From 110a3ebf572c543424d5361fe9d81e525690e779 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 9 Oct 2015 12:26:57 +0200
Subject: [PATCH] Added check also to libs
---
.../nl/lumc/sasc/biopet/core/MultiSampleQScript.scala | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index abeb787a5..5c316d274 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -47,6 +47,8 @@ trait MultiSampleQScript extends SummaryQScript {
/** Adds the library jobs */
final def addAndTrackJobs(): Unit = {
+ if (nameRegex.findFirstIn(libId) == None)
+ Logging.addError(s"Library '$libId' contains illegal chars, may only exist alphanumeric, '-' or '_' chars")
currentSample = Some(sampleId)
currentLib = Some(libId)
addJobs()
@@ -90,8 +92,8 @@ trait MultiSampleQScript extends SummaryQScript {
/** Adds sample jobs */
final def addAndTrackJobs(): Unit = {
- if (sampleRegex.findFirstIn(sampleId) == None)
- Logging.addError(s"Sample '$sampleId' contains illegal chars")
+ if (nameRegex.findFirstIn(sampleId) == None)
+ Logging.addError(s"Sample '$sampleId' contains illegal chars, may only exist alphanumeric, '-' or '_' chars")
currentSample = Some(sampleId)
addJobs()
qscript.addSummarizable(this, "pipeline", Some(sampleId))
@@ -131,7 +133,7 @@ trait MultiSampleQScript extends SummaryQScript {
/** Returns a list of all sampleIDs */
protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
- protected lazy val sampleRegex = """^[a-zA-Z0-9-_]+$""".r
+ protected lazy val nameRegex = """^[a-zA-Z0-9-_]+$""".r
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
--
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