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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.mail
import java.nio.file.FileSystems
import java.nio.file.Files
import java.nio.file.Path
import groovy.transform.CompileStatic
import groovy.transform.EqualsAndHashCode
import groovy.transform.ToString
import groovy.util.logging.Slf4j
import nextflow.file.FileHelper
import nextflow.util.MemoryUnit
/**
* Model a mail attachment
*/
@Slf4j
@CompileStatic
@ToString(includeNames = true)
@EqualsAndHashCode
class Attachment {
private static final MemoryUnit MAX_SIZE = MemoryUnit.of('20MB')
/**
* The attachment file
*/
private File file
/**
* The attachment as classpath resource
*/
private String resource
/**
* Attachment content parameters
*/
private Map params
static Attachment resource(Map params, String path) {
def result = new Attachment()
result.resource = path
result.params = params != null ? params : [:]
return result
}
protected Attachment() {}
Attachment( attach ) {
this([:], attach)
}
Attachment( Map params, attach ) {
if( attach instanceof File ) {
this.file = attach
}
else if( attach instanceof Path ) {
this.file = toFile0(attach)
}
else if( attach instanceof String || attach instanceof GString ) {
this.file = new File(attach.toString())
}
else if( attach != null )
throw new IllegalArgumentException("Invalid attachment argument: $attach [${attach.getClass()}]")
this.params = params != null ? params : [:]
}
File getFile() { file }
String getResource() { resource }
String getContentId() { params.contentId }
String getDescription() { params.description }
String getDisposition() { params.disposition }
String getFileName() {
if( params.fileName )
return params.fileName
if( file )
return file.getName()
if( resource ) {
def str = resource
def p = str.indexOf(':')
if( p!=-1 )
str = resource.substring(p+1)
p = str.lastIndexOf('/')
if( p!=-1 )
str = str.substring(p+1)
return str
}
return null
}
private File toFile0(Path source) {
checkPath(source)
if ( source.fileSystem == FileSystems.default )
return source.toFile()
final tempDir = Files.createTempDirectory('nf-mail-attach')
tempDir.toFile().deleteOnExit()
final target = tempDir.resolve(source.getName())
FileHelper.copyPath(source, target)
return target.toFile()
}
private void checkPath(Path source) {
final attrs = FileHelper.readAttributes(source)
if( !attrs )
return
final size = MemoryUnit.of(attrs.size())
if( size>MAX_SIZE ) {
log.warn("Mail attachment should not be bigger than ${MAX_SIZE} - check file: ${source.toUriString()}")
}
if( attrs.isDirectory() ) {
throw new IllegalArgumentException("Mail attachment cannot be a directory - offending path: ${source.toUriString()}")
}
}
}
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