Enabling writing and running of tests with scalatest. (#789)

.travis.yml

@@ -10,7 +10,7 @@ cache:
     - $HOME/.m2
 jdk:
   - oraclejdk8
-script: ./gradlew testSRA jacocoTestReport;
+script: ./gradlew test jacocoTestReport;
 after_success:
   - bash <(curl -s https://codecov.io/bash)
   - echo "TRAVIS_BRANCH='$TRAVIS_BRANCH'";

build.gradle

@@ -5,20 +5,21 @@ buildscript {
 }
 
 plugins {
-    id "java"
+    id 'java'
+    id 'scala'
     id 'maven'
     id 'signing'
     id 'jacoco'
     id 'com.palantir.git-version' version '0.5.1'
     id 'com.github.johnrengelman.shadow' version '1.2.3'
+    id 'com.github.maiflai.scalatest' version '0.15'
 }
 
 repositories {
     mavenCentral()
 }
 
 jacocoTestReport {
-    dependsOn test
     group = "Reporting"
     description = "Generate Jacoco coverage reports after running tests."
     additionalSourceDirs = files(sourceSets.main.allJava.srcDirs)
@@ -29,10 +30,6 @@ jacocoTestReport {
     }
 }
 
-jacoco {
-    toolVersion = "0.7.5.201505241946"
-}
-
 dependencies {
     compile "org.apache.commons:commons-jexl:2.1.1"
     compile "commons-logging:commons-logging:1.1.1"
@@ -41,6 +38,9 @@ dependencies {
     compile "org.tukaani:xz:1.5"
     compile "gov.nih.nlm.ncbi:ngs-java:1.2.4"
 
+    testCompile "org.scala-lang:scala-library:2.12.1"
+    testCompile "org.scalatest:scalatest_2.12:3.0.1"
+    testRuntime 'org.pegdown:pegdown:1.4.2' // Necessary for generating HTML reports with ScalaTest
     testCompile "org.testng:testng:6.9.9"
     testCompile "com.google.jimfs:jimfs:1.1"
 }
@@ -67,70 +67,46 @@ jar {
 
 import org.gradle.internal.os.OperatingSystem;
 
-tasks.withType(Test) {
-    outputs.upToDateWhen { false } // tests will always rerun
-    useTestNG()
-
-    // set heap size for the test JVM(s)
-    minHeapSize = "1G"
-    maxHeapSize = "2G"
+tasks.withType(Test) { task ->
+    task.outputs.upToDateWhen { false } // tests will always rerun
 
-    jvmArgs '-Djava.awt.headless=true'  //this prevents awt from displaying a java icon while the tests are running
+    // Always run serially because there are some very badly behaved tests in HTSJDK that
+    // will cause errors and even deadlocks if run multi-threaded
+    task.maxParallelForks = 1
 
-    if (System.env.CI == "true") {  //if running under a CI output less into the logs
-        int count = 0
+    // set heap size for the test JVM(s)
+    task.minHeapSize = "1G"
+    task.maxHeapSize = "2G"
 
-        beforeTest { descriptor ->
-            count++
-            if( count % 100 == 0) {
-                logger.lifecycle("Finished "+ Integer.toString(count++) + " tests")
-            }
-        }
-    } else {
-        // show standard out and standard error of the test JVM(s) on the console
-        testLogging.showStandardStreams = true
-        beforeTest { descriptor ->
-            logger.lifecycle("Running Test: " + descriptor)
-        }
+    task.jvmArgs '-Djava.awt.headless=true'  //this prevents awt from displaying a java icon while the tests are running
+}
 
-        // listen to standard out and standard error of the test JVM(s)
-        onOutput { descriptor, event ->
-            logger.lifecycle("Test: " + descriptor + " produced standard out/err: " + event.message )
-        }
-    }
+test {
+    description = "Runs the unit tests other than the SRA tests"
 
     testLogging {
-        testLogging {
-            events "skipped", "failed"
-            exceptionFormat = "full"
-        }
-        afterSuite { desc, result ->
-            if (!desc.parent) { // will match the outermost suite
-                println "Results: ${result.resultType} (${result.testCount} tests, ${result.successfulTestCount} successes, ${result.failedTestCount} failures, ${result.skippedTestCount} skipped)"
-            }
-        }
+        events "failed", "skipped"
     }
-}
 
-test {
-    description = "Runs the unit tests other than the SRA tests"
+    if (System.env.CI == "true") {
+        jvmArgs += '-Dsamjdk.sra_libraries_download=true'
+    }
 
-    useTestNG {
-        if( OperatingSystem.current().isUnix() ){
-            excludeGroups "slow", "broken", "sra"
-        } else {
-            excludeGroups "slow", "broken", "unix", "sra"
-        }
+    tags {
+        exclude "slow"
+        exclude "broken"
+        if (System.env.CI == "false") exclude "sra"
+        if (!OperatingSystem.current().isUnix()) exclude "unix"
     }
 }
 
 task testSRA(type: Test) {
-    jvmArgs '-Dsamjdk.sra_libraries_download=true'
+    description = "Run the SRA tests"
+    jvmArgs += '-Dsamjdk.sra_libraries_download=true'
 
-    description "Run the SRA tests"
-    useTestNG {
-        configFailurePolicy 'continue'
-        includeGroups "sra"
+    tags {
+        exclude "slow"
+        exclude "broken"
     }
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Tue Nov 29 15:10:15 EST 2016
+#Fri Jan 20 17:10:11 EST 2017
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-3.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-3.2.1-all.zip

src/test/java/htsjdk/HtsjdkTest.java

@@ -0,0 +1,10 @@
+package htsjdk;
+
+import org.scalatest.testng.TestNGSuite;
+
+/**
+ * Base class for all Java tests in HTSJDK.
+ */
+public class HtsjdkTest extends TestNGSuite {
+
+}

src/test/java/htsjdk/cram/io/ExternalCompressionTest.java

@@ -1,16 +1,15 @@
-package htsjdk.samtools.cram.io;
+package htsjdk.cram.io;
 
-import org.apache.commons.compress.utils.IOUtils;
+import htsjdk.HtsjdkTest;
+import htsjdk.samtools.cram.io.ExternalCompression;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.nio.file.Files;
 
-public class ExternalCompressionTest {
+public class ExternalCompressionTest extends HtsjdkTest {
     public static final File BZIP2_FILE = new File("src/test/resources/htsjdk/samtools/cram/io/bzip2-test.bz2");
     public static final byte [] TEST_BYTES = "This is a simple string to test BZip2".getBytes();
 

src/test/java/htsjdk/samtools/AbstractBAMFileIndexTest.java

@@ -1,11 +1,12 @@
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import org.testng.annotations.Test;
 
 import java.io.IOException;
 
-public class AbstractBAMFileIndexTest {
+public class AbstractBAMFileIndexTest extends HtsjdkTest {
 
     /**
      * @see <a href="https://github.com/samtools/htsjdk/issues/73">https://github.com/samtools/htsjdk/issues/73</a>
@@ -59,4 +60,4 @@ public int read() throws IOException {
         buffer.readInteger();
         buffer.readBytes(new byte[10000]);
     }
-}
+}

src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java

@@ -1,5 +1,6 @@
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import htsjdk.samtools.util.CloserUtil;
 import org.testng.annotations.Test;
 import static org.testng.Assert.assertEquals;
@@ -10,7 +11,7 @@
  * Test the fix of a bug reported by s-andrews in which the use of an arithmetic rather than a logical right shift in BinaryCigarCodec.binaryCigarToCigarElement()
  * causes an overflow in the CIGAR when reading a BAM file for a read that spans a very large intron.
  */
-public class BAMCigarOverflowTest {
+public class BAMCigarOverflowTest extends HtsjdkTest {
     private static final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools");
 
     @Test

src/test/java/htsjdk/samtools/BAMFileIndexTest.java

@@ -23,6 +23,7 @@
  */
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.CloserUtil;
 import htsjdk.samtools.util.StopWatch;
@@ -46,7 +47,7 @@
 /**
  * Test BAM file indexing.
  */
-public class BAMFileIndexTest {
+public class BAMFileIndexTest extends HtsjdkTest {
     private final File BAM_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam");
     private final boolean mVerbose = false;
 
