Merge remote-tracking branch 'remotes/origin/develop' into feature-VarscanIntoShiva

Conflicts:
	public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala

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

@@ -15,13 +15,9 @@
  */
 package nl.lumc.sasc.biopet.core.extensions
 
-import java.io.{ File, FileOutputStream }
-
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.utils.rscript.Rscript
 
-import scala.sys.process._
-
 /**
  * General rscript extension
  *

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

@@ -184,6 +184,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     map.toMap
   }
 }
+
 object WriteSummary {
   /** Retrive checksum from file */
   def parseChecksum(checksumFile: File): String = {

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala

@@ -19,6 +19,7 @@ class ReferenceTest extends TestNGSuite with Matchers with MockitoSugar {
 
   @Test
   def testDefault: Unit = {
+    Logging.errors.clear()
     make(config :: testReferenceNoIndex :: Nil).referenceFasta()
     Logging.checkErrors(true)
 

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala

+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.File
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 14/01/16.
+ */
+class SummarizableTest extends TestNGSuite with Matchers {
+  @Test
+  def testDefaultMerge: Unit = {
+    val summarizable = new Summarizable {
+      def summaryFiles: Map[String, File] = ???
+      def summaryStats: Any = ???
+    }
+    intercept[IllegalStateException] {
+      summarizable.resolveSummaryConflict("1", "1", "key")
+    }
+  }
+
+  def testOverrideMerge: Unit = {
+    val summarizable = new Summarizable {
+      def summaryFiles: Map[String, File] = ???
+      def summaryStats: Any = ???
+      override def resolveSummaryConflict(v1: Any, v2: Any, key: String) = v1
+    }
+    summarizable.resolveSummaryConflict("1", "1", "key") shouldBe "1"
+  }
+}

