Fix code inspection warnings in core

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

@@ -19,9 +19,9 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Argument
 
 /**
- * Created by pjvan_thof on 2/16/15.
- *
  * Default implementation for sample and library arguments for pipelines, mainly used for typecasting.
+ *
+ * @author Peter van 't Hof
  */
 trait SampleLibraryTag extends Configurable {
   @Argument(doc = "Sample ID", shortName = "sample", required = false)

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

@@ -43,7 +43,7 @@ class Config(var map: Map[String, Any],
    */
   def loadConfigEnv(valueName: String, default: Boolean) {
     sys.env.get(valueName) match {
-      case Some(globalFiles) => {
+      case Some(globalFiles) =>
         for (globalFile <- globalFiles.split(":")) {
           val file: File = new File(globalFile)
           if (file.exists) {
@@ -51,14 +51,13 @@ class Config(var map: Map[String, Any],
             loadConfigFile(file, default)
           } else logger.warn(valueName + " value found but file '" + file + "' does not exist, no global config is loaded")
         }
-      }
       case _ => logger.info(valueName + " value not found, no global config is loaded")
     }
   }
 
   /** Loading default value for biopet */
   def loadDefaultConfig() {
-    loadConfigEnv("BIOPET_CONFIG", true)
+    loadConfigEnv("BIOPET_CONFIG", default = true)
   }
 
   /**
@@ -94,7 +93,7 @@ class Config(var map: Map[String, Any],
   protected[config] var notFoundCache: List[ConfigValueIndex] = List()
   protected[config] var foundCache: Map[ConfigValueIndex, ConfigValue] = Map()
   protected[config] var defaultCache: Map[ConfigValueIndex, ConfigValue] = Map()
-  protected[config] def clearCache: Unit = {
+  protected[config] def clearCache(): Unit = {
     notFoundCache = List()
     foundCache = Map()
     defaultCache = Map()
@@ -114,16 +113,16 @@ class Config(var map: Map[String, Any],
    * @return True if exist
    */
   def contains(requestedIndex: ConfigValueIndex): Boolean =
-    if (notFoundCache.contains(requestedIndex)) return false
-    else if (foundCache.contains(requestedIndex)) return true
+    if (notFoundCache.contains(requestedIndex)) false
+    else if (foundCache.contains(requestedIndex)) true
     else {
       val value = Config.getValueFromMap(map, requestedIndex)
       if (value.isDefined && value.get.value != None) {
         foundCache += (requestedIndex -> value.get)
-        return true
+        true
       } else {
         notFoundCache +:= requestedIndex
-        return false
+        false
       }
     }
 
@@ -201,7 +200,7 @@ class Config(var map: Map[String, Any],
     writeMapToJsonFile(fullEffectiveWithNotFound, "effective.full.notfound")
   }
 
-  override def toString(): String = map.toString
+  override def toString: String = map.toString()
 }
 
 object Config extends Logging {
@@ -210,7 +209,7 @@ object Config extends Logging {
   /**
    * Merge 2 config objects
    * @param config1 prio over config 2
-   * @param config2
+   * @param config2 Low prio map
    * @return Merged config
    */
   def mergeConfigs(config1: Config, config2: Config): Config = new Config(mergeMaps(config1.map, config2.map))
@@ -234,7 +233,7 @@ object Config extends Logging {
 
     def tailSearch(path: List[String]): Option[ConfigValue] = {
       val p = getFromPath(path)
-      if (p != None) p
+      if (p.isDefined) p
       else if (path == Nil) None
       else {
         val p = initSearch(path)
@@ -261,6 +260,6 @@ object Config extends Logging {
       else skipNested(path, tail.tail)
     }
 
-    return tailSearch(startIndex.path)
+    tailSearch(startIndex.path)
   }
 }
\ No newline at end of file

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

@@ -56,7 +56,7 @@ class ConfigValue(val requestIndex: ConfigValueIndex, val foundIndex: ConfigValu
     else if (!default) output += ", foundIndex = (" + foundIndex + ")"
     else output += ", default value is used"
 
-    return output
+    output
   }
 }
 

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

@@ -45,10 +45,6 @@ trait Configurable extends ImplicitConversions {
   /**
    * Creates path with a prefix for sample and library
    * "samples" -> "sampleID" -> "libraries" -> "libraryID" -> rest of path
-   * @param sample
-   * @param library
-   * @param submodule
-   * @return
    */
   def getConfigPath(sample: String = null, library: String = null, submodule: String = null) = {
     (if (sample != null) "samples" :: sample :: Nil else Nil) :::
@@ -92,9 +88,9 @@ trait Configurable extends ImplicitConversions {
       val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
       val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
       val m = if (submodule != null) submodule else configName
-      val p = (if (path == null) getConfigPath(s, l, submodule) ::: subPath else path)
+      val p = if (path == null) getConfigPath(s, l, submodule) ::: subPath else path
       val d = {
-        val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
+        val value = Config.getValueFromMap(defaults, ConfigValueIndex(m, p, key, freeVar))
         if (value.isDefined) value.get.value else default
       }
       if (d == null) globalConfig(m, p, key, freeVar = freeVar)
@@ -119,9 +115,9 @@ trait Configurable extends ImplicitConversions {
       val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
       val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
       val m = if (submodule != null) submodule else configName
-      val p = (if (path == null) getConfigPath(s, l, submodule) ::: subPath else path)
+      val p = if (path == null) getConfigPath(s, l, submodule) ::: subPath else path
 
