Commit c8a93931 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add placeholders

parent 5e98e38a
...@@ -26,7 +26,6 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output} ...@@ -26,7 +26,6 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import scala.collection.mutable import scala.collection.mutable
import scala.io.Source import scala.io.Source
import slick.driver.H2Driver.api._
import scala.concurrent.Await import scala.concurrent.Await
import scala.concurrent.duration.Duration import scala.concurrent.duration.Duration
...@@ -86,8 +85,17 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co ...@@ -86,8 +85,17 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
/** Function to create summary */ /** Function to create summary */
def run(): Unit = { def run(): Unit = {
val summaryDb = SummaryDb.openSqliteSummary(qscript.summaryDbFile) val db = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
//TODO: Add stats
//TODO: Add Files
//TODO: Add executables
db.close()
///////////////// OLD //////////////////
for (((name, sampleId, libraryId), summarizables) <- qscript.summarizables; summarizable <- summarizables) { for (((name, sampleId, libraryId), summarizables) <- qscript.summarizables; summarizable <- summarizables) {
summarizable.addToQscriptSummary(qscript, name) summarizable.addToQscriptSummary(qscript, name)
} }
...@@ -127,7 +135,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co ...@@ -127,7 +135,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
val map = Map(qscript.summaryName -> Map( val map = Map(qscript.summaryName -> Map(
"settings" -> settings, "settings" -> settings,
"files" -> Map("pipeline" -> files), "files" -> Map("pipeline" -> files),
"executables" -> executables.toMap) "executables" -> executables)
) )
qscript match { qscript match {
...@@ -179,7 +187,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co ...@@ -179,7 +187,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
val writer = new PrintWriter(out) val writer = new PrintWriter(out)
writer.println(ConfigUtils.mapToJson(combinedMap).nospaces) writer.println(ConfigUtils.mapToJson(combinedMap).nospaces)
writer.close() writer.close()
summaryDb.close() ///////////////// OLD //////////////////
} }
def prefixSampleLibrary(map: Map[String, Any], sampleId: Option[String], libraryId: Option[String]): Map[String, Any] = { def prefixSampleLibrary(map: Map[String, Any], sampleId: Option[String], libraryId: Option[String]): Map[String, Any] = {
......
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