Switch templates to scalaz

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp

@@ -4,6 +4,8 @@
 #import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
+#import(scalaz._)
+#import(Scalaz._)
 <%@ var summary: SummaryDb %>
 <%@ var sampleId: Option[Int] = None %>
 <%@ var libId: Option[Int] = None %>
@@ -87,7 +89,7 @@
                         "Duplicates" -> List("flagstats", "Duplicates"),
                         "NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
                         )
-                        val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
+                        val results = summary.getStatKeys(runId, "bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
                         val total = results("All").getOrElse(0L).asInstanceOf[Long]
                         val mapped = results("Mapped").getOrElse(0L).asInstanceOf[Long]
                         val duplicates = results("Duplicates").getOrElse(0L).asInstanceOf[Long]

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp

@@ -4,6 +4,8 @@
 #import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
+#import(scalaz._)
+#import(Scalaz._)
 <%@ var summary: SummaryDb %>
 <%@ var sampleId: Option[Int] = None %>
 <%@ var libId: Option[Int] = None %>
@@ -82,7 +84,7 @@
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{
                         val statsPaths = fields.map(x => x -> List("clipping", "general", x)).toMap
-                        val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
+                        val results = summary.getStatKeys(runId, "bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
                     }#
                     #for (field <- fields)
                         <td>${results(field)}</td>

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp

@@ -4,6 +4,8 @@
 #import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
+#import(scalaz._)
+#import(Scalaz._)
 <%@ var summary: SummaryDb %>
 <%@ var sampleId: Option[Int] = None %>
 <%@ var libId: Option[Int] = None %>
@@ -84,7 +86,7 @@
                         #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                         #{
                             val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
-                            val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("CollectInsertSizeMetrics")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
+                            val results = summary.getStatKeys(runId, "bammetrics".right, Some("CollectInsertSizeMetrics".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
                         }#
                         #for (field <- fields)
                             <td>${results(field)}</td>

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp

@@ -4,6 +4,8 @@
 #import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
+#import(scalaz._)
+#import(Scalaz._)
 <%@ var summary: SummaryDb %>
 <%@ var sampleId: Option[Int] = None %>
 <%@ var libId: Option[Int] = None %>
@@ -83,7 +85,7 @@
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{
                         val statsPaths = fields.map(x => x -> List("mapping_quality", "general", x)).toMap
-                        val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
+                        val results = summary.getStatKeys(runId, "bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
                     }#
                     #for (field <- fields)
                         <td>${results(field)}</td>

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp

@@ -4,6 +4,8 @@
 #import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
+#import(scalaz._)
+#import(Scalaz._)
 <%@ var summary: SummaryDb %>
 <%@ var sampleId: Option[Int] = None %>
 <%@ var libId: Option[Int] = None %>
@@ -73,7 +75,7 @@
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{
                         val statsPaths = fields.map(x => x -> List("metrics", x)).toMap
-                        val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("wgs")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
+                        val results = summary.getStatKeys(runId, "bammetrics".right, Some("wgs".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths)
                     }#
                     #for (field <- fields)
                         <td>${results(field)}</td>

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp

@@ -2,7 +2,8 @@
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(scala.concurrent.Await)
 #import(scala.concurrent.duration.Duration)
-
+#import(scalaz._)
+#import(Scalaz._)
 <%@ var summary: SummaryDb %>
 <%@ var rootPath: String %>
 <%@ var pipeline: String %>
@@ -10,7 +11,7 @@
 
 #{
 
-    val settings = summary.getSettingKeys(runId, Right(pipeline),
+    val settings = summary.getSettingKeys(runId, pipeline.right,
       keyValues = Map(
         "contigs" -> List("reference", "contigs"),
         "species" -> List("reference", "species"),
@@ -18,7 +19,7 @@
     ))
     val contigs = settings.getOrElse("contigs", Some(Map())).getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
 
-    val referenceFile = Await.result(summary.getFile(runId, Right(pipeline), None, None, None, key = "referenceFasta"), Duration.Inf)
+    val referenceFile = Await.result(summary.getFile(runId, pipeline.right, None, None, None, key = "referenceFasta"), Duration.Inf)
 }#
 
 <table class="table">

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp

@@ -5,6 +5,8 @@
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
 #import(java.io.File)
+#import(scalaz._)
+#import(Scalaz._)
 <%@ var summary: SummaryDb %>
 <%@ var runId: Int %>
 <%@ var sampleId: Option[Int] = None %>
@@ -18,7 +20,7 @@
 #{
     val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
     val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf)
-    val settings = summary.getSettingsForLibraries(runId, Right("flexiprep"), keyValues = Map(
+    val settings = summary.getSettingsForLibraries(runId, "flexiprep".right, keyValues = Map(
     "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
     settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
     val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
@@ -26,7 +28,7 @@
     val librariesCount = libraries.size
 
     val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
-    summary.getSettingKeys(runId, Right("flexiprep"), None, sampleId.map(Left(_)), libId.map(Left(_)), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
+    summary.getSettingKeys(runId, "flexiprep".right, None, sampleId.map(_.left), libId.map(_.left), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
     else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
 }#
 #if (showIntro)
@@ -137,8 +139,8 @@
                     #if (read == "R2") </tr><tr> #end
                     #{
                         val statsPaths = Map("num_total" -> List("bases", "num_total"))
-                        val seqstatStats = summary.getStatKeys(runId, Right("flexiprep"), Some(Right("seqstat_" + read)), sample = Some(Left(sample.id)), library = Some(Left(lib.id)), keyValues = statsPaths)
-                        val seqstatQcStats = summary.getStatKeys(runId, Right("flexiprep"), Some(Right("seqstat_" + read + "_qc")), sample = Some(Left(sample.id)), library = Some(Left(lib.id)), keyValues = statsPaths)
+                        val seqstatStats = summary.getStatKeys(runId, "flexiprep".right, Some(("seqstat_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = statsPaths)
+                        val seqstatQcStats = summary.getStatKeys(runId, "flexiprep".right, Some(("seqstat_" + read + "_qc").right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = statsPaths)
 
