Move Executable function outside of class

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -5,13 +5,15 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.{ Version, CommandLineResources, Reference, BiopetJavaCommandLineFunction }
+import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
 trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference with Version {
   memoryLimit = Option(3)
 
+  var executable: String = config("java", default = "java", submodule = "java", freeVar = false)
+
   override def subPath = "gatk" :: super.subPath
 
   jarFile = config("gatk_jar")
@@ -20,6 +22,7 @@ trait GatkGeneral extends CommandLineGATK with CommandLineResources with Referen
 
   override def defaultCoreMemory = 4.0
   override def faiRequired = true
+  override def dictRequired = true
 
   if (config.contains("intervals")) intervals = config("intervals").asFileList
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
@@ -39,5 +42,8 @@ trait GatkGeneral extends CommandLineGATK with CommandLineResources with Referen
   override def versionExitcode = List(0, 1)
   def versionCommand = "java" + " -jar " + jarFile + " -version"
 
-  override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
+  override def getVersion = {
+    executable = BiopetCommandLineFunction.preProcessExecutable(executable).path
+    super.getVersion.collect { case v => "Gatk " + v }
+  }
 }

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -91,50 +91,19 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
   }
 
-  /** can override this value is executable may not be converted to CanonicalPath */
+  /**
+   * Can override this value is executable may not be converted to CanonicalPath
+   * @deprecated
+   */
   val executableToCanonicalPath = true
 
   /**
    * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
    */
   protected[core] def preProcessExecutable() {
-    if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
-      if (executable != null) {
-        if (!BiopetCommandLineFunction.executableCache.contains(executable)) {
-          try {
-            val oldExecutable = executable
-            val buffer = new StringBuffer()
-            val cmd = Seq("which", executable)
-            val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
-            if (process.exitValue == 0) {
-              executable = buffer.toString
-              val file = new File(executable)
-              if (executableToCanonicalPath) executable = file.getCanonicalPath
-              else executable = file.getAbsolutePath
-            } else Logging.addError("executable: '" + executable + "' not found, please check config")
-            BiopetCommandLineFunction.executableCache += oldExecutable -> executable
-            BiopetCommandLineFunction.executableCache += executable -> executable
-          } catch {
-            case ioe: java.io.IOException =>
-              logger.warn(s"Could not use 'which' on '$executable', check on executable skipped: " + ioe)
-          }
-        } else executable = BiopetCommandLineFunction.executableCache(executable)
-
-        if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
-          if (new File(executable).exists()) {
-            val is = new FileInputStream(executable)
-            val cnt = is.available
-            val bytes = Array.ofDim[Byte](cnt)
-            is.read(bytes)
-            is.close()
-            val temp = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
-            BiopetCommandLineFunction.executableMd5Cache += executable -> temp
-          } else BiopetCommandLineFunction.executableMd5Cache += executable -> "file_does_not_exist"
-        }
-      }
-    }
-    val md5 = BiopetCommandLineFunction.executableMd5Cache.get(executable)
-    addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
+    val exe = BiopetCommandLineFunction.preProcessExecutable(executable)
+    executable = exe.path
+    addJobReportBinding("md5sum_exe", exe.md5.getOrElse("N/A"))
   }
 
   /** executes checkExecutable method and fill job report */
@@ -230,7 +199,49 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 }
 
 /** stores global caches */
-object BiopetCommandLineFunction {
+object BiopetCommandLineFunction extends Logging {
   private[core] val executableMd5Cache: mutable.Map[String, String] = mutable.Map()
   private[core] val executableCache: mutable.Map[String, String] = mutable.Map()
+
+  private case class Executable(path: String, md5: Option[String])
+  def preProcessExecutable(executable: String): Executable = {
+    if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
+      if (executable != null) {
+        if (!BiopetCommandLineFunction.executableCache.contains(executable)) {
+          try {
+            val oldExecutable = executable
+            val buffer = new StringBuffer()
+            val cmd = Seq("which", executable)
+            val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
+            if (process.exitValue == 0) {
+              val file = new File(buffer.toString)
+              BiopetCommandLineFunction.executableCache += executable -> file.getAbsolutePath
+            } else {
+              Logging.addError("executable: '" + executable + "' not found, please check config")
+              BiopetCommandLineFunction.executableCache += executable -> executable
+            }
+          } catch {
+            case ioe: java.io.IOException =>
+              logger.warn(s"Could not use 'which' on '$executable', check on executable skipped: " + ioe)
+              BiopetCommandLineFunction.executableCache += executable -> executable
+          }
+        }
+
+        if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
+          val newExe = BiopetCommandLineFunction.executableCache(executable)
+          if (new File(newExe).exists()) {
+            val is = new FileInputStream(executable)
+            val cnt = is.available
+            val bytes = Array.ofDim[Byte](cnt)
+            is.read(bytes)
+            is.close()
+            val temp = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
+            BiopetCommandLineFunction.executableMd5Cache += newExe -> temp
+          } else BiopetCommandLineFunction.executableMd5Cache += newExe -> "file_does_not_exist"
+        }
+      }
+    }
+    Executable(BiopetCommandLineFunction.executableCache(executable),
+      BiopetCommandLineFunction.executableMd5Cache.get(executable))
+  }
 }