Merge remote-tracking branch 'origin/fix-BIOPET-587' into fix-BIOPET-587

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -62,7 +62,6 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
         currentSample = Some(sampleId)
         currentLib = Some(libId)
         addJobs()
-        qscript.addSummarizable(this, "pipeline", Some(sampleId), Some(libId))
         currentLib = None
         currentSample = None
       }
@@ -170,7 +169,6 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
         Logging.addError(s"Sample '$sampleId' $nameError")
       currentSample = Some(sampleId)
       addJobs()
-      qscript.addSummarizable(this, "pipeline", Some(sampleId))
       currentSample = None
     }
 

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

@@ -22,6 +22,7 @@ import nl.lumc.sasc.biopet.core.extensions.{ CheckChecksum, Md5sum }
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import org.broadinstitute.gatk.queue.QScript
 import nl.lumc.sasc.biopet.LastCommitHash
+import nl.lumc.sasc.biopet.utils.ConfigUtils
 
 import scala.collection.mutable
 import scala.concurrent.Await
@@ -64,7 +65,8 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
    * @param libraryId Id of libary
    * @param forceSingle If true it replaces summarizable instead of adding to it
    */
-  def addSummarizable(summarizable: Summarizable, name: String,
+  def addSummarizable(summarizable: Summarizable,
+                      name: String,
                       sampleId: Option[String] = None,
                       libraryId: Option[String] = None,
                       forceSingle: Boolean = false): Unit = {
@@ -90,7 +92,7 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
       val id = reader.getLines().next().toInt
       reader.close()
       id
-    } else createRun
+    } else createRun()
   }
 
   private def runIdFile = root match {
@@ -104,7 +106,11 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
       case q: BiopetQScript => q.outputDir
       case _                => throw new IllegalStateException("Root should be a BiopetQscript")
     }
-    val id = Await.result(db.createRun(summaryName, dir.getAbsolutePath, nl.lumc.sasc.biopet.Version,
+    val name = root match {
+      case q: SummaryQScript => q.summaryName
+      case _                 => throw new IllegalStateException("Root should be a SummaryQScript")
+    }
+    val id = Await.result(db.createRun(name, dir.getAbsolutePath, nl.lumc.sasc.biopet.Version,
       LastCommitHash, new Date(System.currentTimeMillis())), Duration.Inf)
     runIdFile.getParentFile.mkdir()
     val writer = new PrintWriter(runIdFile)
@@ -183,6 +189,22 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
       case _ => add(writeSummary)
     }
 
+    qscript match {
+      case q: MultiSampleQScript =>
+        // Global level
+        for ((key, file) <- qscript.summaryFiles) addChecksum(file)
+
+        for ((sampleName, sample) <- q.samples) {
+          // Sample level
+          for ((key, file) <- sample.summaryFiles) addChecksum(file)
+          for ((libName, lib) <- sample.libraries) {
+            // Library level
+            for ((key, file) <- lib.summaryFiles) addChecksum(file)
+          }
+        }
+      case q => for ((key, file) <- q.summaryFiles) addChecksum(file)
+    }
+
     addedJobs = true
   }
 }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -149,14 +149,14 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
           // Sample level
           val sampleId = Await.result(db.getSampleId(qscript.summaryRunId, sampleName), Duration.Inf).getOrElse(throw new IllegalStateException("Sample should already exist in database"))
           for ((key, file) <- sample.summaryFiles.par)
-            Await.result(createFile(db, q.summaryRunId, pipelineId, Some(sampleId), None, None, key, file, outputDir), Duration.Inf)
+            Await.result(createFile(db, q.summaryRunId, pipelineId, None, Some(sampleId), None, key, file, outputDir), Duration.Inf)
           db.createOrUpdateSetting(qscript.summaryRunId, pipelineId, None, Some(sampleId), None, ConfigUtils.mapToJson(sample.summarySettings).nospaces)
 
