#! /usr/bin/env python

# All the vanilla python package dependencies of Umbrella can be satisfied by a standard installation of Python 2.{6,7} or Python 3.
"""
Umbrella is a tool for specifying and materializing comprehensive execution environments, from the hardware all the way up to software and data.  A user simply invokes Umbrella with the desired task, and Umbrella determines the minimum mechanism necessary to run the task, whether it be direct execution, a system container, a local virtual machine, or submission to a cloud or grid environment.  We present the overall design of Umbrella and demonstrate its use to precisely execute a high energy physics application and a ray-tracing application across many platforms using a combination of Parrot, Chroot, Docker, VMware, Condor, and Amazon EC2.

Copyright (C) 2003-2004 Douglas Thain and the University of Wisconsin
Copyright (C) 2005- The University of Notre Dame
This software is distributed under the GNU General Public License.
See the file COPYING for details.

Implementation Logics of Different Execution Engines:
    If the sandbox type is Parrot, create the mountlist file and set PARROT_MOUNT_FILE; set PATH; set PARROT_LDSO_PATH if a separate OS image is needed; parrotize the user's command into `parrot_run user_cmd`.
    If the sandbox type is Docker, transfer the OS image into a Docker image; use volume to mount all the software and data dependencies into a container; set PATH; dockerize the user's command into `docker run user_cmd`. To use Docker, a separate OS image is needed.
    If the sandbox type is chroot, create mountpoints for software and data dependencies inside the OS image directory and mount software and data into the OS image, set PATH, chrootize the user's command into `chroot user_cmd`.

Implementation Logic of Dependency Sources:
    HTTP/HTTPS: Download the dependency into Umbrella local cache.
    CVMFS: check whether the mountpoint already exists on the execution node, if yes, do not need to set mountpoint for this dependency and directly process the next dependency; if no, parrot will be used to deliver cvmfs for the application.
        If Parrot is needed to access cvmfs, and the sandbox type is Parrot,
            Do all the work mentioned above for Parrot execution engine + add SITEINFO into mountlist file.
        If Parrot is needed to access cvmfs, and the sandbox type is Docker,
            Do all the work mentioned above for Docker execution engine + add SITEINFO into mountlist file + parrotize the user's command. First parrotize the user's command, then dockerize the user's command.
        If Parrot is needed to access cvmfs, and the sandbox type is chroot,
            Do all the work mentioned above for chroot execution engine + add SITEINFO into mountlist file + parrotize the user's command. First parrotize the user's command, then chrootize the user's command.
    ROOT: If the user expects the root file to be access at runtime without downloading. Umbrella does nothing if a ROOT file through ROOT protocol is needed, because ROOT supports data access during runtime without downloading first. Inside the umbrella specification file, the user only needs to specify the mount_env attribute.
        If the user expects the root file to be downloaded first, then the user needs to specify both the mount_env and mountpoint attributes inside the umbrella specification.

    Git: If the user's application needs git to do `git clone <repo_url>; git checkout <branch_name/commit_id>`, then the user does not need to specify mountpoint attribute inside the umbrella specification.
        If the user's application does not explicitly require git, but umbrella tries to pull some dependencies from a remote git repository, then the user needs to specify both the mount_env and mountpoint attributes inside the umbrella specification.

mount_env and mountpoint:
If only mountpoint is set to A in a specification, the dependency will be downloaded into the umbrella local cache with the file path of D, and a new mountpoint will be added into mount_dict (mount_dict[A] = D).
If only mount_env is set to B in a specification, the dependency will not be downloaded, meta_search will be executed to get one remote storage location, C, of the dependency, a new environment variable will be set (env_para_dict[B] = C).
If mountpoint is set to A and mount_env is set to B in a specification, the dependency will be downloaded into the umbrella local cache with the file path of D, and a new mountpoint will be added into mount_dict (mount_dict[A] = D) and a new environment variable will also be set (env_para_dict[B] = A).

Local path inside the umbrella local cache:
Case 1: the dependency is delivered as a git repository through http/https/git protocol.
        dest = os.path.dirname(sandbox_dir) + "/cache/" + git_commit + '/' + repo_name
    Note: git_commit is optional in the metadata database. If git_commit is not specified in the metadata database, then:
        dest = os.path.dirname(sandbox_dir) + "/cache/" + repo_name
Case 2: the dependency is delivered not as a git repository through http/https protocol.
        dest = os.path.dirname(sandbox_dir) + "/cache/" + checksum + "/" + name
    Note: checksum is required to be specified in the metadata database. If it is not specified, umbrella will complain and exit.
Case 3: SITECONF info necessary for CVMFS cms repository access through Parrot. For this case, we use a hard-coded path.
        dest = os.path.dirname(sandbox_dir) + "/cache/" + checksum + "/SITECONF"
"""

from __future__ import print_function
import sys
from stat import *
from pprint import pprint
import subprocess
import platform
import re
import tarfile
from optparse import OptionParser
import os
import hashlib
import difflib
import sqlite3
import shutil
import datetime
import time
import getpass
import grp
import logging
import multiprocessing
import resource
import tempfile
import gzip
import imp
import socket

try:
    from StringIO import StringIO       # python 2.x
except ImportError:
    from io import StringIO             # python 3.x

try:
    from urllib import urlretrieve         # python 2.x
except ImportError:
    from urllib.request import urlretrieve # python 3.x

try:
    from urlparse import urlsplit         # python 2.x
except ImportError:
    from urllib.parse import urlsplit   # python 3.x


