Display a warning message for Beta and Exerimental tools.

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

@@ -24,10 +24,9 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.InetAddress;
-import java.net.MalformedURLException;
 import java.net.URL;
-import java.net.URLClassLoader;
 import java.text.DecimalFormat;
+import java.lang.Thread;
 import java.time.Duration;
 import java.time.ZonedDateTime;
 import java.util.ArrayList;
@@ -175,6 +174,8 @@ public Object instanceMainPostParseArgs() {
             printStartupMessage(startDateTime);
         }
 
+        printProductionWarning();
+
         try {
             return runTool();
         } finally {
@@ -278,6 +279,61 @@ protected void printStartupMessage(final ZonedDateTime startDateTime) {
         catch (final Exception e) { /* Unpossible! */ }
     }
 
+    /**
+     * If this tool is either Experimental or Beta, return a warning message advising against use in production
+     * environment.
+     * @param useTerminalColor true if the message should include highlighting terminal colorization
+     * @return a warning message if the tool is Beta or Experimental, otherwise null
+     */
+    protected String getProductionWarning(final boolean useTerminalColor) {
+        final String KNRM = "\u001B[0m"; // reset
+        final String BOLDRED = "\u001B[1m\u001B[31m";
+        final int BORDER_LENGTH = 60;
+
+        String warningMessage = null;
+        if (isBetaFeature()) {
+            warningMessage = String.format(
+                    "\n\n%s   %s\n\n   Warning: %s is a BETA tool and is not yet ready for use in production\n\n   %s%s\n\n",
+                    useTerminalColor ? BOLDRED : "",
+                    Utils.dupChar('!', BORDER_LENGTH),
+                    this.getClass().getSimpleName(),
+                    Utils.dupChar('!', BORDER_LENGTH),
+                    useTerminalColor ? KNRM : ""
+            );
+        }
+        else if (isExperimentalFeature()) {
+            warningMessage = String.format(
+                    "\n\n%s   %s\n\n   Warning: %s is an EXPERIMENTAL tool and should not be used for production\n\n   %s%s\n\n",
+                    useTerminalColor ? BOLDRED : "",
+                    Utils.dupChar('!', BORDER_LENGTH),
+                    this.getClass().getSimpleName(),
+                    Utils.dupChar('!', BORDER_LENGTH),
+                    useTerminalColor ? KNRM : ""
+            );
+        }
+        return warningMessage;
+    }
+
+    /**
+     * If a tool is either Experimental or Beta, log a warning against use in production a environment.
+     */
+    protected void printProductionWarning() {
+        final String warningMessage = getProductionWarning(!(System.console() == null));
+        if (warningMessage != null) {
+            logger.warn(warningMessage);
+        }
+    }
+
+    /**
+     * @return true if this tool has {@code BetaFeature} status.
+     */
+    public boolean isBetaFeature() { return this.getClass().getAnnotation(BetaFeature.class) != null; }
+
+    /**
+     * @return true if this tool has {@code ExperimentalFeature} status.
+     */
+    public boolean isExperimentalFeature() { return this.getClass().getAnnotation(ExperimentalFeature.class) != null; }
+
     /**
      * @return The name of this toolkit. The default implementation uses "Implementation-Title" from the
      *         jar manifest, or (if that's not available) the package name.

src/test/java/org/broadinstitute/hellbender/cmdline/CommandLineProgramUnitTest.java

@@ -145,4 +145,69 @@ private File createTempExpansionTestFile(final String extension, final String fi
         }
         return tempFile;
     }
+
+    @CommandLineProgramProperties(
+            summary = "ExperimentalTool",
+            oneLineSummary = "ExperimentalTool",
+            programGroup = TestProgramGroup.class
+    )
+    @ExperimentalFeature
+    private static class TestExperimentalTool extends CommandLineProgram {
+
+        @Override
+        protected Object doWork() {
+            return null;
+        }
+    }
+
+    @CommandLineProgramProperties(
+            summary = "BetaTool",
+            oneLineSummary = "BetaTool",
+            programGroup = TestProgramGroup.class
+    )
+    @BetaFeature
+    private static class TestBetaTool extends CommandLineProgram {
+        @Override
+        protected Object doWork() {
+            return null;
+        }
+    }
+
+    @CommandLineProgramProperties(
+            summary = "ProductionTool",
+            oneLineSummary = "ProductionTool",
+            programGroup = TestProgramGroup.class
+    )
+    private static class TestProductionTool extends CommandLineProgram {
+        @Override
+        protected Object doWork() {
+            return null;
+        }
+    }
+
+    @DataProvider(name = "toolMaturityLevels")
+    public Object[][] getToolMaturityLevels() {
+        return new Object[][]{
+                {new TestExperimentalTool(), true, false, "EXPERIMENTAL"},
+                {new TestBetaTool(), false, true, "BETA"},
+                {new TestProductionTool(), false, false, null}
+        };
+    }
+
+    @Test(dataProvider = "toolMaturityLevels")
+    public void testToolMaturityLevel(
+            final CommandLineProgram clp,
+            final boolean isExperimental,
+            final boolean isBeta,
+            final String warningSentinel)
+    {
+        Assert.assertEquals(clp.isBetaFeature(), isBeta);
+        Assert.assertEquals(clp.isExperimentalFeature(), isExperimental);
+        if (warningSentinel == null) {
+            Assert.assertEquals(clp.getProductionWarning(true), null);
+        } else {
+            Assert.assertTrue(clp.getProductionWarning(true).contains(warningSentinel));
+        }
+    }
+
 }