Commit 2546ec16 authored by Sander Bollen's avatar Sander Bollen

throw error when no libraries in config

parent 98890af0
...@@ -52,7 +52,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript => ...@@ -52,7 +52,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
/** Adds the library jobs */ /** Adds the library jobs */
final def addAndTrackJobs(): Unit = { final def addAndTrackJobs(): Unit = {
if (nameRegex.findFirstIn(libId) == None) if (nameRegex.findFirstIn(libId).isEmpty)
Logging.addError(s"Library '$libId' $nameError") Logging.addError(s"Library '$libId' $nameError")
currentSample = Some(sampleId) currentSample = Some(sampleId)
currentLib = Some(libId) currentLib = Some(libId)
...@@ -139,9 +139,13 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript => ...@@ -139,9 +139,13 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
*/ */
def makeLibrary(id: String): Library def makeLibrary(id: String): Library
/** returns a set with library names */ /** returns a set with library names or throws error when not found */
protected def libIds: Set[String] = { protected def libIds: Set[String] = {
ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet val ids = ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
if (ids.isEmpty) {
throw new IllegalArgumentException("No libraries found in config")
}
ids
} }
/** Name overules the one from qscript */ /** Name overules the one from qscript */
...@@ -151,7 +155,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript => ...@@ -151,7 +155,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
/** Adds sample jobs */ /** Adds sample jobs */
final def addAndTrackJobs(): Unit = { final def addAndTrackJobs(): Unit = {
if (nameRegex.findFirstIn(sampleId) == None) if (nameRegex.findFirstIn(sampleId).isEmpty)
Logging.addError(s"Sample '$sampleId' $nameError") Logging.addError(s"Sample '$sampleId' $nameError")
currentSample = Some(sampleId) currentSample = Some(sampleId)
addJobs() addJobs()
......
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