Moved the test name and the job queue into the spec.

Defaulting to the hour queue for running pipeline tests.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5122 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -3,12 +3,12 @@ package org.broadinstitute.sting.queue.pipeline
 import org.broadinstitute.sting.utils.Utils
 import org.testng.Assert
 import org.broadinstitute.sting.commandline.CommandLineProgram
-import org.broadinstitute.sting.queue.QCommandLine
 import java.io.File
 import org.broadinstitute.sting.queue.util.{TextFormatUtils, ProcessController}
 import java.util.Date
 import java.text.SimpleDateFormat
 import org.broadinstitute.sting.{WalkerTest, BaseTest}
+import org.broadinstitute.sting.queue.{QException, QCommandLine}
 
 object PipelineTest {
 
@@ -54,11 +54,14 @@ object PipelineTest {
 
   val run = System.getProperty("pipeline.run") == "run"
 
-  def executeTest(name: String, pipelineTest: PipelineTestSpec) {
+  def executeTest(pipelineTest: PipelineTestSpec) {
+    val name = pipelineTest.name
+    if (name == null)
+      throw new QException("PipelineTestSpec.name is null.")
     println(Utils.dupString('-', 80));
-    executeTest(name, pipelineTest.args, pipelineTest.expectedException)
+    executeTest(name, pipelineTest.args, pipelineTest.jobQueue, pipelineTest.expectedException)
     if (run) {
-      assertMatchingMD5s(name, pipelineTest.fileMD5s)
+      assertMatchingMD5s(name, pipelineTest.fileMD5s.map{case (file, md5) => new File(runDir(name), file) -> md5})
       if (pipelineTest.evalSpec != null)
         validateEval(name, pipelineTest.evalSpec)
       println("  => %s PASSED".format(name))
@@ -109,14 +112,21 @@ object PipelineTest {
    * execute the test
    * @param name the name of the test
    * @param args the argument list
+   * @param jobQueue the queue to run the job on.  Defaults to hour if jobQueue is null.
    * @param expectedException the expected exception or null if no exception is expected.
    */
-  def executeTest(name: String, args: String, expectedException: Class[_]) {
+  def executeTest(name: String, args: String, jobQueue: String, expectedException: Class[_]) {
     var command = Utils.escapeExpressions(args)
 
     // add the logging level to each of the integration test commands
 
     command = Utils.appendArray(command, "-bsub", "-l", "WARN", "-startFromScratch", "-tempDir", tempDir(name), "-runDir", runDir(name))
+
+    if (jobQueue == null)
+      command = Utils.appendArray(command, "-jobQueue", "hour")
+    else
+      command = Utils.appendArray(command, "-jobQueue", jobQueue)
+
     if (run)
       command = Utils.appendArray(command, "-run")
 

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

@@ -2,13 +2,16 @@ package org.broadinstitute.sting.queue.pipeline
 
 import java.io.File
 
-class PipelineTestSpec {
+class PipelineTestSpec(var name: String = null) {
 
   /** The arguments to pass to the Queue test, ex: "-S scala/qscript/examples/HelloWorld.scala" */
   var args: String = _
 
+  /** Job Queue to run the test.  Default is null which means use hour. */
+  var jobQueue: String = _
+
   /** Expected MD5 results for each file path. */
-  var fileMD5s = Map.empty[File, String]
+  var fileMD5s = Map.empty[String, String]
 
   /** VariantEval validations to run on a VCF after the pipeline has completed. */
   var evalSpec: PipelineTestEvalSpec = _
@@ -16,7 +19,7 @@ class PipelineTestSpec {
   /** Expected exception from the test. */
   var expectedException: Class[_ <: Exception] = null
 
-  def this(args: String, fileMD5s: Traversable[(File, String)]) = {
+  def this(args: String, fileMD5s: Traversable[(String, String)]) = {
     this()
     this.args = args
     this.fileMD5s = fileMD5s.toMap

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

@@ -7,14 +7,13 @@ import org.broadinstitute.sting.BaseTest
 class ExampleCountLociPipelineTest {
   @Test
   def testCountLoci {
-    var testName = "countloci"
     var testOut = "count.out"
     val spec = new PipelineTestSpec
-    // TODO: Use a variable instead of "hour"
-    spec.args = "-S scala/qscript/examples/ExampleCountLoci.scala -gatk %s -R %s -I %s -o %s -jobQueue hour".format(
+    spec.name = "countloci"
+    spec.args = "-S scala/qscript/examples/ExampleCountLoci.scala -gatk %s -R %s -I %s -o %s".format(
       PipelineTest.currentGATK, BaseTest.hg18Reference, BaseTest.validationDataLocation + "small_bam_for_countloci.bam", testOut
     )
-    spec.fileMD5s += PipelineTest.fileMD5(testName, testOut, "67823e4722495eb10a5e4c42c267b3a6")
-    PipelineTest.executeTest(testName, spec)
+    spec.fileMD5s += testOut -> "67823e4722495eb10a5e4c42c267b3a6"
+    PipelineTest.executeTest(spec)
   }
 }

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

@@ -6,9 +6,9 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 class HelloWorldPipelineTest {
   @Test
   def testHelloWorld {
-    var testName = "helloworld"
     val spec = new PipelineTestSpec
-    spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld -jobQueue hour"
-    PipelineTest.executeTest(testName, spec)
+    spec.name = "helloworld"
+    spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld"
+    PipelineTest.executeTest(spec)
   }
 }

scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala

@@ -27,8 +27,6 @@ class FullCallingPipelineTest {
     dataset.validations :+= new DoubleValidation("eval.dbsnp.all.called.known.titv.tiTvRatio", 3.7426)
     dataset.validations :+= new DoubleValidation("eval.dbsnp.all.called.novel.titv.tiTvRatio", 3.3077)
 
-    dataset.jobQueue = "hour"
-
     dataset
   }
 
@@ -101,11 +99,10 @@ class FullCallingPipelineTest {
       cleanType = "uncleaned"
     }
     
-    if (dataset.jobQueue != null)
-      pipelineCommand += " -jobQueue " + dataset.jobQueue
-
     val pipelineSpec = new PipelineTestSpec
+    pipelineSpec.name = testName
     pipelineSpec.args = pipelineCommand
+    pipelineSpec.jobQueue = dataset.jobQueue
 
     pipelineSpec.evalSpec = new PipelineTestEvalSpec
     pipelineSpec.evalSpec.vcf = new File(PipelineTest.runDir(testName) + "SnpCalls/%s.%s.annotated.handfiltered.vcf".format(projectName, cleanType))
@@ -115,7 +112,7 @@ class FullCallingPipelineTest {
     pipelineSpec.evalSpec.validations = dataset.validations
 
     // Run the test, at least checking if the command compiles
-    PipelineTest.executeTest(testName, pipelineSpec)
+    PipelineTest.executeTest(pipelineSpec)
   }
 
   class PipelineDataset(