From 0832f655216ed33ef5fd6519b0e0cd0023d5107a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 Oct 2015 17:43:46 +0200
Subject: [PATCH] Changed error message
---
.../nl/lumc/sasc/biopet/core/MultiSampleQScript.scala | 8 ++++++--
1 file changed, 6 insertions(+), 2 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 6c60565a1..f60aeeca8 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
@@ -48,7 +48,7 @@ trait MultiSampleQScript extends SummaryQScript {
/** Adds the library jobs */
final def addAndTrackJobs(): Unit = {
if (nameRegex.findFirstIn(libId) == None)
- Logging.addError(s"Library '$libId' does not conform to '$nameRegex'")
+ Logging.addError(s"Library '$libId' $nameError")
currentSample = Some(sampleId)
currentLib = Some(libId)
addJobs()
@@ -93,7 +93,7 @@ trait MultiSampleQScript extends SummaryQScript {
/** Adds sample jobs */
final def addAndTrackJobs(): Unit = {
if (nameRegex.findFirstIn(sampleId) == None)
- Logging.addError(s"Sample '$sampleId' does not conform to '$nameRegex'")
+ Logging.addError(s"Sample '$sampleId' $nameError")
currentSample = Some(sampleId)
addJobs()
qscript.addSummarizable(this, "pipeline", Some(sampleId))
@@ -134,6 +134,10 @@ trait MultiSampleQScript extends SummaryQScript {
protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
protected lazy val nameRegex = """^[a-zA-Z0-9][a-zA-Z0-9-_]+[a-zA-Z0-9]$""".r
+ protected lazy val nameError = " name invalid." +
+ "Name must have at least 3 characters," +
+ "must begin and end with an alphanumeric character, " +
+ "and must not have whitespace."
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
--
GitLab