Fixing BIOPET-542 and BIOPET-615

91336909 · Peter van 't Hof · a085648e · 91336909 · 91336909 · 91336909
Commit 91336909 authored Mar 14, 2017 by Peter van 't Hof
3 changed files
--- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
+++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
 #import(nl.lumc.sasc.biopet.utils.IoUtils)
-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(org.apache.commons.io.FileUtils)
+#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)
+#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] = None %>
-<%@ var libId: Option[String] = None %>
+<%@ var summary: SummaryDb %>
+<%@ var sampleId: Option[Int] = None %>
 <%@ var sampleLevel: Boolean = true %>
-<%@ var rootPath: String %>
+<%@ var libId: Option[Int] = None %>
 <%@ var outputDir: File %>
+<%@ var rootPath: String %>
 <%@ var metricsTag: String = "bammetrics" %>
 <%@ var target: Option[String] %>
+<%@ var runId: Int %>
+<%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
 #{
-    val samples = sampleId match {
-        case Some(sample) => List(sample.toString)
-        case _ => summary.samples.toList
-    }
+    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
 }#


 <table class="table">
 <thead><tr>
    <th>sample</th>
-    <th>mean</th>
-    <th>median</th>
-    <th>max</th>
-    <th>horizontal</th>
-    <th>frac min 10x</th>
-    <th>frac min 20x</th>
-    <th>frac min 30x</th>
-    <th>frac min 40x</th>
-    <th>frac min 50x</th>
+    #for (field <- fields)
+        <th>${field}</th>
+    #end
 </tr></thead>
 <tbody>
-    #for (sample <- samples.toList.sorted)
+    #for (sample <- samples.sortBy(_.name))
        #{
-            val libs = (libId, sampleLevel) match {
-            case (_, true) => List("")
-            case (Some(libId), _) => List(libId.toString)
-            case _ => summary.libraries(sample).toList
+            val libs: List[Option[Int]] = (libId, sampleLevel) match {
+                case (_, true) => List(None)
+                case (Some(_), _) => List(libId)
+                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
            }
        }#
-        <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
+        <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
        #for (libId <- libs)
            #if (libs.head != libId) <tr> #end
-                #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
                #{
-                    val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List(metricsTag, "stats", target.get + "_cov_stats", "coverage", "_all")
-                    val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
-                    val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
-                    val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
+                    val moduleName = target.get + "_cov_stats"
+                    val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
+                    val values = summary.getStatKeys(runId, PipelineName(metricsTag), ModuleName(moduleName), SampleId(sample.id), libId.map(LibraryId).getOrElse(NoLibrary), statsPaths)
                }#
-                <td>${summary.getValue((prefixPath ::: "mean" :: Nil):_*)}</td>
-                <td>${summary.getValue((prefixPath ::: "median" :: Nil):_*)}</td>
-                <td>${summary.getValue((prefixPath ::: "max" :: Nil):_*)}</td>
-                <td>${summary.getValue((prefixPath ::: "horizontal" :: Nil):_*)}</td>
-                <td>${summary.getValue((prefixPath ::: "frac_min_10x" :: Nil):_*)}</td>
-                <td>${summary.getValue((prefixPath ::: "frac_min_20x" :: Nil):_*)}</td>
-                <td>${summary.getValue((prefixPath ::: "frac_min_30x" :: Nil):_*)}</td>
-                <td>${summary.getValue((prefixPath ::: "frac_min_40x" :: Nil):_*)}</td>
-                <td>${summary.getValue((prefixPath ::: "frac_min_50x" :: Nil):_*)}</td>
+                #for (field <- fields)
+                    <th>${values(field)}</th>
+                #end
            </tr>
        #end
    #end

--- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
+++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
 #import(nl.lumc.sasc.biopet.utils.IoUtils)
-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(org.apache.commons.io.FileUtils)
+#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)
+#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] %>
-<%@ var libId: Option[String] = None %>
+<%@ var summary: SummaryDb %>
+<%@ var sampleId: Option[Int] %>
+<%@ var libId: Option[Int] = None %>
 <%@ var outputDir: File %>
 <%@ var metricsTag: String = "bammetrics" %>
 <%@ var target: Option[String] %>
+<%@ var runId: Int %>
+<%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
 #{
-    val originalPlot = new File(summary.getValue(sampleId, libId, metricsTag, "files", target.get + "_cov_stats", "plot", "path")
-        .getOrElse(throw new IllegalArgumentException("No plot found in summary")).toString)
+    val moduleName = target.get + "_cov_stats"
+
+    val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
+    val plotFile = Await.result(summary.getFile(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), "plot"), Duration.Inf)
+    val originalPlot = new File(plotFile.get.path)
    val plot = new File(outputDir, target.get + "_cov_stats.png")

-    val values = summary.getValue(sampleId, libId, metricsTag, "stats", target.get + "_cov_stats", "coverage", "_all")
-        .getOrElse(throw new IllegalArgumentException("No plot found in summary")).asInstanceOf[Map[String, Any]]
+    val values = summary.getStatKeys(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), statsPaths)

    if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
 }#
-
 <img src="${plot.getName}">

 <table class="table">
 <thead><tr>
-    <th>mean</th>
-    <th>median</th>
-    <th>max</th>
-    <th>horizontal</th>
-    <th>frac min 10x</th>
-    <th>frac min 20x</th>
-    <th>frac min 30x</th>
-    <th>frac min 40x</th>
-    <th>frac min 50x</th>
+#for (field <- fields)
+    <th>${field}</th>
+#end
 </tr></thead>
 <tbody>
 <tr>
-    <td>${values.get("mean")}</td>
-    <td>${values.get("median")}</td>
-    <td>${values.get("max")}</td>
-    <td>${values.get("horizontal")}</td>
-    <td>${values.get("frac_min_10x")}</td>
-    <td>${values.get("frac_min_20x")}</td>
-    <td>${values.get("frac_min_30x")}</td>
-    <td>${values.get("frac_min_40x")}</td>
-    <td>${values.get("frac_min_50x")}</td>
+    #for (field <- fields)
+        <th>${values(field)}</th>
+    #end
 </tr>
 </tbody>
 </table>
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
@@ -66,8 +66,9 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {

  /** Generate a page with all target coverage stats */
  def regionsPage: Option[(String, ReportPage)] = {
-    val roi = summary.getSetting(runId, "shiva").get("regions_of_interest")
-    val amplicon = summary.getSetting(runId, "shiva").get("amplicon_bed")
+    val shivaSettings = Await.result(summary.getSetting(runId, "shiva"), Duration.Inf).get
+    val roi = shivaSettings.get("regions_of_interest")
+    val amplicon = shivaSettings.get("amplicon_bed")

    var regionPages: Map[String, ReportPage] = Map()