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biopet.biopet
Commits
c8ac4699
Commit
c8ac4699
authored
Mar 03, 2017
by
Peter van 't Hof
Browse files
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Begin to convert to scalaz \/
parent
df4cf4cd
Changes
5
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Showing
5 changed files
with
148 additions
and
132 deletions
+148
-132
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+18
-16
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
...sc/biopet/core/extensions/PythonCommandLineFunction.scala
+1
-1
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
+12
-10
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
...cala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
+92
-83
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
.../nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
+25
-22
No files found.
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
c8ac4699
...
...
@@ -25,6 +25,8 @@ import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
scala.concurrent.ExecutionContext.Implicits.global
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
import
scalaz._
import
Scalaz._
class
BammetricsReport
(
val
parent
:
Configurable
)
extends
ReportBuilderExtension
{
def
builder
=
BammetricsReport
...
...
@@ -64,14 +66,14 @@ object BammetricsReport extends ReportBuilder {
//val pipelineId: Int = summary.getPipelineId(runId, metricsTag).map(_.get)
val
wgsExecuted
=
summary
.
getStatsSize
(
runId
,
Right
(
metricsTag
),
Some
(
Right
(
"wgs"
)),
sample
=
sampleId
.
map
(
Left
(
_
)),
library
=
libId
.
map
(
Left
(
_
)
))
>=
1
val
rnaExecuted
=
summary
.
getStatsSize
(
runId
,
Right
(
metricsTag
),
Some
(
Right
(
"rna"
)),
sample
=
sampleId
.
map
(
Left
(
_
)),
library
=
libId
.
map
(
Left
(
_
)
))
>=
1
val
wgsExecuted
=
summary
.
getStatsSize
(
runId
,
metricsTag
.
right
,
Some
(
"wgs"
.
right
),
sample
=
sampleId
.
map
(
_
.
left
),
library
=
libId
.
map
(
_
.
left
))
>=
1
val
rnaExecuted
=
summary
.
getStatsSize
(
runId
,
metricsTag
.
right
,
Some
(
"rna"
.
right
),
sample
=
sampleId
.
map
(
_
.
left
),
library
=
libId
.
map
(
_
.
left
))
>=
1
val
insertsizeMetrics
=
summary
.
getStatKeys
(
runId
,
Right
(
metricsTag
),
Some
(
Right
(
"CollectInsertSizeMetrics"
)
),
sample
=
sampleId
.
map
(
Left
(
_
)),
library
=
libId
.
map
(
Left
(
_
)
),
Map
(
"metrics"
->
List
(
"metrics"
)))
val
insertsizeMetrics
=
summary
.
getStatKeys
(
runId
,
metricsTag
.
right
,
Some
(
"CollectInsertSizeMetrics"
.
right
),
sample
=
sampleId
.
map
(
_
.
left
),
library
=
libId
.
map
(
_
.
left
),
Map
(
"metrics"
->
List
(
"metrics"
)))
.
exists
(
_
.
_2
.
isDefined
)
val
targetSettings
=
summary
.
getSettingKeys
(
runId
,
Right
(
metricsTag
),
None
,
sample
=
sampleId
.
map
(
Left
(
_
)),
library
=
libId
.
map
(
Left
(
_
)
),
val
targetSettings
=
summary
.
getSettingKeys
(
runId
,
metricsTag
.
right
,
None
,
sample
=
sampleId
.
map
(
_
.
left
),
library
=
libId
.
map
(
_
.
left
),
Map
(
"amplicon_name"
->
List
(
"amplicon_name"
),
"roi_name"
->
List
(
"roi_name"
)))
val
targets
=
(
targetSettings
(
"amplicon_name"
),
...
...
@@ -132,10 +134,10 @@ object BammetricsReport extends ReportBuilder {
)
val
results
:
Map
[(
Int
,
Option
[
Int
])
,
Map
[
String
,
Option
[
Any
]]]
=
if
(
libraryLevel
)
{
summary
.
getStatsForLibraries
(
runId
,
Right
(
"bammetrics"
),
Some
(
Right
(
"bamstats"
)
),
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
.
right
,
Some
(
"bamstats"
.
right
),
sampleId
=
sampleId
,
keyValues
=
statsPaths
).
map
(
x
=>
(
x
.
_1
.
_1
,
Some
(
x
.
_1
.
_2
))
->
x
.
_2
)
}
else
summary
.
getStatsForSamples
(
runId
,
Right
(
"bammetrics"
),
Some
(
Right
(
"bamstats"
)
),
sample
=
sampleId
.
map
(
Left
(
_
)
),
keyValues
=
statsPaths
).
map
(
x
=>
(
x
.
