diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 4a5b25f7a5b816fe32ad39897a334a6e13fe1eda..a9cb89d93e36333d91e0d030a95328ac31802435 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/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 +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 93cf7ebb16e397db26ad8912a92c74b40cd5c80e..ba0dc2c6d956e4db78189afa3542ebbc7911266b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/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")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index fed5e514be34618f41d2e8348eba6d15e67fab29..7bda8792544eea2d863ab06192b51b55ae900077 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index 47e7d1af8d21add7744613806ea7520d82cbf04d..2c9165036824f135f9552b69fa3b4085be25fc93 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/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
}