making gatk --version print the version

build.gradle

@@ -376,6 +376,7 @@ tasks.withType(Jar) {
     manifest {
         attributes 'Implementation-Title': 'The Genome Analysis Toolkit (GATK)',
                 'Implementation-Version': version,
+                'Toolkit-Short-Name' : 'GATK',
                 'Main-Class': project.mainClassName,
                 'Picard-Version': picardVersion,
                 'htsjdk-Version': htsjdkVersion

src/main/java/org/broadinstitute/hellbender/Main.java

@@ -17,6 +17,8 @@
 import java.io.PrintStream;
 import java.io.Serializable;
 import java.util.*;
+import java.util.jar.Attributes;
+import java.util.jar.Manifest;
 
 /**
  * This is the main class of Hellbender and is the way of executing individual command line programs.
@@ -338,6 +340,8 @@ private CommandLineProgram extractCommandLineProgram( final String[] args,
 
         if (args.length < 1 || args[0].equals("-h") || args[0].equals("--help")) {
             printUsage(System.out, classes, commandLineName);
+        } else if ( args.length == 1 && (args[0].equals("-" + SpecialArgumentsCollection.VERSION_FULLNAME) || args[0].equals("--" + SpecialArgumentsCollection.VERSION_FULLNAME))) {
+            printVersionInfo(System.out);
         } else {
             if (simpleNameToClass.containsKey(args[0])) {
                 final Class<?> clazz = simpleNameToClass.get(args[0]);
@@ -545,4 +549,23 @@ public String getSuggestedAlternateCommand(final Set<Class<?>> classes, final St
         }
         return message.toString();
     }
+
+    /**
+     * Prints version information for the toolkit, including versions of important libraries.
+     * Subclasses may override to change this behavior.
+     */
+    protected void printVersionInfo(PrintStream out){
+        final String toolkitName = RuntimeUtils.getToolkitName(this.getClass());
+        final String version = RuntimeUtils.getVersion(this.getClass());
+        System.out.println(String.format("%s v%s", toolkitName, version));
+        final Manifest manifest = RuntimeUtils.getManifest(this.getClass());
+        if( manifest != null){
+            final Attributes manifestAttributes = manifest.getMainAttributes();
+            final String htsjdkVersion = manifestAttributes.getValue("htsjdk-Version");
+            final String picardVersion = manifestAttributes.getValue("Picard-Version");
+            out.println("HTSJDK Version: " + (htsjdkVersion != null ? htsjdkVersion : "unknown"));
+            out.println("Picard Version: " + (picardVersion != null ? picardVersion : "unknown"));
+        }
+
+    }
 }

src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgram.java

@@ -22,11 +22,10 @@
 import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
 import org.broadinstitute.hellbender.utils.help.HelpConstants;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
+import org.broadinstitute.hellbender.utils.runtime.RuntimeUtils;
 
 import java.io.IOException;
-import java.io.InputStream;
 import java.net.InetAddress;
-import java.net.URL;
 import java.nio.file.*;
 import java.text.DecimalFormat;
 import java.time.Duration;
@@ -293,7 +292,7 @@ protected void printStartupMessage(final ZonedDateTime startDateTime) {
 
     /**
      * If this tool is either Experimental or Beta, return a warning message advising against use in production
-     * environment.
+     * envirogetnment.
      * @param useTerminalColor true if the message should include highlighting terminal colorization
      * @return a warning message if the tool is Beta or Experimental, otherwise null
      */
@@ -353,17 +352,21 @@ protected void warnOnToolStatus() {
      * May be overridden by subclasses to provide a custom implementation if desired.
      */
     protected String getToolkitName() {
-        final String implementationTitle = getClass().getPackage().getImplementationTitle();
-        return implementationTitle != null ? implementationTitle : getClass().getPackage().getName();
+        return RuntimeUtils.getToolkitName(this.getClass());
     }
 
