Commit d37ebc75 authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent 91dfe546
......@@ -14,20 +14,20 @@
*/
package nl.lumc.sasc.biopet.pipelines.basty
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.{Raxml, RunGubbins}
import nl.lumc.sasc.biopet.extensions.gatk.{BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator}
import nl.lumc.sasc.biopet.extensions.{ Raxml, RunGubbins }
import nl.lumc.sasc.biopet.extensions.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.extensions.tools.{BastyGenerateFasta, VcfStats}
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.extensions.tools.{ BastyGenerateFasta, VcfStats }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
/**
* Created by pjvanthof on 27/09/16.
......
......@@ -61,7 +61,6 @@ class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
}
val tempDir = Files.createTempDir()
tempDir.deleteOnExit()
val args = Array("-s", dbFile.getAbsolutePath, "-o", tempDir.getAbsolutePath)
......
......@@ -21,7 +21,7 @@ import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{DataProvider, Test}
import org.testng.annotations.{ DataProvider, Test }
import scala.concurrent.Await
import scala.concurrent.duration.Duration
......
......@@ -14,20 +14,20 @@
*/
package nl.lumc.sasc.biopet.core.summary
import java.io.{File, PrintWriter}
import java.io.{ File, PrintWriter }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
import nl.lumc.sasc.biopet.utils.summary.Summary
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.queue.{QScript, QSettings}
import org.broadinstitute.gatk.queue.{ QScript, QSettings }
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import WriteSummaryTest._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import org.apache.commons.io.FileUtils
import org.testng.annotations.{AfterClass, Test}
import org.testng.annotations.{ AfterClass, Test }
import scala.concurrent.Await
import scala.concurrent.duration.Duration
......
......@@ -72,7 +72,6 @@ class SummaryDbTest extends TestNGSuite with Matchers {
Await.result(db.getLibraries(), Duration.Inf) shouldBe empty
val libraryId = Await.result(db.createLibrary("test_lib", runId, sampleId), Duration.Inf)
Await.result(db.getLibraries(), Duration.Inf) shouldBe Seq(Schema.Library(libraryId, "test_lib", runId, sampleId, None))
Await.result(db.getLibraryName(libraryId), Duration.Inf) shouldBe Some("test_lib")
Await.result(db.getLibraryId(runId, sampleId, "test_lib"), Duration.Inf) shouldBe Some(libraryId)
......@@ -328,21 +327,20 @@ class SummaryDbTest extends TestNGSuite with Matchers {
val libraryId = Await.result(db.createLibrary("test_library", runId, sampleId), Duration.Inf)
Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path", "md5", link = false, 1), Duration.Inf)
Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,None,None,None,"key","path","md5",link = false,1))
Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path","md5",link = false,1))
Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0, 0, None, None, None, "key", "path", "md5", link = false, 1))
Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0, 0, None, None, None, "key", "path", "md5", link = false, 1))
Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path2", "md5", link = false, 1), Duration.Inf)
Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,None,None,None,"key","path2","md5",link = false,1))
Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path2","md5",link = false,1))
Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0, 0, None, None, None, "key", "path2", "md5", link = false, 1))
Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0, 0, None, None, None, "key", "path2", "md5", link = false, 1))
// Test join queries
Await.result(db.createOrUpdateFile(runId, pipelineId, Some(moduleId), Some(sampleId), Some(libraryId), "key", "path3", "md5", link = false, 1), Duration.Inf)
Await.result(db.getFile(runId, Right("test_pipeline"), Some(Right("test_module")), Some(Right("test_sample")), Some(Right("test_library")), "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,Some(moduleId), Some(sampleId), Some(libraryId),"key","path3","md5",link = false,1))
Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path2","md5",link = false,1), Schema.File(0,0,Some(moduleId), Some(sampleId), Some(libraryId),"key","path3","md5",link = false,1))
Await.result(db.getFile(runId, Right("test_pipeline"), Some(Right("test_module")), Some(Right("test_sample")), Some(Right("test_library")), "key"), Duration.Inf) shouldBe Some(Schema.File(0, 0, Some(moduleId), Some(sampleId), Some(libraryId), "key", "path3", "md5", link = false, 1))
Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0, 0, None, None, None, "key", "path2", "md5", link = false, 1), Schema.File(0, 0, Some(moduleId), Some(sampleId), Some(libraryId), "key", "path3", "md5", link = false, 1))
db.close()
}
@Test
def testExecutable(): Unit = {
val dbFile = File.createTempFile("summary.", ".db")
......
......@@ -18,12 +18,12 @@ import java.io.File
import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.centrifuge.{Centrifuge, CentrifugeKreport}
import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
......
......@@ -17,13 +17,13 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
/**
* Created by pjvanthof on 04/02/16.
......
......@@ -23,7 +23,7 @@ import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, Test}
import org.testng.annotations.{ AfterClass, Test }
/**
* Created by pjvan_thof on 13-5-16.
......
......@@ -14,22 +14,22 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, BiopetPipe}
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetPipe }
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import nl.lumc.sasc.biopet.extensions.tools.{BaseCounter, WipeReads}
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.extensions.tools.{ BaseCounter, WipeReads }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.utils.camelize
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends TestNGSuite with Matchers {
......
......@@ -24,7 +24,7 @@ import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, Test}
import org.testng.annotations.{ AfterClass, Test }
/**
* Created by pjvan_thof on 4/11/16.
......
......@@ -23,7 +23,7 @@ import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, Test}
import org.testng.annotations.{ AfterClass, Test }
/**
* Created by pjvan_thof on 31-5-16.
......
......@@ -14,17 +14,17 @@
*/
package nl.lumc.sasc.biopet.pipelines.kopisu
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.freec.{FreeC, FreeCAssessSignificancePlot, FreeCCNVPlot}
import nl.lumc.sasc.biopet.extensions.freec.{ FreeC, FreeCAssessSignificancePlot, FreeCCNVPlot }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
import scala.collection.mutable.ListBuffer
......
......@@ -14,19 +14,19 @@
*/
package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge
import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, MergeSamFiles}
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
/**
* Created by pjvanthof on 15/05/16.
......
......@@ -14,16 +14,16 @@
*/
package nl.lumc.sasc.biopet.pipelines.sage
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
/**
* Created by pjvanthof on 28/09/16.
......
......@@ -14,21 +14,21 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import java.nio.file.Paths
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerCaller, BreakdancerConfig, BreakdancerVCF}
import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerCaller, BreakdancerConfig, BreakdancerVCF }
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import nl.lumc.sasc.biopet.extensions.pindel.{PindelCaller, PindelConfig, PindelVCF}
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.extensions.pindel.{ PindelCaller, PindelConfig, PindelVCF }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
import scala.collection.mutable.ListBuffer
......
......@@ -14,19 +14,19 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.gatk.{BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator}
import nl.lumc.sasc.biopet.extensions.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
/**
* Class for testing shiva
......
......@@ -19,22 +19,22 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.BiopetPipe
import nl.lumc.sasc.biopet.extensions.Freebayes
import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge}
import nl.lumc.sasc.biopet.extensions.gatk.{CombineVariants, GenotypeConcordance, HaplotypeCaller, UnifiedGenotyper}
import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance, HaplotypeCaller, UnifiedGenotyper }
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats}
import nl.lumc.sasc.biopet.extensions.vt.{VtDecompose, VtNormalize}
import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
import scala.collection.mutable.ListBuffer
......
......@@ -25,7 +25,7 @@ import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, Test}
import org.testng.annotations.{ AfterClass, Test }
/**
* Created by pjvan_thof on 4/11/16.
......
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