Start to convert report class

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -63,7 +63,7 @@ class BamMetrics(val parent: Configurable) extends QScript
   override def reportClass = {
     val bammetricsReport = new BammetricsReport(this)
     bammetricsReport.outputDir = new File(outputDir, "report")
-    bammetricsReport.summaryFile = summaryFile
+    bammetricsReport.summaryDbFile = summaryDbFile
     bammetricsReport.args = if (libId.isDefined) Map(
       "sampleId" -> sampleId.getOrElse("."),
       "libId" -> libId.getOrElse("."))

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala

@@ -14,6 +14,9 @@
  */
 package nl.lumc.sasc.biopet.core.report
 
+import scala.concurrent.Await
+import scala.concurrent.duration.Duration
+
 /**
  * This trait will generate a report with added function to generate sample and library pages for those existing in the summary.
  *
@@ -22,7 +25,7 @@ package nl.lumc.sasc.biopet.core.report
 trait MultisampleReportBuilder extends ReportBuilder {
 
   /** Method to generate a single sample page */
-  def samplePage(sampleId: String, args: Map[String, Any]): ReportPage
+  def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage
 
   /** Default list of samples, can be override */
   def samplesSections: List[(String, ReportSection)] = {
@@ -32,7 +35,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
   }
 
   /** Method to generate a single library page */
-  def libraryPage(sampleId: String, libraryId: String, args: Map[String, Any]): ReportPage
+  def libraryPage(sampleId: Int, libraryId: Int, args: Map[String, Any]): ReportPage
 
   /** Default list of libraries, can be override */
   def librariesSections: List[(String, ReportSection)] = {
@@ -43,22 +46,25 @@ trait MultisampleReportBuilder extends ReportBuilder {
 
   /** Generate the samples page including a single sample page for each sample in the summary */
   def generateSamplesPage(args: Map[String, Any]): ReportPage = {
-    val samplePages = summary.samples
+    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samplePages = samples.map(_.id)
       .map(sampleId => sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId))))
       .toList
-    ReportPage(samplePages, samplesSections, args)
+    ReportPage(samplePages.map(x => samples.find(_.name == x._1).get.name -> x._2), samplesSections, args)
   }
 
   /** Generate the libraries page for a single sample with a subpage for eacht library */
   def generateLibraryPage(args: Map[String, Any]): ReportPage = {
     val sampleId = args("sampleId") match {
-      case Some(x) => x.toString
+      case Some(x: Int) => x
       case None    => throw new IllegalStateException("Sample not found")
     }
 
-    val libPages = summary.libraries(sampleId)
+    val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = Some(sampleId)), Duration.Inf)
+
+    val libPages = libraries.map(_.id)
       .map(libId => libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId))))
       .toList
-    ReportPage(libPages, librariesSections, args)
+    ReportPage(libPages.map(x => libraries.find(_.name == x._1).get.name -> x._2), librariesSections, args)
   }
 }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.core.report
 import java.io._
 
 import nl.lumc.sasc.biopet.core.ToolCommandFunction
-import nl.lumc.sasc.biopet.utils.summary.Summary
-import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand }
+import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
+import nl.lumc.sasc.biopet.utils.{IoUtils, Logging, ToolCommand}
 import org.broadinstitute.gatk.utils.commandline.Input
-import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
+import org.fusesource.scalate.{TemplateEngine, TemplateSource}
 
 import scala.collection.mutable
 import scala.language.postfixOps
@@ -38,7 +38,9 @@ trait ReportBuilderExtension extends ToolCommandFunction {
   def toolObject = builder
 
   @Input(required = true)
-  var summaryFile: File = _
+  var summaryDbFile: File = _
+
+  var runId: Option[Int] = None
 
   /** OutputDir for the report  */
   var outputDir: File = _
@@ -58,7 +60,8 @@ trait ReportBuilderExtension extends ToolCommandFunction {
   /** Command to generate the report */
   override def cmdLine: String = {
     super.cmdLine +
-      required("--summary", summaryFile) +
+      required("--summaryDb", summaryDbFile) +
+      optional("--runId", runId) +
       required("--outputDir", outputDir) +
       args.map(x => required("-a", x._1 + "=" + x._2)).mkString
   }
@@ -66,8 +69,9 @@ trait ReportBuilderExtension extends ToolCommandFunction {
 
 trait ReportBuilder extends ToolCommand {
 
-  case class Args(summary: File = null,
+  case class Args(summaryDbFile: File = null,
                   outputDir: File = null,
+                  runId: Int = 0,
                   pageArgs: mutable.Map[String, Any] = mutable.Map()) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
@@ -78,8 +82,8 @@ trait ReportBuilder extends ToolCommand {
        """.stripMargin
     )
 
