Skip to content

B
biopet.biopet
Commit 346fcbff authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files
Options

Switch to use of traits

parent 0bc5bbe7
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 219 additions and 221 deletions
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ 346fcbff
......@@ -21,12 +21,12 @@ import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportBuilderExtension,
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.rscript.{ LinePlot, StackedBarPlot }
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
import scala.concurrent.ExecutionContext.Implicits.global
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
class BammetricsReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = BammetricsReport
......@@ -66,14 +66,15 @@ object BammetricsReport extends ReportBuilder {
//val pipelineId: Int = summary.getPipelineId(runId, metricsTag).map(_.get)
val wgsExecuted = summary.getStatsSize(runId, Some(metricsTag.right), Some(Some("wgs".right)), sample = sampleId.map(x => Some(x.left)), library = libId.map(x => Some(x.left))) >= 1
val rnaExecuted = summary.getStatsSize(runId, Some(metricsTag.right), Some(Some("rna".right)), sample = sampleId.map(x => Some(x.left)), library = libId.map(x => Some(x.left))) >= 1
val wgsExecuted = summary.getStatsSize(runId, metricsTag, "wgs", sample = sampleId.map(SampleId), library = libId.map(LibraryId)) >= 1
val rnaExecuted = summary.getStatsSize(runId, metricsTag, "rna", sample = sampleId.map(SampleId), library = libId.map(LibraryId)) >= 1
val insertsizeMetrics = summary.getStatKeys(runId, metricsTag.right, Some("CollectInsertSizeMetrics".right),
sample = sampleId.map(_.left), library = libId.map(_.left), Map("metrics" -> List("metrics")))
val insertsizeMetrics = summary.getStatKeys(runId, metricsTag, "CollectInsertSizeMetrics",
sampleId.map(SampleId).getOrElse(NoSample), libId.map(LibraryId).getOrElse(NoLibrary), Map("metrics" -> List("metrics")))
.exists(_._2.isDefined)
val targetSettings = summary.getSettingKeys(runId, metricsTag.right, None, sample = sampleId.map(_.left), library = libId.map(_.left),
val targetSettings = summary.getSettingKeys(runId, metricsTag, NoModule,
sample = sampleId.map(SampleId).getOrElse(NoSample), library = libId.map(LibraryId).getOrElse(NoLibrary),
Map("amplicon_name" -> List("amplicon_name"), "roi_name" -> List("roi_name")))
val targets = (
targetSettings("amplicon_name"),
......@@ -134,10 +135,10 @@ object BammetricsReport extends ReportBuilder {
)
val results: Map[(Int, Option[Int]), Map[String, Option[Any]]] = if (libraryLevel) {
summary.getStatsForLibraries(runId, "bammetrics".right, Some("bamstats".right),
summary.getStatsForLibraries(runId, "bammetrics", "bamstats",
sampleId = sampleId, keyValues = statsPaths).map(x => (x._1._1, Some(x._1._2)) -> x._2)
} else summary.getStatsForSamples(runId, "bammetrics".right, Some("bamstats".right),
sample = sampleId.map(_.left), keyValues = statsPaths).map(x => (x._1, None) -> x._2)
} else summary.getStatsForSamples(runId, "bammetrics", "bamstats",
sample = sampleId.map(SampleId), keyValues = statsPaths).map(x => (x._1, None) -> x._2)
for (((s, l), result) <- results) {
val sampleName: String = summary.getSampleName(s).map(_.get)
......@@ -177,8 +178,8 @@ object BammetricsReport extends ReportBuilder {
statsPaths: Map[String, List[String]],
xKey: String,
yKey: String,
pipeline: \/[Int, String],
module: Option[\/[Int, String]],
pipeline: PipelineQuery,
module: ModuleQuery,
