nextflow.file.FileSystemPathFactory.groovy Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of nf-commons Show documentation
Show all versions of nf-commons Show documentation
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
The newest version!
/*
* Copyright 2013-2024, Seqera Labs
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package nextflow.file
import java.nio.file.Path
import groovy.transform.CompileStatic
import groovy.transform.stc.ClosureParams
import groovy.transform.stc.SimpleType
import groovy.util.logging.Slf4j
import nextflow.plugin.Plugins
import org.pf4j.ExtensionPoint
/**
* Define extension methods for supporting pluggable file remote file systems e.g. AWS S3 or Google Storage
*
* @author Paolo Di Tommaso
*/
@Slf4j
@CompileStatic
abstract class FileSystemPathFactory implements ExtensionPoint {
/**
* Converts path uri string to the corresponding {@link Path} object
*
* @param uri
* A fully qualified path uri including the protocol scheme
* @return
* A {@link Path} for the given path or {@code null} if protocol is unknown
*/
abstract protected Path parseUri(String uri)
/**
* Converts a {@link Path} object to a fully qualified uri string
*
* @param path
* The {@link Path} object to be converted
* @return
* The uri string corresponding to the specified path or {@code null}
* if the no provider is found
*/
abstract protected String toUriString(Path path)
/**
* Bash helper library that implements the support for third-party storage
* to be included in the job command wrapper script
*
* @return The Bash snippet implementing the support for third-party such as AWS S3
* or {@code null} if not supported
*/
abstract protected String getBashLib(Path target)
/**
* The name of a Bash helper function to upload a file to a remote file storage
*
* @return The name of the upload function or {@code null} if not supported
*/
abstract protected String getUploadCmd(String source, Path target)
static Path parse(String uri) {
lookup0 { it.parseUri(uri) }
}
static String getUriString(Path path) {
lookup0 { it.toUriString(path) }
}
static String bashLib(Path target) {
lookup0 { it.getBashLib(target) }
}
static String uploadCmd(String source, Path target) {
lookup0 { it.getUploadCmd(source, target) }
}
private static List factories0() {
final factories = new ArrayList(10)
final itr = Plugins.getPriorityExtensions(FileSystemPathFactory).iterator()
while( itr.hasNext() )
factories.add(itr.next())
log.trace "File system path factories: ${factories}"
return factories
}
private static T lookup0( @ClosureParams(value = SimpleType, options = ['nextflow.file.FileSystemPathFactory']) Closure criteria) {
final factories = factories0()
for( int i=0; i