Merge branch 'feature-report_core_testing' into 'develop'

Feature report core testing



See merge request !330

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

@@ -93,9 +93,9 @@ trait ReportBuilder extends ToolCommand {
   private var total = 0
 
   private var _sampleId: Option[String] = None
-  protected def sampleId = _sampleId
+  protected[report] def sampleId = _sampleId
   private var _libId: Option[String] = None
-  protected def libId = _libId
+  protected[report] def libId = _libId
 
   case class ExtFile(resourcePath: String, targetPath: String)
 
@@ -152,6 +152,8 @@ trait ReportBuilder extends ToolCommand {
     total = ReportBuilder.countPages(indexPage)
     logger.info(total + " pages to be generated")
 
+    done = 0
+
     logger.info("Generate pages")
     val jobs = generatePage(summary, indexPage, cmdArgs.outputDir,
       args = pageArgs ++ cmdArgs.pageArgs.toMap ++
@@ -216,7 +218,7 @@ object ReportBuilder {
   protected val engine = new TemplateEngine()
 
   /** Cache of temp file for templates from the classpath / jar */
-  private var templateCache: Map[String, File] = Map()
+  private[report] var templateCache: Map[String, File] = Map()
 
   /** This will give the total number of pages including all nested pages */
   def countPages(page: ReportPage): Int = {

public/biopet-core/src/test/resources/empty_summary.json

+{
+  "samples": {
+    "sampleName": {
+      "libraries": {
+        "libName": {
+
+        }
+      }
+    }
+  }
+}
\ No newline at end of file

public/biopet-core/src/test/resources/template.ssp

+<%@ var arg: String%>
+${arg}
\ No newline at end of file

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

+package nl.lumc.sasc.biopet.core.report
+
+import java.io.File
+import java.nio.file.Paths
+
+import com.google.common.io.Files
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 24/02/16.
+ */
+class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @Test
+  def testGeneratePages(): Unit = {
+    val builder = new MultisampleReportBuilder {
+      def reportName: String = "test"
+      def indexPage: ReportPage = ReportPage("Samples" -> generateSamplesPage(Map()) :: Nil, Nil, Map())
+
+      def samplePage(sampleId: String, args: Map[String, Any]): ReportPage =
+        ReportPage("Libraries" -> generateLibraryPage(Map("sampleId" -> Some(sampleId))) :: Nil, Nil, Map())
+
+      def libraryPage(sampleId: String, libraryId: String, args: Map[String, Any]) = ReportPage(Nil, Nil, Map())
+    }
+
+    val tempDir = Files.createTempDir()
+    tempDir.deleteOnExit()
+    val args = Array("-s", resourcePath("/empty_summary.json"), "-o", tempDir.getAbsolutePath)
+    builder.main(args)
+    builder.extFiles.foreach(x => new File(tempDir, "ext" + File.separator + x.targetPath) should exist)
+
+    def createFile(path: String*) = new File(tempDir, path.mkString(File.separator))
+
+    createFile("index.html") should exist
+    createFile("Samples", "index.html") should exist
+    createFile("Samples", "sampleName", "index.html") should exist
+    createFile("Samples", "sampleName", "Libraries", "index.html") should exist
+    createFile("Samples", "sampleName", "Libraries", "libName", "index.html") should exist
+  }
+
+}

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

+package nl.lumc.sasc.biopet.core.report
+
+import java.io.File
+import java.nio.file.Paths
+
+import com.google.common.io.Files
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ DataProvider, Test }
+
+/**
+ * Created by pjvanthof on 24/02/16.
+ */
+class ReportBuilderTest extends TestNGSuite with Matchers {
+
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @DataProvider(name = "testGeneratePages")
+  def generatePageProvider = {
+    val sample = Array(Some("sampleName"), None)
+    val lib = Array(Some("libName"), None)
+    val nested = Array(false, true)
+    for (s <- sample; l <- lib; n <- nested) yield Array(s, l, n)
+  }
+
+  @Test(dataProvider = "testGeneratePages")
+  def testGeneratePages(sample: Option[String], lib: Option[String], nested: Boolean): Unit = {
+    val builder = new ReportBuilder {
+      def reportName: String = "test"
+      def indexPage: ReportPage = ReportPage(
+        (if (nested) "p1" -> ReportPage(Nil, Nil, Map()) :: Nil else Nil), Nil, Map())
+    }
+
+    val tempDir = Files.createTempDir()
+    tempDir.deleteOnExit()
+    val args = Array("-s", resourcePath("/empty_summary.json"), "-o", tempDir.getAbsolutePath) ++
+      sample.map(x => Array("-a", s"sampleId=$x")).getOrElse(Array()) ++
+      lib.map(x => Array("-a", s"libId=$x")).getOrElse(Array())
+    builder.main(args)
+    builder.sampleId shouldBe sample
+    builder.libId shouldBe lib
+    builder.extFiles.foreach(x => new File(tempDir, "ext" + File.separator + x.targetPath) should exist)
+    new File(tempDir, "index.html") should exist
+    new File(tempDir, "p1" + File.separator + "index.html").exists() shouldBe nested
+  }
+
+  @Test
+  def testCountPages: Unit = {
+    ReportBuilder.countPages(ReportPage(Nil, Nil, Map())) shouldBe 1
+    ReportBuilder.countPages(ReportPage(
+      "p1" -> ReportPage(Nil, Nil, Map()) :: Nil,
+      Nil, Map())) shouldBe 2
+    ReportBuilder.countPages(ReportPage(
+      "p1" -> ReportPage(Nil, Nil, Map()) :: "p2" -> ReportPage(Nil, Nil, Map()) :: Nil,
+      Nil, Map())) shouldBe 3
+    ReportBuilder.countPages(ReportPage(
+      "p1" -> ReportPage("p1" -> ReportPage(Nil, Nil, Map()) :: Nil, Nil, Map()) :: Nil,
+      Nil, Map())) shouldBe 3
+    ReportBuilder.countPages(ReportPage(
+      "p1" -> ReportPage(Nil, Nil, Map()) :: "p2" -> ReportPage("p1" -> ReportPage(Nil, Nil, Map()) :: Nil, Nil, Map()) :: Nil,
+      Nil, Map())) shouldBe 4
+  }
+
+  @Test
+  def testRenderTemplate: Unit = {
+    ReportBuilder.templateCache = Map()
+    ReportBuilder.templateCache shouldBe empty
+    ReportBuilder.renderTemplate("/template.ssp", Map("arg" -> "test")) shouldBe "test"
+    ReportBuilder.templateCache.size shouldBe 1
+    ReportBuilder.renderTemplate("/template.ssp", Map("arg" -> "bla")) shouldBe "bla"
+    ReportBuilder.templateCache.size shouldBe 1
+  }
+}

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

+package nl.lumc.sasc.biopet.core.report
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 24/02/16.
+ */
+class ReportSectionTest extends TestNGSuite with Matchers {
+
+  @Test
+  def testSectionRender: Unit = {
+    ReportSection("/template.ssp", Map("arg" -> "test")).render() shouldBe "test"
+    ReportSection("/template.ssp").render(Map("arg" -> "test")) shouldBe "test"
+  }
+}