xlabel: Option[String] = None,
ylabel: Option[String] = None,
title: Option[String] = None,
......@@ -189,7 +190,7 @@ object BammetricsReport extends ReportBuilder {
val results: Map[(Int, Option[Int]), Map[String, Option[Array[Any]]]] = if (libraryLevel) {
summary.getStatsForLibraries(runId, pipeline, module, sampleId = sampleId, keyValues = statsPaths)
.map(x => (x._1._1, Some(x._1._2)) -> x._2.map(x => x._1 -> x._2.map(ConfigUtils.any2list(_).toArray)))
} else summary.getStatsForSamples(runId, pipeline, module, sample = sampleId.map(_.left), keyValues = statsPaths)
} else summary.getStatsForSamples(runId, pipeline, module, sample = sampleId.map(SampleId), keyValues = statsPaths)
.map(x => (x._1, None) -> x._2.map(x => x._1 -> x._2.map(ConfigUtils.any2list(_).toArray)))
val tables: Array[Map[String, Array[Any]]] = results.map {
......@@ -199,7 +200,7 @@ object BammetricsReport extends ReportBuilder {
val libraryName = library.flatMap(l => Await.result(summary.getLibraryName(l), Duration.Inf))
Map(
yKey -> map(yKey).getOrElse(Array()),
(sampleName + libraryName.map("-" + _) getOrElse ("")) -> map(xKey).getOrElse(Array())
(sampleName + libraryName.map("-" + _).getOrElse("")) -> map(xKey).getOrElse(Array())
)
}.toArray
......@@ -233,7 +234,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary(outputDir, prefix, summary, libraryLevel, sampleId, libraryId, statsPaths,
"insert_size", "count", "bammetrics".right, Some("CollectInsertSizeMetrics".right),
"insert_size", "count", "bammetrics", "CollectInsertSizeMetrics",
"Insert size", "Reads", "Insert size")
}
......@@ -249,7 +250,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary(outputDir, prefix, summary, libraryLevel, sampleId, libraryId, statsPaths,
"mapping_quality", "count", "bammetrics".right, Some("bamstats".right),
"mapping_quality", "count", "bammetrics", "bamstats",
"Mapping quality", "Reads", "Mapping quality")
}
......@@ -265,7 +266,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary(outputDir, prefix, summary, libraryLevel, sampleId, libraryId, statsPaths,
"clipping", "count", "bammetrics".right, Some("bamstats".right),
"clipping", "count", "bammetrics", "bamstats",
"Clipping", "Reads", "Clipping")
}
......@@ -290,7 +291,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary(outputDir, prefix, summary, libraryLevel, sampleId, libraryId, statsPaths,
"coverage", "count", "bammetrics".right, Some("wgs".right),
"coverage", "count", "bammetrics", "wgs",
"Coverage", "Bases", "Whole genome coverage")
}
......@@ -315,7 +316,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary(outputDir, prefix, summary, libraryLevel, sampleId, libraryId, statsPaths,
"coverage", "count", "bammetrics".right, Some("rna".right),
"coverage", "count", "bammetrics", "rna",
"Relative position", "Coverage", "Rna coverage")
}
......
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
View file @ 346fcbff
......@@ -19,21 +19,20 @@ 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.summary.Summary
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import org.broadinstitute.gatk.queue.function.CommandLineFunction
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 nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ NoLibrary, NoSample }
import org.apache.commons.io.FileUtils
import org.testng.annotations.{ AfterClass, Test }
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scala.util.matching.Regex
import scalaz._
import Scalaz._
/**
* Created by pjvanthof on 15/01/16.
