Changes method name

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

@@ -13,8 +13,8 @@
 </tr></thead>
 <tbody>
 <tr>
-<td>${summary.getLibraryValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "path")}</td>
-<td>${summary.getLibraryValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "md5")}</td>
+<td>${summary.getValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "path")}</td>
+<td>${summary.getValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "md5")}</td>
 </tr>
 </tbody>
 </table>
\ No newline at end of file

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

@@ -10,11 +10,11 @@
 <%@ var metricsTag: String = "bammetrics" %>
 <%@ var target: String %>
 #{
-    val originalPlot = new File(summary.getLibraryValue(sampleId, libId, metricsTag, "files", target + "_cov_stats", "plot", "path")
+    val originalPlot = new File(summary.getValue(sampleId, libId, metricsTag, "files", target + "_cov_stats", "plot", "path")
         .getOrElse(throw new IllegalArgumentException("No plot found in summary")).toString)
     val plot = new File(outputDir, target + "_cov_stats.png")
 
-    val values = summary.getLibraryValue(sampleId, libId, metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
+    val values = summary.getValue(sampleId, libId, metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
         .getOrElse(throw new IllegalArgumentException("No plot found in summary")).asInstanceOf[Map[String, Any]]
 
     if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -42,8 +42,8 @@ object BammetricsReport extends ReportBuilder {
                      libId: Option[String],
                      metricsTag: String = "bammetrics") = {
     val targets = (
-      summary.getLibraryValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
-      summary.getLibraryValue(sampleId, libId, "bammetrics", "settings", "roi_name")
+      summary.getValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
+      summary.getValue(sampleId, libId, "bammetrics", "settings", "roi_name")
     ) match {
         case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
         case (_, Some(roi: List[_])) => roi.map(_.toString)

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp

@@ -6,7 +6,7 @@
 <%@ var libId: Option[String] = None %>
 <%@ var pipeline: String = summary.getValue("meta", "pipeline_name").getOrElse("").toString %>
 #{
-    val executables = summary.getLibraryValue(sampleId, libId, pipeline, "executables").getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
+    val executables = summary.getValue(sampleId, libId, pipeline, "executables").getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
 }#
 
 <table class="table">

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala

@@ -55,7 +55,7 @@ class Summary(file: File) {
 
   //TODO: rename method
   /** Get value on nested path with prefix depending is sampleId and/or libId is None or not */
-  def getLibraryValue(sampleId: Option[String], libId: Option[String], path: String*): Option[Any] = {
+  def getValue(sampleId: Option[String], libId: Option[String], path: String*): Option[Any] = {
     (sampleId, libId) match {
       case (Some(sample), Some(lib)) => getLibraryValue(sample, lib, path: _*)
       case (Some(sample), _)         => getSampleValue(sample, path: _*)

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

@@ -48,8 +48,8 @@
             #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
-                    <td>${removeDir(summary.getLibraryValue(Some(sample), (if (sampleLevel) None else Some(libId)), pipelineName, "files", "pipeline", fileTag, "path"))}</td>
-                    <td>${summary.getLibraryValue(Some(sample), (if (sampleLevel) None else Some(libId)), pipelineName, "files", "pipeline", fileTag, "md5")}</td>
+                    <td>${removeDir(summary.getValue(Some(sample), (if (sampleLevel) None else Some(libId)), pipelineName, "files", "pipeline", fileTag, "path"))}</td>
+                    <td>${summary.getValue(Some(sample), (if (sampleLevel) None else Some(libId)), pipelineName, "files", "pipeline", fileTag, "md5")}</td>
                 </tr>
             #end
         #end

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

@@ -9,7 +9,7 @@
 <%@ var rootPath: String %>
 <%@ var outputDir: File %>
 #{
-    val variantCallers = summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "settings", "variantcallers").get.asInstanceOf[List[String]]
+    val variantCallers = summary.getValue(sampleId, libId, "shivavariantcalling", "settings", "variantcallers").get.asInstanceOf[List[String]]
     val pipelineOutputDir = summary.getValue("meta", "output_dir").getOrElse("").toString
     def removeDir(value: Option[Any]): Option[Any] = {
         value.collect { case a =>
@@ -31,15 +31,15 @@
         #if (variantCallers.size > 1)
             <tr>
                 <td>Final (merged)</td>
-                <td>${removeDir(summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "path"))}</td>
-                <td>${summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "md5")}</td>
+                <td>${removeDir(summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "path"))}</td>
+                <td>${summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "md5")}</td>
             </tr>
         #end
         #for (variantCaller <- variantCallers)
             <tr>
                 <td>${variantCaller}</td>
-                <td>${removeDir(summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "path"))}</td>
-                <td>${summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "md5")}</td>
+                <td>${removeDir(summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "path"))}</td>
+                <td>${summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "md5")}</td>
             </tr>
         #end
     </tbody>