From 0db8718734daaeba5307a9e3f6b644cee56bec13 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 May 2016 17:13:20 +0200
Subject: [PATCH] Added tests for deps
---
.../biopet/core/WriteDependenciesTest.scala | 23 ++++++++++++++++---
1 file changed, 20 insertions(+), 3 deletions(-)
diff --git a/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala b/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
index 351cc6b6e..c40f615c2 100644
--- a/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
+++ b/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import java.nio.file.Files
+import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.function.QFunction
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
@@ -26,11 +27,27 @@ class WriteDependenciesTest extends TestNGSuite with Matchers {
}
@Test
- def test: Unit = {
+ def testDeps: Unit = {
val outputFile = File.createTempFile("deps.", ".json")
outputFile.deleteOnExit()
- WriteDependencies.writeDependencies(Qfunc(file1 :: Nil, file2 :: Nil) :: Qfunc(file2 :: Nil, file3 :: Nil) :: Nil, outputFile)
- println(Source.fromFile(outputFile).getLines().mkString("\n"))
+ val func1 = Qfunc(file1 :: Nil, file2 :: Nil)
+ val func2 = Qfunc(file2 :: Nil, file3 :: Nil)
+ WriteDependencies.writeDependencies(func1 :: func2 :: Nil, outputFile)
+ val deps = ConfigUtils.fileToConfigMap(outputFile)
+ deps("jobs") shouldBe a[Map[_, _]]
+ val jobs = deps("jobs").asInstanceOf[Map[String, Map[String, Any]]]
+ jobs.count(_._1.contains("Qfunc")) shouldBe 2
+
+ deps("files") shouldBe a[List[_]]
+ val files = deps("files").asInstanceOf[List[Map[String, Any]]]
+ val paths = files.map(x => x.get("path")).flatten
+ assert(paths.contains(file1.toString))
+ assert(paths.contains(file2.toString))
+ assert(paths.contains(file3.toString))
+
+ files.find(_.get("path") == Some(file1.toString)).flatMap(_.get("pipeline_input")) shouldBe Some(true)
+ files.find(_.get("path") == Some(file2.toString)).flatMap(_.get("pipeline_input")) shouldBe Some(false)
+ files.find(_.get("path") == Some(file3.toString)).flatMap(_.get("pipeline_input")) shouldBe Some(false)
}
}
--
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