_1
,
None
)
->
x
.
_2
)
}
else
summary
.
getStatsForSamples
(
runId
,
"bammetrics"
.
right
,
Some
(
"bamstats"
.
right
),
sample
=
sampleId
.
map
(
_
.
left
),
keyValues
=
statsPaths
).
map
(
x
=>
(
x
.
_1
,
None
)
->
x
.
_2
)
for
(((
s
,
l
),
result
)
<-
results
)
{
val
sampleName
:
String
=
summary
.
getSampleName
(
s
).
map
(
_
.
get
)
...
...
@@ -175,8 +177,8 @@ object BammetricsReport extends ReportBuilder {
statsPaths
:
Map
[
String
,
List
[
String
]],
xKey
:
String
,
yKey
:
String
,
pipeline
:
Either
[
Int
,
String
],
module
:
Option
[
Either
[
Int
,
String
]],
pipeline
:
\/
[
Int
,
String
]
,
module
:
Option
[
\/
[
Int
,
String
]],
xlabel
:
Option
[
String
]
=
None
,
ylabel
:
Option
[
String
]
=
None
,
title
:
Option
[
String
]
=
None
,
...
...
@@ -187,7 +189,7 @@ object BammetricsReport extends ReportBuilder {
val
results
:
Map
[(
Int
,
Option
[
Int
])
,
Map
[
String
,
Option
[
Array
[
Any
]]]]
=
if
(
libraryLevel
)
{
summary
.
getStatsForLibraries
(
runId
,
pipeline
,
module
,
sampleId
=
sampleId
,
keyValues
=
statsPaths
)
.
map
(
x
=>
(
x
.
_1
.
_1
,
Some
(
x
.
_1
.
_2
))
->
x
.
_2
.
map
(
x
=>
x
.
_1
->
x
.
_2
.
map
(
ConfigUtils
.
any2list
(
_
).
toArray
)))
}
else
summary
.
getStatsForSamples
(
runId
,
pipeline
,
module
,
sample
=
sampleId
.
map
(
Left
(
_
)
),
keyValues
=
statsPaths
)
}
else
summary
.
getStatsForSamples
(
runId
,
pipeline
,
module
,
sample
=
sampleId
.
map
(
_
.
left
),
keyValues
=
statsPaths
)
.
map
(
x
=>
(
x
.
_1
,
None
)
->
x
.
_2
.
map
(
x
=>
x
.
_1
->
x
.
_2
.
map
(
ConfigUtils
.
any2list
(
_
).
toArray
)))
val
tables
:
Array
[
Map
[
String
,
Array
[
Any
]]]
=
results
.
map
{
...
...
@@ -231,7 +233,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary
(
outputDir
,
prefix
,
summary
,
libraryLevel
,
sampleId
,
libraryId
,
statsPaths
,
"insert_size"
,
"count"
,
Right
(
"bammetrics"
),
Some
(
Right
(
"CollectInsertSizeMetrics"
)
),
"insert_size"
,
"count"
,
"bammetrics"
.
right
,
Some
(
"CollectInsertSizeMetrics"
.
right
),
"Insert size"
,
"Reads"
,
"Insert size"
)
}
...
...
@@ -247,7 +249,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary
(
outputDir
,
prefix
,
summary
,
libraryLevel
,
sampleId
,
libraryId
,
statsPaths
,
"mapping_quality"
,
"count"
,
Right
(
"bammetrics"
),
Some
(
Right
(
"bamstats"
)
),
"mapping_quality"
,
"count"
,
"bammetrics"
.
right
,
Some
(
"bamstats"
.
right
),
"Mapping quality"
,
"Reads"
,
"Mapping quality"
)
}
...
...
@@ -263,7 +265,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary
(
outputDir
,
prefix
,
summary
,
libraryLevel
,
sampleId
,
libraryId
,
statsPaths
,
"clipping"
,
"count"
,
Right
(
"bammetrics"
),
Some
(
Right
(
"bamstats"
)
),
"clipping"
,
"count"
,
"bammetrics"
.
right
,
Some
(
"bamstats"
.
right
),
"Clipping"
,
"Reads"
,
"Clipping"
)
}
...
...
@@ -288,7 +290,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary
(
outputDir
,
prefix
,
summary
,
libraryLevel
,
sampleId
,
libraryId
,
statsPaths
,
"coverage"
,
"count"
,
Right
(
"bammetrics"
),
Some
(
Right
(
"wgs"
)
),
"coverage"
,
"count"
,
"bammetrics"
.
right
,
Some
(
"wgs"
.
right
),
"Coverage"
,
"Bases"
,
"Whole genome coverage"
)
}
...