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala

+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
+import nl.lumc.sasc.biopet.core.extensions.Md5sum
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
+import org.broadinstitute.gatk.queue.QScript
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+import SummaryQScriptTest._
+
+/**
+ * Created by pjvanthof on 14/01/16.
+ */
+class SummaryQScriptTest extends TestNGSuite with Matchers {
+  @Test
+  def testNoJobs: Unit = {
+    SummaryQScript.md5sumCache.clear()
+    val script = makeQscript()
+    script.addSummaryJobs()
+    SummaryQScript.md5sumCache shouldBe empty
+  }
+
+  @Test
+  def testFiles: Unit = {
+    SummaryQScript.md5sumCache.clear()
+    val file = new File(s".${File.separator}bla")
+    val script = makeQscript(files = Map("file" -> file))
+    script.addSummaryJobs()
+    SummaryQScript.md5sumCache should not be empty
+    SummaryQScript.md5sumCache.toMap shouldBe Map(
+      new File(s".${File.separator}bla") -> new File(s".${File.separator}bla.md5"))
+    script.functions.size shouldBe 2
+    assert(script.functions
+      .filter(_.isInstanceOf[Md5sum])
+      .map(_.asInstanceOf[Md5sum])
+      .exists(_.cmdLine.contains(" || ")))
+  }
+
+  @Test
+  def testDuplicateFiles: Unit = {
+    SummaryQScript.md5sumCache.clear()
+    val file = new File(s".${File.separator}bla")
+    val script = makeQscript(files = Map("file" -> file, "file2" -> file))
+    script.addSummaryJobs()
+    SummaryQScript.md5sumCache should not be empty
+    SummaryQScript.md5sumCache.toMap shouldBe Map(
+      new File(s".${File.separator}bla") -> new File(s".${File.separator}bla.md5"))
+    script.functions.size shouldBe 2
+    assert(script.functions
+      .filter(_.isInstanceOf[Md5sum])
+      .map(_.asInstanceOf[Md5sum])
+      .exists(_.cmdLine.contains(" || ")))
+  }
+
+  @Test
+  def testAddSummarizable: Unit = {
+    SummaryQScript.md5sumCache.clear()
+    val file = new File(s".${File.separator}bla")
+    val script = makeQscript()
+    script.addSummarizable(makeSummarizable(files = Map("file" -> file, "file2" -> file)), "test")
+    script.summarizables.size shouldBe 1
+    script.addSummaryJobs()
+    SummaryQScript.md5sumCache should not be empty
+    SummaryQScript.md5sumCache.toMap shouldBe Map(
+      new File(s".${File.separator}bla") -> new File(s".${File.separator}bla.md5"))
+    script.functions.size shouldBe 2
+    assert(script.functions
+      .filter(_.isInstanceOf[Md5sum])
+      .map(_.asInstanceOf[Md5sum])
+      .exists(_.cmdLine.contains(" || ")))
+  }
+
+  @Test
+  def testInputFile: Unit = {
+    SummaryQScript.md5sumCache.clear()
+    val file = new File(s".${File.separator}bla")
+    val script = makeQscript()
+    script.addSummarizable(makeSummarizable(files = Map("file" -> file, "file2" -> file)), "test")
+    script.summarizables.size shouldBe 1
+    script.inputFiles :+= InputFile(file, Some("md5sum"))
+    script.inputFiles :+= InputFile(file, None)
+    script.addSummaryJobs()
+    SummaryQScript.md5sumCache should not be empty
+    SummaryQScript.md5sumCache.toMap shouldBe Map(
+      new File(s".${File.separator}bla") -> new File(s".${File.separator}bla.md5"))
+    script.functions.size shouldBe 3
+    assert(script.functions
+      .filter(_.isInstanceOf[Md5sum])
+      .map(_.asInstanceOf[Md5sum])
+      .exists(_.cmdLine.contains(" || ")))
+  }
+
+  @Test
+  def testAddQscript: Unit = {
+    SummaryQScript.md5sumCache.clear()
+    val script = makeQscript()
+    script.addSummaryQScript(script)
+    script.summaryQScripts.head shouldBe script
+  }
+}
+
+object SummaryQScriptTest {
+  def makeQscript(settings: Map[String, Any] = Map(),
+                  files: Map[String, File] = Map(),
+                  c: Map[String, Any] = Map()) =
+    new SummaryQScript with QScript {
+      outputDir = new File(".")
+      override def globalConfig = new Config(c)
+      def summarySettings: Map[String, Any] = settings
+      def summaryFiles: Map[String, File] = files
+      val tempFile = File.createTempFile("summary", ".json")
+      tempFile.deleteOnExit()
+      def summaryFile: File = tempFile
+      def init(): Unit = ???
+      def biopetScript(): Unit = ???
+      def root: Configurable = null
+    }
+
+  def makeSummarizable(files: Map[String, File] = Map(), stats: Map[String, Any] = Map()) = new Summarizable {
+    def summaryFiles: Map[String, File] = files
+    def summaryStats: Any = stats
+  }
+}
\ No newline at end of file

