade.phase>
</properties>
@ -73,7 +74,7 @@
<executions>
<execution>
<id>unpack</id>
<phase>process-resources</phase>
<phase>${gatk.unpack.phase}</phase>
<goals>
<goal>unpack</goal>
</goals>
@ -261,6 +262,8 @@
</property>
</activation>
<properties>
<gatk.jar.phase>none</gatk.jar.phase>
<gatk.unpack.phase>none</gatk.unpack.phase>
<gatk.shade.phase>none</gatk.shade.phase>
</properties>
</profile>

4
public/package-tests/pom.xml
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@ -102,6 +102,7 @@
<!-- TODO: Using additionalClasspathElement while debugging exclusion issue above -->
<additionalClasspathElements>
<additionalClasspathElement>${gatk.basedir}/public/gatk-tools-public/target/gatk-tools-public-${project.version}-tests.jar</additionalClasspathElement>
<additionalClasspathElement>${gatk.basedir}/public/gatk-queue/target/gatk-queue-${project.version}-tests.jar</additionalClasspathElement>
</additionalClasspathElements>
</configuration>
<executions>
@ -142,7 +143,8 @@
<testClassesDirectory>${gatk.packagetests.testClasses}</testClassesDirectory>
<!-- TODO: Using additionalClasspathElement while debugging exclusion issue above -->
<additionalClasspathElements>
<additionalClasspathElement>${gatk.basedir}/public/gatk-framework/target/gatk-framework-${project.version}-tests.jar</additionalClasspathElement>
<additionalClasspathElement>${gatk.basedir}/public/gatk-tools-public/target/gatk-tools-public-${project.version}-tests.jar</additionalClasspathElement>
<additionalClasspathElement>${gatk.basedir}/public/gatk-queue/target/gatk-queue-${project.version}-tests.jar</additionalClasspathElement>
</additionalClasspathElements>
</configuration>
<executions>