Fix static test blocks and @BeforeSuite usages to prevent excessive c…

…ode execution when tests aren't included in a suite.
broadinstitute · Sep 7, 2017 · 3868349 · 3868349
1 parent f7ce97b
commit 3868349
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Showing 8 changed files with 16 additions and 22 deletions.
diff --git a/src/test/java/org/broadinstitute/hellbender/BwaMemIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/BwaMemIntegrationTest.java
@@ -2,22 +2,20 @@
 
 import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex;
 import org.broadinstitute.hellbender.utils.test.BaseTest;
-import org.testng.annotations.AfterSuite;
-import org.testng.annotations.BeforeSuite;
-import org.testng.annotations.Test;
+import org.testng.annotations.*;
 
 public class BwaMemIntegrationTest extends BaseTest {
 
     private BwaMemIndex index;
 
-    @BeforeSuite
+    @BeforeClass
     public void loadIndex() {
         final String imageFile = createTempFile(b37_reference_20_21, ".img").toString();
         BwaMemIndex.createIndexImageFromFastaFile(b37_reference_20_21, imageFile);
         index = new BwaMemIndex(imageFile);
     }
 
-    @AfterSuite
+    @AfterClass
     public void unloadIndex() {
         index.close();
         index = null;

diff --git a/...adinstitute/hellbender/tools/coveragemodel/germline/GermlineCNVCallerIntegrationTest.java b/...adinstitute/hellbender/tools/coveragemodel/germline/GermlineCNVCallerIntegrationTest.java
@@ -21,7 +21,7 @@
 import org.broadinstitute.hellbender.utils.SparkToggleCommandLineProgram;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.param.ParamUtils;
-import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 import javax.annotation.Nonnull;
@@ -105,7 +105,7 @@ public class GermlineCNVCallerIntegrationTest extends CommandLineProgramTest {
     private static SexGenotypeDataCollection LEARNING_SEX_GENOTYPES_DATA;
     private static SexGenotypeDataCollection CALLING_SEX_GENOTYPES_DATA;
 
-    @BeforeSuite
+    @BeforeClass
     public void init() throws IOException {
         LEARNING_SEX_GENOTYPES_DATA = new SexGenotypeDataCollection(TEST_LEARNING_SAMPLE_SEX_GENOTYPES_FILE);
         CALLING_SEX_GENOTYPES_DATA = new SexGenotypeDataCollection(TEST_CALLING_SAMPLE_SEX_GENOTYPES_FILE);

diff --git a/...adinstitute/hellbender/tools/walkers/genotyper/GenotypeLikelihoodCalculatorsUnitTest.java b/...adinstitute/hellbender/tools/walkers/genotyper/GenotypeLikelihoodCalculatorsUnitTest.java
@@ -2,7 +2,7 @@
 
 import org.broadinstitute.hellbender.utils.test.BaseTest;
 import org.testng.Assert;
-import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -14,7 +14,7 @@ public final class GenotypeLikelihoodCalculatorsUnitTest extends BaseTest {
 
     GenotypeLikelihoodCalculators calcs;
 
-    @BeforeSuite
+    @BeforeClass
     public void init(){
         calcs = new GenotypeLikelihoodCalculators();
     }

diff --git a/...a/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java b/...a/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java
@@ -9,7 +9,7 @@
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.test.BaseTest;
 import org.testng.Assert;
-import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -44,7 +44,7 @@ protected static List<AFCalculator> createAFCalculators(final List<AFCalculatorI
         return AFCalculators;
     }
 
-    @BeforeSuite
+    @BeforeClass
     public void before() {
         AA1 = makePL(Arrays.asList(A, A), 0, 20, 20);
         AB1 = makePL(Arrays.asList(A, C), 20, 0, 20);

diff --git a/...te/hellbender/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/...te/hellbender/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
@@ -3,7 +3,7 @@
 import htsjdk.variant.variantcontext.*;
 import org.broadinstitute.hellbender.utils.test.BaseTest;
 import org.testng.Assert;
-import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -18,7 +18,7 @@ public final class GeneralPloidyAFCalculationModelUnitTest extends BaseTest {
     static final int numSamples = 4;
     static final int samplePloidy = 4;   // = 2*samplesPerPool
 
-    @BeforeSuite
+    @BeforeClass
     public void before() {
         // legacy diploid cases
         AA1 = new double[]{-5.0, -20.0, -20.0};

diff --git a/.../hellbender/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/.../hellbender/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
@@ -17,7 +17,7 @@
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 import org.broadinstitute.hellbender.utils.test.BaseTest;
 import org.testng.Assert;
-import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -31,7 +31,7 @@ public final class PairHMMLikelihoodCalculationEngineUnitTest extends BaseTest {
 
     Allele Aref, T, C, G, Cref, ATC, ATCATC;
 
-    @BeforeSuite
+    @BeforeClass
     public void setup() {
         // alleles
         Aref = Allele.create("A", true);

diff --git a/src/test/java/org/broadinstitute/hellbender/utils/recalibration/QualQuantizerUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/recalibration/QualQuantizerUnitTest.java
@@ -6,7 +6,7 @@
 import org.broadinstitute.hellbender.utils.QualityUtils;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.testng.Assert;
-import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -16,10 +16,6 @@
 
 
 public final class QualQuantizerUnitTest extends BaseTest {
-    @BeforeSuite
-    public void before() {
-
-    }
 
     // --------------------------------------------------------------------------------
     //

diff --git a/...est/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtilsUnitTest.java b/...est/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtilsUnitTest.java
@@ -19,7 +19,7 @@
 import org.broadinstitute.hellbender.utils.test.BaseTest;
 import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils;
 import org.testng.Assert;
-import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -36,7 +36,7 @@ public final class GATKVariantContextUtilsUnitTest extends BaseTest {
     Allele Anoref;
     Allele GT;
 
-    @BeforeSuite
+    @BeforeClass
     public void setup() throws IOException {
         // alleles
         Aref = Allele.create("A", true);