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biopet.biopet
Commits
a10bd09e
Commit
a10bd09e
authored
Mar 05, 2015
by
Peter van 't Hof
Browse files
Change getVersion to Option[String]
parent
15e4e777
Changes
2
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
a10bd09e
...
...
@@ -135,10 +135,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
protected
val
versionExitcode
=
List
(
0
)
/** Executes the version command */
private
def
getVersionInternal
:
String
=
{
if
(
versionCommand
==
null
||
versionRegex
==
null
)
return
"N/A"
private
def
getVersionInternal
:
Option
[
String
]
=
{
if
(
versionCommand
==
null
||
versionRegex
==
null
)
return
None
val
exe
=
new
File
(
versionCommand
.
trim
.
split
(
" "
)(
0
))
if
(!
exe
.
exists
())
return
"N/A"
if
(!
exe
.
exists
())
return
None
val
stdout
=
new
StringBuffer
()
val
stderr
=
new
StringBuffer
()
def
outputLog
=
"Version command: \n"
+
versionCommand
+
...
...
@@ -147,25 +147,28 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
val
process
=
Process
(
versionCommand
).
run
(
ProcessLogger
(
stdout
append
_
+
"\n"
,
stderr
append
_
+
"\n"
))
if
(!
versionExitcode
.
contains
(
process
.
exitValue
))
{
logger
.
warn
(
"getVersion give exit code "
+
process
.
exitValue
+
", version not found \n"
+
outputLog
)
return
"N/A"
return
None
}
for
(
line
<-
stdout
.
toString
.
split
(
"\n"
)
++
stderr
.
toString
.
split
(
"\n"
))
{
line
match
{
case
versionRegex
(
m
)
=>
return
m
case
versionRegex
(
m
)
=>
return
Some
(
m
)
case
_
=>
}
}
logger
.
warn
(
"getVersion give a exit code "
+
process
.
exitValue
+
" but no version was found, executable correct? \n"
+
outputLog
)
return
"N/A"
return
None
}
/** Get version from cache otherwise execute the version command */
def
getVersion
:
String
=
{
def
getVersion
:
Option
[
String
]
=
{
if
(!
BiopetCommandLineFunctionTrait
.
executableCache
.
contains
(
executable
))
preProcesExecutable
if
(!
BiopetCommandLineFunctionTrait
.
versionCache
.
contains
(
executable
))
BiopetCommandLineFunctionTrait
.
versionCache
+=
executable
->
getVersionInternal
return
BiopetCommandLineFunctionTrait
.
versionCache
(
executable
)
if
(!
BiopetCommandLineFunctionTrait
.
versionCache
.
contains
(
versionCommand
))
getVersionInternal
match
{
case
Some
(
version
)
=>
BiopetCommandLineFunctionTrait
.
versionCache
+=
versionCommand
->
version
case
_
=>
}
BiopetCommandLineFunctionTrait
.
versionCache
.
get
(
versionCommand
)
}
/**
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
View file @
a10bd09e
...
...
@@ -64,8 +64,8 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
// otherwise, use default contaminants file (depending on FastQC version)
case
None
=>
val
defaultContams
=
getVersion
match
{
case
"v0.11.2"
=>
new
File
(
fastqcDir
+
"/Configuration/contaminant_list.txt"
)
case
_
=>
new
File
(
fastqcDir
+
"/Contaminants/contaminant_list.txt"
)
case
Some
(
"v0.11.2"
)
=>
new
File
(
fastqcDir
+
"/Configuration/contaminant_list.txt"
)
case
_
=>
new
File
(
fastqcDir
+
"/Contaminants/contaminant_list.txt"
)
}
config
(
"contaminants"
,
default
=
defaultContams
)
}
...
...
@@ -76,8 +76,8 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
// otherwise, check if adapters are already present (depending on FastQC version)
case
None
=>
val
defaultAdapters
=
getVersion
match
{
case
"v0.11.2"
=>
Option
(
new
File
(
fastqcDir
+
"/Configuration/adapter_list.txt"
))
case
_
=>
None
case
Some
(
"v0.11.2"
)
=>
Option
(
new
File
(
fastqcDir
+
"/Configuration/adapter_list.txt"
))
case
_
=>
None
}
defaultAdapters
.
collect
{
case
adp
=>
config
(
"adapters"
,
default
=
adp
)
}
}
...
...
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