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biopet.biopet
Commits
62c8519c
Commit
62c8519c
authored
10 years ago
by
Peter van 't Hof
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changed output on getVersion on fail
parent
fe70b7cc
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+5
-3
5 additions, 3 deletions
...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
with
5 additions
and
3 deletions
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+
5
−
3
View file @
62c8519c
...
...
@@ -85,10 +85,12 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if
(
versionCommand
==
null
||
versionRegex
==
null
)
return
"N/A"
val
stdout
=
new
StringBuffer
()
val
stderr
=
new
StringBuffer
()
def
outputLog
=
"\n output log: \n stdout: \n"
+
stdout
.
toString
+
"\n stderr: \n"
+
stderr
.
toString
def
outputLog
=
"Version command: \n"
+
versionCommand
+
"\n output log: \n stdout: \n"
+
stdout
.
toString
+
"\n stderr: \n"
+
stderr
.
toString
val
process
=
Process
(
versionCommand
).
run
(
ProcessLogger
(
stdout
append
_
,
stderr
append
_
))
if
(!
versionExitcode
.
contains
(
process
.
exitValue
))
{
logger
.
warn
(
"Version
command: '"
+
versionCommand
+
"'
give exit code "
+
process
.
exitValue
+
", version not found"
+
outputLog
)
logger
.
warn
(
"
get
Version give exit code "
+
process
.
exitValue
+
", version not found
\n
"
+
outputLog
)
return
"N/A"
}
for
(
line
<-
stdout
.
toString
.
split
(
"\n"
)
++
stderr
.
toString
.
split
(
"\n"
))
{
...
...
@@ -97,7 +99,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
case
_
=>
}
}
logger
.
warn
(
"Version
command: '"
+
versionCommand
+
"'
give a exit code "
+
process
.
exitValue
+
" but no version was found, executable correct?"
+
outputLog
)
logger
.
warn
(
"
get
Version give a exit code "
+
process
.
exitValue
+
" but no version was found, executable correct?
\n
"
+
outputLog
)
return
"N/A"
}
...
...
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