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala

+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.{ PrintWriter, File }
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
+import nl.lumc.sasc.biopet.utils.summary.Summary
+import org.broadinstitute.gatk.queue.function.CommandLineFunction
+import org.broadinstitute.gatk.queue.{ QScript, QSettings }
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import WriteSummaryTest._
+import org.testng.annotations.Test
+
+import scala.util.matching.Regex
+
+/**
+ * Created by pjvanthof on 15/01/16.
+ */
+class WriteSummaryTest extends TestNGSuite with Matchers {
+
+  @Test
+  def testWrongRoot(): Unit = {
+    intercept[IllegalArgumentException] {
+      makeWriter(null)
+    }
+  }
+
+  /** This is a basic summary test, no matter the content this should always be true */
+  def basicSummaryTest(summary: Summary,
+                       name: String,
+                       sampleId: Option[String] = None,
+                       libId: Option[String] = None): Unit = {
+    summary.getValue(sampleId, libId, name) should not be None
+    summary.getValue(sampleId, libId, name, "files", "pipeline").get shouldBe a[Map[_, _]]
+    summary.getValue(sampleId, libId, name, "settings").get shouldBe a[Map[_, _]]
+    summary.getValue(sampleId, libId, name, "executables").get shouldBe a[Map[_, _]]
+
+    summary.getValue("meta") should not be None
+    summary.getValue("meta", "pipeline_name") shouldBe Some(name)
+    summary.getValue("meta", "last_commit_hash") shouldBe Some(nl.lumc.sasc.biopet.LastCommitHash)
+    summary.getValue("meta", "pipeline_version") shouldBe Some(nl.lumc.sasc.biopet.Version)
+    summary.getValue("meta", "output_dir") shouldBe Some(new File(".").getAbsolutePath)
+    summary.getValue("meta", "summary_creation") should not be None
+  }
+
+  def createFakeCheckSum(file: File): Unit = {
+    file.getParentFile.mkdirs()
+    val writer = new PrintWriter(file)
+    writer.println("checksum  file")
+    writer.close()
+    file.deleteOnExit()
+  }
+
+  @Test
+  def testEmpty(): Unit = {
+    val qscript = makeQscript(name = "test")
+    val writer = makeWriter(qscript)
+    writer.freezeFieldValues()
+    writer.deps shouldBe empty
+    writer.run()
+
+    val summary = new Summary(writer.out)
+    basicSummaryTest(summary, "test")
+  }
+
+  @Test
+  def testMergeQscript(): Unit = {
+    val qscript = makeQscript(name = "test")
+    val qscript2 = makeQscript(name = "test2")
+    qscript.addSummaryQScript(qscript2)
+    val summaryWriter = new PrintWriter(qscript2.summaryFile)
+    summaryWriter.println("""{ "test2": "value" }""")
+    summaryWriter.close()
+    val writer = makeWriter(qscript)
+    writer.freezeFieldValues()
+    writer.run()
+
+    val summary = new Summary(writer.out)
+    basicSummaryTest(summary, "test")
+    summary.getValue("test2") shouldBe Some("value")
+  }
+
+  @Test
+  def testSingleJob(): Unit = {
+    val qscript = makeQscript("test")
+    val writer = makeWriter(qscript)
+    val summarizable = makeSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+    qscript.addSummarizable(summarizable, "tool_1")
+    qscript.addSummaryJobs()
+    createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+    writer.freezeFieldValues()
+    writer.run()
+
+    val summary = new Summary(writer.out)
+    basicSummaryTest(summary, "test")
+    summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
+    summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+  }
+
+  @Test
+  def testSingleJavaJob(): Unit = {
+    val qscript = makeQscript("test")
+    val writer = makeWriter(qscript)
+    val summarizable = makeJavaCommand(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+    qscript.add(summarizable)
+    qscript.addSummarizable(summarizable, "tool_1")
+    qscript.addSummaryJobs()
+    createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+    writer.freezeFieldValues()
+    writer.run()
+
+    val summary = new Summary(writer.out)
+    basicSummaryTest(summary, "test")
+    summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
+    summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+    summary.getValue("test", "executables", "java_command", "version") shouldBe Some("test version")
+  }
+
+  @Test
+  def testVersion(): Unit = {
+    val qscript = makeQscript("test")
+    val writer = makeWriter(qscript)
+    val summarizable = makeVersionSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+    qscript.add(summarizable)
