From 8a5bf774fff5c7a79de3e4a62695a2c2c93fd554 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 31 Aug 2015 17:26:06 +0200
Subject: [PATCH] SummaryToTsvTest
---
.../sasc/biopet/tools/SamplesTsvToJson.scala | 4 +-
.../src/test/resources/test.summary.json | 17 +++++
.../sasc/biopet/tools/MpileupToVcfTest.scala | 3 +-
.../sasc/biopet/tools/PrefixFastqTest.scala | 3 +-
.../biopet/tools/SamplesTsvToJsonTest.scala | 17 ++---
.../sasc/biopet/tools/SummaryToTsvTest.scala | 73 +++++++++++++++++++
6 files changed, 101 insertions(+), 16 deletions(-)
create mode 100644 public/biopet-framework/src/test/resources/test.summary.json
create mode 100644 public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
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 1dde5ba87..ad5f07c98 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
@@ -44,7 +44,7 @@ object SamplesTsvToJson extends ToolCommand {
println(jsonString)
}
- def mapFromFile(inputFile: File) : Map[String, Any] = {
+ def mapFromFile(inputFile: File): Map[String, Any] = {
val reader = Source.fromFile(inputFile)
val lines = reader.getLines().toList.filter(!_.isEmpty)
val header = lines.head.split("\t")
@@ -78,7 +78,7 @@ object SamplesTsvToJson extends ToolCommand {
librariesValues.foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
}
- def stringFromInputs(inputs: List[File]) : String = {
+ def stringFromInputs(inputs: List[File]): String = {
val map = inputs.map(f => mapFromFile(f)).foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
mapToJson(map).spaces2
}
diff --git a/public/biopet-framework/src/test/resources/test.summary.json b/public/biopet-framework/src/test/resources/test.summary.json
new file mode 100644
index 000000000..aff9e962e
--- /dev/null
+++ b/public/biopet-framework/src/test/resources/test.summary.json
@@ -0,0 +1,17 @@
+{
+ "samples" : {
+ "016" : {
+ "libraries" : {
+ "L001" : {
+ "flexiprep" : {
+ "settings" : {
+ "skip_trim" : false,
+ "skip_clip" : false,
+ "paired" : true
+ }
+ }
+ }
+ }
+ }
+ }
+}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
index 6f6fef89b..032f9a913 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
@@ -13,7 +13,6 @@ import org.testng.annotations.Test
import scala.collection.JavaConversions._
-
/**
* Created by ahbbollen on 27-8-15.
*/
@@ -52,7 +51,7 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def extraValidateOutVcf() = {
val tmp = File.createTempFile("mpileup", ".vcf")
- val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath, "--minDP", "1" ,"--minAP", "1")
+ val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath, "--minDP", "1", "--minAP", "1")
main(args)
val vcfReader = new VCFFileReader(tmp, false)
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
index 7f85dc9f8..41db9e3ae 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
@@ -11,7 +11,6 @@ import org.testng.annotations.Test
import scala.collection.JavaConversions._
-
/**
* Created by ahbbollen on 28-8-15.
*/
@@ -41,7 +40,7 @@ class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
val reader = new FastqReader(temp)
- for (read <- reader.iterator()){
+ for (read <- reader.iterator()) {
read.getReadString.startsWith("AAA") shouldBe true
}
}
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 5a21bafa1..6fba307e3 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
@@ -8,7 +8,6 @@ import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
-
/**
* Created by ahbbollen on 28-8-15.
*/
@@ -28,22 +27,22 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testNoSampleColumn() = {
val tsv = resourcePath("/no_sample.tsv")
- val thrown = the [IllegalStateException] thrownBy main(Array("-i", tsv))
- thrown.getMessage should equal ("Sample column does not exist in: " + tsv)
+ val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv))
+ thrown.getMessage should equal("Sample column does not exist in: " + tsv)
}
@Test
def testNumberInLibs = {
val tsv = resourcePath("/number.tsv")
- val thrown = the [IllegalStateException] thrownBy main(Array("-i", tsv))
- thrown.getMessage should equal ("Sample or library may not start with a number")
+ val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv))
+ thrown.getMessage should equal("Sample or library may not start with a number")
}
@Test
def testSampleIDs = {
val tsv = resourcePath("/same.tsv")
- val thrown = the [IllegalStateException] thrownBy main(Array("-i", tsv))
- thrown.getMessage should equal ("Combination of Sample_ID_1 and Lib_ID_1 is found multiple times")
+ val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv))
+ thrown.getMessage should equal("Combination of Sample_ID_1 and Lib_ID_1 is found multiple times")
}
@@ -52,7 +51,7 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
val tsv = new File(resourcePath("/sample.tsv"))
val json = stringFromInputs(List(tsv))
- json should equal (
+ json should equal(
"""|{
| "samples" : {
| "Sample_ID_1" : {
@@ -73,6 +72,4 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
|}""".stripMargin)
}
-
-
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
new file mode 100644
index 000000000..5bf947eb0
--- /dev/null
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
@@ -0,0 +1,73 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import nl.lumc.sasc.biopet.tools.SamplesTsvToJson._
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import nl.lumc.sasc.biopet.core.summary.Summary
+
+
+/**
+ * Created by ahbbollen on 31-8-15.
+ */
+class SummaryToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
+ import SummaryToTsv._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ @Test
+ def testMain = {
+ val tsv = resourcePath("/test.summary.json")
+
+ noException should be thrownBy main(Array("-s", tsv, "-p", "something=flexiprep:settings:skip_trim",
+ "-m", "root"))
+ noException should be thrownBy main(Array("-s", tsv, "-p", "something=flexiprep:settings:skip_trim",
+ "-m", "sample"))
+ noException should be thrownBy main(Array("-s", tsv, "-p", "something=flexiprep:settings:skip_trim",
+ "-m", "lib"))
+ }
+
+ @Test
+ def testHeader = {
+ val tsv = resourcePath("/test.summary.json")
+ val path = List("something=flexiprep:settings:skip_trim")
+
+ val paths = path.map(x => {
+ val split = x.split("=", 2)
+ split(0) -> split(1).split(":")
+ }).toMap
+
+ createHeader(paths) should equal("\tsomething")
+ }
+
+ @Test
+ def testLine = {
+ val tsv = resourcePath("/test.summary.json")
+ val path = List("something=flexiprep:settings:skip_trim")
+
+ val paths = path.map(x => {
+ val split = x.split("=", 2)
+ split(0) -> split(1).split(":")
+ }).toMap
+
+ val summary = new Summary(new File(tsv))
+ val values = fetchValues(summary, paths)
+
+ val line = values.head._2.keys.map(x => createLine(paths, values, x)).head
+ line should equal("value\t")
+ val sample_values = fetchValues(summary, paths, true, false)
+ val sample_line = sample_values.head._2.keys.map(x => createLine(paths, sample_values, x)).head
+ sample_line should equal("016\t")
+
+ val lib_values = fetchValues(summary, paths, false, true)
+ val lib_line = lib_values.head._2.keys.map(x => createLine(paths, lib_values, x)).head
+ lib_line should equal("016-L001\tfalse")
+ }
+
+}
--
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