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
9e21462b
Commit
9e21462b
authored
Jan 16, 2015
by
Peter van 't Hof
Browse files
Remove old report
parent
7bd7b5a9
Changes
2
Hide whitespace changes
Inline
Side-by-side
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
]
=
{
...
...
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