@@ -78,8 +79,7 @@ public void testSpecificQueries()
     }
 
     @Test(groups = {"slow"})
-    public void testRandomQueries()
-            throws Exception {
+    public void testRandomQueries() throws Exception {
         runRandomTest(BAM_FILE, 1000, new Random());
     }
 

src/test/java/htsjdk/samtools/BAMFileWriterTest.java

@@ -23,6 +23,7 @@
  */
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.CloserUtil;
 import org.testng.Assert;
@@ -35,7 +36,7 @@
  * Test that BAM writing doesn't blow up.  For presorted writing, the resulting BAM file is read and contents are
  * compared with the original SAM file.
  */
-public class BAMFileWriterTest {
+public class BAMFileWriterTest extends HtsjdkTest {
 
     private SAMRecordSetBuilder getRecordSetBuilder(final boolean sortForMe, final SAMFileHeader.SortOrder sortOrder) {
         final SAMRecordSetBuilder ret = new SAMRecordSetBuilder(sortForMe, sortOrder);

src/test/java/htsjdk/samtools/BAMIndexWriterTest.java

@@ -23,6 +23,7 @@
  */
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import htsjdk.samtools.util.CloserUtil;
 import htsjdk.samtools.util.IOUtil;
 import org.testng.annotations.DataProvider;
@@ -38,7 +39,7 @@
 /**
  * Test BAM file index creation
  */
-public class BAMIndexWriterTest {
+public class BAMIndexWriterTest extends HtsjdkTest {
     // Two input files for basic test
     private final String BAM_FILE_LOCATION = "src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam";
     private final String BAI_FILE_LOCATION = "src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai";

src/test/java/htsjdk/samtools/BAMIteratorTest.java

@@ -23,6 +23,7 @@
  */
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.CloserUtil;
 import org.testng.Assert;
@@ -34,7 +35,7 @@
 /**
  * @author alecw@broadinstitute.org
  */
-public class BAMIteratorTest {
+public class BAMIteratorTest extends HtsjdkTest {
     private static final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools");
 
     @Test(dataProvider = "dataProvider")

src/test/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilterTest.java

@@ -1,13 +1,14 @@
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
 import java.util.Random;
 
-public class BAMQueryMultipleIntervalsIteratorFilterTest {
+public class BAMQueryMultipleIntervalsIteratorFilterTest extends HtsjdkTest {
 
     private final byte[] BASES = {'A', 'C', 'G', 'T'};
     private final Random random = new Random();

src/test/java/htsjdk/samtools/BAMRemoteFileTest.java

@@ -23,6 +23,7 @@
  */
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import htsjdk.samtools.util.CloserUtil;
 import htsjdk.samtools.util.TestUtil;
 import org.testng.annotations.Test;
@@ -40,7 +41,7 @@
 /**
  * Test BAM file indexing.
  */
-public class BAMRemoteFileTest {
+public class BAMRemoteFileTest extends HtsjdkTest {
     private final File BAM_INDEX_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai");
     private final File BAM_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam");
     private final String BAM_URL_STRING = TestUtil.BASE_URL_FOR_HTTP_TESTS + "index_test.bam";

src/test/java/htsjdk/samtools/BinTest.java

@@ -24,12 +24,13 @@
 
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
 import java.util.Collections;
 
-public class BinTest {
+public class BinTest extends HtsjdkTest {
     @Test
     public void testEmptyBin() {
         // Construct a new empty bin and ensure that the bin list is empty, not null.

src/test/java/htsjdk/samtools/CRAMBAIIndexerTest.java

@@ -1,5 +1,6 @@
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import htsjdk.samtools.cram.build.ContainerFactory;
 import htsjdk.samtools.cram.structure.Container;
 import htsjdk.samtools.cram.structure.CramCompressionRecord;
@@ -17,7 +18,7 @@
 /**
  * Created by vadim on 12/01/2016.
  */
-public class CRAMBAIIndexerTest {
+public class CRAMBAIIndexerTest extends HtsjdkTest {
 
     private static CramCompressionRecord createRecord(int recordIndex, int seqId, int start) {
         byte[] bases = "AAAAA".getBytes();

src/test/java/htsjdk/samtools/CRAMCRAIIndexerTest.java

@@ -1,5 +1,6 @@
 package htsjdk.samtools;
 
+import htsjdk.HtsjdkTest;
 import htsjdk.samtools.cram.CRAIEntry;
 import htsjdk.samtools.cram.build.CramContainerIterator;
 import htsjdk.samtools.cram.ref.ReferenceSource;
@@ -17,7 +18,7 @@
  * Companion to CRAMBAIIndexerTest, for testing CRAI indices created on cram
  * streams;
  */
-public class CRAMCRAIIndexerTest {
+public class CRAMCRAIIndexerTest extends HtsjdkTest {
 
     @Test
     public void testCRAIIndexerFromContainer() throws IOException {
@@ -180,4 +181,4 @@ private long getIteratorCount(Iterator<SAMRecord> it) {
         return count;
     }
 
-}
+}