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biopet.biopet
Commits
9b522749
Commit
9b522749
authored
Jan 17, 2017
by
Peter van 't Hof
Browse files
Change to option types
parent
89846ab2
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
9b522749
...
...
@@ -177,51 +177,51 @@ object BiopetQScript {
require
(
outputDir
.
getAbsoluteFile
.
canWrite
,
s
"No premision to write outputdir: $outputDir"
)
}
def
safeInputs
(
function
:
QFunction
)
:
Seq
[
File
]
=
{
def
safeInputs
(
function
:
QFunction
)
:
Option
[
Seq
[
File
]
]
=
{
try
{
function
.
inputs
Some
(
function
.
inputs
)
}
catch
{
case
e
:
NullPointerException
=>
Seq
()
case
e
:
NullPointerException
=>
None
}
}
def
safeOutputs
(
function
:
QFunction
)
:
Seq
[
File
]
=
{
def
safeOutputs
(
function
:
QFunction
)
:
Option
[
Seq
[
File
]
]
=
{
try
{
function
.
outputs
Some
(
function
.
outputs
)
}
catch
{
case
e
:
NullPointerException
=>
Seq
()
case
e
:
NullPointerException
=>
None
}
}
def
safeDoneFiles
(
function
:
QFunction
)
:
Seq
[
File
]
=
{
def
safeDoneFiles
(
function
:
QFunction
)
:
Option
[
Seq
[
File
]
]
=
{
try
{
function
.
doneOutputs
Some
(
function
.
doneOutputs
)
}
catch
{
case
e
:
NullPointerException
=>
Seq
()
case
e
:
NullPointerException
=>
None
}
}
def
safeFailFiles
(
function
:
QFunction
)
:
Seq
[
File
]
=
{
def
safeFailFiles
(
function
:
QFunction
)
:
Option
[
Seq
[
File
]
]
=
{
try
{
function
.
failOutputs
Some
(
function
.
failOutputs
)
}
catch
{
case
e
:
NullPointerException
=>
Seq
()
case
e
:
NullPointerException
=>
None
}
}
def
safeIsDone
(
function
:
QFunction
)
:
Boolean
=
{
def
safeIsDone
(
function
:
QFunction
)
:
Option
[
Boolean
]
=
{
try
{
function
.
isDone
Some
(
function
.
isDone
)
}
catch
{
case
e
:
NullPointerException
=>
fals
e
case
e
:
NullPointerException
=>
Non
e
}
}
def
safeIsFail
(
function
:
QFunction
)
:
Boolean
=
{
def
safeIsFail
(
function
:
QFunction
)
:
Option
[
Boolean
]
=
{
try
{
function
.
isFail
Some
(
function
.
isFail
)
}
catch
{
case
e
:
NullPointerException
=>
fals
e
case
e
:
NullPointerException
=>
Non
e
}
}
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
9b522749
...
...
@@ -91,12 +91,12 @@ object WriteDependencies extends Logging with Configurable {
val
files
:
mutable.Map
[
File
,
QueueFile
]
=
mutable
.
Map
()
for
(
function
<-
functions
)
{
for
(
input
<-
BiopetQScript
.
safeInputs
(
function
))
{
for
(
input
<-
BiopetQScript
.
safeInputs
(
function
)
.
getOrElse
(
Seq
())
)
{
val
file
=
files
.
getOrElse
(
input
,
QueueFile
(
input
))
file
.
addInputJob
(
function
)
files
+=
input
->
file
}
for
(
output
<-
BiopetQScript
.
safeOutputs
(
function
))
{
for
(
output
<-
BiopetQScript
.
safeOutputs
(
function
)
.
getOrElse
(
Seq
())
)
{
val
file
=
files
.
getOrElse
(
output
,
QueueFile
(
output
))
file
.
addOutputJob
(
function
)
files
+=
output
->
file
...
...
@@ -113,13 +113,13 @@ object WriteDependencies extends Logging with Configurable {
case
s
:
WriteSummary
if
s.qscript.root
=
=
null
=>
true
case
_
=>
false
}),
"intermediate"
->
f
.
isIntermediate
,
"depends_on_intermediate"
->
BiopetQScript
.
safeOutputs
(
f
).
exists
(
files
(
_
).
isIntermediate
),
"depends_on_jobs"
->
BiopetQScript
.
safeOutputs
(
f
).
toList
.
flatMap
(
files
(
_
).
outputJobNames
).
distinct
,
"output_used_by_jobs"
->
BiopetQScript
.
safeOutputs
(
f
).
toList
.
flatMap
(
files
(
_
).
inputJobNames
).
distinct
,
"outputs"
->
BiopetQScript
.
safeOutputs
(
f
).
toList
,
"inputs"
->
BiopetQScript
.
safeOutputs
(
f
).
toList
,
"done_files"
->
BiopetQScript
.
safeDoneFiles
(
f
).
toList
,
"fail_files"
->
BiopetQScript
.
safeFailFiles
(
f
).
toList
,
"depends_on_intermediate"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
exists
(
files
(
_
).
isIntermediate
),
"depends_on_jobs"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
toList
.
flatMap
(
files
(
_
).
outputJobNames
).
distinct
,
"output_used_by_jobs"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
toList
.
flatMap
(
files
(
_
).
inputJobNames
).
distinct
,
"outputs"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
toList
,
"inputs"
->
BiopetQScript
.
safeOutputs
(
f
).
getOrElse
(
Seq
()).
toList
,
"done_files"
->
BiopetQScript
.
safeDoneFiles
(
f
).
getOrElse
(
Seq
()).
toList
,
"fail_files"
->
BiopetQScript
.
safeFailFiles
(
f
).
getOrElse
(
Seq
()).
toList
,
"stdout_file"
->
f
.
jobOutputFile
,
"done_at_start"
->
BiopetQScript
.
safeIsDone
(
f
),
"fail_at_start"
->
BiopetQScript
.
safeIsFail
(
f
))
...
...
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