           for ((libName, lib) <- sample.libraries) {
             // Library level
             val libId = Await.result(db.getLibraryId(qscript.summaryRunId, sampleId, libName), Duration.Inf).getOrElse(throw new IllegalStateException("Library should already exist in database"))
             for ((key, file) <- lib.summaryFiles.par)
-              Await.result(createFile(db, q.summaryRunId, pipelineId, Some(sampleId), Some(libId), None, key, file, outputDir), Duration.Inf)
+              Await.result(createFile(db, q.summaryRunId, pipelineId, None, Some(sampleId), Some(libId), key, file, outputDir), Duration.Inf)
             db.createOrUpdateSetting(qscript.summaryRunId, pipelineId, None, Some(sampleId), Some(libId), ConfigUtils.mapToJson(lib.summarySettings).nospaces)
           }
         }

gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-<%@ var summary: Summary %>
-<%@ var rootPath: String %>
-
+#import(scala.concurrent.Await)
+#import(scala.concurrent.duration.Duration)
+<%@ var summary: SummaryDb %>
+<%@ var runId: Int %>
+#{
+    val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
+    val samples = Await.result(summary.getSamples(Some(runId)), Duration.Inf)
+}#
 <table class="table">
 <tbody>
     <tr><th>Pipeline</th><td>Gears</td></tr>
-    <tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
-    <tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
-    <tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
+    <tr><th>Version</th><td>${run.version}</td></tr>
+    <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
+    <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
+    <tr><th>Number of samples</th><td>${samples.size}</td></tr>
 </tbody>
 </table>
 <br/>

gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-<%@ var summary: Summary %>
-<%@ var rootPath: String %>
+#import(scala.concurrent.Await)
+#import(scala.concurrent.duration.Duration)
+<%@ var summary: SummaryDb %>
+<%@ var runId: Int %>
 <%@ var sampleId: Option[String] = None %>
 <%@ var libId: Option[String] = None %>
-
+#{
+    val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
+}#
 <table class="table">
 <tbody>
-    <tr><th>Pipeline</th><td>Gears</td></tr>
-    <tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
-    <tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
-    <tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
+    <tr><th>Pipeline</th><td>GearsSingle</td></tr>
+    <tr><th>Version</th><td>${run.version}</td></tr>
+    <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
+    <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
     #if(sampleId.isDefined) <tr><th>Sample</th><td>${sampleId}</td></tr> #end
     #if(libId.isDefined) <tr><th>Library</th><td>${libId}</td></tr> #end
 </tbody>

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

@@ -14,6 +14,8 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gears
 
+import java.io.File
+
 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
@@ -57,10 +59,10 @@ object GearsReport extends MultisampleReportBuilder {
         )), Map()))
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-        )), Map("biomFile" -> qiimeClosesOtuTable.get)))
+        )), Map("biomFile" -> new File(qiimeClosesOtuTable.get.path))))
       else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-        )), Map("biomFile" -> qiimeOpenOtuTable.get)))
+        )), Map("biomFile" -> new File(qiimeOpenOtuTable.get.path))))
       else Nil) ::: List("Samples" -> generateSamplesPage(pageArgs)) ++
         Map(
           "Versions" -> ReportPage(List(), List(
@@ -97,10 +99,10 @@ object GearsReport extends MultisampleReportBuilder {
       )), Map()))
     else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-      )), Map("biomFile" -> qiimeClosesOtuTable.get)))
+      )), Map("biomFile" -> new File(qiimeClosesOtuTable.get.path))))
     else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-      )), Map("biomFile" -> qiimeOpenOtuTable.get)))
+      )), Map("biomFile" -> new File(qiimeOpenOtuTable.get.path))))
     else Nil) ::: List(
       "Libraries" -> generateLibraryPage(args)
     ), List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
@@ -133,10 +135,10 @@ object GearsReport extends MultisampleReportBuilder {
         )), Map()))
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-        )), Map("biomFile" -> qiimeClosesOtuTable.get)))
+        )), Map("biomFile" -> new File(qiimeClosesOtuTable.get.path))))
       else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
-        )), Map("biomFile" -> qiimeOpenOtuTable.get)))
+        )), Map("biomFile" -> new File(qiimeOpenOtuTable.get.path))))
       else Nil), List(
         "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
         "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")

mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp

 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(scala.concurrent.Await)
 #import(scala.concurrent.duration.Duration)
 <%@ var summary: SummaryDb %>
 <%@ var rootPath: String %>
-<%@ var pipeline: String %>
 <%@ var runId: Int %>
 <%@ var sampleId: Option[Int] %>
 <%@ var libId: Option[Int] %>
 #{
     val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
-    val settings = summary.getSettingKeys(runId, Right(pipeline),
+    val settings = summary.getSettingKeys(runId, run.name,
     keyValues = Map(
     "contigs" -> List("reference", "contigs"),
     "species" -> List("reference", "species"),
@@ -19,13 +20,13 @@
 }#
 <table class="table">
 <tbody>
-    <tr><th>Pipeline</th><td>${pipeline}</td></tr>
+    <tr><th>Pipeline</th><td>Mapping</td></tr>
     <tr><th>Version</th><td>${run.version}</td></tr>
     <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
     <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
     <tr><th>Reference</th><td>${settings.get("species")} - ${settings.get("name")}</td></tr>
-    <tr><th>Sample</th><td>${sampleId}</td></tr>
-    <tr><th>Library</th><td>${libId}</td></tr>
+    <tr><th>Sample</th><td>${Await.result(summary.getSampleName(sampleId.get), Duration.Inf)}</td></tr>
+    <tr><th>Library</th><td>${Await.result(summary.getLibraryName(libId.get), Duration.Inf)}</td></tr>
 </tbody>
 </table>
 <br/>

shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-<%@ var summary: Summary %>
-<%@ var rootPath: String %>
-
+#import(scala.concurrent.Await)
+#import(scala.concurrent.duration.Duration)
+<%@ var summary: SummaryDb %>
+<%@ var runId: Int %>
+#{
+    val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
+    val samples = Await.result(summary.getSamples(Some(runId)), Duration.Inf)
+    val settings = summary.getSettingKeys(runId, run.name,
+    keyValues = Map(
+        "contigs" -> List("reference", "contigs"),
+        "species" -> List("reference", "species"),
+        "name" -> List("reference", "name"),
+        "annotation" -> List("annotation"),
+        "multisample_variantcalling" -> List("multisample_variantcalling"),
+        "sv_calling" -> List("sv_calling"),
+        "variantcallers" -> List("variantcallers")
+    ))
+}#
 <table class="table">
 <tbody>
     <tr><th>Pipeline</th><td>Shiva</td></tr>
-    <tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
-    <tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
-    <tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
+    <tr><th>Pipeline</th><td>Gears</td></tr>
+    <tr><th>Version</th><td>${run.version}</td></tr>
+    <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
+    <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
     <tr>
         <th>Variantcallers</th>
-        <td>${summary.getValue("shivavariantcalling", "settings", "variantcallers").getOrElse(List("None")).asInstanceOf[List[String]].mkString(", ")}</td>
+        <td>${settings.get("variantcallers")}</td>
     </tr>
-    <tr><th>Reference</th><td>${summary.getValue("shiva", "settings", "reference", "species")} - ${summary.getValue("shiva", "settings", "reference", "name")}</td></tr>
-    <tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
-    <tr><th>Annotation</th><td>${summary.getValue("shiva", "settings", "annotation")}</td></tr>
-    <tr><th>Multisample variantcalling</th><td>${summary.getValue("shiva", "settings", "multisample_variantcalling")}</td></tr>
-    <tr><th>Sv calling</th><td>${summary.getValue("shiva", "settings", "sv_calling")}</td></tr>
+    <tr><th>Reference</th><td>${settings.get("species")} - ${settings.get("name")}</td></tr>
+    <tr><th>Number of samples</th><td>${samples.size}</td></tr>
+    <tr><th>Annotation</th><td>${settings.get("annotation")}</td></tr>
+    <tr><th>Multisample variantcalling</th><td>${settings.get("multisample_variantcalling")}</td></tr>
+    <tr><th>Sv calling</th><td>${settings.get("sv_calling")}</td></tr>
 </tbody>
 </table>
 <br/>