     /**
-     * @return An abbreviated name of the toolkit for this tool. Subclasses may override to provide
-     *         a custom toolkit name.
+     * @return An abbreviated name of the toolkit for this tool. Looks for "Tool-Short-Name" in the manifest by default.
+     *         Uses {@link #DEFAULT_TOOLKIT_SHORT_NAME} if the manifest is unavailable.
+     * Subclasses may override to do something different.
      */
     protected String getToolkitShortName() {
-        // TODO: stored in the jar manifest, like {@link CommandLineProgram#getToolkitName}
-        return DEFAULT_TOOLKIT_SHORT_NAME;
+        final Manifest manifest = RuntimeUtils.getManifest(this.getClass());
+        if( manifest != null){
+            return manifest.getMainAttributes().getValue("Toolkit-Short-Name");
+        } else {
+            return DEFAULT_TOOLKIT_SHORT_NAME;
+        }
     }
 
     /**
@@ -373,10 +376,7 @@ protected String getToolkitShortName() {
      * May be overridden by subclasses to provide a custom implementation if desired.
      */
     public String getVersion() {
-        String versionString = this.getClass().getPackage().getImplementationVersion();
-        return versionString != null ?
-                versionString :
-                "Unavailable";
+       return RuntimeUtils.getVersion(this.getClass());
     }
 
     /**
@@ -394,21 +394,13 @@ protected String getSupportInformation() {
      * May be overridden by subclasses to provide a custom implementation if desired.
      */
     protected void printLibraryVersions() {
-        try {
-            final String classPath = getClass().getResource(getClass().getSimpleName() + ".class").toString();
-            if (classPath.startsWith("jar")) {
-                final String manifestPath = classPath.substring(0, classPath.lastIndexOf("!") + 1) + "/META-INF/MANIFEST.MF";
-                try ( final InputStream manifestStream = new URL(manifestPath).openStream() ) {
-                    final Attributes manifestAttributes = new Manifest(manifestStream).getMainAttributes();
-                    final String htsjdkVersion = manifestAttributes.getValue("htsjdk-Version");
-                    final String picardVersion = manifestAttributes.getValue("Picard-Version");
-
-                    logger.info("HTSJDK Version: " + (htsjdkVersion != null ? htsjdkVersion : "unknown"));
-                    logger.info("Picard Version: " + (picardVersion != null ? picardVersion : "unknown"));
-                }
-            }
-        }
-        catch (IOException ignored) {
+        final Manifest manifest = RuntimeUtils.getManifest(this.getClass());
+        if( manifest != null ){
+                final Attributes manifestAttributes = manifest.getMainAttributes();
+                final String htsjdkVersion = manifestAttributes.getValue("htsjdk-Version");
+                final String picardVersion = manifestAttributes.getValue("Picard-Version");
+                logger.info("HTSJDK Version: " + (htsjdkVersion != null ? htsjdkVersion : "unknown"));
+                logger.info("Picard Version: " + (picardVersion != null ? picardVersion : "unknown"));
         }
     }
 
@@ -426,9 +418,8 @@ protected void printSettings() {
         }
         else {
             // At DEBUG verbosity, print all the HTSJDK defaults:
-            Defaults.allDefaults().entrySet().stream().forEach(e->
-                    logger.info("HTSJDK " + Defaults.class.getSimpleName() + "." + e.getKey() + " : " + e.getValue())
-            );
+            Defaults.allDefaults()
+                    .forEach((key, value) -> logger.info("HTSJDK " + Defaults.class.getSimpleName() + "." + key + " : " + value));
         }
 
         // Log the configuration options:

src/main/java/org/broadinstitute/hellbender/utils/runtime/RuntimeUtils.java

@@ -1,10 +1,13 @@
 package org.broadinstitute.hellbender.utils.runtime;
 
 import org.apache.commons.lang3.StringUtils;
+import org.broadinstitute.hellbender.utils.Utils;
 
 import java.io.File;
-
-import org.broadinstitute.hellbender.utils.Utils;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.jar.Manifest;
 
 public final class RuntimeUtils {
     public static final String[] PATHS;
@@ -50,4 +53,44 @@ public static String toolDisplayName(final Class<?> toolClass) {
                 toolClass.getSimpleName();
     }
 
