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gatk-3.8
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Writes output to file

This commit is contained in:
Mark DePristo 2011-08-24 13:52:05 -04:00
parent 3ae68e2397
commit d047c19ad1
2 changed files with 8 additions and 5 deletions
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4
public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
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@ -115,7 +115,9 @@ class QCommandLine extends CommandLineProgram with Logging {
// walk over each script, calling onExecutionDone // walk over each script, calling onExecutionDone
for (script <- allQScripts) { for (script <- allQScripts) {
script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success) script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success)
JobLogging.printLogs(qGraph.getFunctionsAndStatus(script.functions)) val reportFile = new File("joblogging.gatkreport.txt")
logger.info("Writing JobLogging GATKReport to file " + reportFile)
JobLogging.printLogs(qGraph.getFunctionsAndStatus(script.functions), reportFile)
} }
if (!qGraph.success) { if (!qGraph.success) {

9
public/scala/src/org/broadinstitute/sting/queue/util/JobLogging.scala
View File

@ -27,6 +27,7 @@ import org.broadinstitute.sting.queue.function.QFunction
import org.broadinstitute.sting.gatk.report.{GATKReportTable, GATKReport} import org.broadinstitute.sting.gatk.report.{GATKReportTable, GATKReport}
import org.broadinstitute.sting.utils.exceptions.UserException import org.broadinstitute.sting.utils.exceptions.UserException
import org.broadinstitute.sting.queue.engine.JobRunInfo import org.broadinstitute.sting.queue.engine.JobRunInfo
import java.io.{FileOutputStream, PrintStream, File}
/** /**
* A mixin to add Job info to the class * A mixin to add Job info to the class
@ -70,10 +71,10 @@ trait JobLogging extends QFunction {
} }
object JobLogging { object JobLogging {
def printLogs(jobs: Map[QFunction, JobRunInfo]) { def printLogs(jobs: Map[QFunction, JobRunInfo], dest: File) {
val jobLogs: List[JobLogging] = jobLoggingSublist(jobs.keys.toList) val jobLogs: List[JobLogging] = jobLoggingSublist(jobs.keys.toList)
jobLogs.foreach((job: JobLogging) => job.addRunInfo(jobs.get(job).get)) jobLogs.foreach((job: JobLogging) => job.addRunInfo(jobs.get(job).get))
printJobLogging(jobLogs) printJobLogging(jobLogs, new PrintStream(new FileOutputStream(dest)))
} }
private def jobLoggingSublist(l: List[QFunction]): List[JobLogging] = { private def jobLoggingSublist(l: List[QFunction]): List[JobLogging] = {
@ -89,7 +90,7 @@ object JobLogging {
* Prints the JobLogging logs to a GATKReport. First splits up the * Prints the JobLogging logs to a GATKReport. First splits up the
* logs by group, and for each group generates a GATKReportTable * logs by group, and for each group generates a GATKReportTable
*/ */
private def printJobLogging(logs: List[JobLogging]) { private def printJobLogging(logs: List[JobLogging], stream: PrintStream) {
// create the report // create the report
val report: GATKReport = new GATKReport val report: GATKReport = new GATKReport
@ -108,7 +109,7 @@ object JobLogging {
} }
} }
report.print(System.out) report.print(stream)
} }
private def groupLogs(logs: List[JobLogging]): Map[String, List[JobLogging]] = { private def groupLogs(logs: List[JobLogging]): Map[String, List[JobLogging]] = {