+    qscript.addSummarizable(summarizable, "tool_1")
+    qscript.addSummaryJobs()
+    createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+    writer.freezeFieldValues()
+    writer.run()
+
+    val summary = new Summary(writer.out)
+    basicSummaryTest(summary, "test")
+    summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
+    summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+    summary.getValue("test", "executables", "version_command", "version") shouldBe Some("test version")
+  }
+
+  @Test
+  def testSampleLibrary(): Unit = {
+    val qscript = makeSampleLibraryQscript("test", s = Some("sampleName"), l = Some("libName"))
+    val writer = makeWriter(qscript)
+    val summarizable = makeSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+    qscript.addSummarizable(summarizable, "tool_1")
+    qscript.addSummaryJobs()
+    createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+    writer.freezeFieldValues()
+    writer.deps shouldBe empty
+    writer.run()
+
+    val summary = new Summary(writer.out)
+    basicSummaryTest(summary, "test", sampleId = Some("sampleName"), libId = Some("libName"))
+    summary.getValue(Some("sampleName"), Some("libName"), "test", "stats", "tool_1", "key") shouldBe Some("value")
+    summary.getValue(Some("sampleName"), Some("libName"), "test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+  }
+
+  @Test
+  def testSample(): Unit = {
+    val qscript = makeSampleLibraryQscript("test", s = Some("sampleName"))
+    val writer = makeWriter(qscript)
+    val summarizable = makeSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+    qscript.addSummarizable(summarizable, "tool_1")
+    qscript.addSummaryJobs()
+    createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+    writer.freezeFieldValues()
+    writer.deps shouldBe empty
+    writer.run()
+
+    val summary = new Summary(writer.out)
+    basicSummaryTest(summary, "test", sampleId = Some("sampleName"), libId = None)
+    summary.getValue(Some("sampleName"), None, "test", "stats", "tool_1", "key") shouldBe Some("value")
+    summary.getValue(Some("sampleName"), None, "test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+  }
+
+  @Test
+  def testMultisampleQscript(): Unit = {
+    val qscript = makeMultisampleQscript("test", multisampleConfig)
+    val writer = makeWriter(qscript)
+    val summarizable = makeSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+    qscript.addSummarizable(summarizable, "tool_1")
+    qscript.addSummaryJobs()
+    createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+    writer.freezeFieldValues()
+    writer.deps shouldBe empty
+    writer.run()
+
+    val summary = new Summary(writer.out)
+    basicSummaryTest(summary, "test")
+    summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
+    summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+
+    summary.getValue(Some("sampleName"), Some("libName"), "test") should not be None
+  }
+
+}
+
+object WriteSummaryTest {
+  def makeWriter(root: Configurable, c: Map[String, Any] = Map()) = new WriteSummary(root) {
+    override def globalConfig = new Config(c)
+    override def outputs = Seq()
+    override def inputs = Seq()
+    qSettings = new QSettings {
+      jobName = "test"
+      jobTempDir = Files.createTempDir()
+      jobTempDir.deleteOnExit()
+      jobPriority = Some(1)
+    }
+    override def absoluteCommandDirectory() {}
+  }
+
+  def makeQscript(name: String,
+                  settings: Map[String, Any] = Map(),
+                  files: Map[String, File] = Map(),
+                  c: Map[String, Any] = Map()) =
+    new SummaryQScript with QScript {
+      summaryName = name
+      outputDir = new File(".").getAbsoluteFile
+      override def globalConfig = new Config(c)
+      def summarySettings: Map[String, Any] = settings
+      def summaryFiles: Map[String, File] = files
+      val tempFile = File.createTempFile("summary", ".json")
+      tempFile.deleteOnExit()
+      def summaryFile: File = tempFile
+      def init(): Unit = {}
+      def biopetScript(): Unit = {}
+      def root: Configurable = null
+    }
+
+  def makeSampleLibraryQscript(name: String,
+                               settings: Map[String, Any] = Map(),
+                               files: Map[String, File] = Map(),
+                               c: Map[String, Any] = Map(),
+                               s: Option[String] = None,
+                               l: Option[String] = None) =
