From 684fe7c88803cd0a23bea33df3dd30243cef0e60 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 14 Jan 2016 23:37:42 +0100
Subject: [PATCH] Adding tests for input files for summary
---
.../biopet/core/summary/WriteSummary.scala | 1 +
.../core/summary/SummaryQScriptTest.scala | 40 +++++++++++++++++++
2 files changed, 41 insertions(+)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index 02c860fdb..bb6e1bf56 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/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 = {
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 1f3aec58a..ef97c8af8 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
@@ -2,6 +2,8 @@ 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, QSettings}
import org.broadinstitute.gatk.queue.function.QFunction
@@ -32,6 +34,10 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
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
@@ -44,6 +50,10 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
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
@@ -58,9 +68,39 @@ class SummaryQScriptTest extends TestNGSuite with Matchers {
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 {
--
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