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biopet.biopet
Commits
a32ce842
Commit
a32ce842
authored
Feb 13, 2017
by
Peter van 't Hof
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Added executables
parent
eb3a77c1
Changes
3
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3 changed files
with
44 additions
and
4 deletions
+44
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+15
-2
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryDb.scala
...n/scala/nl/lumc/sasc/biopet/utils/summary/SummaryDb.scala
+25
-0
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
...n/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
+4
-2
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
a32ce842
...
...
@@ -129,8 +129,6 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
Await
.
result
(
createFile
(
db
,
qscript
.
summaryRunId
,
pipelineId
,
Some
(
moduleId
),
sampleId
,
libId
,
key
,
file
,
outputDir
),
Duration
.
Inf
)
}
//TODO: Add executables
qscript
match
{
case
tag
:
SampleLibraryTag
=>
val
sampleId
=
tag
.
sampleId
.
flatMap
(
name
=>
Await
.
result
(
db
.
getSampleId
(
qscript
.
summaryRunId
,
name
),
Duration
.
Inf
))
...
...
@@ -165,6 +163,21 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
db
.
createOrUpdateSetting
(
qscript
.
summaryRunId
,
pipelineId
,
None
,
None
,
None
,
ConfigUtils
.
mapToJson
(
q
.
summarySettings
).
nospaces
)
}
for
((
name
,
f
)
<-
qscript
.
functions
.
flatMap
(
_
match
{
case
c
:
Configurable
with
Version
=>
Some
(
c
)
case
_
=>
None
}).
groupBy
(
_
.
configNamespace
))
yield
{
f
match
{
case
f
:
BiopetJavaCommandLineFunction
with
Version
=>
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
name
,
f
.
getVersion
,
f
.
getJavaVersion
,
javaMd5
=
BiopetCommandLineFunction
.
executableMd5Cache
.
get
(
f
.
executable
),
jarPath
=
Some
(
f
.
jarFile
.
getAbsolutePath
))
case
f
:
BiopetCommandLineFunction
with
Version
=>
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
name
,
f
.
getVersion
,
Option
(
f
.
executable
))
case
f
:
Configurable
with
Version
=>
db
.
createOrUpdateExecutable
(
qscript
.
summaryRunId
,
name
,
f
.
getVersion
)
case
_
=>
None
}
}
db
.
close
()
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryDb.scala
View file @
a32ce842
...
...
@@ -272,6 +272,31 @@ class SummaryDb(db: Database) extends Closeable {
if
(
r
==
0
)
createFile
(
runId
,
pipelineId
,
moduleId
,
sampleId
,
libId
,
key
,
path
,
md5
,
link
,
size
)
else
db
.
run
(
filter
.
update
(
File
(
runId
,
pipelineId
,
moduleId
,
sampleId
,
libId
,
key
,
path
,
md5
,
link
,
size
)))
}
def
executablesFilter
(
runId
:
Option
[
Int
],
toolName
:
Option
[
String
])
=
{
val
l
:
List
[
Option
[
Query
[
Executables
,
Executables
#
TableElementType
,
Seq
]
=>
Query
[
Executables
,
Executables
#
TableElementType
,
Seq
]]]
=
List
(
runId
.
map
(
x
=>
y
=>
y
.
filter
(
_
.
runId
===
x
)),
toolName
.
map
(
x
=>
y
=>
y
.
filter
(
_
.
toolName
===
x
))
)
l
.
flatten
.
foldLeft
(
executables
.
subquery
)((
a
,
b
)
=>
b
(
a
))
}
def
getFiles
(
runId
:
Option
[
Int
],
toolName
:
Option
[
String
])
=
{
db
.
run
(
executablesFilter
(
runId
,
toolName
).
result
)
}
def
createExecutable
(
runId
:
Int
,
toolName
:
String
,
version
:
Option
[
String
]
=
None
,
path
:
Option
[
String
]
=
None
,
javaVersion
:
Option
[
String
]
=
None
,
exeMd5
:
Option
[
String
]
=
None
,
javaMd5
:
Option
[
String
]
=
None
,
jarPath
:
Option
[
String
]
=
None
)
=
{
db
.
run
(
executables
.
forceInsert
(
Executable
(
runId
,
toolName
,
version
,
path
,
javaVersion
,
exeMd5
,
javaMd5
,
jarPath
)))
}
def
createOrUpdateExecutable
(
runId
:
Int
,
toolName
:
String
,
version
:
Option
[
String
]
=
None
,
path
:
Option
[
String
]
=
None
,
javaVersion
:
Option
[
String
]
=
None
,
exeMd5
:
Option
[
String
]
=
None
,
javaMd5
:
Option
[
String
]
=
None
,
jarPath
:
Option
[
String
]
=
None
)
=
{
val
filter
=
executablesFilter
(
Some
(
runId
),
Some
(
toolName
))
val
r
=
Await
.
result
(
db
.
run
(
filter
.
size
.
result
),
Duration
.
Inf
)
if
(
r
==
0
)
createExecutable
(
runId
,
toolName
,
version
,
javaVersion
,
exeMd5
,
javaMd5
)
else
db
.
run
(
filter
.
update
(
Executable
(
runId
,
toolName
,
version
,
path
,
javaVersion
,
exeMd5
,
javaMd5
,
jarPath
)))
}
}
object
SummaryDb
{
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala
View file @
a32ce842
...
...
@@ -118,16 +118,18 @@ object Schema {
}
val
files
=
TableQuery
[
Files
]
case
class
Executable
(
runId
:
Int
,
toolName
:
String
,
version
:
Option
[
String
],
javaVersion
:
Option
[
String
],
exeMd5
:
Option
[
String
],
javaMd5
:
Option
[
String
])
case
class
Executable
(
runId
:
Int
,
toolName
:
String
,
version
:
Option
[
String
],
path
=
Option
[
String
],
javaVersion
:
Option
[
String
],
exeMd5
:
Option
[
String
],
javaMd5
:
Option
[
String
],
jarPath
:
Option
[
String
])
class
Executables
(
tag
:
Tag
)
extends
Table
[
Executable
](
tag
,
"Executables"
)
{
def
runId
=
column
[
Int
](
"runId"
)
def
toolName
=
column
[
String
](
"toolName"
)
def
version
=
column
[
Option
[
String
]](
"version"
)
def
path
=
column
[
Option
[
String
]](
"path"
)
def
javaVersion
=
column
[
Option
[
String
]](
"javaVersion"
)
def
exeMd5
=
column
[
Option
[
String
]](
"exeMd5"
)
def
javaMd5
=
column
[
Option
[
String
]](
"javaMd5"
)
def
jarPath
=
column
[
Option
[
String
]](
"jarPath"
)
def
*
=
(
runId
,
toolName
,
version
,
javaVersion
,
exeMd5
,
javaMd5
)
<>
(
Executable
.
tupled
,
Executable
.
unapply
)
def
*
=
(
runId
,
toolName
,
version
,
path
,
javaVersion
,
exeMd5
,
javaMd5
,
jarPath
)
<>
(
Executable
.
tupled
,
Executable
.
unapply
)
def
idx
=
index
(
"idx_executables"
,
(
runId
,
toolName
),
unique
=
true
)
}
...
...
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