#if sys.version_info < (2,6,) or sys.version_info >= (3,):
#    sys.exit("Umbrella depends on [python2.6, python3).")

found_requests = None
try:
    imp.find_module('requests')
    found_requests = True
    import requests
    import requests.packages.urllib3
except ImportError:
    found_requests = False


found_boto3 = None
try:
    imp.find_module('boto3')
    found_boto3 = True
    import boto3
except ImportError:
    found_boto3 = False


found_botocore = None
try:
    imp.find_module('botocore')
    found_botocore = True
    import botocore
except ImportError:
    found_botocore = False

s3_url = 'https://s3.amazonaws.com'

import json

# cctools binary is hosted at: /afs/crc.nd.edu/group/ccl/web/hep-case-study/parrot
cctools_binary_source = "http://ccl.cse.nd.edu/research/data/hep-case-study/parrot"

#Replace the version of cctools inside umbrella is easy: set cctools_binary_version.
cctools_binary_version = "d68f960d"

parrot_path = ""

#set cms_siteconf_url to be the url for the siteconf your application depends
#the url and format settings here should be consistent with the function set_cvmfs_cms_siteconf
cms_siteconf_url = "http://ccl.cse.nd.edu/research/data/hep-case-study/2efd5cbb3424fe6b4a74294c84d0fb43/SITECONF.tar.gz"
cms_siteconf_format = "tgz"

tempfile_list = [] #a list of temporary file created by umbrella and need to be removed before umbrella ends.
tempdir_list = [] #a list of temporary dir created by umbrella and need to be removed before umbrella ends.

pac_manager = {
"yum": ("-y install", "info")
}

upload_count = 0

def subprocess_error(cmd, rc, stdout, stderr):
    """Print the command, return code, stdout, and stderr; and then directly exit.

    Args:
        cmd: the executed command.
        rc: the return code.
        stdout: the standard output of the command.
        stderr: standard error of the command.

    Returns:
        directly exit the program.
    """
    cleanup(tempfile_list, tempdir_list)
    sys.exit("`%s` fails with the return code of %d, \nstdout: %s, \nstderr: %s\n" % (cmd, rc, stdout, stderr))

def func_call(cmd, utils_list=None):
    """ Execute a command and return the return code, stdout, stderr.

    Args:
        cmd: the command needs to execute using the subprocess module.
        utils_list: a list of executables used in the cmd

    Returns:
        a tuple including the return code, stdout, stderr.
    """

    # first check whether all the executables in utils_list exist or not
    if dependency_check_list(utils_list) == -1:
        cleanup(tempfile_list, tempdir_list)
        sys.exit(-1)

    logging.debug("Start to execute command: %s", cmd)
    p = subprocess.Popen(cmd, stdout = subprocess.PIPE, shell = True)
    (stdout, stderr) = p.communicate()
    rc = p.returncode
    logging.debug("returncode: %d\nstdout: %s\nstderr: %s", rc, stdout, stderr)
    return (rc, stdout, stderr)

def func_call_withenv(cmd, env_dict, utils_list=None):
    """ Execute a command with a special setting of the environment variables and return the return code, stdout, stderr.

    Args:
        cmd: the command needs to execute using the subprocess module.
        env_dict: the environment setting.
        utils_list: a list of executables used in the cmd

    Returns:
        a tuple including the return code, stdout, stderr.
    """

    # first check whether all the executables in utils_list exist or not
    if dependency_check_list(utils_list) == -1:
        cleanup(tempfile_list, tempdir_list)
        sys.exit(-1)

    logging.debug("Start to execute command: %s", cmd)
    logging.debug("The environment variables for executing the command is:")
    logging.debug(env_dict)

    p = subprocess.Popen(cmd, env = env_dict, stdout = subprocess.PIPE, shell = True)
    (stdout, stderr) = p.communicate()
    rc = p.returncode
    logging.debug("returncode: %d\nstdout: %s\nstderr: %s", rc, stdout, stderr)
    return (rc, stdout, stderr)

def which_exec(name):
    """The implementation of shell which command

    Args:
        name: the name of the executable to be found.