-    opt[File]('s', "summary") unbounded () required () maxOccurs 1 valueName "<file>" action { (x, c) =>
-      c.copy(summary = x)
+    opt[File]('s', "summaryDb") unbounded () required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(summaryDbFile = x)
     } validate {
       x => if (x.exists) success else failure("Summary JSON file not found!")
     } text "Biopet summary JSON file"
@@ -88,17 +92,27 @@ trait ReportBuilder extends ToolCommand {
       c.copy(outputDir = x)
     } text "Output HTML report files to this directory"
 
+    opt[Int]("runId") unbounded () maxOccurs 1 valueName "<int>" action { (x, c) =>
+      c.copy(runId = x)
+    }
+
     opt[Map[String, String]]('a', "args") unbounded () action { (x, c) =>
       c.copy(pageArgs = c.pageArgs ++ x)
     }
   }
 
   /** summary object internaly */
-  private var setSummary: Summary = _
+  private var setSummary: SummaryDb = _
 
   /** Retrival of summary, read only */
   final def summary = setSummary
 
+  /** summary object internaly */
+  private var setRunId: Int = 0
+
+  /** Retrival of summary, read only */
+  final def runId = setRunId
+
   /** default args that are passed to all page withing the report */
   def pageArgs: Map[String, Any] = Map()
 
@@ -165,7 +179,8 @@ trait ReportBuilder extends ToolCommand {
     )
 
     logger.info("Parsing summary")
-    setSummary = new Summary(cmdArgs.summary)
+    setSummary = SummaryDb.openSqliteSummary(cmdArgs.summaryDbFile)
+    setRunId = cmdArgs.runId
 
     total = ReportBuilder.countPages(indexPage)
     logger.info(total + " pages to be generated")
@@ -175,7 +190,7 @@ trait ReportBuilder extends ToolCommand {
     logger.info("Generate pages")
     val jobs = generatePage(summary, indexPage, cmdArgs.outputDir,
       args = pageArgs ++ cmdArgs.pageArgs.toMap ++
-        Map("summary" -> summary, "reportName" -> reportName, "indexPage" -> indexPage))
+        Map("summary" -> summary, "reportName" -> reportName, "indexPage" -> indexPage, "runId" -> cmdArgs.runId))
 
     logger.info(jobs + " Done")
   }
@@ -196,7 +211,7 @@ trait ReportBuilder extends ToolCommand {
    * @param args Args to add to this sub page, are args from current page are passed automaticly
    * @return Number of pages including all subpages that are rendered
    */
-  def generatePage(summary: Summary,
+  def generatePage(summary: SummaryDb,
                    page: ReportPage,
                    outputDir: File,
                    path: List[String] = Nil,

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala

@@ -36,10 +36,10 @@ class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
       def reportName: String = "test"
       def indexPage: ReportPage = ReportPage("Samples" -> generateSamplesPage(Map()) :: Nil, Nil, Map())
 
-      def samplePage(sampleId: String, args: Map[String, Any]): ReportPage =
+      def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage =
         ReportPage("Libraries" -> generateLibraryPage(Map("sampleId" -> Some(sampleId))) :: Nil, Nil, Map())
 
-      def libraryPage(sampleId: String, libraryId: String, args: Map[String, Any]) = ReportPage(Nil, Nil, Map())
+      def libraryPage(sampleId: Int, libraryId: Int, args: Map[String, Any]) = ReportPage(Nil, Nil, Map())
     }
 
     val tempDir = Files.createTempDir()

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala

@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.utils.config
 
 import java.io.{ File, PrintWriter }
 
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
 
 import scala.concurrent.Future

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala

@@ -15,7 +15,7 @@ import java.sql.Date
  *
  * Created by pjvanthof on 05/02/2017.
  */
-class SummaryDb(db: Database) extends Closeable {
+class SummaryDb(val db: Database) extends Closeable {
 
   def close(): Unit = db.close()
 
@@ -75,6 +75,11 @@ class SummaryDb(db: Database) extends Closeable {
     getSamples(runId = Some(runId), name = Some(sampleName)).map(_.headOption.map(_.id))
   }
 
+  /** Return samplId of a specific runId + sampleName */
+  def getSampleName(sampleId: Int): Future[Option[Int]] = {
+    getSamples(sampleId = Some(sampleId)).map(_.headOption.map(_.id))
+  }
+
   /** Return sample tags of a specific sample as a map */
   def getSampleTags(sampleId: Int): Future[Option[Map[String, Any]]] = {
     db.run(samples.filter(_.id === sampleId).map(_.tags).result)
@@ -184,7 +189,7 @@ class SummaryDb(db: Database) extends Closeable {
   }
 
   /** Return a Query for [[Stats]] */
-  private def statsFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
+  def statsFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
                           sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
     var f: Query[Stats, Stats#TableElementType, Seq] = stats
     runId.foreach(r => f = f.filter(_.runId === r))
@@ -215,7 +220,7 @@ class SummaryDb(db: Database) extends Closeable {
   }
 
