Merge branch 'feature-fix_java_version' into 'develop'

Feature fix java version

Fix for #144

See merge request !185

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

@@ -37,7 +37,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
 
   var vmem: Option[String] = config("vmem")
   protected val defaultCoreMemory: Double = 1.0
-  var vmemFactor: Double = config("vmem_factor", default = 1.5)
+  protected val defaultVmemFactor: Double = 1.4
+  var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
 
   var residentFactor: Double = config("resident_factor", default = 1.2)
 
@@ -156,7 +157,13 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   protected val versionExitcode = List(0)
 
   /** Executes the version command */
-  private def getVersionInternal: Option[String] = {
+  private[core] def getVersionInternal(): Option[String] = {
+    if (versionCommand == null || versionRegex == null) None
+    else getVersionInternal(versionCommand, versionRegex)
+  }
+
+  /** Executes the version command */
+  private[core] def getVersionInternal(versionCommand: String, versionRegex: Regex): Option[String] = {
     if (versionCommand == null || versionRegex == null) return None
     val exe = new File(versionCommand.trim.split(" ")(0))
     if (!exe.exists()) return None
@@ -221,7 +228,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
 /** stores global caches */
 object BiopetCommandLineFunctionTrait {
   import scala.collection.mutable.Map
-  private val versionCache: Map[String, String] = Map()
+  private[core] val versionCache: Map[String, String] = Map()
   private[core] val executableMd5Cache: Map[String, String] = Map()
-  private val executableCache: Map[String, String] = Map()
+  private[core] val executableCache: Map[String, String] = Map()
 }

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

@@ -25,6 +25,8 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
   javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
   javaGCTimeLimit = config("java_gc_timelimit")
 
+  override protected val defaultVmemFactor: Double = 2.0
+
   /** Constructs java opts, this adds scala threads */
   override def javaOpts = super.javaOpts +
     optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)
@@ -37,6 +39,19 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
     return cmd
   }
 
+  def javaVersionCommand: String = executable + " -version"
+
+  def getJavaVersion: Option[String] = {
+    if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
+      preProcesExecutable
+    if (!BiopetCommandLineFunctionTrait.versionCache.contains(javaVersionCommand))
+      getVersionInternal(javaVersionCommand, """java version "(.*)"""".r) match {
+        case Some(version) => BiopetCommandLineFunctionTrait.versionCache += javaVersionCommand -> version
+        case _             =>
+      }
+    BiopetCommandLineFunctionTrait.versionCache.get(javaVersionCommand)
+  }
+
   override def setupRetry(): Unit = {
     super.setupRetry()
     javaMemoryLimit = memoryLimit

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

@@ -74,11 +74,13 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
             case f: BiopetJavaCommandLineFunction => {
               f.configName -> Map("version" -> f.getVersion.getOrElse(None),
                 "java_md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
-                "jar_md5" -> SummaryQScript.md5sumCache.getOrElse(f.jarFile, None))
+                "java_version" -> f.getJavaVersion,
+                "jar_path" -> f.jarFile)
             }
             case f: BiopetCommandLineFunction => {
               f.configName -> Map("version" -> f.getVersion.getOrElse(None),
-                "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None))
+                "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
+                "path" -> f.executable)
             }
             case _ => throw new IllegalStateException("This should not be possible")
           }

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -72,8 +72,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
     /** Sample specific files to add to summary */
     def summaryFiles: Map[String, File] = {
       preProcessBam match {
-        case Some(preProcessBam) => Map("preProcessBam" -> preProcessBam)
-        case _                   => Map()
+        case Some(b) => Map("preProcessBam" -> b)
+        case _       => Map()
       }
     }
 
@@ -88,9 +88,9 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
       /** Library specific files to add to the summary */
       def summaryFiles: Map[String, File] = {
         (bamFile, preProcessBam) match {
-          case (Some(bamFile), Some(preProcessBam)) => Map("bamFile" -> bamFile, "preProcessBam" -> preProcessBam)
-          case (Some(bamFile), _)                   => Map("bamFile" -> bamFile)
-          case _                                    => Map()
+          case (Some(b), Some(pb)) => Map("bamFile" -> b, "preProcessBam" -> pb)
+          case (Some(b), _)        => Map("bamFile" -> b)
+          case _                   => Map()
         }
       }
 
@@ -116,10 +116,9 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
           case (false, true) => // Starting from bam file
             config("bam_to_fastq", default = false).asBoolean match {
               case true => makeMapping // bam file will be converted to fastq
-              case false => {
+              case false =>
                 val file = new File(libDir, sampleId + "-" + libId + ".final.bam")
                 (None, Some(file), preProcess(file))
-              }
             }
           case _ => (None, None, None)
         }
@@ -137,7 +136,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
             mapping.input_R2 = config("R2")
           })
           case (false, true) => config("bam_to_fastq", default = false).asBoolean match {
-            case true => {
+            case true =>
               val samToFastq = SamToFastq(qscript, config("bam"),
                 new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
                 new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
@@ -147,8 +146,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
                 mapping.input_R1 = samToFastq.fastqR1
                 mapping.input_R2 = Some(samToFastq.fastqR2)
               })
-            }
-            case false => {
+            case false =>
               val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
               val readGroups = inputSam.getFileHeader.getReadGroups
 
@@ -157,7 +155,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
                 if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
                 readGroup.getSample == sampleId && readGroup.getLibrary == libId
               })
-              inputSam.close
+              inputSam.close()
 
               if (!readGroupOke) {
                 if (config("correct_readgroups", default = false).asBoolean) {
@@ -181,15 +179,13 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
                 bamLn.deps :+= baiLn.output
                 add(bamLn)
               }
-
-            }
           }
           case _ => logger.warn("Sample: " + sampleId + "  Library: " + libId + ", no reads found")
         }
 
         mapping.foreach(mapping => {
-          mapping.init
-          mapping.biopetScript
+          mapping.init()
+          mapping.biopetScript()
           addAll(mapping.functions) // Add functions of mapping to curent function pool
           addSummaryQScript(mapping)
         })
@@ -234,13 +230,13 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
       }
     }
 
-    lazy val preProcessBam: Option[File] = addDoublePreProcess(libraries.map(lib => {
+    lazy val preProcessBam: Option[File] = addDoublePreProcess(libraries.flatMap(lib => {
       (lib._2.bamFile, lib._2.preProcessBam) match {
         case (_, Some(file)) => Some(file)
         case (Some(file), _) => Some(file)
         case _               => None
       }
-    }).flatten.toList)
+    }).toList)
 
     lazy val variantcalling = if (config("single_sample_variantcalling", default = false).asBoolean) {
       Some(makeVariantcalling(multisample = true))
@@ -255,8 +251,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
         bamMetrics.sampleId = Some(sampleId)
         bamMetrics.inputBam = preProcessBam.get
         bamMetrics.outputDir = sampleDir
-        bamMetrics.init
-        bamMetrics.biopetScript
+        bamMetrics.init()
+        bamMetrics.biopetScript()
         addAll(bamMetrics.functions)
         addSummaryQScript(bamMetrics)
 
@@ -281,7 +277,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
   def addMultiSampleJobs(): Unit = {
     variantcalling.foreach(vc => {
       vc.outputDir = new File(outputDir, "variantcalling")
-      vc.inputBams = samples.map(_._2.preProcessBam).flatten.toList
+      vc.inputBams = samples.flatMap(_._2.preProcessBam).toList
       vc.init
       vc.biopetScript
       addAll(vc.functions)