    Returns:
        If the executable is found, returns its fullpath.
        If PATH is not set, directly exit.
        Otherwise, returns None.
    """
    if 'PATH' not in os.environ.keys():
        cleanup(tempfile_list, tempdir_list)
        logging.critical("The environment variable PATH is not set!")
        sys.exit("The environment variable PATH is not set!")
    for path in os.environ["PATH"].split(":"):
        fullpath = path + '/' + name
        if os.path.exists(fullpath) and os.path.isfile(fullpath):
            return fullpath
    return None

def md5_cal(filename, block_size=2**20):
    """Calculate the md5sum of a file

    Args:
        filename: the name of the file
        block_size: the size of each block

    Returns:
        If the calculation fails for any reason, directly exit.
        Otherwise, return the md5 value of the content of the file
    """
    try:
        with open(filename, 'rb') as f:
            md5 = hashlib.md5()
            while True:
                data = f.read(block_size)
                if not data:
                    break
                md5.update(data)
            return md5.hexdigest().lower()
    except Exception as e:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("Computing the checksum of %s fails: %s.", filename, e)
        sys.exit("md5_cal(" + filename + ") failed.\n" + e)

def url_download(url, dest):
    """ Download url into dest

    Args:
        url: the url needed to be downloaded.
        dest: the path where the content from the url should be put.

    Returns:
        If the url is downloaded successfully, return None;
        Otherwise, directly exit.
    """
    logging.debug("Start to download %s to %s ...." % (url, dest))
    urlretrieve(url, dest)

def dependency_download(name, url, checksum, checksum_tool, dest, format_remote_storage, action):
    """Download a dependency from the url and verify its integrity.

    Args:
        name: the file name of the dependency. If its format is plain text, then filename is the same with the archived name. If its format is tgz, the filename should be the archived name with the trailing .tgz/.tar.gz removed.
        url: the storage location of the dependency.
        checksum: the checksum of the dependency.
        checksum_tool: the tool used to calculate the checksum, such as md5sum.
        dest: the destination of the dependency where the downloaded dependency will be put.
        format_remote_storage: the file format of the dependency, such as .tgz.
        action: the action on the downloaded dependency. Options: none, unpack. "none" leaves the downloaded dependency at it is. "unpack" uncompresses the dependency.

    Returns:
        If the url is a broken link or the integrity of the downloaded data is bad, directly exit.
        Otherwise, return None.
    """
    print("Download software from %s into the umbrella local cache (%s)" % (url, dest))
    logging.debug("Download software from %s into the umbrella local cache (%s)", url, dest)
    dest_dir = os.path.dirname(dest)
    dest_uncompress = dest #dest_uncompress is the path of the uncompressed-version dependency

    if format_remote_storage == "plain":
        filename = name
    elif format_remote_storage == "tgz":
        filename = "%s.tar.gz" % name

    dest = os.path.join(dest_dir, filename) #dest is the path of the compressed-version dependency

    if not os.path.exists(dest_dir):
        os.makedirs(dest_dir)

    if not os.path.exists(dest):
        #download the dependency from the url
        #this method currently will fail when the data size is larger than the memory size, use subprocess + wget can solve it
        url_download(url, dest)
        #if it exists, the uncompressed-version directory will be deleted first
        if action == "unpack" and format_remote_storage != 'plain' and os.path.exists(dest_uncompress):
            shutil.rmtree(dest_uncompress)
            logging.debug("the uncompressed-version directory exists already, first delete it")

    #calculate the checkusm of the compressed-version dependency
    if checksum_tool == "md5sum":
        local_checksum = md5_cal(dest)
        logging.debug("The checksum of %s is: %s", dest, local_checksum)
        if not local_checksum == checksum:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("The version of %s is incorrect! Please first delete it and its unpacked directory!!", dest)
            sys.exit("the version of " + dest + " is incorrect! Please first delete it and its unpacked directory!!\n")
    elif not checksum_tool:
        logging.debug("the checksum of %s is not provided!", url)
    else:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("%s is not supported currently!", checksum_tool)
        sys.exit(checksum_tool + "is not supported currently!")

    #if the uncompressed-version dependency does not exist, uncompress the dependency
    if action == "unpack" and (not os.path.exists(dest_uncompress)) and format_remote_storage == "tgz":
        logging.debug("Uncompressing %s into %s ....", dest, dest_uncompress)
        tfile = tarfile.open(dest, "r:gz")
        tfile.extractall(dest_dir)

def extract_tar(src, dest, form):
    """Extract a tgz file from src to dest

    Args:
        src: the location of a tgz file
        dest: the location where the uncompressed data will be put
        form: the format the tarball. Such as: tar, tgz

    Returns:
        None
    """
    if form == "tar":
        tfile = tarfile.open(src, "r")
    elif form == "tgz":
        tfile = tarfile.open(src, "r:gz")
    tfile.extractall(dest)

def meta_search(meta_json, name, id=None):
    """Search the metadata information of an dependency in the meta_json
    First find all the items with the required name in meta_json.
    Then find the right one whose id satisfied the requirement.
    If no id parameter is problem, then the first matched one will be returned.

    Args:
        meta_json: the json object including all the metadata of dependencies.
        name: the name of the dependency.
        id: the id attribute of the dependency. Defaults to None.

