Adding empty summary test

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

@@ -5,8 +5,7 @@ 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, QSettings}
-import org.broadinstitute.gatk.queue.function.QFunction
+import org.broadinstitute.gatk.queue.QScript
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test

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

+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.File
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
+import nl.lumc.sasc.biopet.utils.summary.Summary
+import org.broadinstitute.gatk.queue.{QScript, QSettings}
+import org.broadinstitute.gatk.queue.function.QFunction
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import WriteSummaryTest._
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+  * Created by pjvanthof on 15/01/16.
+  */
+class WriteSummaryTest extends TestNGSuite with Matchers {
+
+  def testWrongRoot: Unit = {
+    intercept[IllegalArgumentException] {
+      makeWriter(null)
+    }
+  }
+
+  @Test
+  def testEmpty: Unit = {
+    val qscript = makeQscript()
+    val writer = makeWriter(qscript)
+    writer.freezeFieldValues()
+
+    writer.run()
+
+    val summary = new Summary(writer.out)
+
+    summary.getValue("test") should not be None
+    summary.getValue("test", "files") shouldBe Some(Map("pipeline" -> Map()))
+    summary.getValue("test", "settings") shouldBe Some(Map())
+    summary.getValue("test", "executables") shouldBe Some(Map())
+
+    summary.getValue("meta") should not be None
+    summary.getValue("meta", "pipeline_name") shouldBe Some("test")
+    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
+  }
+}
+
+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(settings: Map[String, Any] = Map(),
+                  files: Map[String, File] = Map(),
+                  c: Map[String, Any] = Map()) =
+    new SummaryQScript 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
+    }
+
+  def makeSummarizable(files: Map[String, File] = Map(), stats: Map[String, Any] = Map()) = new Summarizable {
+    def summaryFiles: Map[String, File] = files
+    def summaryStats: Any = stats
+  }
+}
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