-      globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
+      globalConfig.contains(m, p, key, freeVar) || Config.getValueFromMap(defaults, ConfigValueIndex(m, p, key, freeVar)).isDefined
     }
   }
 }

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

 package nl.lumc.sasc.biopet.core.report
 
 /**
- * Created by pjvan_thof on 3/30/15.
+ * This trait will generate a report with added function to generate sample and library pages for those existing in the summary.
+ *
+ * @author pjvan_thof
  */
 trait MultisampleReportBuilder extends ReportBuilder {
 
@@ -28,7 +30,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
   /** Generate the samples page including a single sample page for each sample in the summary */
   def generateSamplesPage(args: Map[String, Any]): ReportPage = {
     val samplePages = summary.samples
-      .map(sampleId => (sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId)))))
+      .map(sampleId => sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId))))
       .toList
     ReportPage(samplePages, samplesSections, args)
   }
@@ -41,7 +43,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
     }
 
     val libPages = summary.libraries(sampleId)
-      .map(libId => (libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId)))))
+      .map(libId => libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId))))
       .toList
     ReportPage(libPages, libririesSections, args)
   }

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

@@ -10,7 +10,9 @@ import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
 import scala.collection.mutable
 
 /**
- * Created by pjvan_thof on 3/27/15.
+ * This trait is meant to make an extension for a report object
+ *
+ * @author pjvan_thof
  */
 trait ReportBuilderExtension extends ToolCommandFuntion {
 
@@ -28,8 +30,8 @@ trait ReportBuilderExtension extends ToolCommandFuntion {
 
   override val defaultCoreMemory = 3.0
 
-  override def beforeGraph: Unit = {
-    super.beforeGraph
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
     jobOutputFile = new File(outputDir, ".report.log.out")
     javaMainClass = builder.getClass.getName.takeWhile(_ != '$')
   }
@@ -87,18 +89,16 @@ trait ReportBuilder extends ToolCommand {
     require(cmdArgs.outputDir.isDirectory, "Output dir is not a directory")
 
     cmdArgs.pageArgs.get("sampleId") match {
-      case Some(s: String) => {
+      case Some(s: String) =>
         cmdArgs.pageArgs += "sampleId" -> Some(s)
         _sampleId = Some(s)
-      }
       case _ =>
     }
 
     cmdArgs.pageArgs.get("libId") match {
-      case Some(l: String) => {
+      case Some(l: String) =>
         cmdArgs.pageArgs += "libId" -> Some(l)
         _libId = Some(l)
-      }
       case _ =>
     }
 
@@ -121,7 +121,7 @@ trait ReportBuilder extends ToolCommand {
     )
 
     for (resource <- extFiles.par) {
-      IoUtils.copyStreamToFile(getClass.getResourceAsStream(resourceDir + resource), new File(extOutputDir, resource), true)
+      IoUtils.copyStreamToFile(getClass.getResourceAsStream(resourceDir + resource), new File(extOutputDir, resource), createDirs = true)
     }
 
     logger.info("Parsing summary")
@@ -184,7 +184,7 @@ trait ReportBuilder extends ToolCommand {
 
     done += 1
     if (done % 100 == 0) logger.info(done + " Done, " + (done.toDouble / total * 100) + "%")
-    jobs.fold(0)(_ + _) + 1
+    jobs.sum + 1
   }
 }
 
@@ -210,18 +210,13 @@ object ReportBuilder {
   def renderTemplate(location: String, args: Map[String, Any] = Map()): String = {
     Logging.logger.info("Rendering: " + location)
 
-    if (location == "/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp") {
-      println("hier dus")
-    }
-
     val templateFile: File = templateCache.get(location) match {
       case Some(template) => template
-      case _ => {
+      case _ =>
         val tempFile = File.createTempFile("ssp-template", new File(location).getName)
         IoUtils.copyStreamToFile(getClass.getResourceAsStream(location), tempFile)
         templateCache += location -> tempFile
         tempFile
-      }
     }
     engine.layout(TemplateSource.fromFile(templateFile), args)
   }