    Returns:
        If one item is found in meta_json, return the item, which is a dictionary.
        If no item satisfied the requirement on meta_json, directly exit.
    """
    if name in meta_json.keys():
        if not id:
            for item in meta_json[name]:
                return meta_json[name][item]
        else:
            if id in meta_json[name].keys():
                return meta_json[name][id]
            else:
                cleanup(tempfile_list, tempdir_list)
                logging.debug("meta_json does not has <%s> with the id <%s>", name, id)
                sys.exit("meta_json does not has <%s> with the id <%s>" % (name, id))
    else:
        cleanup(tempfile_list, tempdir_list)
        logging.debug("meta_json does not include %s", name)
        sys.exit("meta_json does not include %s\n" % name)

def attr_check(name, item, attr, check_len = 0):
    """Check and obtain the attr of an item.

    Args:
        name: the name of the dependency.
        item: an item from the metadata database
        attr: an attribute
        check_len: if set to 1, also check whether the length of the attr is > 0; if set to 0, ignore the length checking.

    Returns:
        If the attribute check is successful, directly return the attribute.
        Otherwise, directly exit.
    """
    logging.debug("check the %s attr of the following item:", attr)
    logging.debug(item)
    if attr in item.keys():
        if check_len == 1:
            if len(item[attr]) <= 0:
                cleanup(tempfile_list, tempdir_list)
                logging.debug("The %s attr of the item is empty.", attr)
                sys.exit("The %s attr of the item (%s) is empty." % (item, attr))

            #when multiple options are available, currently the first one will be picked.
            #we can add filter here to control the choice.
            if attr == 'source':
                return source_filter(item[attr], ['osf', 's3'], name)
            else:
                return item[attr][0]
        else:
            return item[attr]
    else:
        cleanup(tempfile_list, tempdir_list)
        logging.debug("This item doesn not have %s attr!", attr)
        sys.exit("the item (%s) does not have %s attr!" % (item, attr))

def source_filter(sources, filters, name):
    """Filter the download urls of a dependency.
    The reason why this filtering process is necessary is: some urls are not
    accessible by the current umbrella runtime. For example, if some urls points to
    OSF, but the execution node has no requests python package installed. In this
    case, all the download urls pointing to OSF are ignored.

    Args:
        sources: a list of download urls
        filters: a list of protocols which are not supported by the current umbrella runtime.
        name: the name of the dependency.

    Returns:
        If all the download urls are not available, exit directly.
        Otherwise, return the first available url.
    """
    l = []
    for s in sources:
        filtered = 0
        for item in filters:
            if s[:len(item)] == item:
                filtered = 1
                break
        if not filtered:
            l.append(s)

    if len(l) == 0:
        return sources[0]
    else:
        return l[0]

def cctools_download(sandbox_dir, hardware_platform, linux_distro, action):
    """Download cctools

    Args:
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        hardware_platform: the architecture of the required hardware platform (e.g., x86_64).
        linux_distro: the linux distro.  For Example: redhat6, centos6.
        action: the action on the downloaded dependency. Options: none, unpack. "none" leaves the downloaded dependency at it is. "unpack" uncompresses the dependency.

    Returns:
        the path of the downloaded cctools in the umbrella local cache. For example: /tmp/umbrella_test/cache/d19376d92daa129ff736f75247b79ec8/cctools-4.9.0-redhat6-x86_64
    """
    name = "cctools-%s-%s-%s" % (cctools_binary_version, hardware_platform, linux_distro)
    source = "%s/%s.tar.gz" % (cctools_binary_source, name)
    global parrot_path
    cctools_dest = os.path.dirname(sandbox_dir) + "/cache/" + name
    dependency_download(name, source, None, None, cctools_dest, "tgz", "unpack")
    parrot_path = cctools_dest + "/bin/parrot_run"
    return parrot_path

def set_cvmfs_cms_siteconf(sandbox_dir):
    """Download cvmfs SITEINFO and set its mountpoint.

    Args:
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.

    Returns:
        cvmfs_cms_siteconf_mountpoint: a string in the format of '/cvmfs/cms.cern.ch/SITECONF/local <SITEINFO dir in the umbrella local cache>/local'
    """
    dest = os.path.dirname(sandbox_dir) + "/cache/cms_siteconf/SITECONF"
    dependency_download("SITECONF.tar.gz", cms_siteconf_url, "", "", dest, cms_siteconf_format, "unpack")
    cvmfs_cms_siteconf_mountpoint = '/cvmfs/cms.cern.ch/SITECONF/local %s/local' % dest
    return cvmfs_cms_siteconf_mountpoint

def is_dir(path):
    """Judge whether a path is directory or not.
    If the path is a dir, directly return. Otherwise, exit directly.

