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biopet.biopet
Commits
6c9f45d0
Commit
6c9f45d0
authored
Jun 04, 2015
by
Peter van 't Hof
Browse files
Move copy functions to IoUtils
parent
2b7ffba3
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
6c9f45d0
...
...
@@ -5,10 +5,9 @@ import java.net.URL
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.summary.Summary
import
org.apache.commons.io.IOUtils
import
org.broadinstitute.gatk.utils.commandline.Input
import
org.fusesource.scalate.
{
TemplateSource
,
TemplateEngine
}
import
scala.collection.JavaConversions._
import
nl.lumc.sasc.biopet.utils.IoUtils
/**
* Created by pjvan_thof on 3/27/15.
...
...
@@ -92,7 +91,7 @@ trait ReportBuilder extends ToolCommand {
)
for
(
resource
<-
extFiles
.
par
)
{
ReportBuilder
.
copyStreamToFile
(
getClass
.
getResourceAsStream
(
resourceDir
+
resource
),
new
File
(
extOutputDir
,
resource
),
true
)
IoUtils
.
copyStreamToFile
(
getClass
.
getResourceAsStream
(
resourceDir
+
resource
),
new
File
(
extOutputDir
,
resource
),
true
)
}
logger
.
info
(
"Parsing summary"
)
...
...
@@ -162,37 +161,11 @@ object ReportBuilder {
case
Some
(
template
)
=>
template
case
_
=>
{
val
tempFile
=
File
.
createTempFile
(
"ssp-template"
,
new
File
(
location
).
getName
)
copyStreamToFile
(
getClass
.
getResourceAsStream
(
location
),
tempFile
)
IoUtils
.
copyStreamToFile
(
getClass
.
getResourceAsStream
(
location
),
tempFile
)
templateCache
+=
location
->
tempFile
tempFile
}
}
engine
.
layout
(
TemplateSource
.
fromFile
(
templateFile
),
args
)
}
//TODO: move to utils
def
copyFile
(
in
:
File
,
out
:
File
,
createDirs
:
Boolean
=
false
)
:
Unit
=
{
copyStreamToFile
(
new
FileInputStream
(
in
),
out
,
createDirs
)
}
def
copyStreamToFile
(
in
:
InputStream
,
out
:
File
,
createDirs
:
Boolean
=
false
)
:
Unit
=
{
if
(
createDirs
)
out
.
getParentFile
.
mkdirs
()
val
os
=
new
FileOutputStream
(
out
)
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
in
,
os
)
os
.
close
()
in
.
close
()
}
def
copyDir
(
inputDir
:
File
,
externalDir
:
File
)
:
Unit
=
{
require
(
inputDir
.
isDirectory
)
externalDir
.
mkdirs
()
for
(
srcFile
<-
inputDir
.
listFiles
)
{
if
(
srcFile
.
isDirectory
)
copyDir
(
new
File
(
inputDir
,
srcFile
.
getName
),
new
File
(
externalDir
,
srcFile
.
getName
))
else
{
val
newFile
=
new
File
(
externalDir
,
srcFile
.
getName
)
copyFile
(
srcFile
,
newFile
)
}
}
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
0 → 100644
View file @
6c9f45d0
package
nl.lumc.sasc.biopet.utils
import
java.io.
{
FileOutputStream
,
InputStream
,
FileInputStream
,
File
}
/**
* Created by pjvan_thof on 6/4/15.
*/
object
IoUtils
{
def
copyFile
(
in
:
File
,
out
:
File
,
createDirs
:
Boolean
=
false
)
:
Unit
=
{
copyStreamToFile
(
new
FileInputStream
(
in
),
out
,
createDirs
)
}
def
copyStreamToFile
(
in
:
InputStream
,
out
:
File
,
createDirs
:
Boolean
=
false
)
:
Unit
=
{
if
(
createDirs
)
out
.
getParentFile
.
mkdirs
()
val
os
=
new
FileOutputStream
(
out
)
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
in
,
os
)
os
.
close
()
in
.
close
()
}
def
copyDir
(
inputDir
:
File
,
externalDir
:
File
)
:
Unit
=
{
require
(
inputDir
.
isDirectory
)
externalDir
.
mkdirs
()
for
(
srcFile
<-
inputDir
.
listFiles
)
{
if
(
srcFile
.
isDirectory
)
copyDir
(
new
File
(
inputDir
,
srcFile
.
getName
),
new
File
(
externalDir
,
srcFile
.
getName
))
else
{
val
newFile
=
new
File
(
externalDir
,
srcFile
.
getName
)
copyFile
(
srcFile
,
newFile
)
}
}
}
}
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