...
@@ -313,7 +315,7 @@ object BammetricsReport extends ReportBuilder {
)
writePlotFromSummary
(
outputDir
,
prefix
,
summary
,
libraryLevel
,
sampleId
,
libraryId
,
statsPaths
,
"coverage"
,
"count"
,
Right
(
"bammetrics"
),
Some
(
Right
(
"rna"
)
),
"coverage"
,
"count"
,
"bammetrics"
.
right
,
Some
(
"rna"
.
right
),
"Relative position"
,
"Coverage"
,
"Rna coverage"
)
}
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
View file @
c8ac4699
...
...
@@ -14,7 +14,7 @@
*/
package
nl.lumc.sasc.biopet.core.extensions
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.utils.Logging
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
View file @
c8ac4699
...
...
@@ -32,6 +32,8 @@ import org.testng.annotations.{ AfterClass, Test }
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
import
scala.util.matching.Regex
import
scalaz._
import
Scalaz._
/**
* Created by pjvanthof on 15/01/16.
...
...
@@ -98,8 +100,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)
),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
@Test
...
...
@@ -119,8 +121,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)
),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
@Test
...
...
@@ -140,8 +142,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)
),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
@Test
...
...
@@ -161,8 +163,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
Some
(
Right
(
"sampleName"
)),
Some
(
Right
(
"libName"
)
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
Some
(
Right
(
"sampleName"
)),
Some
(
Right
(
"libName"
)
),
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
Some
(
"sampleName"
.
right
),
Some
(
"libName"
.
right
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
Some
(
"sampleName"
.
right
),
Some
(
"libName"
.
right
),
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
@Test
...
...
@@ -202,8 +204,8 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)
),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
"test"
.
right
,
Some
(
"tool_1"
.
right
),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
@AfterClass
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
View file @
c8ac4699
This diff is collapsed.
Click to expand it.
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
View file @
c8ac4699
...
...
@@ -10,6 +10,9 @@ import org.testng.annotations.Test
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
import
scalaz._
import
Scalaz._
/**
* Testing voor [[SummaryDb]]
* Created by pjvanthof on 14/02/2017.
...
...
@@ -133,9 +136,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
db
.
createTables
()
Await
.
result
(
db
.
createOrUpdateSetting
(
0
,
0
,
None
,
None
,
None
,
"""{"content": "test" }"""
),
Duration
.
Inf
)
Await
.
result
(
db
.
getSetting
(
0
,
Left
(
0
)
,
None
,
None
,
None
),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test"
))
Await
.
result
(
db
.
getSetting
(
0
,
0.
left
,
None
,
None
,
None
),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test"
))
Await
.
result
(
db
.
createOrUpdateSetting
(
0
,
0
,
None
,
None
,
None
,
"""{"content": "test2" }"""
),
Duration
.
Inf
)
Await
.
result
(
db
.
getSetting
(
0
,
Left
(
0
)
,
None
,
None
,
None
),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test2"
))
Await
.
result
(
db
.
getSetting
(
0
,
0.
left
,
None
,
None
,
None
),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test2"
))
db
.
close
()
}
...
...
@@ -155,9 +158,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }"""
.
stripMargin
),
Duration
.
Inf
)
db
.
getSettingKeys
(
0
,
Left
(
0
),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)
),
keyValues
=
Map
())
shouldBe
Map
()
db
.
getSettingKeys
(
0
,
Left
(
0
),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
(
"content"
->
Some
(
"test"
))
db
.
getSettingKeys
(
0
,
Left
(
0
),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)
),
keyValues
=
Map
(
"content"
->
List
(
"content2"
,
"key"
)))
shouldBe
Map
(
"content"
->
Some
(
"value"
))
db
.
getSettingKeys
(
0
,
0.
left
,
Some
(
0.
left
),
Some
(
0.
left
),
Some
(
0.
left
),
keyValues
=
Map
())
shouldBe
Map
()
db
.
getSettingKeys
(
0
,
0.
left
,
Some
(
0.
left
),
Some
(
0.
left
),
Some
(
0.
left
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
(
"content"
->
Some
(
"test"
))
db
.
getSettingKeys
(
0
,
0.
left
,
Some
(
0.
left
),
Some
(
0.
left
),
Some
(
0.
left
),
keyValues
=
Map
(
"content"
->
List
(
"content2"
,
"key"
)))
shouldBe
Map
(
"content"
->
Some
(
"value"
))
db
.
close
()
}
...
...
@@ -180,8 +183,8 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }"""
.
stripMargin
),
Duration
.