    Args:
        path: a path

    Returns:
        None
    """
    if os.path.isdir(path):
        pass
    else:
        cleanup(tempfile_list, tempdir_list)
        logging.debug("%s is not a directory!", path)
        sys.exit("%s is not a directory!" % path)

def git_dependency_download(repo_url, dest, git_branch, git_commit):
    """Prepare a dependency from a git repository.
    First check whether dest exist or not: if dest exists, then checkout to git_branch and git_commit;
    otherwise, git clone url, and then checkout to git_branch and git_commit.

    Args:
        repo_url: the url of the remote git repository
        dest: the local directory where the git repository will be cloned into
        git_branch: the branch name of the git repository
        git_commit: the commit id of the repository

    Returns:
        dest: the local directory where the git repository is
    """
    dest = remove_trailing_slashes(dest)

    scheme, netloc, path, query, fragment = urlsplit(repo_url)
    repo_name = os.path.basename(path)
    if repo_name[-4:] == '.git':
        repo_name = repo_name[:-4]

    dest = dest + '/' + repo_name
    if os.path.exists(dest):
        is_dir(dest)
    else:
        dir = os.path.dirname(dest)
        if os.path.exists(dir):
            is_dir(dir)
        else:
            os.makedirs(dir)
        os.chdir(dir)

        cmd = "git clone %s" % repo_url
        rc, stdout, stderr = func_call(cmd, ["git"])
        if rc != 0:
            subprocess_error(cmd, rc, stdout, stderr)

    os.chdir(dest)
    if git_branch:
        cmd = "git checkout %s" % git_branch
        rc, stdout, stderr = func_call(cmd, ["git"])
        if rc != 0:
            subprocess_error(cmd, rc, stdout, stderr)

    if git_commit:
        cmd = "git checkout %s" % git_commit
        rc, stdout, stderr = func_call(cmd, ["git"])
        if rc != 0:
            subprocess_error(cmd, rc, stdout, stderr)
    return dest

def git_dependency_parser(item, repo_url, sandbox_dir):
    """Parse a git dependency

    Args:
        item: an item from the metadata database
        repo_url: the url of the remote git repository
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.

    Returns:
        dest: the path of the downloaded data dependency in the umbrella local cache.
    """
    logging.debug("This dependency is stored as a git repository: ")
    logging.debug(item)
    git_branch = ''
    if "branch" in item.keys():
        git_branch = item["branch"]
    git_commit = ''
    if "commit" in item.keys():
        git_commit = item["commit"]
    dest = os.path.dirname(sandbox_dir) + "/cache/" + git_commit
    dest = git_dependency_download(repo_url, dest, git_branch, git_commit)
    return dest

def data_dependency_process(name, id, meta_json, sandbox_dir, action, osf_auth):
    """Download a data dependency

    Args:
        name: the item name in the data section
        id: the id attribute of the processed dependency
        meta_json: the json object including all the metadata of dependencies.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        action: the action on the downloaded dependency. Options: none, unpack. "none" leaves the downloaded dependency at it is. "unpack" uncompresses the dependency.
        osf_auth: the osf authentication info including osf_username and osf_password.

    Returns:
        dest: the path of the downloaded data dependency in the umbrella local cache.
    """
    item = meta_search(meta_json, name, id)
    source = attr_check(name, item, "source", 1)
    if source[:4] == 'git+':
        dest = git_dependency_parser(item, source[4:], sandbox_dir)
    elif source[:4] == 'osf+':
        checksum = attr_check(name, item, "checksum").lower()
        form = attr_check(name, item, "format")
        dest = os.path.dirname(sandbox_dir) + "/cache/" + checksum + "/" + name
        try:
            logging.debug("Trying to download %s as a normal url ,,,", source)
            dependency_download(name, source[4:], checksum, "md5sum", dest, form, action)
        except:
            logging.debug("Fails to download %s as a normal url ,,,", source)
            if len(osf_auth) < 2:
                cleanup(tempfile_list, tempdir_list)
                logging.debug("Please use --osf_user and --osf_pass to specify your osf authentication info!")
                sys.exit("Please use --osf_user and --osf_pass to specify your osf authentication info!")
            if form == "tgz":
                osf_download(osf_auth[0], osf_auth[1], source[4:], dest + ".tar.gz")
            else:
                osf_download(osf_auth[0], osf_auth[1], source[4:], dest)
            dependency_download(name, dest, checksum, "md5sum", dest, form, action)
    elif source[:3] == "s3+":
        checksum = attr_check(name, item, "checksum").lower()
        form = attr_check(name, item, "format")
        dest = os.path.dirname(sandbox_dir) + "/cache/" + checksum + "/" + name
        try:
            logging.debug("Trying to download %s as a normal url ,,,", source)
            dependency_download(name, source[3:], checksum, "md5sum", dest, form, action)
        except:
            logging.debug("Fails to download %s as a normal url ,,,", source)
            if form == "tgz":
                s3_download(source[3:], dest + ".tar.gz")
            else:
                s3_download(source[3:], dest)
            dependency_download(name, dest, checksum, "md5sum", dest, form, action)
    else:
        checksum = attr_check(name, item, "checksum").lower()
        form = attr_check(name, item, "format")
        dest = os.path.dirname(sandbox_dir) + "/cache/" + checksum + "/" + name
        dependency_download(name, source, checksum, "md5sum", dest, form, action)
    return dest

def check_cvmfs_repo(repo_name):
    """ Check whether a cvmfs repo is installed on the host or not

    Args:
        repo_name: a cvmfs repo name. For example: "/cvmfs/cms.cern.ch".

