From 61bde6210b6f01e3e1caa0ff478c3ac119237ad0 Mon Sep 17 00:00:00 2001 From: kshakir Date: Tue, 4 Dec 2012 12:32:00 -0500 Subject: [PATCH] Restored RemoteFile push and pull in base QScript. --- .../src/org/broadinstitute/sting/queue/QScript.scala | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/public/scala/src/org/broadinstitute/sting/queue/QScript.scala b/public/scala/src/org/broadinstitute/sting/queue/QScript.scala index 5b67ae913..d709d1fb4 100755 --- a/public/scala/src/org/broadinstitute/sting/queue/QScript.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/QScript.scala @@ -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 */