+    /**
+     * @param clazz class to use when looking up the Implementation-Title
+     * @return The name of this toolkit, uses "Implementation-Title" from the
+     *         jar manifest of the given class, or (if that's not available) the package name.
+     */
+    public static String getToolkitName(Class<?> clazz) {
+        final String implementationTitle = clazz.getPackage().getImplementationTitle();
+        return implementationTitle != null ? implementationTitle : clazz.getPackage().getName();
+    }
+
+    /**
+     * @return load the manifest file associated with the given class or null if loading fails
+     */
+    public static Manifest getManifest(Class<?> clazz) {
+        final URL resourceURL = clazz.getResource(clazz.getSimpleName() + ".class");
+        if( resourceURL == null) {
+            return null;
+        }
+        final String classPath = resourceURL.toString();
+        if (classPath.startsWith("jar")) {
+            final String manifestPath = classPath.substring(0, classPath.lastIndexOf("!") + 1) + "/META-INF/MANIFEST.MF";
+            try ( final InputStream manifestStream = new URL(manifestPath).openStream() ) {
+                return new Manifest(manifestStream);
+            } catch (IOException e) {
+                return null;
+            }
+        } else {
+            return null;
+        }
+    }
+
+    /**
+     * @return get the implementation version of the given class
+     */
+    public static String getVersion(Class<?> clazz){
+        String versionString = clazz.getPackage().getImplementationVersion();
+        return versionString != null ? versionString : "Unavailable";
+    }
+
+
 }

src/test/java/org/broadinstitute/hellbender/MainTest.java

@@ -109,4 +109,10 @@ public void testNonZeroPicardReturnValue() {
         }
     }
 
+    @Test
+    public void testVersion(){
+        //assert that --version doesn't crash.
+        Assert.assertNull(new Main().instanceMain(new String[]{"--version"}));
+    }
+
 }

src/test/java/org/broadinstitute/hellbender/utils/runtime/RuntimeUtilsUnitTest.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.utils.runtime;
 
 import org.broadinstitute.hellbender.GATKBaseTest;
+import org.broadinstitute.hellbender.Main;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
@@ -14,4 +15,11 @@ public void testWhichExists() {
     public void testWhichNotExists() {
         Assert.assertNull(RuntimeUtils.which("does_not_exist"), "Found nonexistent binary: does_not_exist");
     }
+
+    @Test
+    public void testGetToolkitName(){
+        final String toolkitName = RuntimeUtils.getToolkitName(Main.class);
+        // test that it's one of the valid outcomes of getToolkitName, tests in intellij don't necessarily build the correct manifest but the docker tests might\
+        Assert.assertTrue(toolkitName.equals("The Genome Analysis Toolkit (GATK)") || toolkitName.equals("org.broadinstitute.hellbender"));
+    }
 }

src/test/java/org/broadinstitute/hellbender/utils/runtime/StreamingProcessControllerUnitTest.java

@@ -103,25 +103,6 @@ public void testStartupCommandExecution() throws IOException {
         Assert.assertEquals(getLineFromTempFile(tempFile), "some output");
     }
 
-    @Test(groups = "python", timeOut = 10000)
-    public void testStderrRedirect() {
-        final StreamingProcessController controller = initializePythonControllerWithAckFIFO(true);
-
-        // write to stderr, but we expect to get it from stdout due to redirection
-        controller.writeProcessInput("import sys" + NL + "sys.stderr.write('error output to stderr\\n')" + NL);
-        boolean ack = requestAndWaitForAck(controller);
-        Assert.assertTrue(ack);
-
-        ProcessOutput po = controller.getProcessOutput();
-
-        Assert.assertNotNull(po.getStdout());
-        Assert.assertNotNull(po.getStdout().getBufferString());
-        Assert.assertNotNull(po.getStdout().getBufferString().contains("error output to stderr"));
-
-        controller.terminate();
-        Assert.assertFalse(controller.getProcess().isAlive());
-    }
-
     @Test(timeOut = 10000)
     public void testFIFOLifetime() {
         // cat is a red herring here; we're just testing that a FIFO is created, and then deleted after termination