......@@ -100,8 +99,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir)
summary.getStatKeys(qscript.summaryRunId, "test".right, Some("tool_1".right), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test".right, Some("tool_1".right), None, None, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
summary.getStatKeys(qscript.summaryRunId, "test", "tool_1", keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test", "tool_1", key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
}
@Test
......@@ -121,8 +120,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir)
summary.getStatKeys(qscript.summaryRunId, "test".right, Some("tool_1".right), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test".right, Some("tool_1".right), None, None, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
summary.getStatKeys(qscript.summaryRunId, "test", "tool_1", keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test", "tool_1", NoSample, NoLibrary, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
}
@Test
......@@ -142,8 +141,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir)
summary.getStatKeys(qscript.summaryRunId, "test".right, Some("tool_1".right), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test".right, Some("tool_1".right), None, None, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
summary.getStatKeys(qscript.summaryRunId, "test", "tool_1", keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test", "tool_1", key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
}
@Test
......@@ -163,8 +162,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir)
summary.getStatKeys(qscript.summaryRunId, "test".right, Some("tool_1".right), Some("sampleName".right), Some("libName".right), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test".right, Some("tool_1".right), Some("sampleName".right), Some("libName".right), key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
summary.getStatKeys(qscript.summaryRunId, "test", "tool_1", "sampleName", "libName", keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test", "tool_1", "sampleName", "libName", key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
}
@Test
......@@ -204,8 +203,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir)
summary.getStatKeys(qscript.summaryRunId, "test".right, Some("tool_1".right), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test".right, Some("tool_1".right), None, None, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
summary.getStatKeys(qscript.summaryRunId, "test", "tool_1", keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
Await.result(summary.getFile(qscript.summaryRunId, "test", "tool_1", key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
}
@AfterClass
......
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
View file @ 346fcbff
......@@ -9,9 +9,8 @@ import org.testng.annotations.Test
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
import SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ NoLibrary, NoModule, NoSample }
/**
* Testing voor [[SummaryDb]]
......@@ -140,9 +139,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
db.createTables()
Await.result(db.createOrUpdateSetting(0, 0, None, None, None, """{"content": "test" }"""), Duration.Inf)
Await.result(db.getSetting(0, 0.left, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.getSetting(0, 0, NoModule, NoSample, NoLibrary), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.createOrUpdateSetting(0, 0, None, None, None, """{"content": "test2" }"""), Duration.Inf)
Await.result(db.getSetting(0, 0.left, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
Await.result(db.getSetting(0, 0, NoModule, NoSample, NoLibrary), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
db.close()
}
......@@ -162,9 +161,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }""".stripMargin), Duration.Inf)
db.getSettingKeys(0, 0.left, Some(0.left), Some(0.left), Some(0.left), keyValues = Map()) shouldBe Map()
db.getSettingKeys(0, 0.left, Some(0.left), Some(0.left), Some(0.left), keyValues = Map("content" -> List("content"))) shouldBe Map("content" -> Some("test"))