    Returns:
        If the cvmfs repo is installed,  returns the string including the mountpoint of cvmfs cms repo. For example: "/cvmfs/cms.cern.ch".
        Otherwise, return an empty string.
    """
    logging.debug("Check whether a cvmfs repo is installed on the host or not")
    cmd = "df -h|grep '^cvmfs'|grep "+ "'" + repo_name + "'" + "|rev| cut -d' '  -f1|rev"
    rc, stdout, stderr = func_call(cmd, ["df", "grep", "rev", "cut"])
    if rc == 0:
        return stdout[:-1]
    else:
        return ''

def dependency_process(name, id, action, meta_json, sandbox_dir, osf_auth):
    """ Process each explicit and implicit dependency.

    Args:
        name: the item name in the software section
        id: the id attribute of the processed dependency
        action: the action on the downloaded dependency. Options: none, unpack. "none" leaves the downloaded dependency at it is. "unpack" uncompresses the dependency.
        meta_json: the json object including all the metadata of dependencies.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        osf_auth: the osf authentication info including osf_username and osf_password.

    Returns:
        mount_value: the actual storage path of one dependency.
    """
    mount_value = ''

    item = meta_search(meta_json, name, id)
    source = attr_check(name, item, "source", 1)
    logging.debug("%s is chosen to deliver %s", source, name)

    if source[:4] == "git+":
        dest = git_dependency_parser(item, source[4:], sandbox_dir)
        mount_value = dest
    elif source[:4] == "osf+":
        checksum = attr_check(name, item, "checksum").lower()
        form = attr_check(name, item, "format")
        dest = os.path.dirname(sandbox_dir) + "/cache/" + checksum + "/" + name

        #first download it as a normal url
        try:
            logging.debug("Trying to download %s as a normal url ,,,", source)
            dependency_download(name, source[4:], checksum, "md5sum", dest, form, action)
        except:
            logging.debug("Fails to download %s as a normal url ,,,", source)
            if len(osf_auth) < 2:
                cleanup(tempfile_list, tempdir_list)
                logging.debug("Please use --osf_user and --osf_pass to specify your osf authentication info!")
                sys.exit("Please use --osf_user and --osf_pass to specify your osf authentication info!")
            if form == "tgz":
                osf_download(osf_auth[0], osf_auth[1], source[4:], dest + ".tar.gz")
            else:
                osf_download(osf_auth[0], osf_auth[1], source[4:], dest)
            dependency_download(name, dest, checksum, "md5sum", dest, form, action)
        mount_value = dest
    elif source[:3] == "s3+":
        checksum = attr_check(name, item, "checksum").lower()
        form = attr_check(name, item, "format")
        dest = os.path.dirname(sandbox_dir) + "/cache/" + checksum + "/" + name
        try:
            logging.debug("Trying to download %s as a normal url ,,,", source)
            dependency_download(name, source[3:], checksum, "md5sum", dest, form, action)
        except:
            logging.debug("Fails to download %s as a normal url ,,,", source)
            if form == "tgz":
                s3_download(source[3:], dest + ".tar.gz")
            else:
                s3_download(source[3:], dest)
            dependency_download(name, dest, checksum, "md5sum", dest, form, action)
        mount_value = dest
    elif source[:5] == "cvmfs":
        pass
    else:
        checksum = attr_check(name, item, "checksum").lower()
        form = attr_check(name, item, "format")
        dest = os.path.dirname(sandbox_dir) + "/cache/" + checksum + "/" + name
        dependency_download(name, source, checksum, "md5sum", dest, form, action)
        mount_value = dest
    return mount_value

def env_parameter_init(hardware_spec, kernel_spec, os_spec):
    """ Set the environment parameters according to the specification file.

    Args:
        hardware_spec: the hardware section in the specification for the user's task.
        kernel_spec: the kernel section in the specification for the user's task.
        os_spec: the os section in the specification for the user's task.

