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feat: save results directly to cloud storage #30

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feat: save results directly to cloud storage #30

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38 changes: 37 additions & 1 deletion modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,8 @@

package nextflow.processor

import nextflow.util.CacheHelper

import java.nio.file.FileAlreadyExistsException
import java.nio.file.FileSystem
import java.nio.file.FileSystems
Expand All @@ -25,6 +27,7 @@ import java.nio.file.LinkOption
import java.nio.file.NoSuchFileException
import java.nio.file.Path
import java.nio.file.PathMatcher
import java.nio.file.Paths
import java.util.concurrent.ExecutorService

import groovy.transform.CompileDynamic
Expand Down Expand Up @@ -127,7 +130,16 @@ class PublishDir {
}

void setPath( Path obj ) {
this.path = obj.complete()
def path = obj.complete()

if(path.getFileSystem().provider() == FileSystems.default.provider()) {
log.info("path.toString(): " + path.toUriString() + " is local file system")
this.path = applyS3PrefixForLocalPath(path)
log.info("path.toString(): " + path.toUriString() + " is conveerted to S3 path ${this.path.toUriString()}")
} else {
log.info("path.toString(): " + path.toUriString() + " is other file system")
this.path = path
}
}

void setMode( String str ) {
Expand Down Expand Up @@ -513,5 +525,29 @@ class PublishDir {
}
}

private Path applyS3PrefixForLocalPath(Path path) {
def s3Prefix = getS3PrefixForPublishDir()
if(!s3Prefix) {
log.info("No s3 prefix defined for publishDir - returning original path: " + path.toUriString())
return path
}

def rootDir = Paths.get("").toAbsolutePath().normalize().toUriString()
log.info("path.toString(): " + path.toUriString() + " is root dir ${rootDir}")

def pathStr = path.toUriString()
pathStr = pathStr.startsWith(rootDir) ? pathStr.substring(rootDir.length()) : pathStr
String normalizedLocalPath = pathStr.startsWith('/') ? pathStr.substring(1) : pathStr
if (s3Prefix.endsWith('/')) s3Prefix = s3Prefix.substring(0, s3Prefix.length() - 1)

return FileHelper.asPath("${s3Prefix}/${normalizedLocalPath}")
}

/**
* Get S3 prefix for redirecting publishDir local paths to S3
*/
@CompileStatic
private String getS3PrefixForPublishDir() {
return Global.session.config.navigate('lifebit.results', '') as String
}
}
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