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biopet.biopet
Commit b34b4b44 authored by Peter van 't Hof's avatar Peter van 't Hof
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Explict test noException

parent 4fa9758a
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Showing with 12 additions and 12 deletions
generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala
View file @ b34b4b44
......@@ -46,21 +46,21 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
def testNcbiAssembly(): Unit = {
val pipeline = initPipeline(Map())
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("ncbi_assembly_id" -> "id")))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
def testSingleFasta(): Unit = {
val pipeline = initPipeline(Map())
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri")))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
def testMultiFasta(): Unit = {
val pipeline = initPipeline(Map())
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> List("uri", "uri2", "uri3.gz"))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
......@@ -68,7 +68,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(Map("download_annotations" -> true))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
"dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf.gz")))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
......@@ -76,7 +76,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(Map("download_annotations" -> true))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
"dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf.gz", "contig_map" -> Map("1" -> "chr1"))))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
......@@ -84,7 +84,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(Map("download_annotations" -> true))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
"dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf", "contig_map" -> Map("1" -> "chr1"))))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
......@@ -92,7 +92,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(Map("download_annotations" -> true))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
"dbsnp" -> Map("version" -> Map(("vcf_uri" -> "uri.vcf"))))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
......@@ -100,7 +100,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(Map("download_annotations" -> true))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
"dbsnp" -> Map("version" -> Map("vcf_uri" -> List("uri.vcf.gz", "uri2.vcf.gz"))))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
......@@ -108,7 +108,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(Map("download_annotations" -> true))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
"vep" -> Map("version" -> Map("cache_uri" -> "something/human_vep_80_hg19.tar.gz")))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
......@@ -116,7 +116,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(Map("download_annotations" -> true))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
"gene_annotation" -> Map("version" -> Map("gtf_uri" -> "bla.gf.gz")))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
......@@ -124,7 +124,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(Map("download_annotations" -> true))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
"gene_annotation" -> Map("version" -> Map("gtf_uri" -> "bla.gf")))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
@Test
......@@ -132,7 +132,7 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(Map("download_annotations" -> true))
pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
"gene_annotation" -> Map("version" -> Map("gff_uri" -> "bla.gf")))))
pipeline.script()
noException should be thrownBy pipeline.script()
}
}
......
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