From 51f894334c4b497bd6472921ff5da45f32d838eb Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 11 Apr 2016 09:02:38 +0200
Subject: [PATCH] Added spec parsing unit test
---
.../src/test/resources/specs/files.specs | 26 +++++++++++++++++
.../src/test/resources/specs/test.gens | 0
.../src/test/resources/specs/test.gens_info | 0
.../resources/specs/test.gens_info_by_sample | 0
.../test/resources/specs/test.gens_summary | 0
.../test/resources/specs/test.gens_warnings | 0
.../pipelines/gwastest/GwasTestTest.scala | 29 +++++++++++++++++++
7 files changed, 55 insertions(+)
create mode 100644 public/gwas-test/src/test/resources/specs/files.specs
create mode 100644 public/gwas-test/src/test/resources/specs/test.gens
create mode 100644 public/gwas-test/src/test/resources/specs/test.gens_info
create mode 100644 public/gwas-test/src/test/resources/specs/test.gens_info_by_sample
create mode 100644 public/gwas-test/src/test/resources/specs/test.gens_summary
create mode 100644 public/gwas-test/src/test/resources/specs/test.gens_warnings
diff --git a/public/gwas-test/src/test/resources/specs/files.specs b/public/gwas-test/src/test/resources/specs/files.specs
new file mode 100644
index 000000000..6385b4296
--- /dev/null
+++ b/public/gwas-test/src/test/resources/specs/files.specs
@@ -0,0 +1,26 @@
+{
+ files = (
+ {
+ chromosome = "chrQ";
+ name = "imputation_06/test";
+ orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr1";
+ },
+ {
+ chromosome = "chrQ";
+ name = "imputation_06/test";
+ orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr1";
+ },
+ {
+ chromosome = "chrQ";
+ name = "imputation_06/test";
+ orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr22";
+ },
+ {
+ chromosome = "chrQ";
+ name = "imputation_06/test";
+ orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr22";
+ }
+ );
+ jids = ( "2102064" );
+ type = "tped3col";
+}
\ No newline at end of file
diff --git a/public/gwas-test/src/test/resources/specs/test.gens b/public/gwas-test/src/test/resources/specs/test.gens
new file mode 100644
index 000000000..e69de29bb
diff --git a/public/gwas-test/src/test/resources/specs/test.gens_info b/public/gwas-test/src/test/resources/specs/test.gens_info
new file mode 100644
index 000000000..e69de29bb
diff --git a/public/gwas-test/src/test/resources/specs/test.gens_info_by_sample b/public/gwas-test/src/test/resources/specs/test.gens_info_by_sample
new file mode 100644
index 000000000..e69de29bb
diff --git a/public/gwas-test/src/test/resources/specs/test.gens_summary b/public/gwas-test/src/test/resources/specs/test.gens_summary
new file mode 100644
index 000000000..e69de29bb
diff --git a/public/gwas-test/src/test/resources/specs/test.gens_warnings b/public/gwas-test/src/test/resources/specs/test.gens_warnings
new file mode 100644
index 000000000..e69de29bb
diff --git a/public/gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala b/public/gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
index 23bf7b43c..01b098d6f 100644
--- a/public/gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
+++ b/public/gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
@@ -32,6 +32,35 @@ class GwasTestTest extends TestNGSuite with Matchers {
pipeline.script()
}
+ @Test
+ def testFromGens: Unit = {
+ val pipeline = initPipeline(GwasTestTest.config ++
+ Map("input_gens" -> List(Map("genotypes" -> GwasTestTest.vcfFile, "contig" -> "chrQ"))
+ )
+ )
+ pipeline.script()
+ }
+
+ @Test
+ def testWrongContig: Unit = {
+ val pipeline = initPipeline(GwasTestTest.config ++
+ Map("input_gens" -> List(Map("genotypes" -> GwasTestTest.vcfFile, "contig" -> "chrBla"))
+ )
+ )
+ intercept[IllegalStateException] {
+ pipeline.script()
+ }
+ }
+
+ @Test
+ def testFromSpecs: Unit = {
+ val pipeline = initPipeline(GwasTestTest.config ++
+ Map("imute_specs_file" -> GwasTestTest.resourcePath("/specs/files.specs"))
+ )
+ pipeline.script()
+ }
+
+
@Test
def testEmpty: Unit = {
val pipeline = initPipeline(GwasTestTest.config)
--
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