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biopet.biopet
Commits
13dd6e6a
Commit
13dd6e6a
authored
Nov 17, 2014
by
bow
Browse files
Merge branch 'feature-no_output_test' into 'develop'
Feature no output test For #58 See merge request !52
parents
827de641
5c47970a
Changes
4
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biopet-framework/src/main/resources/log4j.properties
0 → 100644
View file @
13dd6e6a
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger
=
INFO, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1
=
org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout
=
org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern
=
%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
View file @
13dd6e6a
package
nl.lumc.sasc.biopet.core
import
java.text.SimpleDateFormat
import
java.util.Calendar
import
org.apache.log4j.Logger
import
org.apache.log4j.WriterAppender
import
org.apache.log4j.helpers.DateLayout
trait
Logging
{
def
logger
=
Logging
.
logger
}
object
Logging
{
val
logger
=
Logger
.
getLogger
(
"Logging"
)
val
logLayout
=
new
DateLayout
()
{
val
ignoresThrowable
=
false
def
format
(
event
:
org.apache.log4j.spi.LoggingEvent
)
:
String
=
{
val
calendar
:
Calendar
=
Calendar
.
getInstance
calendar
.
setTimeInMillis
(
event
.
getTimeStamp
)
val
formatter
:
SimpleDateFormat
=
new
SimpleDateFormat
(
"yyyy-MM-dd HH:mm:ss"
);
val
formattedDate
:
String
=
formatter
.
format
(
calendar
.
getTime
)
var
logLevel
=
event
.
getLevel
.
toString
while
(
logLevel
.
size
<
6
)
logLevel
+=
" "
val
className
=
event
.
getLocationInformation
.
getClassName
.
split
(
"\\."
).
last
.
split
(
"\\$"
).
head
logLevel
+
" ["
+
formattedDate
+
"] ["
+
className
+
"] "
+
event
.
getMessage
+
"\n"
}
}
val
stderrAppender
=
new
WriterAppender
(
logLayout
,
sys
.
process
.
stderr
)
logger
.
setLevel
(
org
.
apache
.
log4j
.
Level
.
INFO
)
logger
.
addAppender
(
Logging
.
stderrAppender
)
val
logger
=
Logger
.
getRootLogger
}
\ No newline at end of file
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
View file @
13dd6e6a
package
nl.lumc.sasc.biopet.core
import
org.apache.log4j.WriterAppender
import
java.io.File
trait
ToolCommand
extends
MainCommand
with
Logging
{
abstract
class
AbstractArgs
{
}
abstract
class
AbstractOptParser
extends
scopt
.
OptionParser
[
Args
](
commandName
)
{
opt
[
Unit
](
"log_nostderr"
)
foreach
{
_
=>
logger
.
removeAppender
(
Logging
.
stderrAppender
)
}
text
(
"No output to stderr"
)
opt
[
File
](
"log_file"
)
foreach
{
x
=>
logger
.
addAppender
(
new
WriterAppender
(
Logging
.
logLayout
,
new
java
.
io
.
PrintStream
(
x
)))
}
text
(
"Log file"
)
valueName
(
"<file>"
)
opt
[
String
](
'l'
,
"log_level"
)
foreach
{
x
=>
x
.
toLowerCase
match
{
case
"debug"
=>
logger
.
setLevel
(
org
.
apache
.
log4j
.
Level
.
DEBUG
)
...
...
biopet-framework/src/test/resources/log4j.properties
0 → 100644
View file @
13dd6e6a
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger
=
ERROR, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1
=
org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout
=
org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern
=
%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
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