+    new SummaryQScript with QScript with SampleLibraryTag {
+      sampleId = s
+      libId = l
+      summaryName = "test"
+      outputDir = new File(".").getAbsoluteFile
+      override def globalConfig = new Config(c)
+      def summarySettings: Map[String, Any] = settings
+      def summaryFiles: Map[String, File] = files
+      val tempFile = File.createTempFile("summary", ".json")
+      tempFile.deleteOnExit()
+      def summaryFile: File = tempFile
+      def init(): Unit = {}
+      def biopetScript(): Unit = {}
+      def root: Configurable = null
+    }
+
+  def makeMultisampleQscript(name: String,
+                             c: Map[String, Any],
+                             settings: Map[String, Any] = Map(),
+                             files: Map[String, File] = Map()) =
+    new MultiSampleQScript with QScript {
+      summaryName = "test"
+      outputDir = new File(".").getAbsoluteFile
+      override def globalConfig = new Config(c)
+      def summarySettings: Map[String, Any] = settings
+      def summaryFiles: Map[String, File] = files
+      val tempFile = File.createTempFile("summary", ".json")
+      tempFile.deleteOnExit()
+      def summaryFile: File = tempFile
+      def init(): Unit = {}
+      def biopetScript(): Unit = {}
+      def root: Configurable = null
+
+      class Sample(id: String) extends AbstractSample(id) {
+        class Library(id: String) extends AbstractLibrary(id) {
+          protected def addJobs(): Unit = {}
+          def summaryFiles: Map[String, File] = files
+          def summaryStats: Any = Map()
+        }
+
+        def makeLibrary(id: String): Library = new Library(id)
+        protected def addJobs(): Unit = {}
+        def summaryFiles: Map[String, File] = files
+        def summaryStats: Any = Map()
+      }
+
+      def makeSample(id: String): Sample = new Sample(id)
+
+      def addMultiSampleJobs(): Unit = {}
+    }
+
+  val multisampleConfig = Map("samples" -> Map("sampleName" -> Map("libraries" -> Map("libName" -> Map()))))
+
+  def makeSummarizable(files: Map[String, File] = Map(), stats: Map[String, Any] = Map()) = new Summarizable {
+    def summaryFiles: Map[String, File] = files
+    def summaryStats: Any = stats
+  }
+
+  def makeJavaCommand(files: Map[String, File] = Map(),
+                      stats: Map[String, Any] = Map(),
+                      c: Map[String, Any] = Map()) = new BiopetJavaCommandLineFunction with Summarizable with Version {
+    override def globalConfig = new Config(c)
+    override def configName = "java_command"
+    def root: Configurable = null
+    def summaryStats: Map[String, Any] = stats
+    def summaryFiles: Map[String, File] = files
+
+    def versionCommand: String = "echo test version"
+    def versionRegex: Regex = """(.*)""".r
+    override def getVersion = Some("test version")
+
+    override def outputs = Seq()
+    override def inputs = Seq()
+    qSettings = new QSettings {
+      jobName = "test"
+      jobTempDir = Files.createTempDir()
+      jobTempDir.deleteOnExit()
+      jobPriority = Some(1)
+    }
+    override def absoluteCommandDirectory() {}
+  }
+
+  def makeVersionSummarizable(files: Map[String, File] = Map(),
+                              stats: Map[String, Any] = Map(),
+                              c: Map[String, Any] = Map()) =
+    new CommandLineFunction with Configurable with Summarizable with Version {
+      override def globalConfig = new Config(c)
+      override def configName = "version_command"
+      def root: Configurable = null
+
+      def summaryFiles: Map[String, File] = files
+      def summaryStats: Any = stats
+
+      def versionCommand: String = "echo test version"
+      def versionRegex: Regex = """(.*)""".r
+      override def getVersion = Some("test version")
+
+      def commandLine: String = ""
+
+      override def outputs = Seq()
+      override def inputs = Seq()
+      qSettings = new QSettings {
+        jobName = "test"
+        jobTempDir = Files.createTempDir()
+        jobTempDir.deleteOnExit()
+        jobPriority = Some(1)
+      }
+      override def absoluteCommandDirectory() {}
+    }
+
+}
\ No newline at end of file

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

@@ -26,18 +26,19 @@ import scala.collection.mutable
 import scala.io.Source
 
 /**
- * Extension for cutadept
- * Based on version 1.5
+ * Extension for cutadapt
+ * Started with version 1.5
+ * Updated to version 1.9 (18-01-2016 by wyleung)
  */