                         val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
                         val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp

@@ -5,6 +5,8 @@
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(org.apache.commons.io.FileUtils)
 #import(java.io.File)
+#import(scalaz._)
+#import(Scalaz._)
 <%@ var summary: SummaryDb %>
 <%@ var runId: Int %>
 <%@ var sampleId: Option[Int] %>
@@ -12,7 +14,7 @@
 <%@ var plot: String %>
 <%@ var outputDir: File %>
 #{
-    val settings = summary.getSettingKeys(runId, Right("flexiprep"), None, sampleId.map(Left(_)), libId.map(Left(_)), keyValues = Map(
+    val settings = summary.getSettingKeys(runId, "flexiprep".right, None, sampleId.map(_.left), libId.map(_.left), keyValues = Map(
     "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
 
     val paired: Boolean = settings("paired") == Some(true)
@@ -20,7 +22,7 @@
     val skipTrim: Boolean = settings("skip_trim") == Some(true)
 
     def getPlot(read:String) = {
-        val file = Await.result(summary.getFile(runId, Right("flexiprep"), Some(Right(read)), sampleId.map(Left(_)), libId.map(Left(_)), plot), Duration.Inf)
+        val file = Await.result(summary.getFile(runId, "flexiprep".right, Some(read.right), sampleId.map(_.left), libId.map(_.left), plot), Duration.Inf)
         file.collect {
             case path => {
                 val file = new File(path.path.toString)
@@ -32,7 +34,7 @@
     }
 
     def plotAvailable(read:String) = {
-        val file = Await.result(summary.getFile(runId, Right("flexiprep"), Some(Right(read)), sampleId.map(Left(_)), libId.map(Left(_)), plot), Duration.Inf)
+        val file = Await.result(summary.getFile(runId, "flexiprep".right, Some(read.right), sampleId.map(_.left), libId.map(_.left), plot), Duration.Inf)
         file.map(x => new File(x.path).exists()).getOrElse(false)
     }
 

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

@@ -4,6 +4,8 @@
 #import(scala.concurrent.duration.Duration)
 #import(java.io.File)
 #import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
+#import(scalaz._)
+#import(Scalaz._)
 <%@ var summary: SummaryDb %>
 <%@ var runId: Int %>
 <%@ var sampleId: Option[Int] = None %>
@@ -17,7 +19,7 @@
 #{
     val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
     val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf)
-    val settings = summary.getSettingsForLibraries(runId, Right("flexiprep"), keyValues = Map(
+    val settings = summary.getSettingsForLibraries(runId, "flexiprep".right, keyValues = Map(
     "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
     settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
     val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
@@ -25,7 +27,7 @@
     val librariesCount = libraries.size
 
     val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
-        summary.getSettingKeys(runId, Right("flexiprep"), None, sampleId.map(Left(_)), libId.map(Left(_)), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
+        summary.getSettingKeys(runId, "flexiprep".right, None, sampleId.map(_.left), libId.map(_.left), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
     else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
 }#
 
@@ -142,15 +144,15 @@
                     #if (read == "R2") </tr><tr> #end
                     #{
                         val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
-                        val seqstatStats = summary.getStatKeys(runId, Right("flexiprep"), Some(Right("seqstat_" + read)), sample = Some(Left(sample.id)), library = Some(Left(lib.id)), keyValues = seqstatPaths)
-                        val seqstatQcStats = summary.getStatKeys(runId, Right("flexiprep"), Some(Right("seqstat_" + read + "_qc")), sample = Some(Left(sample.id)), library = Some(Left(lib.id)), keyValues = seqstatPaths)
+                        val seqstatStats = summary.getStatKeys(runId, "flexiprep".right, Some(("seqstat_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = seqstatPaths)
+                        val seqstatQcStats = summary.getStatKeys(runId, "flexiprep".right, Some(("seqstat_" + read + "_qc").right), sample = Some(sample.id.left), library = Some(lib.id.left), 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.getStatKeys(runId, Right("flexiprep"), Some(Right("clipping_" + read)), sample = Some(Left(sample.id)), library = Some(Left(lib.id)), keyValues = clippingPaths)
+                        val clippingStats = summary.getStatKeys(runId, "flexiprep".right, Some(("clipping_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = clippingPaths)
 
                         val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read))
-                        val trimmingStats = summary.getStatKeys(runId, Right("flexiprep"), Some(Right("trimming")), sample = Some(Left(sample.id)), library = Some(Left(lib.id)), keyValues = trimmingPaths)
+                        val trimmingStats = summary.getStatKeys(runId, "flexiprep".right, Some("trimming".right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = trimmingPaths)
 
                         val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
                         val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong