Error cache now also works on executables

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

@@ -66,7 +66,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     super.freezeFieldValues()
   }
 
-  protected def checkExecutable {
+  protected[core] def checkExecutable {
     if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
       try if (executable != null) {
         if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
@@ -79,8 +79,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
             val file = new File(executable)
             executable = file.getCanonicalPath
           } else {
-            logger.error("executable: '" + executable + "' not found, please check config")
-            throw new QException("executable: '" + executable + "' not found, please check config")
+            BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
           }
           BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
           BiopetCommandLineFunctionTrait.executableCache += executable -> executable
@@ -101,9 +100,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
         case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
       }
     }
-    val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache(executable)
-    if (md5 == null) addJobReportBinding("md5sum_exe", md5)
-    else addJobReportBinding("md5sum_exe", "None")
+    val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache.get(executable)
+    addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
   }
 
   final protected def preCmdInternal {
@@ -120,6 +118,11 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   protected val versionExitcode = List(0) // Can select multiple
   private def getVersionInternal: String = {
     if (versionCommand == null || versionRegex == null) return "N/A"
+    val exe = new File(versionCommand.trim.split(" ")(0))
+    if (!exe.exists()) {
+      //BiopetQScript.addError("executable '" + exe + "' does not exist")
+      return "N/A"
+    }
     val stdout = new StringBuffer()
     val stderr = new StringBuffer()
     def outputLog = "Version command: \n" + versionCommand +

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

@@ -33,7 +33,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
 
   var outputDir: String = {
     val temp = Config.getValueFromMap(Config.global.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
-    if (temp.isEmpty) throw new IllegalArgumentException("No output_dir defined in config")
+    if (temp.isEmpty) ""
     else {
       val t = temp.get.value.toString
       if (!t.endsWith("/")) t + "/" else t
@@ -54,7 +54,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
 
   final def script() {
     outputDir = config("output_dir")
-    if (!outputDir.endsWith("/")) outputDir += "/"
+    if (outputDir.isEmpty) outputDir = new File(".").getAbsolutePath()
+    else if (!outputDir.endsWith("/")) outputDir += "/"
     init
     biopetScript
 
@@ -63,11 +64,15 @@ trait BiopetQScript extends Configurable with GatkLogging {
       case _                            =>
     }
     for (function <- functions) function match {
-      case f: BiopetCommandLineFunctionTrait => f.afterGraph
+      case f: BiopetCommandLineFunctionTrait => {
+        f.checkExecutable
+        f.afterGraph
+      }
       case _                                 =>
     }
 
-    Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+    if (new File(outputDir).canWrite) Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+    else BiopetQScript.addError("Output dir: '" + outputDir + "' is not writeable")
 
     BiopetQScript.checkErrors
   }
@@ -82,15 +87,23 @@ trait BiopetQScript extends Configurable with GatkLogging {
 object BiopetQScript extends Logging {
   private val errors: ListBuffer[Exception] = ListBuffer()
 
-  def addError(msg: String): Unit = {
+  def addError(error: String, debug: String = null): Unit = {
+    val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
     errors.append(new Exception(msg))
   }
 
   protected def checkErrors: Unit = {
     if (!errors.isEmpty) {
-      for (e <- errors) {
-        logger.error(e.getMessage)
-        logger.debug(e.getStackTrace.mkString("Stack trace:\n", "\n", "\n"))
+      logger.error("*************************")
+      logger.error("Biopet found some errors:")
+      if (logger.isDebugEnabled) {
+        for (e <- errors) {
+          logger.error(e.getMessage)
+          logger.debug(e.getStackTrace.mkString("Stack trace:\n", "\n", "\n"))
+        }
+      } else {
+        val set = errors.map(_.getMessage).toSet
+        set.toList.sorted.foreach(logger.error(_))
       }
       throw new IllegalStateException("Biopet found errors")
     }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

@@ -51,7 +51,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   override def afterGraph {
     this.checkExecutable
 
-    val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
+    val fastqcDir = new File(executable).getParent
 
     contaminants = contaminants match {
       // user-defined contaminants file take precedence

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -335,8 +335,8 @@ object ConfigUtils extends Logging {
       val exist = valueExists(value)
       if (!exist)
         BiopetQScript.addError("Value does not exist but is required, key: " + value.requestIndex.key +
-          "  module: " + value.requestIndex.module +
-          (if (value.requestIndex.path != Nil) "  path: " + value.requestIndex.path.mkString("->") else ""))
+          "  module: " + value.requestIndex.module,
+          (if (value.requestIndex.path != Nil) "  path: " + value.requestIndex.path.mkString("->") else null))
       exist
     }