diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
index 56d9d56ab76c7fe1d302932cb37227fe9d84756b..1be487ff6d1309685d004d4b2f8f8b5523a93d75 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
@@ -7,8 +7,8 @@ import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
/**
- * Created by pjvanthof on 14/01/16.
- */
+ * Created by pjvanthof on 14/01/16.
+ */
class SummarizableTest extends TestNGSuite with Matchers {
@Test
def testDefaultMerge: Unit = {
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
index 39afff6b3b3280c858d3c7184f282b06081594ab..a53fe068f9537cdce91a75f45ef9393631377d0d 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
@@ -4,7 +4,7 @@ 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 nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
import org.broadinstitute.gatk.queue.QScript
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
@@ -12,8 +12,8 @@ import org.testng.annotations.Test
import SummaryQScriptTest._
/**
- * Created by pjvanthof on 14/01/16.
- */
+ * Created by pjvanthof on 14/01/16.
+ */
class SummaryQScriptTest extends TestNGSuite with Matchers {
@Test
def testNoJobs: Unit = {
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
index 82d7c6a2957e480ec224e2a194512a7d5b9ab29c..4bb196c162ddb93c85b19d1364d34789fb77e8b9 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
@@ -1,52 +1,198 @@
package nl.lumc.sasc.biopet.core.summary
-import java.io.File
+import java.io.{ PrintWriter, File }
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
+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.{QScript, QSettings}
-import org.broadinstitute.gatk.queue.function.QFunction
+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.io.Source
+import scala.util.matching.Regex
/**
- * Created by pjvanthof on 15/01/16.
- */
+ * Created by pjvanthof on 15/01/16.
+ */
class WriteSummaryTest extends TestNGSuite with Matchers {
- def testWrongRoot: Unit = {
+ @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()
+ 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")
+ }
- 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())
+ @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()
- 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
+ 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 {
@@ -63,10 +209,33 @@ object WriteSummaryTest {
override def absoluteCommandDirectory() {}
}
- def makeQscript(settings: Map[String, Any] = Map(),
+ 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)
@@ -75,13 +244,103 @@ object WriteSummaryTest {
val tempFile = File.createTempFile("summary", ".json")
tempFile.deleteOnExit()
def summaryFile: File = tempFile
- def init(): Unit = ???
- def biopetScript(): Unit = ???
+ 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