From abed23bb2d4198f68146d2d5f64c4519af6ac3b1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Nov 2015 12:36:04 +0100
Subject: [PATCH] Better error handeling on wrong values
---
.../biopet/pipelines/gentrap/Gentrap.scala | 25 +++++++++++--------
1 file changed, 15 insertions(+), 10 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 298fd7770..a57ec9f2a 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -42,6 +42,7 @@ import scalaz.Scalaz._
* Gentrap pipeline
* Generic transcriptome analysis pipeline
*
+ * @author Peter van 't Hof <p.j.van_t_hof@lumc.nl>
* @author Wibowo Arindrarto <w.arindrarto@lumc.nl>
*/
class Gentrap(val root: Configurable) extends QScript
@@ -65,7 +66,7 @@ class Gentrap(val root: Configurable) extends QScript
if (config.contains("expression_measures"))
config("expression_measures")
.asStringList
- .map { makeExpMeasure }
+ .flatMap { makeExpMeasure }
.toSet
else {
Logging.addError("'expression_measures' is missing in the config")
@@ -76,7 +77,7 @@ class Gentrap(val root: Configurable) extends QScript
/** Strandedness modes */
var strandProtocol: StrandProtocol.Value = {
if (config.contains("strand_protocol"))
- makeStrandProtocol(config("strand_protocol").asString)
+ makeStrandProtocol(config("strand_protocol").asString).getOrElse(StrandProtocol.NonSpecific)
else {
Logging.addError("'strand_protocol' is missing in the config")
StrandProtocol.NonSpecific
@@ -894,22 +895,26 @@ object Gentrap extends PipelineCommand {
.mkString("")
/** Conversion from raw user-supplied expression measure string to enum value */
- private def makeExpMeasure(rawName: String): ExpMeasures.Value = {
+ private def makeExpMeasure(rawName: String): Option[ExpMeasures.Value] = {
try {
- ExpMeasures.withName(camelize(rawName))
+ Some(ExpMeasures.withName(camelize(rawName)))
} catch {
- case nse: NoSuchElementException => throw new IllegalArgumentException("Invalid expression measure: " + rawName)
- case e: Exception => throw e
+ case nse: NoSuchElementException =>
+ Logging.addError(s"Invalid expression measure: $rawName")
+ None
+ case e: Exception => throw e
}
}
/** Conversion from raw user-supplied expression measure string to enum value */
- private def makeStrandProtocol(rawName: String): StrandProtocol.Value = {
+ private def makeStrandProtocol(rawName: String): Option[StrandProtocol.Value] = {
try {
- StrandProtocol.withName(camelize(rawName))
+ Some(StrandProtocol.withName(camelize(rawName)))
} catch {
- case nse: NoSuchElementException => throw new IllegalArgumentException("Invalid strand protocol: " + rawName)
- case e: Exception => throw e
+ case nse: NoSuchElementException =>
+ Logging.addError(s"Invalid strand protocol: $rawName")
+ None
+ case e: Exception => throw e
}
}
}
--
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