diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp index a9c4a8eebb863f8f29682e638479e4185a2f5be0..6497546891055ccdc882cbf2be5b609a7c1ae229 100644 --- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp +++ b/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 diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp index 3230b72db233d96d59ea68d7056e6de384e1cfe3..ddb6817dd9e8dc90345881517637cbac53fcea56 100644 --- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp +++ b/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) diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala index 03e0d5faaeb6d77256dd64b4bc9656d57fccd5d6..5de15a7d58ae45039fc56e3892af7f85c4296791 100644 --- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala +++ b/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) diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp index 66456d792464970e9c72e845fc55f20d617c9cc6..e3eaba475acffa68c38293624e09e436e8976f62 100644 --- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp +++ b/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"> diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala index d1ebec6bc7ac0eeec23c671a2508414c981b2f02..d6d2fcc9a1b4c5cae18e71e2052b8a747cc10bed 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala +++ b/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: _*) diff --git a/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp b/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp index 4570ad240a6220dd06eb4412fc1456d426b36ffe..3c9926d4e4dd9234ee25a87ca4cf1a5df38f3a78 100644 --- a/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp +++ b/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 diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp index a17e87c9e17596abbdba6ca55110779ac6d246d8..3514498749d8c55e7b6839263875e31a3aa3b877 100644 --- a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp +++ b/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>