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stage files to tmp files, then atomically move #1713

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Aug 21, 2020
Merged

stage files to tmp files, then atomically move #1713

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stage files to tmp files, then atomically move
jchorl Aug 19, 2020
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jchorl Aug 20, 2020
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11 changes: 10 additions & 1 deletion modules/nextflow/src/main/groovy/nextflow/file/FilePorter.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@

package nextflow.file

import java.nio.file.Files
import java.nio.file.NoSuchFileException
import java.nio.file.Path
import java.util.concurrent.ExecutionException
Expand Down Expand Up @@ -284,8 +285,16 @@ class FilePorter {
log.debug "Local cache found for foreign file ${source.toUriString()} at ${target.toUriString()}"
return target
}

log.debug "Copying foreign file ${source.toUriString()} to work dir: ${target.toUriString()}"
return FileHelper.copyPath(source, target)

// copy to a temp file first and move to ensure that a partial copy doesn't get cached as completed.
// use the target parent dir as the temp dir because it'lll have the same permissions.
def tmpFile = target.getParent().resolve( "temp-${UUID.randomUUID()}" )
log.debug "Using temp file ${tmpFile.toUriString()} for ${target.toUriString()}"

FileHelper.copyPath(source, tmpFile)
return FileHelper.movePath(tmpFile, target)
}

synchronized String getMessageAndClear() {
Expand Down