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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
/*
* 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.http
import java.nio.file.FileSystem
import java.nio.file.LinkOption
import java.nio.file.Path
import java.nio.file.Paths
import java.nio.file.ProviderMismatchException
import java.nio.file.WatchEvent
import java.nio.file.WatchKey
import java.nio.file.WatchService
import groovy.transform.CompileStatic
/**
* Implements a {@link Path} for http/ftp protocols
*
* @author Emilio Palumbo
* @author Paolo Di Tommaso
*/
@CompileStatic
class XPath implements Path {
static final public Set ALL_SCHEMES = ['ftp','http','https'] as Set
private static final String[] EMPTY = []
private XFileSystem fs
private Path path
private String query
XPath(XFileSystem fs, String path) {
this(fs, path, EMPTY)
}
XPath(XFileSystem fs, String path, String[] more) {
this.fs = fs
this.query = query(path)
this.path = Paths.get(stripQuery(path) ?:'/', more)
}
private XPath(XFileSystem fs, Path path, String query=null) {
this.fs = fs
this.path = path
this.query = query
}
private URI getBaseUri() {
fs?.getBaseUri()
}
private XPath createXPath(String path) {
fs && path.startsWith('/') ? new XPath(fs, path) : new XPath(null, path)
}
@Override
FileSystem getFileSystem() {
return fs
}
@Override
boolean isAbsolute() {
return path.isAbsolute()
}
@Override
Path getRoot() {
return createXPath("/")
}
@Override
Path getFileName() {
final result = path?.getFileName()?.toString()
return result ? new XPath(null, result) : null
}
@Override
Path getParent() {
String result = path.parent ? path.parent.toString() : null
if( result ) {
if( result != '/' ) result += '/'
return createXPath(result)
}
return null
}
@Override
int getNameCount() {
return path.toString() ? path.nameCount : 0
}
@Override
Path getName(int index) {
return new XPath(null, path.getName(index).toString())
}
@Override
Path subpath(int beginIndex, int endIndex) {
return new XPath(null, path.subpath(beginIndex, endIndex).toString())
}
@Override
Path normalize() {
return new XPath(fs, path.normalize(), query)
}
@Override
boolean startsWith(Path other) {
return startsWith(other.toString())
}
@Override
boolean startsWith(String other) {
return path.startsWith(other)
}
@Override
boolean endsWith(Path other) {
return endsWith(other.toString())
}
@Override
boolean endsWith(String other) {
return path.endsWith(other)
}
@Override
Path resolve(Path other) {
if( this.class != other.class )
throw new ProviderMismatchException()
def that = (XPath)other
if( that.fs && this.fs != that.fs )
return other
else if( that.path ) {
def newPath = this.path.resolve(that.path)
return new XPath(fs, newPath, that.query)
}
else {
return this
}
}
@Override
Path resolve(String other) {
resolve(get(other))
}
@Override
Path resolveSibling(Path other) {
if( this.class != other.class )
throw new ProviderMismatchException()
def that = (XPath)other
if( that.fs && this.fs != that.fs )
return other
if( that.path ) {
final Path newPath = this.path.resolveSibling(that.path)
return newPath.isAbsolute() ? new XPath(fs, newPath) : new XPath(null, newPath)
}
else {
return this
}
}
@Override
Path resolveSibling(String other) {
resolveSibling(get(other))
}
@Override
Path relativize(Path other) {
def otherPath = ((XPath)other).path
return createXPath(path.relativize(otherPath).toString())
}
@Override
URI toUri() {
final String concat = query!=null ? "$path?$query" : path.toString()
return baseUri ? new URI("$baseUri$concat") : new URI(concat)
}
@Override
Path toAbsolutePath() {
return this
}
@Override
Path toRealPath(LinkOption... options) throws IOException {
return this
}
@Override
File toFile() {
throw new UnsupportedOperationException()
}
@Override
String toString() {
return path.toString()
}
@Override
WatchKey register(WatchService watcher, WatchEvent.Kind[] events, WatchEvent.Modifier... modifiers) throws IOException {
throw new UnsupportedOperationException("Register not supported by XFileSystem")
}
@Override
WatchKey register(WatchService watcher, WatchEvent.Kind... events) throws IOException {
throw new UnsupportedOperationException("Register not supported by XFileSystem")
}
@Override
Iterator iterator() {
final len = getNameCount()
new Iterator() {
int index
Path current = len ? getName(index++) : null
@Override
boolean hasNext() {
return current != null
}
@Override
Path next() {
final result = current
current = index other.toUri().toString()
}
@Override
boolean equals(Object other) {
if (other.class != XPath) {
return false
}
final that = (XPath)other
return this.fs == that.fs && this.path == that.path && this.query == that.query
}
/**
* @return The unique hash code for this path
*/
@Override
int hashCode() {
return Objects.hash(fs,path,query)
}
/**
* Path factory method.
*
* @param str
* A fully qualified URI path string, e.g. {@code http://www.host.name/data.file.txt}
* @return
* The corresponding {@link XPath} object
* @throws
* ProviderMismatchException When the URI scheme does not match any supported protocol, i.e. {@code ftp},
* {@code http}, {@code https}
*/
static XPath get(String str) {
if( str == null )
return null
def uri = new URI(null,null,str,null,null)
if( uri.scheme && !ALL_SCHEMES.contains(uri.scheme))
throw new ProviderMismatchException()
uri.authority ? (XPath)Paths.get(uri) : new XPath(null, str)
}
static String stripQuery(String uri) {
if(!uri)
return null
final p = uri.indexOf('?')
return p>0 ? uri.substring(0,p) : (p==0 ? null : uri)
}
static String query(String uri) {
if(!uri)
return null
final p = uri.indexOf('?')
return p!=-1 && p