db.getSettingKeys(0, 0.left, Some(0.left), Some(0.left), Some(0.left), keyValues = Map("content" -> List("content2", "key"))) shouldBe Map("content" -> Some("value"))
db.getSettingKeys(0, 0, 0, 0, 0, keyValues = Map()) shouldBe Map()
db.getSettingKeys(0, 0, 0, 0, 0, keyValues = Map("content" -> List("content"))) shouldBe Map("content" -> Some("test"))
db.getSettingKeys(0, 0, 0, 0, 0, keyValues = Map("content" -> List("content2", "key"))) shouldBe Map("content" -> Some("value"))
db.close()
}
......@@ -187,8 +186,8 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }""".stripMargin), Duration.Inf)
db.getSettingsForSamples(0, 0.left, Some(0.left), keyValues = Map()) shouldBe Map(0 -> Map())
db.getSettingsForSamples(0, 0.left, Some(0.left), keyValues = Map("content" -> List("content"))) shouldBe Map(0 -> Map("content" -> Some("test")))
db.getSettingsForSamples(0, 0, 0, keyValues = Map()) shouldBe Map(0 -> Map())
db.getSettingsForSamples(0, 0, 0, keyValues = Map("content" -> List("content"))) shouldBe Map(0 -> Map("content" -> Some("test")))
db.close()
}
......@@ -212,8 +211,8 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }""".stripMargin), Duration.Inf)
db.getSettingsForLibraries(0, 0.left, Some(0.left), keyValues = Map()) shouldBe Map((0, 0) -> Map())
db.getSettingsForLibraries(0, 0.left, Some(0.left), keyValues = Map("content" -> List("content"))) shouldBe Map((0, 0) -> Map("content" -> Some("test")))
db.getSettingsForLibraries(0, 0, 0, keyValues = Map()) shouldBe Map((0, 0) -> Map())
db.getSettingsForLibraries(0, 0, 0, keyValues = Map("content" -> List("content"))) shouldBe Map((0, 0) -> Map("content" -> Some("test")))
db.close()
}
......@@ -234,15 +233,15 @@ class SummaryDbTest extends TestNGSuite with Matchers {
Await.result(db.getStatsSize(), Duration.Inf) shouldBe 0
Await.result(db.createOrUpdateStat(runId, pipelineId, None, None, None, """{"content": "test" }"""), Duration.Inf)
Await.result(db.getStat(runId, pipelineId.left, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.getStat(runId, pipelineId, NoModule, NoSample, NoLibrary), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.getStatsSize(), Duration.Inf) shouldBe 1
Await.result(db.createOrUpdateStat(runId, pipelineId, None, None, None, """{"content": "test2" }"""), Duration.Inf)
Await.result(db.getStat(runId, pipelineId.left, None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
Await.result(db.getStat(runId, pipelineId, NoModule, NoSample, NoLibrary), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
Await.result(db.getStatsSize(), Duration.Inf) shouldBe 1
// Test join queries
Await.result(db.createOrUpdateStat(runId, pipelineId, Some(moduleId), Some(sampleId), Some(libraryId), """{"content": "test3" }"""), Duration.Inf)
Await.result(db.getStat(runId, "test_pipeline".right, Some("test_module".right), Some("test_sample".right), Some("test_library".right)), Duration.Inf) shouldBe Some(Map("content" -> "test3"))
Await.result(db.getStat(runId, "test_pipeline", "test_module", "test_sample", "test_library"), Duration.Inf) shouldBe Some(Map("content" -> "test3"))
Await.result(db.getStatsSize(), Duration.Inf) shouldBe 2
db.close()
......@@ -264,9 +263,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }""".stripMargin), Duration.Inf)
db.getStatKeys(0, 0.left, Some(0.left), Some(0.left), Some(0.left), keyValues = Map()) shouldBe Map()
db.getStatKeys(0, 0.left, Some(0.left), Some(0.left), Some(0.left), keyValues = Map("content" -> List("content"))) shouldBe Map("content" -> Some("test"))
db.getStatKeys(0, 0.left, Some(0.left), Some(0.left), Some(0.left), keyValues = Map("content" -> List("content2", "key"))) shouldBe Map("content" -> Some("value"))
db.getStatKeys(0, 0, 0, 0, 0, keyValues = Map()) shouldBe Map()
db.getStatKeys(0, 0, 0, 0, 0, keyValues = Map("content" -> List("content"))) shouldBe Map("content" -> Some("test"))
db.getStatKeys(0, 0, 0, 0, 0, keyValues = Map("content" -> List("content2", "key"))) shouldBe Map("content" -> Some("value"))
db.close()
}
......@@ -289,8 +288,8 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }""".stripMargin), Duration.Inf)
db.getStatsForSamples(0, 0.left, Some(0.left), keyValues = Map()) shouldBe Map(0 -> Map())
