Enabled the parameterize option for debugging PipelineTest MD5s.

Fixed escaping expressions that have more than one space between arguments.
Updated example to match the wiki.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5516 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/Utils.java

@@ -319,7 +319,7 @@ public class Utils {
         else if (args.indexOf('\"') != -1)
             return escapeExpressions(args, "\"");
         else
-            return args.split(" ");
+            return args.trim().split(" +");
     }
 
     /**
@@ -335,13 +335,13 @@ public class Utils {
         for (int i = 0; i < split.length - 1; i += 2) {
             arg = split[i].trim();
             if (arg.length() > 0) // if the unescaped arg has a size
-                command = Utils.concatArrays(command, arg.split(" "));
+                command = Utils.concatArrays(command, arg.split(" +"));
             command = Utils.concatArrays(command, new String[]{split[i + 1]});
         }
         arg = split[split.length - 1].trim();
         if (split.length % 2 == 1) // if the command ends with a delimiter
             if (arg.length() > 0) // if the last unescaped arg has a size
-                command = Utils.concatArrays(command, arg.split(" "));
+                command = Utils.concatArrays(command, arg.split(" +"));
         return command;
     }
 

java/test/org/broadinstitute/sting/utils/UtilsUnitTest.java

@@ -86,6 +86,18 @@ public class UtilsUnitTest extends BaseTest {
     public void testEscapeExpressions() {
         String[] expected, actual;
 
+        expected = new String[] {"one", "two", "three"};
+        actual = Utils.escapeExpressions("one two three");
+        Assert.assertEquals(actual, expected);
+        actual = Utils.escapeExpressions(" one two three");
+        Assert.assertEquals(actual, expected);
+        actual = Utils.escapeExpressions("one two three ");
+        Assert.assertEquals(actual, expected);
+        actual = Utils.escapeExpressions(" one two three ");
+        Assert.assertEquals(actual, expected);
+        actual = Utils.escapeExpressions("  one  two  three  ");
+        Assert.assertEquals(actual, expected);
+
         expected = new String[] {"one", "two", "three four", "five", "six"};
         actual = Utils.escapeExpressions("one two 'three four' five six");
         Assert.assertEquals(actual, expected);
@@ -95,6 +107,8 @@ public class UtilsUnitTest extends BaseTest {
         Assert.assertEquals(actual, expected);
         actual = Utils.escapeExpressions(" one two 'three four' five six ");
         Assert.assertEquals(actual, expected);
+        actual = Utils.escapeExpressions("  one  two  'three four'  five  six  ");
+        Assert.assertEquals(actual, expected);
 
         expected = new String[] {"one two", "three", "four"};
         actual = Utils.escapeExpressions("'one two' three four");
@@ -105,6 +119,8 @@ public class UtilsUnitTest extends BaseTest {
         Assert.assertEquals(actual, expected);
         actual = Utils.escapeExpressions(" 'one two' three four ");
         Assert.assertEquals(actual, expected);
+        actual = Utils.escapeExpressions("  'one two'  three  four  ");
+        Assert.assertEquals(actual, expected);
 
         expected = new String[] {"one", "two", "three four"};
         actual = Utils.escapeExpressions("one two 'three four'");
@@ -115,5 +131,7 @@ public class UtilsUnitTest extends BaseTest {
         Assert.assertEquals(actual, expected);
         actual = Utils.escapeExpressions(" one two 'three four' ");
         Assert.assertEquals(actual, expected);
+        actual = Utils.escapeExpressions("  one  two  'three four'  ");
+        Assert.assertEquals(actual, expected);
     }
 }

scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala

@@ -150,7 +150,7 @@ object PipelineTest extends BaseTest with Logging {
     println(Utils.dupString('-', 80));
     executeTest(name, pipelineTest.args, pipelineTest.jobQueue, pipelineTest.expectedException)
     if (run) {
-      assertMatchingMD5s(name, pipelineTest.fileMD5s.map{case (file, md5) => new File(runDir(name), file) -> md5})
+      assertMatchingMD5s(name, pipelineTest.fileMD5s.map{case (file, md5) => new File(runDir(name), file) -> md5}, pipelineTest.parameterize)
       if (pipelineTest.evalSpec != null)
         validateEval(name, pipelineTest.evalSpec)
       println("  => %s PASSED".format(name))
@@ -159,11 +159,11 @@ object PipelineTest extends BaseTest with Logging {
       println("  => %s PASSED DRY RUN".format(name))
   }
 
-  private def assertMatchingMD5s(name: String, fileMD5s: Traversable[(File, String)]) {
+  private def assertMatchingMD5s(name: String, fileMD5s: Traversable[(File, String)], parameterize: Boolean) {
     var failed = 0
     for ((file, expectedMD5) <- fileMD5s) {
-      val calculatedMD5 = BaseTest.testFileMD5(name, file, expectedMD5, false)
+      val calculatedMD5 = BaseTest.testFileMD5(name, file, expectedMD5, parameterize)
-      if (expectedMD5 != "" && expectedMD5 != calculatedMD5)
+      if (!parameterize && expectedMD5 != "" && expectedMD5 != calculatedMD5)
         failed += 1
     }
     if (failed > 0)

scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala

@@ -19,6 +19,9 @@ class PipelineTestSpec(var name: String = null) {
   /** Expected exception from the test. */
   var expectedException: Class[_ <: Exception] = null
 
+  /** If true will check the MD5s without failing. */
+  var parameterize = false
+
   def this(args: String, fileMD5s: Traversable[(String, String)]) = {
     this()
     this.args = args

scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala

@@ -31,12 +31,14 @@ import org.broadinstitute.sting.BaseTest
 class ExampleCountLociPipelineTest {
   @Test
   def testCountLoci {
-    var testOut = "count.out"
+    val testOut = "count.out"
     val spec = new PipelineTestSpec
     spec.name = "countloci"
-    spec.args = "-S scala/qscript/examples/ExampleCountLoci.scala -R %s -I %s -o %s".format(
+    spec.args = Array(
-      BaseTest.hg18Reference, BaseTest.validationDataLocation + "small_bam_for_countloci.bam", testOut
+      " -S scala/qscript/examples/ExampleCountLoci.scala",
-    )
+      " -R " + BaseTest.hg18Reference,
+      " -I " + BaseTest.validationDataLocation + "small_bam_for_countloci.bam",
+      " -o " + testOut).mkString
     spec.fileMD5s += testOut -> "67823e4722495eb10a5e4c42c267b3a6"
     PipelineTest.executeTest(spec)
   }