When /etc/mailname is unreadable fall back to the hostname.

Implicit conversions for String to/from File.
Small updates to the example QScripts.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5614 348d0f76-0448-11de-a6fe-93d51630548a

scala/qscript/examples/ExampleUnifiedGenotyper.scala

@@ -36,14 +36,12 @@ class ExampleUnifiedGenotyper extends QScript {
   // and then reuse this trait on each CommandLineGATK function below.
   trait UnifiedGenotyperArguments extends CommandLineGATK {
     this.reference_sequence = qscript.referenceFile
-    this.intervals = List(qscript.intervals)
-    //  is how you set the value for an scala Option.
+    this.intervals = if (qscript.intervals == null) Nil else List(qscript.intervals)
     // Set the memory limit to 2 gigabytes on each command.
     this.memoryLimit = 2
   }
 
-
-  def script = {
+  def script() {
     // Create the four function that we can run.
     val genotyper = new UnifiedGenotyper with UnifiedGenotyperArguments
     val variantFilter = new VariantFiltration with UnifiedGenotyperArguments

scala/qscript/examples/HelloWorld.scala

@@ -1,7 +1,7 @@
 import org.broadinstitute.sting.queue.QScript
 
 class HelloWorld extends QScript {
-  def script = {
+  def script() {
     add(new CommandLineFunction {
       def commandLine = "echo hello world"
     })

scala/src/org/broadinstitute/sting/queue/QScript.scala

@@ -24,15 +24,15 @@
 
 package org.broadinstitute.sting.queue
 
-import util.{PrimitiveOptionConversions, Logging}
 import org.broadinstitute.sting.queue.function.QFunction
-import org.broadinstitute.sting.utils.text.XReadLines
 import annotation.target.field
+import io.Source
+import util.{StringFileConversions, PrimitiveOptionConversions, Logging}
 
 /**
  * Defines a Queue pipeline as a collection of CommandLineFunctions.
  */
-trait QScript extends Logging with PrimitiveOptionConversions {
+trait QScript extends Logging with PrimitiveOptionConversions with StringFileConversions  {
 
   // Type aliases so users don't have to import
   type File = java.io.File
@@ -55,7 +55,7 @@ trait QScript extends Logging with PrimitiveOptionConversions {
   /**
    * Builds the CommandLineFunctions that will be used to run this script and adds them to this.functions directly or using the add() utility method.
    */
-  def script: Unit
+  def script()
 
   /**
    * The command line functions that will be executed for this QScript.
@@ -72,17 +72,6 @@ trait QScript extends Logging with PrimitiveOptionConversions {
   protected def swapExt(file: File, oldExtension: String, newExtension: String) =
     new File(file.getName.stripSuffix(oldExtension) + newExtension)
 
-  /**
-   * Exchanges the extension on a file.
-   * @param dir New directory for the file.
-   * @param file File to look for the extension.
-   * @param oldExtension Old extension to strip off, if present.
-   * @param newExtension New extension to append.
-   * @return new File with the new extension in dir.
-   */
-  protected def swapExt(dir: String, file: File, oldExtension: String, newExtension: String) =
-    new File(dir, file.getName.stripSuffix(oldExtension) + newExtension)
-
   /**
    * Exchanges the extension on a file.
    * @param dir New directory for the file.
@@ -103,13 +92,11 @@ trait QScript extends Logging with PrimitiveOptionConversions {
     this.functions ++= functions
   }
 
-  def addAll(functions: List[QFunction] ) = {
+  def addAll(functions: List[QFunction]) {
     functions.foreach( f => add(f) )
   }
 
-  def extractFileEntries(in: File): List[File] = {
-    return collection.JavaConversions.asScalaIterator((new XReadLines(in))).toList.map( new File(_) )
-  }
+  def extractFileEntries(in: File): List[File] = Source.fromFile(in).getLines().toList
 }
 