Inf
)
db
.
getSettingsForSamples
(
0
,
Left
(
0
),
Some
(
Left
(
0
)
),
keyValues
=
Map
())
shouldBe
Map
(
0
->
Map
())
db
.
getSettingsForSamples
(
0
,
Left
(
0
),
Some
(
Left
(
0
)
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
(
0
->
Map
(
"content"
->
Some
(
"test"
)))
db
.
getSettingsForSamples
(
0
,
0.
left
,
Some
(
0.
left
),
keyValues
=
Map
())
shouldBe
Map
(
0
->
Map
())
db
.
getSettingsForSamples
(
0
,
0.
left
,
Some
(
0.
left
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
(
0
->
Map
(
"content"
->
Some
(
"test"
)))
db
.
close
()
}
...
...
@@ -205,8 +208,8 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }"""
.
stripMargin
),
Duration
.
Inf
)
db
.
getSettingsForLibraries
(
0
,
Left
(
0
),
Some
(
Left
(
0
)
),
keyValues
=
Map
())
shouldBe
Map
((
0
,
0
)
->
Map
())
db
.
getSettingsForLibraries
(
0
,
Left
(
0
),
Some
(
Left
(
0
)
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
((
0
,
0
)
->
Map
(
"content"
->
Some
(
"test"
)))
db
.
getSettingsForLibraries
(
0
,
0.
left
,
Some
(
0.
left
),
keyValues
=
Map
())
shouldBe
Map
((
0
,
0
)
->
Map
())
db
.
getSettingsForLibraries
(
0
,
0.
left
,
Some
(
0.
left
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
((
0
,
0
)
->
Map
(
"content"
->
Some
(
"test"
)))
db
.
close
()
}
...
...
@@ -227,15 +230,15 @@ class SummaryDbTest extends TestNGSuite with Matchers {
Await
.
result
(
db
.
getStatsSize
(),
Duration
.
Inf
)
shouldBe
0
Await
.
result
(
db
.
createOrUpdateStat
(
runId
,
pipelineId
,
None
,
None
,
None
,
"""{"content": "test" }"""
),
Duration
.
Inf
)
Await
.
result
(
db
.
getStat
(
runId
,
Left
(
pipelineId
)
,
None
,
None
,
None
),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test"
))
Await
.
result
(
db
.
getStat
(
runId
,
pipelineId
.
left
,
None
,
None
,
None
),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test"
))
Await
.
result
(
db
.
getStatsSize
(),
Duration
.
Inf
)
shouldBe
1
Await
.
result
(
db
.
createOrUpdateStat
(
runId
,
pipelineId
,
None
,
None
,
None
,
"""{"content": "test2" }"""
),
Duration
.
Inf
)
Await
.
result
(
db
.
getStat
(
runId
,
Left
(
pipelineId
)
,
None
,
None
,
None
),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test2"
))
Await
.
result
(
db
.
getStat
(
runId
,
pipelineId
.
left
,
None
,
None
,
None
),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test2"
))
Await
.
result
(
db
.
getStatsSize
(),
Duration
.
Inf
)
shouldBe
1
// Test join queries
Await
.
result
(
db
.
createOrUpdateStat
(
runId
,
pipelineId
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"""{"content": "test3" }"""
),
Duration
.
Inf
)
Await
.
result
(
db
.
getStat
(
runId
,
Right
(
"test_pipeline"
),
Some
(
Right
(
"test_module"
)),
Some
(
Right
(
"test_sample"
)),
Some
(
Right
(
"test_library"
)
)),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test3"
))
Await
.
result
(
db
.
getStat
(
runId
,
"test_pipeline"
.
right
,
Some
(
"test_module"
.
right
),
Some
(
"test_sample"
.
right
),
Some
(
"test_library"
.
right
)),
Duration
.
Inf
)
shouldBe
Some
(
Map
(
"content"
->
"test3"
))
Await
.
result
(
db
.
getStatsSize
(),
Duration
.
Inf
)
shouldBe
2
db
.
close
()
...
...
@@ -257,9 +260,9 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }"""
.
stripMargin
),
Duration
.