db.getStatsForSamples(0, 0.left, Some(0.left), keyValues = Map("content" -> List("content"))) shouldBe Map(0 -> Map("content" -> Some("test")))
db.getStatsForSamples(0, 0, 0, keyValues = Map()) shouldBe Map(0 -> Map())
db.getStatsForSamples(0, 0, 0, keyValues = Map("content" -> List("content"))) shouldBe Map(0 -> Map("content" -> Some("test")))
db.close()
}
......@@ -314,8 +313,8 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }""".stripMargin), Duration.Inf)
db.getStatsForLibraries(0, 0.left, Some(0.left), keyValues = Map()) shouldBe Map((0, 0) -> Map())
db.getStatsForLibraries(0, 0.left, Some(0.left), keyValues = Map("content" -> List("content"))) shouldBe Map((0, 0) -> Map("content" -> Some("test")))
db.getStatsForLibraries(0, 0, 0, keyValues = Map()) shouldBe Map((0, 0) -> Map())
db.getStatsForLibraries(0, 0, 0, keyValues = Map("content" -> List("content"))) shouldBe Map((0, 0) -> Map("content" -> Some("test")))
db.close()
}
......@@ -334,15 +333,15 @@ 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, pipelineId.left, None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0, 0, None, None, None, "key", "path", "md5", link = false, 1))
Await.result(db.getFile(runId, pipelineId, NoModule, NoSample, NoLibrary, "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, pipelineId.left, None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0, 0, None, None, None, "key", "path2", "md5", link = false, 1))
Await.result(db.getFile(runId, pipelineId, NoModule, NoSample, NoLibrary, "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, "test_pipeline".right, Some("test_module".right), Some("test_sample".right), Some("test_library".right), "key"), Duration.Inf) shouldBe Some(Schema.File(0, 0, Some(moduleId), Some(sampleId), Some(libraryId), "key", "path3", "md5", link = false, 1))
Await.result(db.getFile(runId, "test_pipeline", "test_module", "test_sample", "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()
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @ 346fcbff
......@@ -20,11 +20,10 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
class FlexiprepReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = FlexiprepReport
......@@ -97,15 +96,15 @@ object FlexiprepReport extends ReportBuilder {
tsvWriter.println("Library\tAfter_QC\tClipping\tTrimming\tSynced")
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val seqstatStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("seqstat_" + read).right), keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("seqstat_" + read + "_qc").right), keyValues = seqstatPaths)
val seqstatStats = summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read, keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read + "_qc", keyValues = seqstatPaths)
val clippingPaths = Map("num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
"num_reads_discarded_too_long" -> List("num_reads_discarded_too_long"))
val clippingStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("clipping_" + read).right), keyValues = clippingPaths)
val clippingStats = summary.getStatsForLibraries(runId, "flexiprep", "clipping_" + read, keyValues = clippingPaths)
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read))
val trimmingStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some("trimming".right), keyValues = trimmingPaths)
val trimmingStats = summary.getStatsForLibraries(runId, "flexiprep", "trimming", keyValues = trimmingPaths)
val libraries = Await.result(summary.getLibraries(runId = runId, sampleId = sampleId), Duration.Inf)
......@@ -156,8 +155,8 @@ object FlexiprepReport extends ReportBuilder {
tsvWriter.println("Library\tAfter_QC\tDiscarded")
val statsPaths = Map("num_total" -> List("bases", "num_total"))
val seqstatStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("seqstat_" + read).right), keyValues = statsPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, "flexiprep".right, Some(("seqstat_" + read + "_qc").right), keyValues = statsPaths)
val seqstatStats = summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read, keyValues = statsPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read + "_qc", keyValues = statsPaths)
val libraries = Await.result(summary.getLibraries(runId = runId, sampleId = sampleId), Duration.Inf)
......
