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biopet.biopet
Commits
2546ec16
Commit
2546ec16
authored
Nov 16, 2016
by
Sander Bollen
Browse files
throw error when no libraries in config
parent
98890af0
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
2546ec16
...
...
@@ -52,7 +52,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
/** Adds the library jobs */
final
def
addAndTrackJobs
()
:
Unit
=
{
if
(
nameRegex
.
findFirstIn
(
libId
)
==
None
)
if
(
nameRegex
.
findFirstIn
(
libId
)
.
isEmpty
)
Logging
.
addError
(
s
"Library '$libId' $nameError"
)
currentSample
=
Some
(
sampleId
)
currentLib
=
Some
(
libId
)
...
...
@@ -139,9 +139,13 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
*/
def
makeLibrary
(
id
:
String
)
:
Library
/** returns a set with library names */
/** returns a set with library names
or throws error when not found
*/
protected
def
libIds
:
Set
[
String
]
=
{
ConfigUtils
.
getMapFromPath
(
globalConfig
.
map
,
List
(
"samples"
,
sampleId
,
"libraries"
)).
getOrElse
(
Map
()).
keySet
val
ids
=
ConfigUtils
.
getMapFromPath
(
globalConfig
.
map
,
List
(
"samples"
,
sampleId
,
"libraries"
)).
getOrElse
(
Map
()).
keySet
if
(
ids
.
isEmpty
)
{
throw
new
IllegalArgumentException
(
"No libraries found in config"
)
}
ids
}
/** Name overules the one from qscript */
...
...
@@ -151,7 +155,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
/** Adds sample jobs */
final
def
addAndTrackJobs
()
:
Unit
=
{
if
(
nameRegex
.
findFirstIn
(
sampleId
)
==
None
)
if
(
nameRegex
.
findFirstIn
(
sampleId
)
.
isEmpty
)
Logging
.
addError
(
s
"Sample '$sampleId' $nameError"
)
currentSample
=
Some
(
sampleId
)
addJobs
()
...
...
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