UnitTests for RScript

public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java

@@ -32,6 +32,7 @@ import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
 import org.broadinstitute.sting.utils.PathUtils;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.IOException;
@@ -53,11 +54,11 @@ public class RScriptExecutor {
     public static class RScriptArgumentCollection {
         @Advanced
         @Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
-        private String PATH_TO_RSCRIPT = "Rscript";
+        public String PATH_TO_RSCRIPT = "Rscript";
 
         @Advanced
         @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
-        private List<String> PATH_TO_RESOURCES = Arrays.asList("public/R/", "private/R/");
+        public List<String> PATH_TO_RESOURCES = Arrays.asList("public/R/", "private/R/");
     }
 
     final RScriptArgumentCollection myArgs;
@@ -98,7 +99,7 @@ public class RScriptExecutor {
             }
         }
 
-        generateException("Couldn't find script: " + scriptName + " in " + myArgs.PATH_TO_RSCRIPT);
+        generateException("Couldn't find script: " + scriptName + " in " + myArgs.PATH_TO_RESOURCES);
         return null;
     }
 
@@ -112,7 +113,7 @@ public class RScriptExecutor {
 
     private void generateException(String msg, Throwable e) {
         if ( exceptOnError )
-            throw new RuntimeException(msg, e);
+            throw new UserException(msg, e);
         else
             logger.warn(msg + (e == null ? "" : ":" + e.getMessage()));
     }

public/java/test/org/broadinstitute/sting/utils/R/RScriptExecutorUnitTest.java

@@ -0,0 +1,106 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.R;
+
+import org.apache.commons.io.FileUtils;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.walkers.diffengine.DiffElement;
+import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine;
+import org.broadinstitute.sting.gatk.walkers.diffengine.DiffNode;
+import org.broadinstitute.sting.gatk.walkers.diffengine.Difference;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * Basic unit test for RScriptExecutor in reduced reads
+ */
+public class RScriptExecutorUnitTest extends BaseTest {
+    final static String testrscript = "print(\"hello, world\")\n";
+    final static String publicRScript = "plot_Tranches.R";
+    final static String privateRScript = "variantCallQC.R";
+
+    // --------------------------------------------------------------------------------
+    //
+    // Difference testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private void testOne(String script, String pathToRscript, String anotherSearchPath, boolean exceptOnError) {
+        RScriptExecutor.RScriptArgumentCollection collection =
+                new RScriptExecutor.RScriptArgumentCollection();
+        if ( pathToRscript != null )
+            collection.PATH_TO_RSCRIPT = pathToRscript;
+        if ( anotherSearchPath != null ) {
+            List<String> x = new ArrayList<String>(collection.PATH_TO_RESOURCES);
+            x.add(anotherSearchPath);
+            collection.PATH_TO_RESOURCES = x;
+        }
+        RScriptExecutor executor = new RScriptExecutor(collection, exceptOnError);
+        executor.callRScripts(script);
+    }
+
+    @Test
+    public void testPublic() { testOne(publicRScript, null, null, true); }
+
+    @Test
+    public void testPrivate() { testOne(privateRScript, null, null, true); }
+
+    // make sure we don't break finding something in private by adding another directory
+    @Test
+    public void testPrivateWithAdditionalPath1() { testOne(privateRScript, null, "dist", true); }
+
+    // make sure we don't break finding something in private by adding another directory
+    @Test
+    public void testPrivateWithAdditionalPath2() { testOne(privateRScript, null, "doesNotExist", true); }
+
+    @Test(expectedExceptions = UserException.class)
+    public void testNonExistantScriptException() { testOne("does_not_exist.R", null, null, true); }
+
+    @Test()
+    public void testNonExistantScriptNoException() { testOne("does_not_exist.R", null, null, false); }
+
+    @Test(expectedExceptions = UserException.class)
+    public void testNonExistantRScriptException() { testOne(publicRScript, "badRScriptValue", null, true); }
+
+    @Test()
+    public void testNonExistantRScriptNoException() { testOne(publicRScript, "badRScriptValue", null, false); }
+
+    @Test()
+    public void testScriptInNewPath() throws IOException {
+        File t = createTempFile("myTestScript", ".R");
+        FileUtils.writeStringToFile(t, testrscript);
+        testOne(t.getName(), null, t.getParent(), true);
+    }
+}