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biopet.biopet
Commits
9e21462b
Commit
9e21462b
authored
Jan 16, 2015
by
Peter van 't Hof
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Remove old report
parent
7bd7b5a9
Changes
2
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2 changed files
with
1 addition
and
41 deletions
+1
-41
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+1
-7
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+0
-34
No files found.
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
9e21462b
...
...
@@ -57,14 +57,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
case
f
:
BiopetCommandLineFunctionTrait
=>
f
.
afterGraph
case
_
=>
}
val
configReport
=
Config
.
global
.
getReport
val
configReportFile
=
new
File
(
outputDir
+
qSettings
.
runName
+
".configreport.txt"
)
configReportFile
.
getParentFile
.
mkdir
val
writer
=
new
PrintWriter
(
configReportFile
)
writer
.
write
(
configReport
)
writer
.
close
()
Config
.
global
.
writeReport
(
qSettings
.
runName
,
outputDir
+
".log/"
+
qSettings
.
runName
)
for
(
line
<-
configReport
.
split
(
"\n"
))
logger
.
debug
(
line
)
}
def
add
(
functions
:
QFunction*
)
// Gets implemeted at org.broadinstitute.sting.queue.QScript
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
View file @
9e21462b
...
...
@@ -140,40 +140,6 @@ class Config(var map: Map[String, Any]) extends Logging {
}
else
throw
new
IllegalStateException
(
"Value in config could not be found but it seems required, index: "
+
requestedIndex
)
}
//TODO: New version of report is needed
/**
* Makes report for all used values
* @deprecated
* @return Config report
*/
def
getReport
:
String
=
{
val
output
:
StringBuilder
=
new
StringBuilder
output
.
append
(
"Config report, sorted on module:\n"
)
var
modules
:
Map
[
String
,
StringBuilder
]
=
Map
()
for
((
key
,
value
)
<-
foundCache
)
{
val
module
=
key
.
module
if
(!
modules
.
contains
(
module
))
modules
+=
(
module
->
new
StringBuilder
)
modules
(
module
).
append
(
"Found: "
+
value
.
toString
+
"\n"
)
}
for
((
key
,
value
)
<-
defaultCache
)
{
val
module
=
key
.
module
if
(!
modules
.
contains
(
module
))
modules
+=
(
module
->
new
StringBuilder
)
modules
(
module
).
append
(
"Default used: "
+
value
.
toString
+
"\n"
)
}
for
(
value
<-
notFoundCache
)
{
val
module
=
value
.
module
if
(!
modules
.
contains
(
module
))
modules
+=
(
module
->
new
StringBuilder
)
if
(!
defaultCache
.
contains
(
value
))
modules
(
module
).
append
(
"Not Found: "
+
value
.
toString
+
"\n"
)
}
for
((
key
,
value
)
<-
modules
)
{
output
.
append
(
"Config options for module: "
+
key
+
"\n"
)
output
.
append
(
value
.
toString
)
output
.
append
(
"\n"
)
}
return
output
.
toString
}
def
writeReport
(
id
:
String
,
directory
:
String
)
:
Unit
=
{
def
convertIndexValuesToMap
(
input
:
List
[(
ConfigValueIndex
,
Any
)],
forceFreeVar
:
Option
[
Boolean
]
=
None
)
:
Map
[
String
,
Any
]
=
{
...
...
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