Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
21fba762
Commit
21fba762
authored
Feb 12, 2015
by
Peter van 't Hof
Browse files
Fix some small bugs
parent
2a906887
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
21fba762
...
...
@@ -48,7 +48,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
protected
[
core
]
def
beforeCmd
{}
/**
* Can override this method. This is executed after the script is done en queue starts to generate the graph
* Can overr
* ide this method. This is executed after the script is done en queue starts to generate the graph
*/
protected
[
core
]
def
afterGraph
{}
//TODO: function need rename to beforeGraph
...
...
@@ -123,7 +124,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
beforeCmd
addJobReportBinding
(
"cores"
,
if
(
nCoresRequest
.
get
.
toInt
>
0
)
nCoresRequest
.
get
.
toInt
else
1
)
addJobReportBinding
(
"cores"
,
nCoresRequest
match
{
case
Some
(
n
)
if
n
>
0
=>
n
case
_
=>
1
})
addJobReportBinding
(
"version"
,
getVersion
)
}
...
...
@@ -166,6 +170,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/** Get version from cache otherwise execute the version command */
def
getVersion
:
String
=
{
if
(!
BiopetCommandLineFunctionTrait
.
executableCache
.
contains
(
executable
))
checkExecutable
if
(!
BiopetCommandLineFunctionTrait
.
versionCache
.
contains
(
executable
))
BiopetCommandLineFunctionTrait
.
versionCache
+=
executable
->
getVersionInternal
return
BiopetCommandLineFunctionTrait
.
versionCache
(
executable
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
21fba762
...
...
@@ -73,12 +73,14 @@ trait BiopetQScript extends Configurable with GatkLogging {
case
f
:
BiopetCommandLineFunctionTrait
=>
{
f
.
checkExecutable
f
.
afterGraph
f
.
commandLine
}
case
_
=>
}
if
(
outputDir
.
canWrite
)
globalConfig
.
writeReport
(
qSettings
.
runName
,
outputDir
+
".log/"
+
qSettings
.
runName
)
else
BiopetQScript
.
addError
(
"Output dir: '"
+
outputDir
+
"' is not writeable"
)
if
(
outputDir
.
getParentFile
.
canWrite
||
(
outputDir
.
exists
&&
outputDir
.
canWrite
))
globalConfig
.
writeReport
(
qSettings
.
runName
,
new
File
(
outputDir
,
".log/"
+
qSettings
.
runName
))
else
BiopetQScript
.
addError
(
"Parent of output dir: '"
+
outputDir
.
getParent
+
"' is not writeable, outputdir can not be created"
)
BiopetQScript
.
checkErrors
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
View file @
21fba762
...
...
@@ -140,7 +140,8 @@ class Config(var map: Map[String, Any]) extends Logging {
}
else
ConfigValue
(
requestedIndex
,
null
,
null
,
freeVar
)
}
def
writeReport
(
id
:
String
,
directory
:
String
)
:
Unit
=
{
def
writeReport
(
id
:
String
,
directory
:
File
)
:
Unit
=
{
directory
.
mkdirs
()
def
convertIndexValuesToMap
(
input
:
List
[(
ConfigValueIndex
,
Any
)],
forceFreeVar
:
Option
[
Boolean
]
=
None
)
:
Map
[
String
,
Any
]
=
{
input
.
foldLeft
(
Map
[
String
,
Any
]())(
...
...
@@ -155,8 +156,7 @@ class Config(var map: Map[String, Any]) extends Logging {
}
def
writeMapToJsonFile
(
map
:
Map
[
String
,
Any
],
name
:
String
)
:
Unit
=
{
val
file
=
new
File
(
directory
+
"/"
+
id
+
"."
+
name
+
".json"
)
file
.
getParentFile
.
mkdirs
()
val
file
=
new
File
(
directory
,
id
+
"."
+
name
+
".json"
)
val
writer
=
new
PrintWriter
(
file
)
writer
.
write
(
ConfigUtils
.
mapToJson
(
map
).
spaces2
)
writer
.
close
()
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment