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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner

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/*
 * Copyright 2013-2019, Centre for Genomic Regulation (CRG)
 *
 * 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.EqualsAndHashCode
import groovy.transform.PackageScope
import groovy.transform.ToString
import groovy.util.logging.Slf4j

/**
 * Implements a special {@code Path} used to stage files in the work area
 */
@Slf4j
@ToString(includePackage = false, includeNames = true)
@EqualsAndHashCode
@CompileStatic
class FileHolder  {

    final def sourceObj

    final Path storePath

    final String stageName

    FileHolder( Path inputFile ) {
        assert inputFile
        this.sourceObj = inputFile
        this.storePath = real(inputFile)
        this.stageName = norm(inputFile.getFileName())
    }

    FileHolder( def origin, Path path ) {
        assert origin != null
        assert path != null

        this.sourceObj = origin
        this.storePath = path
        this.stageName = norm(path.getFileName())
    }

    protected FileHolder( def source, Path store, def stageName ) {
        this.sourceObj = source
        this.storePath = store
        this.stageName = norm(stageName)
    }

    FileHolder withName( def stageName )  {
        new FileHolder( this.sourceObj, this.storePath, stageName )
    }

    Path getStorePath() { storePath }

    String getStageName() { stageName }

    @PackageScope
    static FileHolder get( def path, def name = null ) {
        Path storePath = path as Path
        def target = name ? name : storePath.getFileName()
        new FileHolder( path, storePath, target )
    }

    /**
     * Make sure the stage name does not start with a slash character
     *
     * @param path
     * @return The normalised path
     */
    static private String norm(path) {
        def result = path.toString()
        return result.startsWith('/') ? result.substring(1) : result
    }

    static private Path real( Path path ) {
        try {
            return path.toRealPath()
        }
        catch( Exception e ) {
            log.trace "Unable to get real path for: $path"
            return path
        }
    }
}