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biopet.biopet
Commit d9c644e7 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added join queries for files

parent 4f941fd2
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Showing with 40 additions and 28 deletions
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
View file @ d9c644e7
......@@ -296,7 +296,7 @@ class SummaryDb(val db: Database) extends Closeable {
}
def settingsFilter(runId: Option[Int] = None, pipeline: Option[Either[Int, String]] = None, module: Option[Option[Either[Int, String]]] = None,
sample: Option[Option[Either[Int, String]]] = None, lib: Option[Option[Either[Int, String]]] = None,
sample: Option[Option[Either[Int, String]]] = None, library: Option[Option[Either[Int, String]]] = None,
mustHaveSample: Boolean = false, mustHaveLibrary: Boolean = false) = {
var f: Query[Settings, Settings#TableElementType, Seq] = settings
runId.foreach(r => f = f.filter(_.runId === r))
......@@ -379,37 +379,50 @@ class SummaryDb(val db: Database) extends Closeable {
}
/** Return a [[Query]] for [[Files]] */
def filesFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None,
def filesFilter(runId: Option[Int] = None, pipeline: Option[Either[Int, String]] = None, module: Option[Option[Either[Int, String]]] = None,
sample: Option[Option[Either[Int, String]]] = None, library: Option[Option[Either[Int, String]]] = None,
key: Option[String] = None, pipelineName: Option[String] = None, moduleName: Option[Option[String]] = None,
sampleName: Option[Option[String]] = None, libraryName: Option[Option[String]] = None) = {
var f: Query[Files, Files#TableElementType, Seq] = files
runId.foreach(r => f = f.filter(_.runId === r))
pipelineId.foreach(r => f = f.filter(_.pipelineId === r))
key.foreach(r => f = f.filter(_.key === r))
moduleId.foreach(r => f = if (r.isDefined) f.filter(_.moduleId === r.get) else f.filter(_.moduleId.isEmpty))
sampleId.foreach(r => f = if (r.isDefined) f.filter(_.sampleId === r.get) else f.filter(_.sampleId.isEmpty))
libId.foreach(r => f = if (r.isDefined) f.filter(_.libraryId === r.get) else f.filter(_.libraryId.isEmpty))
// Join Query's
if (pipelineName.isDefined) f = f.join(pipelines).on(_.pipelineId === _.id).filter(_._2.name === pipelineName.get).map(_._1)
moduleName.foreach(r => if (r.isDefined) f = f.join(modules).on(_.moduleId === _.id).filter(_._2.name === r.get).map(_._1) else f = f.filter(_.moduleId.isEmpty))
sampleName.foreach(r => if (r.isDefined) f = f.join(samples).on(_.sampleId === _.id).filter(_._2.name === r.get).map(_._1) else f = f.filter(_.sampleId.isEmpty))
libraryName.foreach(r => if (r.isDefined) f = f.join(libraries).on(_.libraryId === _.id).filter(_._2.name === r.get).map(_._1) else f = f.filter(_.libraryId.isEmpty))
f = pipeline match {
case Some(Left(id)) => f.filter(_.pipelineId === id)
case Some(Right(name)) => f.join(pipelines).on(_.pipelineId === _.id).filter(_._2.name === name).map(_._1)
case _ => f
}
f = module match {
case Some(Some(Left(id))) => f.filter(_.moduleId === id)
case Some(Some(Right(name))) => f.join(modules).on(_.moduleId === _.id).filter(_._2.name === name).map(_._1)
case Some(None) => f.filter(_.moduleId.isEmpty)
case _ => f
}
f = sample match {
case Some(Some(Left(id))) => f.filter(_.sampleId === id)
case Some(Some(Right(name))) => f.join(samples).on(_.sampleId === _.id).filter(_._2.name === name).map(_._1)
case Some(None) => f.filter(_.sampleId.isEmpty)
case _ => f
}
f = library match {
case Some(Some(Left(id))) => f.filter(_.libraryId === id)
case Some(Some(Right(name))) => f.join(libraries).on(_.libraryId === _.id).filter(_._2.name === name).map(_._1)
case Some(None) => f.filter(_.libraryId.isEmpty)
case _ => f
}
f
}
/** Returns all [[Files]] with the given criteria */
def getFiles(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]],
sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None,
def getFiles(runId: Option[Int] = None, pipeline: Option[Either[Int, String]] = None, module: Option[Option[Either[Int, String]]],
sample: Option[Option[Either[Int, String]]] = None, library: Option[Option[Either[Int, String]]] = None,
key: Option[String] = None): Future[Seq[Schema.File]] = {
db.run(filesFilter(runId, pipelineId, moduleId, sampleId, libId, key).result)
db.run(filesFilter(runId, pipeline, module, sample, library, key).result)
}
def getFile(runId: Int, pipelineName: String, moduleName: Option[String], sampleName: Option[String],
