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Restored RemoteFile push and pull in base QScript.

This commit is contained in:
kshakir 2012-12-04 12:32:00 -05:00
parent 4ced2e4ffc
commit 61bde6210b
1 changed files with 12 additions and 0 deletions
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12
public/scala/src/org/broadinstitute/sting/queue/QScript.scala
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@ -127,14 +127,26 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
* Pull all remote files to the local disk
*/
def pullInputs() {
val inputs = ClassFieldCache.getFieldFiles(this, inputFields)
for (remoteFile <- filterRemoteFiles(inputs)) {
logger.info("Pulling %s from %s".format(remoteFile.getAbsolutePath, remoteFile.remoteDescription))
remoteFile.pullToLocal()
}
}
/**
* Push all remote files from the local disk
*/
def pushOutputs() {
val outputs = ClassFieldCache.getFieldFiles(this, outputFields)
for (remoteFile <- filterRemoteFiles(outputs)) {
logger.info("Pushing %s to %s".format(remoteFile.getAbsolutePath, remoteFile.remoteDescription))
remoteFile.pushToRemote()
}
}
private def filterRemoteFiles(fields: Seq[File]): Seq[RemoteFile] =
fields.filter(field => field != null && field.isInstanceOf[RemoteFile]).map(_.asInstanceOf[RemoteFile])
/**
* @return the inputs or null if there are no inputs
*/