Inf
)
db
.
getStatKeys
(
0
,
Left
(
0
),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)
),
keyValues
=
Map
())
shouldBe
Map
()
db
.
getStatKeys
(
0
,
Left
(
0
),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
(
"content"
->
Some
(
"test"
))
db
.
getStatKeys
(
0
,
Left
(
0
),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)),
Some
(
Left
(
0
)
),
keyValues
=
Map
(
"content"
->
List
(
"content2"
,
"key"
)))
shouldBe
Map
(
"content"
->
Some
(
"value"
))
db
.
getStatKeys
(
0
,
0.
left
,
Some
(
0.
left
),
Some
(
0.
left
),
Some
(
0.
left
),
keyValues
=
Map
())
shouldBe
Map
()
db
.
getStatKeys
(
0
,
0.
left
,
Some
(
0.
left
),
Some
(
0.
left
),
Some
(
0.
left
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
(
"content"
->
Some
(
"test"
))
db
.
getStatKeys
(
0
,
0.
left
,
Some
(
0.
left
),
Some
(
0.
left
),
Some
(
0.
left
),
keyValues
=
Map
(
"content"
->
List
(
"content2"
,
"key"
)))
shouldBe
Map
(
"content"
->
Some
(
"value"
))
db
.
close
()
}
...
...
@@ -282,8 +285,8 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }"""
.
stripMargin
),
Duration
.
Inf
)
db
.
getStatsForSamples
(
0
,
Left
(
0
),
Some
(
Left
(
0
)
),
keyValues
=
Map
())
shouldBe
Map
(
0
->
Map
())
db
.
getStatsForSamples
(
0
,
Left
(
0
),
Some
(
Left
(
0
)
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
(
0
->
Map
(
"content"
->
Some
(
"test"
)))
db
.
getStatsForSamples
(
0
,
0.
left
,
Some
(
0.
left
),
keyValues
=
Map
())
shouldBe
Map
(
0
->
Map
())
db
.
getStatsForSamples
(
0
,
0.
left
,
Some
(
0.
left
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
(
0
->
Map
(
"content"
->
Some
(
"test"
)))
db
.
close
()
}
...
...
@@ -307,8 +310,8 @@ class SummaryDbTest extends TestNGSuite with Matchers {
|}
| }"""
.
stripMargin
),
Duration
.
Inf
)
db
.
getStatsForLibraries
(
0
,
Left
(
0
),
Some
(
Left
(
0
)
),
keyValues
=
Map
())
shouldBe
Map
((
0
,
0
)
->
Map
())
db
.
getStatsForLibraries
(
0
,
Left
(
0
),
Some
(
Left
(
0
)
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
((
0
,
0
)
->
Map
(
"content"
->
Some
(
"test"
)))
db
.
getStatsForLibraries
(
0
,
0.
left
,
Some
(
0.
left
),
keyValues
=
Map
())
shouldBe
Map
((
0
,
0
)
->
Map
())
db
.
getStatsForLibraries
(
0
,
0.
left
,
Some
(
0.
left
),
keyValues
=
Map
(
"content"
->
List
(
"content"
)))
shouldBe
Map
((
0
,
0
)
->
Map
(
"content"
->
Some
(
"test"
)))
db
.
close
()
}
...
...
@@ -327,15 +330,15 @@ class SummaryDbTest extends TestNGSuite with Matchers {
val
libraryId
=
Await
.
result
(
db
.
createLibrary
(
"test_library"
,
runId
,
sampleId
),
Duration
.
Inf
)
Await
.
result
(
db
.
createOrUpdateFile
(
runId
,
pipelineId
,
None
,
None
,
None
,
"key"
,
"path"
,
"md5"
,
link
=
false
,
1
),
Duration
.
Inf
)
Await
.
result
(
db
.
getFile
(
runId
,
Left
(
pipelineId
)
,
None
,
None
,
None
,
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFile
(
runId
,
pipelineId
.
left
,
None
,
None
,
None
,
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFiles
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
createOrUpdateFile
(
runId
,
pipelineId
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
),
Duration
.
Inf
)
Await
.
result
(
db
.
getFile
(
runId
,
Left
(
pipelineId
)
,
None
,
None
,
None
,
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFile
(
runId
,
pipelineId
.
left
,
None
,
None
,
None
,
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFiles
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
))
// Test join queries
Await
.
result
(
db
.
createOrUpdateFile
(
runId
,
pipelineId
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"key"
,
"path3"
,
"md5"
,
link
=
false
,
1
),
Duration
.
Inf
)
Await
.
result
(
db
.
getFile
(
runId
,
Right
(
"test_pipeline"
),
Some
(
Right
(
"test_module"
)),
Some
(
Right
(
"test_sample"
)),
Some
(
Right
(
"test_library"
)
),
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"key"
,
"path3"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFile
(
runId
,
"test_pipeline"
.
right
,
Some
(
"test_module"
.
right
),
Some
(
"test_sample"
.
right
),
Some
(
"test_library"
.
right
),
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"key"
,
"path3"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFiles
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
),
Schema
.
File
(
0
,
0
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"key"
,
"path3"
,
"md5"
,
link
=
false
,
1
))
db
.
close
()
...
...
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