libraryName: Option[String], key: String): Future[Option[Schema.File]] = {
db.run(filesFilter(runId = Some(runId), pipelineName = Some(pipelineName), moduleName = Some(moduleName),
sampleName = Some(sampleName), libraryName = Some(libraryName), key = Some(key)).result).map(_.headOption)
def getFile(runId: Int, pipeline: Either[Int, String], module: Option[Either[Int, String]], sample: Option[Either[Int, String]],
library: Option[Either[Int, String]], key: String): Future[Option[Schema.File]] = {
db.run(filesFilter(Some(runId), Some(pipeline), Some(module), Some(sample), Some(library), Some(key)).result).map(_.headOption)
}
/** Creates a file. This method will raise expection if it already exist */
......@@ -423,7 +436,7 @@ class SummaryDb(val db: Database) extends Closeable {
def createOrUpdateFile(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
sampleId: Option[Int] = None, libId: Option[Int] = None,
key: String, path: String, md5: String, link: Boolean = false, size: Long): Future[Int] = {
val filter = filesFilter(Some(runId), Some(pipelineId), Some(moduleId), Some(sampleId), Some(libId), Some(key))
val filter = filesFilter(Some(runId), Some(Left(pipelineId)), Some(Left(moduleId)), Some(Left(sampleId)), Some(Left(libId)), Some(key))
val r = Await.result(db.run(filter.size.result), Duration.Inf)
if (r == 0) createFile(runId, pipelineId, moduleId, sampleId, libId, key, path, md5, link, size)
else db.run(filter.update(Schema.File(runId, pipelineId, moduleId, sampleId, libId, key, path, md5, link, size)))
......
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @ d9c644e7
......@@ -41,8 +41,8 @@ object GearsReport extends MultisampleReportBuilder {
def indexPage = {
val krakenExecuted = summary.getStatsSize(runId = runId, pipeline = Right("gearskraken"), module = Some(Right("krakenreport")), library = Some(None), mustHaveSample = true) >= samples.size
val centrifugeExecuted = summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")), library = Some(None), mustHaveSample = true) >= samples.size
val qiimeClosesOtuTable = summary.getFile(runId, "gears", None, None, None, key = "qiime_closed_otu_table")
val qiimeOpenOtuTable = summary.getFile(runId, "gears", None, None, None, key = "qiime_open_otu_table")
val qiimeClosesOtuTable = summary.getFile(runId, Right("gears"), None, None, None, key = "qiime_closed_otu_table")
val qiimeOpenOtuTable = summary.getFile(runId, Right("gears"), None, None, None, 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",
......@@ -80,11 +80,10 @@ object GearsReport extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
val sampleName = Await.result(summary.getSampleName(sampleId), Duration.Inf)
val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")), sample = Left(sampleId), library = Some(None)), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")), sample = Left(sampleId), library = None), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", None, sampleName, None, key = "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", None, sampleName, None, key = "qiime_open_otu_table"), Duration.Inf)
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, Right("gears"), None, Some(Left(sampleId)), None, "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, Right("gears"), None, Some(Left(sampleId)), None, "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")
......@@ -117,8 +116,8 @@ object GearsReport extends MultisampleReportBuilder {
val krakenExecuted = Await.result(summary.getStatsSize(runId, Right("gearskraken"), Some(Right("krakenreport")), sample = Some(Left(sampleId)), library = Some(Left(libId))), Duration.Inf) == 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId, Right("gearscentrifuge"), Some(Right("centrifuge_report")), sample = Some(Left(sampleId)), library = Some(Left(libId))), Duration.Inf) == 1
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", None, sName, lName, key = "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", None, sName, lName, key = "qiime_open_otu_table"), Duration.Inf)
val qiimeClosesOtuTable = Await.result(summary.getFile(runId, Right("gears"), None, Some(Left(sampleId)), Some(Left(libId)), "qiime_closed_otu_table"), Duration.Inf)
val qiimeOpenOtuTable = Await.result(summary.getFile(runId, Right("gears"), None, Some(Left(sampleId)), Some(Left(libId)), "qiime_open_otu_table"), Duration.Inf)
ReportPage(
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
......
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