   /** This return a [[Query]] for [[Settings]] */
-  private def settingsFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
+  def settingsFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
                              sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
     var f: Query[Settings, Settings#TableElementType, Seq] = settings
     runId.foreach(r => f = f.filter(_.runId === r))
@@ -249,7 +254,7 @@ class SummaryDb(db: Database) extends Closeable {
   }
 
   /** Return a [[Query]] for [[Files]] */
-  private def filesFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]],
+  def filesFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]],
                           sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None,
                           key: Option[String] = None) = {
     var f: Query[Files, Files#TableElementType, Seq] = files
@@ -287,7 +292,7 @@ class SummaryDb(db: Database) extends Closeable {
   }
 
   /** Returns a [[Query]] for [[Executables]] */
-  private def executablesFilter(runId: Option[Int], toolName: Option[String]) = {
+  def executablesFilter(runId: Option[Int], toolName: Option[String]) = {
     var q: Query[Executables, Executables#TableElementType, Seq] = executables
     runId.foreach(r => q = q.filter(_.runId === r))
     toolName.foreach(r => q = q.filter(_.toolName === r))

carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -103,7 +103,7 @@ class Carp(val parent: Configurable) extends QScript with MultisampleMappingTrai
   override def reportClass: Option[ReportBuilderExtension] = {
     val carp = new CarpReport(this)
     carp.outputDir = new File(outputDir, "report")
-    carp.summaryFile = summaryFile
+    carp.summaryDbFile = summaryDbFile
     Some(carp)
   }
 

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -65,7 +65,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
   override def reportClass: Some[FlexiprepReport] = {
     val flexiprepReport = new FlexiprepReport(this)
     flexiprepReport.outputDir = new File(outputDir, "report")
-    flexiprepReport.summaryFile = summaryFile
+    flexiprepReport.summaryDbFile = summaryDbFile
     flexiprepReport.args = Map(
       "sampleId" -> sampleId.getOrElse("."),
       "libId" -> libId.getOrElse("."))

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala

@@ -33,7 +33,7 @@ class Gears(val parent: Configurable) extends QScript with MultiSampleQScript {
   override def reportClass = {
     val gearsReport = new GearsReport(this)
     gearsReport.outputDir = new File(outputDir, "report")
-    gearsReport.summaryFile = summaryFile
+    gearsReport.summaryDbFile = summaryDbFile
     Some(gearsReport)
   }
 

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala

@@ -73,7 +73,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
   override def reportClass = {
     val gears = new GearsSingleReport(this)
     gears.outputDir = new File(outputDir, "report")
-    gears.summaryFile = summaryFile
+    gears.summaryDbFile = summaryDbFile
     sampleId.foreach(gears.args += "sampleId" -> _)
     libId.foreach(gears.args += "libId" -> _)
     Some(gears)

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -47,7 +47,7 @@ class Gentrap(val parent: Configurable) extends QScript
   override def reportClass: Option[ReportBuilderExtension] = {
     val report = new GentrapReport(this)
     report.outputDir = new File(outputDir, "report")
-    report.summaryFile = summaryFile
+    report.summaryDbFile = summaryDbFile
     Some(report)
   }
 

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -140,7 +140,7 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
   override def reportClass: Some[MappingReport] = {
     val mappingReport = new MappingReport(this)
     mappingReport.outputDir = new File(outputDir, "report")
-    mappingReport.summaryFile = summaryFile
+    mappingReport.summaryDbFile = summaryDbFile
     mappingReport.args = Map(
       "sampleId" -> sampleId.getOrElse("."),
       "libId" -> libId.getOrElse("."))

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala

@@ -63,7 +63,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
   override def reportClass: Option[ReportBuilderExtension] = {
     val report = new MultisampleMappingReport(this)
     report.outputDir = new File(outputDir, "report")
-    report.summaryFile = summaryFile
+    report.summaryDbFile = summaryDbFile
     Some(report)
   }
 

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala

@@ -40,7 +40,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
   override def reportClass: Option[ReportBuilderExtension] = {
     val shiva = new ShivaReport(this)
     shiva.outputDir = new File(outputDir, "report")
-    shiva.summaryFile = summaryFile
+    shiva.summaryDbFile = summaryDbFile
     Some(shiva)
   }
 

tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala

@@ -119,7 +119,7 @@ class TinyCap(val parent: Configurable) extends QScript
   override def reportClass: Option[ReportBuilderExtension] = {
     val report = new TinyCapReport(this)
     report.outputDir = new File(outputDir, "report")
-    report.summaryFile = summaryFile
+    report.summaryDbFile = summaryDbFile
     Some(report)
   }