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

@@ -28,6 +28,8 @@ import scala.collection.mutable
 import scala.io.Source
 
 /**
+ * This will collect and write the summary
+ *
  * Created by pjvan_thof on 2/14/15.
  */
 class WriteSummary(val root: Configurable) extends InProcessFunction with Configurable {
@@ -71,17 +73,15 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
       val executables: Map[String, Any] = {
         (for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunctionTrait]) yield {
           f match {
-            case f: BiopetJavaCommandLineFunction => {
+            case f: BiopetJavaCommandLineFunction =>
               f.configName -> Map("version" -> f.getVersion.getOrElse(None),
                 "java_md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
                 "java_version" -> f.getJavaVersion,
                 "jar_path" -> f.jarFile)
-            }
-            case f: BiopetCommandLineFunction => {
+            case f: BiopetCommandLineFunction =>
               f.configName -> Map("version" -> f.getVersion.getOrElse(None),
                 "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None),
                 "path" -> f.executable)
-            }
             case _ => throw new IllegalStateException("This should not be possible")
           }
 
@@ -127,42 +127,29 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
 
   def prefixSampleLibrary(map: Map[String, Any], sampleId: Option[String], libraryId: Option[String]): Map[String, Any] = {
     sampleId match {
-      case Some(sampleId) => Map("samples" -> Map(sampleId -> (libraryId match {
-        case Some(libraryId) => Map("libraries" -> Map(libraryId -> map))
-        case _               => map
+      case Some(s) => Map("samples" -> Map(s -> (libraryId match {
+        case Some(l) => Map("libraries" -> Map(l -> map))
+        case _       => map
       })))
       case _ => map
     }
   }
 
-  /**
-   * Convert summarizable to a summary map
-   * @param summarizable
-   * @param name
-   * @return
-   */
+  /** Convert summarizable to a summary map */
   def parseSummarizable(summarizable: Summarizable, name: String) = {
     val stats = summarizable.summaryStats
     val files = parseFiles(summarizable.summaryFiles)
 
-    (Map("stats" -> Map(name -> stats))) ++
+    Map("stats" -> Map(name -> stats)) ++
       (if (files.isEmpty) Map[String, Any]() else Map("files" -> Map(name -> files)))
   }
 
-  /**
-   * Parse files map to summary map
-   * @param files
-   * @return
-   */
+  /** Parse files map to summary map */
   def parseFiles(files: Map[String, File]): Map[String, Map[String, Any]] = {
     for ((key, file) <- files) yield key -> parseFile(file)
   }
 
-  /**
-   * parse single file summary map
-   * @param file
-   * @return
-   */
+  /** arse single file summary map */
   def parseFile(file: File): Map[String, Any] = {
     val map: mutable.Map[String, Any] = mutable.Map()
     map += "path" -> file.getAbsolutePath
@@ -170,11 +157,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     map.toMap
   }
 
-  /**
-   * Retrive checksum from file
-   * @param checksumFile
-   * @return
-   */
+  /** Retrive checksum from file */
   def parseChecksum(checksumFile: File): String = {
     Source.fromFile(checksumFile).getLines().toList.head.split(" ")(0)
   }

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

@@ -46,7 +46,8 @@
 package nl.lumc.sasc.biopet.core.workaround
 
 import java.io.{ File, FileOutputStream }
-import java.util.{ Arrays, ResourceBundle }
+import java.util
+import java.util.ResourceBundle
 
 import nl.lumc.sasc.biopet.FullVersion
 import nl.lumc.sasc.biopet.core.Logging
@@ -176,8 +177,8 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
 
       // TODO: Default command plugin argument?
       val remoteFileConverter = (
-        for (commandPlugin <- allCommandPlugins if (commandPlugin.remoteFileConverter != null))
-          yield commandPlugin.remoteFileConverter).headOption.getOrElse(null)
+        for (commandPlugin <- allCommandPlugins if commandPlugin.remoteFileConverter != null)
+          yield commandPlugin.remoteFileConverter).headOption.orNull
 
       if (remoteFileConverter != null)
         loadArgumentsIntoObject(remoteFileConverter)
@@ -198,7 +199,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
             script.mkRemoteOutputs(remoteFileConverter)
         }
 
-        script.functions.foreach(qGraph.add(_))
+        script.functions.foreach(qGraph.add)
         logger.info("Added " + script.functions.size + " functions")
       }
       // Execute the job graph
@@ -281,7 +282,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
    * @return a ScalaCompoundArgumentTypeDescriptor
    */
   override def getArgumentTypeDescriptors =
-    Arrays.asList(new ScalaCompoundArgumentTypeDescriptor)
+    util.Arrays.asList(new ScalaCompoundArgumentTypeDescriptor)
 
   override def getApplicationDetails: ApplicationDetails = {
     new ApplicationDetails(createQueueHeader(),