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biopet.biopet
Commits
7ef47a09
Commit
7ef47a09
authored
Jul 22, 2014
by
Peter van 't Hof
Browse files
Switch to Argonaut library
parent
6294de9f
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-framework/pom.xml
View file @
7ef47a09
...
...
@@ -54,6 +54,11 @@
<artifactId>
gatk-queue-package-distribution
</artifactId>
<version>
3.2
</version>
</dependency>
<dependency>
<groupId>
io.argonaut
</groupId>
<artifactId>
argonaut_2.11
</artifactId>
<version>
6.1-M3
</version>
</dependency>
</dependencies>
<build>
<plugins>
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
View file @
7ef47a09
package
nl.lumc.sasc.biopet.core.config
import
nl.lumc.sasc.biopet.core._
import
scala.util.parsing.json._
import
java.io.File
import
org.broadinstitute.gatk.queue.util.Logging
import
argonaut._
,
Argonaut
.
_
import
scalaz._
,
Scalaz
.
_
class
Config
(
var
map
:
Map
[
String
,
Any
])
extends
Logging
{
logger
.
debug
(
"Init phase of config"
)
...
...
@@ -24,23 +25,45 @@ class Config(var map: Map[String,Any]) extends Logging {
}
def
loadConfigFile
(
configFile
:
File
)
{
var
configJson
=
JSON
.
parseFull
(
scala
.
io
.
Source
.
fromFile
(
configFile
).
mkString
)
logger
.
debug
(
"Jsonfile: "
+
configFile
)
val
jsonText
=
scala
.
io
.
Source
.
fromFile
(
configFile
).
mkString
val
json
=
Parse
.
parseOption
(
jsonText
)
logger
.
debug
(
json
)
val
configJson
=
jsonToMap
(
json
.
get
)
logger
.
debug
(
"Contain: "
+
configJson
)
if
(
configJson
==
None
)
{
throw
new
IllegalStateException
(
"The config JSON file is either not properly formatted or not a JSON file, file: "
+
configFile
)
}
this
.
logger
.
debug
(
"Jsonfile: "
+
configFile
)
this
.
logger
.
debug
(
"Contain: "
+
configJson
)
configJson
.
get
match
{
case
m
:
Map
[
_
,
_
]
=>
{
logger
.
debug
(
m
)
if
(
map
.
isEmpty
)
map
=
m
.
asInstanceOf
[
Map
[
String
,
Any
]]
else
map
=
Config
.
mergeMaps
(
m
.
asInstanceOf
[
Map
[
String
,
Any
]],
map
)
if
(
map
.
isEmpty
)
map
=
configJson
else
map
=
Config
.
mergeMaps
(
configJson
,
map
)
logger
.
debug
(
"New config: "
+
map
)
}
private
def
jsonToMap
(
json
:
Json
)
:
Map
[
String
,
Any
]
=
{
var
output
:
Map
[
String
,
Any
]
=
Map
()
if
(
json
.
isObject
)
{
for
(
key
<-
json
.
objectFieldsOrEmpty
)
{
val
value
:
Any
=
jsonToAny
(
json
.
field
(
key
).
get
)
output
+=
(
key
->
value
)
}
case
null
=>
logger
.
warn
(
"Config "
+
configFile
+
" wrong format"
)
}
this
.
logger
.
debug
(
"config: "
+
map
)
}
else
return
null
return
output
}
private
def
jsonToAny
(
json
:
Json
)
:
Any
=
{
if
(
json
.
isObject
)
return
jsonToMap
(
json
)
else
if
(
json
.
isArray
)
{
var
list
:
List
[
Any
]
=
List
()
for
(
value
<-
json
.
objectValues
.
get
)
list
::=
jsonToAny
(
value
)
return
list
}
else
if
(
json
.
isBool
)
return
json
.
bool
.
get
else
if
(
json
.
isString
)
return
json
.
string
.
get
.
toString
else
if
(
json
.
isNumber
)
{
val
num
=
json
.
number
.
get
if
(
num
.
toString
.
contains
(
"."
))
return
num
.
toDouble
else
return
num
.
toLong
}
else
throw
new
IllegalStateException
(
"Config value type not supported, value: "
+
json
)
}
def
getMap
()
:
Map
[
String
,
Any
]
=
map
...
...
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