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @ 346fcbff
......@@ -17,13 +17,12 @@ package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.report.{ MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ NoLibrary, NoModule, SampleId }
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
/**
* Report for Gears
*
......@@ -41,10 +40,10 @@ object GearsReport extends MultisampleReportBuilder {
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def indexPage = {
val krakenExecuted = summary.getStatsSize(runId = runId, pipeline = Some("gearskraken".right), module = Some(Some("krakenreport".right)), library = Some(None), mustHaveSample = true) >= samples.size
val centrifugeExecuted = summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)), library = Some(None), mustHaveSample = true) >= samples.size
val qiimeClosesOtuTable = summary.getFile(runId, "gears".right, None, None, None, key = "qiime_closed_otu_table")
val qiimeOpenOtuTable = summary.getFile(runId, "gears".right, None, None, None, key = "qiime_open_otu_table")
val krakenExecuted = summary.getStatsSize(runId = runId, pipeline = "gearskraken", module = "krakenreport", library = NoLibrary, mustHaveSample = true) >= samples.size
val centrifugeExecuted = summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report", library = NoLibrary, mustHaveSample = true) >= samples.size
val qiimeClosesOtuTable = summary.getFile(runId, "gears", key = "qiime_closed_otu_table")
val qiimeOpenOtuTable = summary.getFile(runId, "gears", key = "qiime_open_otu_table")
ReportPage(
(if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
......@@ -82,10 +81,10 @@ object GearsReport extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)), sample = Some(Some(sampleId.left)), library = Some(None)), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)), sample = Some(Some(sampleId.left)), library = None), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears".right, None, Some(sampleId.left), None, "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears".right, None, Some(sampleId.left), None, "qiime_open_otu_table"), Duration.Inf)
val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport", sample = sampleId, library = NoLibrary), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report", sample = sampleId, library = None), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", NoModule, sampleId, NoLibrary, "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", NoModule, sampleId, NoLibrary, "qiime_open_otu_table"), Duration.Inf)
ReportPage((if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_report")
......@@ -114,12 +113,12 @@ object GearsReport extends MultisampleReportBuilder {
val sName = Await.result(summary.getSampleName(sampleId), Duration.Inf)
val lName = Await.result(summary.getLibraryName(libId), Duration.Inf)
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Some("flexiprep".right), sample = Some(Some(sampleId.left)), library = Some(Some(libId.left))), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, "flexiprep", sample = sampleId, library = libId), Duration.Inf) >= 1
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)), sample = Some(Some(sampleId.left)), library = Some(Some(libId.left))), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)), sample = Some(Some(sampleId.left)), library = Some(Some(libId.left))), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears".right, None, Some(sampleId.left), Some(libId.left), "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears".right, None, Some(sampleId.left), Some(libId.left), "qiime_open_otu_table"), Duration.Inf)
val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport", sample = sampleId, library = libId), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report", sample = sampleId, library = libId), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", NoModule, sampleId, libId, "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", NoModule, sampleId, libId, "qiime_open_otu_table"), Duration.Inf)
ReportPage(
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
......
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
View file @ 346fcbff
......@@ -16,11 +16,11 @@ package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ LibraryId, SampleId }
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
class GearsSingleReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = GearsSingleReport
......@@ -35,8 +35,8 @@ object GearsSingleReport extends ReportBuilder {
val sampleName = sampleId.flatMap(x => Await.result(summary.getSampleName(x), Duration.Inf))
val libraryName = libId.flatMap(x => Await.result(summary.getLibraryName(x), Duration.Inf))
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)), sample = Some(sampleId.map(_.left)), library = Some(libId.map(_.left))), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)), sample = Some(sampleId.map(_.left)), library = Some(libId.map(_.left))), Duration.Inf) == 1
val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport", sample = sampleId.map(SampleId), library = libId.map(LibraryId)), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report", sample = sampleId.map(SampleId), library = libId.map(LibraryId)), Duration.Inf) == 1
ReportPage(
List(
......