    Returns:
        a tuple including the requirements for hardware, kernel and os.
    """
    hardware_platform = attr_check("hardware", hardware_spec, "arch").lower()

    cpu_cores = 1
    if "cores" in hardware_spec.keys():
        cpu_cores = hardware_spec["cores"].lower()

    memory_size = "1GB"
    if "memory" in hardware_spec.keys():
        memory_size = hardware_spec["memory"].lower()

    disk_size = "1GB"
    if "disk" in hardware_spec.keys():
        disk_size = hardware_spec["disk"].lower()

    kernel_name = attr_check("kernel", kernel_spec, "name").lower()
    kernel_version = attr_check("kernel", kernel_spec, "version").lower()
    kernel_version = re.sub('\s+', '', kernel_version).strip()

    distro_name = attr_check("os", os_spec, "name").lower()
    distro_version = attr_check("os", os_spec, "version").lower()

    os_id = ''
    if "id" in os_spec.keys():
        os_id = os_spec["id"]

    index = distro_version.find('.')
    linux_distro = distro_name + distro_version[:index] #example of linux_distro: redhat6
    return (hardware_platform, cpu_cores, memory_size, disk_size, kernel_name, kernel_version, linux_distro, distro_name, distro_version, os_id)

def compare_versions(v1, v2):
    """ Compare two versions, the format of version is: X.X.X

    Args:
        v1: a version.
        v2: a version.

    Returns:
        0 if v1 == v2; 1 if v1 is newer than v2; -1 if v1 is older than v2.
    """
    list1 = v1.split('.')
    list2 = v2.split('.')
    for i in range(len(list1)):
        list1[i] = int(list1[i])
    for i in range(len(list2)):
        list2[i] = int(list2[i])
    if list1[0] == list2[0]:
        if list1[1] == list2[1]:
            if list1[2] == list2[2]:
                return 0
            elif list1[2] > list2[2]:
                return 1
            else:
                return -1
        elif list1[1] > list2[1]:
            return 1
        else:
            return -1

    elif list1[0] > list2[0]:
        return 1
    else:
        return -1

def verify_kernel(host_kernel_name, host_kernel_version, kernel_name, kernel_version):
    """ Check whether the kernel version of the host machine matches the requirement.
    The kernel_version format supported for now includes: >=2.6.18; [2.6.18, 2.6.32].

    Args:
        host_kernel_name: the name of the OS kernel of the host machine.
        host_kernel_version: the version of the kernel of the host machine.
        kernel_name: the name of the required OS kernel (e.g., linux). Not case sensitive.
        kernel_version: the version of the required kernel (e.g., 2.6.18).

    Returns:
        If the kernel version of the host machine matches the requirement, return None.
        If the kernel version of the host machine does not match the requirement, directly exit.
    """
    if host_kernel_name != kernel_name:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("The required kernel name is %s, the kernel name of the host machine is %s!", kernel_name, host_kernel_name)
        sys.exit("The required kernel name is %s, the kernel name of the host machine is %s!\n" % (kernel_name, host_kernel_name))
    if kernel_version[0] == '[':
        list1 = kernel_version[1:-1].split(',')
        if compare_versions(host_kernel_version, list1[0]) >= 0 and compare_versions(host_kernel_version, list1[1]) <= 0:
            logging.debug("The kernel version matches!")
        else:
            cleanup(tempfile_list, tempdir_list)
            logging.debug("The required kernel version is %s, the kernel version of the host machine is %s!", kernel_version, host_kernel_version)
            sys.exit("The required kernel version is %s, the kernel version of the host machine is %s!\n" % (kernel_version, host_kernel_version))
    elif kernel_version[0] == '>':
        if compare_versions(host_kernel_version, kernel_version[2:]) >= 0:
            logging.debug("The kernel version matches!")
        else:
            cleanup(tempfile_list, tempdir_list)
            logging.debug("The required kernel version is %s, the kernel version of the host machine is %s!", kernel_version, host_kernel_version)
            sys.exit("The required kernel version is %s, the kernel version of the host machine is %s!\n" % (kernel_version, host_kernel_version))
    elif kernel_version[0] == '<':
        if compare_versions(host_kernel_version, kernel_version[2:]) <= 0:
            logging.debug("The kernel version matches!")
        else:
            cleanup(tempfile_list, tempdir_list)
            logging.debug("The required kernel version is %s, the kernel version of the host machine is %s!", kernel_version, host_kernel_version)
            sys.exit("The required kernel version is %s, the kernel version of the host machine is %s!\n" % (kernel_version, host_kernel_version))
    else: #the kernel version is a single value
        if compare_versions(host_kernel_version, kernel_version[2:]) == 0:
            logging.debug("The kernel version matches!")
        else:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("The required kernel version is %s, the kernel version of the host machine is %s!", kernel_version, host_kernel_version)
            sys.exit("The required kernel version is %s, the kernel version of the host machine is %s!\n" % (kernel_version, host_kernel_version))

def env_check(sandbox_dir, sandbox_mode, hardware_platform, cpu_cores, memory_size, disk_size, kernel_name, kernel_version):
    """ Check the matching degree between the specification requirement and the host machine.
    Currently check the following item: sandbox_mode, hardware platform, kernel, OS, disk, memory, cpu cores.
    Other things needed to check: software, and data??

    Args:
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        sandbox_mode: the execution engine.
        hardware_platform: the architecture of the required hardware platform (e.g., x86_64).
        cpu_cores: the number of required  cpus (e.g., 1).
        memory_size: the memory size requirement (e.g., 2GB). Not case sensitive.
        disk_size: the disk size requirement (e.g., 2GB). Not case sensitive.
        kernel_name: the name of the required OS kernel (e.g., linux). Not case sensitive.
        kernel_version: the version of the required kernel (e.g., 2.6.18).