 object QScript {

scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala

@@ -0,0 +1,105 @@
+/*
+ * 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.queue.util
+
+import java.io.{Serializable, File}
+
+/**
+ * Converts String to/from File
+ * The method signatures are based on the compiler errors reported by StringFileConversionsUnitTest.
+ * The implementations are based on the runtime errors reported by StringFileConversionsUnitTest.
+ */
+object StringFileConversions {
+  implicit def stringAsFile(x: String): File = {
+    if (x == null) null else new File(x)
+  }
+
+  implicit def fileAsString(x: File): String = {
+    if (x == null) null else x.getPath
+  }
+
+  // Possible to get the invariants, covariants, contravariants, upper type bounds, lower type bounds
+  // and mixins all correct so this doesn't have to be duplicated with concrete implementations?
+  // http://programming-scala.labs.oreilly.com/ch12.html is your friend.
+
+  implicit def stringsAsFiles(x: List[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable]) = {
+    x.map(_ match {
+      case string: String => stringAsFile(string)
+      case file: File => file
+    })
+  }
+
+  implicit def filesAsStrings(x: List[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable]) = {
+    x.map(_ match {
+      case file: File => fileAsString(file)
+      case string: String => string
+    })
+  }
+
+  implicit def stringsAsFiles(x: Set[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable] with Serializable]) = {
+    x.map(_ match {
+      case string: String => stringAsFile(string)
+      case file: File => file
+    })
+  }
+
+  implicit def filesAsStrings(x: Set[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable] with Serializable]) = {
+    x.map(_ match {
+      case file: File => fileAsString(file)
+      case string: String => string
+    })
+  }
+}
+
+/**
+ * Converts String to/from File
+ * The method signatures are based on the compiler errors reported by StringFileConversionsUnitTest.
+ * The implementations are based on the runtime errors reported by StringFileConversionsUnitTest.
+ */
+trait StringFileConversions {
+  implicit def stringAsFile(x: String): File = {
+    StringFileConversions.stringAsFile(x)
+  }
+
+  implicit def fileAsString(x: File): String = {
+    StringFileConversions.fileAsString(x)
+  }
+
+  implicit def stringsAsFiles(x: List[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable]) = {
+    StringFileConversions.stringsAsFiles(x)
+  }
+
+  implicit def filesAsStrings(x: List[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable]) = {
+    StringFileConversions.filesAsStrings(x)
+  }
+
+  implicit def stringsAsFiles(x: Set[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable] with Serializable]) = {
+    StringFileConversions.stringsAsFiles(x)
+  }
+
+  implicit def filesAsStrings(x: Set[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable] with Serializable]) = {
+    StringFileConversions.filesAsStrings(x)
+  }
+}

scala/src/org/broadinstitute/sting/queue/util/SystemUtils.scala

@@ -32,7 +32,7 @@ import io.Source
 /**
  * A collection of various system utilities.
  */
-object SystemUtils {
+object SystemUtils extends Logging {
   val inetAddress = InetAddress.getLocalHost.getHostAddress
   val canonicalHostName = InetAddress.getLocalHost.getCanonicalHostName
 
@@ -46,7 +46,13 @@ object SystemUtils {
   val mailName = {
     val mailnameFile = new File("/etc/mailname")
     if (mailnameFile.exists)
-      Source.fromFile(mailnameFile).mkString.trim
+      try {
+        Source.fromFile(mailnameFile).mkString.trim
+      } catch {
+        case e: Exception =>
+          logger.error("Unabled to read mail domain. Using hostname.", e)
+          hostName.split('.').takeRight(2).mkString(".")
+      }
     else
       hostName.split('.').takeRight(2).mkString(".")
   }

scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala

@@ -0,0 +1,102 @@
+/*
+ * 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.queue.util
+
+import org.testng.annotations.Test
+import java.io.File
+import org.testng.Assert
+import StringFileConversions._
+
+class StringFileConversionsUnitTest {
+  @Test
+  def testStringToFile() {
+    val file = new File("foo")
+    val string: String = file
+    Assert.assertEquals(string, "foo")
+  }
+
+  @Test
+  def testFileToString() {
+    val string = "foo"
+    val file: File = string
+    Assert.assertEquals(file, new File("foo"))
+  }
+
+  @Test
+  def testStringToFileList() {
+    var files = List(new File("foo"))
+    files :+= "bar"
+    Assert.assertEquals(files, List(new File("foo"), new File("bar")))
+  }
+
+  @Test
+  def testFileToStringList() {
+    var strings = List("foo")
+    strings :+= new File("bar")
+    Assert.assertEquals(strings, List("foo", "bar"))
+  }
+
+  @Test
+  def testStringToFileSet() {
+    var files = Set(new File("foo"))
+    files += "bar"
+    Assert.assertEquals(files, Set(new File("foo"), new File("bar")))
+  }
+
+  @Test
+  def testFileToStringSet() {
+    var strings = Set("foo")
+    strings += new File("bar")
+    Assert.assertEquals(strings, Set("foo", "bar"))
+  }
+
+  @Test
+  def testStringListToFileList() {
+    var files = List(new File("foo"))
+    files ++= List("bar")
+    Assert.assertEquals(files, List(new File("foo"), new File("bar")))
+  }
+
+  @Test
+  def testFileListToStringList() {
+    var strings = List("foo")
+    strings ++= List(new File("bar"))
+    Assert.assertEquals(strings, List("foo", "bar"))
+  }
+
+  @Test
+  def testStringSetToFileSet() {
+    var files = Set(new File("foo"))
+    files ++= Set("bar")
+    Assert.assertEquals(files, Set(new File("foo"), new File("bar")))
+  }
+
+  @Test
+  def testFileSetToStringSet() {
+    var strings = Set("foo")
+    strings ++= Set(new File("bar"))
+    Assert.assertEquals(strings, Set("foo", "bar"))
+  }
+}