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
View file @ 346fcbff
......@@ -18,11 +18,11 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
class MappingReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = MappingReport
......@@ -40,12 +40,13 @@ object MappingReport extends ReportBuilder {
override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def krakenExecuted: Boolean = Await.result(summary.getStatsSize(runId, Some("gears".right), Some(Some("krakenreport".right)),
sample = Some(sampleId.map(_.left)), library = Some(libId.map(_.left))), Duration.Inf) >= 1
def krakenExecuted: Boolean = Await.result(summary.getStatsSize(runId, "gears", "krakenreport",
sample = sampleId.map(SampleId), library = libId.map(LibraryId)), Duration.Inf) >= 1
/** Root page for single BamMetrcis report */
def indexPage = {
val mappingSettings = summary.getSettingKeys(runId, "mapping".right, None, sample = sampleId.map(_.left), library = libId.map(_.left),
val mappingSettings = summary.getSettingKeys(runId, "mapping", NoModule,
sample = sampleId.map(SampleId).getOrElse(NoSample), library = libId.map(LibraryId).getOrElse(NoLibrary),
keyValues = Map("skip_flexiprep" -> List("skip_flexiprep"), "skip_metrics" -> List("skip_metrics")))
val skipFlexiprep = mappingSettings.get("skip_flexiprep").flatten.getOrElse(false) == true
val bamMetricsPage = if (mappingSettings.get("skip_metrics").flatten.getOrElse(false) == true) {
......
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ 346fcbff
......@@ -18,11 +18,11 @@ import nl.lumc.sasc.biopet.core.report.{ MultisampleReportBuilder, ReportBuilder
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ NoLibrary, NoModule }
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import scalaz._
import Scalaz._
/**
* Created by pjvanthof on 11/01/16.
......@@ -50,20 +50,20 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Root page for the carp report */
def indexPage = {
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Some("gearscentrifuge".right), Some(Some("centrifuge_report".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val wgsExecuted = Await.result(summary.getStatsSize(runId, Some("bammetrics".right), Some(Some("wgs".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val rnaExecuted = Await.result(summary.getStatsSize(runId, Some("bammetrics".right), Some(Some("rna".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val insertsizeExecuted = Await.result(summary.getStatsSize(runId, Some("bammetrics".right), Some(Some("CollectInsertSizeMetrics".right)),
library = Some(None), mustHaveSample = true), Duration.Inf) >= 1
val mappingExecuted = Await.result(summary.getStatsSize(runId, Some("mapping".right), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
val mappingSettings = summary.getSettingsForLibraries(runId, "mapping".right, None, keyValues = Map("paired" -> List("paired")))
val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport",
library = NoLibrary, mustHaveSample = true), Duration.Inf) >= 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report",
library = NoLibrary, mustHaveSample = true), Duration.Inf) >= 1
val wgsExecuted = Await.result(summary.getStatsSize(runId, "bammetrics", "wgs",
library = NoLibrary, mustHaveSample = true), Duration.Inf) >= 1
val rnaExecuted = Await.result(summary.getStatsSize(runId, "bammetrics", "rna",
library = NoLibrary, mustHaveSample = true), Duration.Inf) >= 1
val insertsizeExecuted = Await.result(summary.getStatsSize(runId, "bammetrics", "CollectInsertSizeMetrics",
library = NoLibrary, mustHaveSample = true), Duration.Inf) >= 1
val mappingExecuted = Await.result(summary.getStatsSize(runId, "mapping", NoModule, mustHaveLibrary = true), Duration.Inf) >= 1
val mappingSettings = summary.getSettingsForLibraries(runId, "mapping", NoModule, keyValues = Map("paired" -> List("paired")))
val pairedFound = !mappingExecuted || mappingSettings.exists(_._2.exists(_._2 == Option(true)))
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Some("flexiprep".right), mustHaveLibrary = true), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, "flexiprep", mustHaveLibrary = true), Duration.Inf) >= 1
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
......@@ -115,19 +115,19 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Files page, can be used general or at sample level */
def filesPage(sampleId: Option[Int] = None, libraryId: Option[Int] = None): ReportPage = {
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Some("flexiprep".right), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, "flexiprep", NoModule, mustHaveLibrary = true), Duration.Inf) >= 1
ReportPage(List(), Nil, Map())
}
/** Single sample page */
def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
val krakenExecuted = Await.result(summary.getStatsSize(runId, Some("gearskraken".right), Some(Some("krakenreport".right)),