<commit_before>/*
 * Copyright (c) 2013-2015, Centre for Genomic Regulation (CRG).
 * Copyright (c) 2013-2015, <NAME> and the respective authors.
 *
 *   This file is part of 'Nextflow'.
 *
 *   Nextflow is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   Nextflow is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
 */

package nextflow.executor
import static nextflow.processor.TaskStatus.COMPLETED
import static nextflow.processor.TaskStatus.RUNNING
import static nextflow.processor.TaskStatus.SUBMITTED

import java.nio.file.Files
import java.nio.file.Path

import groovy.util.logging.Slf4j
import nextflow.fs.dx.DxFileSystem
import nextflow.fs.dx.DxFileSystemSerializer
import nextflow.fs.dx.DxPath
import nextflow.fs.dx.DxPathSerializer
import nextflow.fs.dx.api.DxApi
import nextflow.processor.TaskHandler
import nextflow.processor.TaskMonitor
import nextflow.processor.TaskPollingMonitor
import nextflow.processor.TaskProcessor
import nextflow.processor.TaskRun
import nextflow.util.Duration
import nextflow.util.KryoHelper
import nextflow.util.PathSerializer

/**
 * Executes script.nf indicated in dxapp.sh in the DnaNexus environment
 *
 * See https://www.dnanexus.com/
 *
 * @author <NAME> <<EMAIL>>
 * @author <NAME> <<EMAIL>>
 */


@Slf4j
@ServiceName('dnanexus')
class DnaNexusExecutor extends Executor {

//    static {
//        // call to force the installation of the DX file system provider
//        FileHelper.getOrInstallProvider(DxFileSystemProvider)
//    }

    @Override
    void register() {
        // -- register the serializer for the Dx file system objects
        KryoHelper.register(DxPath, DxPathSerializer)
        KryoHelper.register(DxFileSystem, DxFileSystemSerializer)
        KryoHelper.register(S3Path, PathSerializer)<commit_msg>Removed unnecessary `S3Path` serialiser registation on DnaNexus executor initialisation <commit_after>/*
 * Copyright (c) 2013-2015, Centre for Genomic Regulation (CRG).
 * Copyright (c) 2013-2015, <NAME> and the respective authors.
 *
 *   This file is part of 'Nextflow'.
 *
 *   Nextflow is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   Nextflow is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
 */

package nextflow.executor
import static nextflow.processor.TaskStatus.COMPLETED
import static nextflow.processor.TaskStatus.RUNNING
import static nextflow.processor.TaskStatus.SUBMITTED

import java.nio.file.Files
import java.nio.file.Path

import groovy.util.logging.Slf4j
import nextflow.fs.dx.DxFileSystem
import nextflow.fs.dx.DxFileSystemSerializer
import nextflow.fs.dx.DxPath
import nextflow.fs.dx.DxPathSerializer
import nextflow.fs.dx.api.DxApi
import nextflow.processor.TaskHandler
import nextflow.processor.TaskMonitor
import nextflow.processor.TaskPollingMonitor
import nextflow.processor.TaskProcessor
import nextflow.processor.TaskRun
import nextflow.util.Duration
import nextflow.util.KryoHelper
/**
 * Executes script.nf indicated in dxapp.sh in the DnaNexus environment
 *
 * See https://www.dnanexus.com/
 *
 * @author <NAME> <<EMAIL>>
 * @author <NAME> <<EMAIL>>
 */


@Slf4j
@ServiceName('dnanexus')
class DnaNexusExecutor extends Executor {

    @Override
    void register() {
        // -- register the serializer for the Dx file system objects
        KryoHelper.register(DxPath, DxPathSerializer)
        KryoHelper.register(DxFileSystem, DxFileSystemSerializer)
{'fraction_non_alphanumeric': 0.0816188107619263, 'fraction_numerical': 0.009043635541487679, 'mean_word_length': 4.061784897025172, 'pattern_counts': {'":': 0, '<': 19, '<?xml version=': 0, '>': 19, 'https://': 2, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6205131', 'n_tokens_mistral': 1326, 'n_tokens_neox': 1284, 'n_words': 423}