From 6f49ff051c7c8422f01eb17a0e74d76be74e453c Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Fri, 28 Aug 2015 13:24:32 +0200
Subject: [PATCH] Fix most of #196. Only documentation remaining
---
.../sasc/biopet/tools/SamplesTsvToJson.scala | 2 +-
.../biopet/tools/SamplesTsvToJsonTest.scala | 27 +++++++++++++++++++
2 files changed, 28 insertions(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
index ccf8f90b1..b2ccbc61c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
@@ -71,7 +71,7 @@ object SamplesTsvToJson extends ToolCommand {
t <- 0 until values.size if !values(t).isEmpty && t != sampleColumn && t != libraryColumn
) yield header(t) -> values(t)).toMap
library match {
- case Some(lib) => Map("samples" -> Map(sample -> Map("libraries" -> Map(library -> valuesMap))))
+ case Some(lib) => Map("samples" -> Map(sample -> Map("libraries" -> Map(library.get -> valuesMap))))
case _ => Map("samples" -> Map(sample -> valuesMap))
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
index f9b32ca38..5a21bafa1 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
@@ -8,6 +8,7 @@ import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
+
/**
* Created by ahbbollen on 28-8-15.
*/
@@ -46,6 +47,32 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
}
+ @Test
+ def testJson = {
+ val tsv = new File(resourcePath("/sample.tsv"))
+ val json = stringFromInputs(List(tsv))
+
+ json should equal (
+ """|{
+ | "samples" : {
+ | "Sample_ID_1" : {
+ | "libraries" : {
+ | "Lib_ID_1" : {
+ | "bam" : "MyFirst.bam"
+ | }
+ | }
+ | },
+ | "Sample_ID_2" : {
+ | "libraries" : {
+ | "Lib_ID_2" : {
+ | "bam" : "MySecond.bam"
+ | }
+ | }
+ | }
+ | }
+ |}""".stripMargin)
+ }
+
}
--
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