    Returns:
        host_linux_distro: the linux distro of the host machine. For Example: redhat6, centos6.
    """
    print("Execution environment checking ...")

    if sandbox_mode not in ["docker", "destructive", "parrot"]:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("Currently local execution engine only support three sandbox techniques: docker, chroot or parrot!")
        sys.exit("Currently local execution engine only support three sandbox techniques: docker, chroot or parrot!\n")

    uname_list = platform.uname() #format of uname_list: (system,node,release,version,machine,processor)
    logging.debug("The platform information of the local machine:")
    logging.debug(uname_list)

    if uname_list[0].lower() != "linux":
        cleanup(tempfile_list, tempdir_list)
        logging.critical("Umbrella only works on Linux machines!")
        sys.exit("Umbrella only works on Linux machines!\n")

    logging.debug("Hardware platform checking ...")
    if hardware_platform != uname_list[4].lower():
        cleanup(tempfile_list, tempdir_list)
        logging.critical("The specification requires %s, but the local machine is %s", hardware_platform, uname_list[4].lower())
        sys.exit("The specification requires " + hardware_platform + ", but the local machine is " + uname_list[4].lower() + "!\n")

    logging.debug("CPU cores checking ...")
    cpu_cores = int(cpu_cores)
    host_cpu_cores = multiprocessing.cpu_count()
    if cpu_cores > host_cpu_cores:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("The specification requires %d cpu cores, but the local machine only has %d cores!", cpu_cores, host_cpu_cores)
        sys.exit("The specification requires %d cpu cores, but the local machine only has %d cores!\n" % (cpu_cores, host_cpu_cores))

    logging.debug("Memory size checking ...")
    memory_size = re.sub('\s+', '', memory_size).strip()
    memory_size = float(memory_size[:-2])

    cmd = "free -tg|grep Total|sed 's/\s\+/ /g'|cut -d' ' -f2"
    rc, stdout, stderr = func_call(cmd, ["free", "grep", "sed", "cut"])
    if rc != 0:
        logging.critical("The return code is %d, memory check fail!", rc)
    else:
        host_memory_size = float(stdout)
        if memory_size > host_memory_size:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("The specification requires %.2f GB memory space, but the local machine only has %.2f GB free memory space!", memory_size, host_memory_size)
            sys.exit("The specification requires %.2f GB memory space, but the local machine only has %.2f GB free memory space!" % (memory_size, host_memory_size))

    logging.debug("Disk space checking ...")
    disk_size = re.sub('\s+', '', disk_size).strip()
    disk_size = float(disk_size[:-2])
    st = os.statvfs(sandbox_dir)
    free_disk = float(st.f_bavail * st.f_frsize) / (1024*1024*1024)
    if disk_size > free_disk:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("The specification requires %.2f GB disk space, but the local machine only has %.2f GB free disk space!", disk_size, free_disk)
        sys.exit("The specification requires %.2f GB disk space, but the local machine only has %.2f GB free disk space!" % (disk_size, free_disk))

    #check kernel
    logging.debug("Kernel checking ...")
    host_kernel_name = uname_list[0].lower()
    index = uname_list[2].find('-')
    host_kernel_version = uname_list[2][:index]
    verify_kernel(host_kernel_name, host_kernel_version, kernel_name, kernel_version)

    #set host_linux_distro. Examples: redhat6, centos6.
    #potential problem: maybe in the future, we need a finer control about the host_linux_distro, like redhat6.5, centos6.5.
    host_linux_distro = None

    dist_list = platform.linux_distribution() # platform.dist() is obsolete.
    logging.debug("The hardware information of the local machine:")
    logging.debug(dist_list)

    if not dist_list[0] or not dist_list[1]:
        host_linux_distro = uname_list[2]
    else:
        dist_name = dist_list[0]
        dist_version = dist_list[1][:dist_list[1].find('.')]
        if dist_list[0] == 'CentOS Linux':
            dist_name = 'centos'
        elif dist_list[0] == 'Red Hat Enterprise Linux Server':
            dist_name = 'redhat'
        elif len(dist_list[0]) >= 16 and dist_list[0][:16] == 'Scientific Linux':
            dist_name = 'redhat'
        host_linux_distro = dist_name + dist_version

    logging.debug("The OS distribution information of the local machine: %s", host_linux_distro)

    if sandbox_mode == "parrot" and not parrot_path:
        check_parrot_binary_support(host_linux_distro)

    return host_linux_distro

def check_parrot_binary_support(host_linux_distro):
    """Check whether a parrot binary for the host machine is provided by cctools.
    Currently, cctools only provided the parrot binary for redhat5-7 and centos5-7.
    If the user the host machine is not any of these, then the user should build their cctools themselves.

    Args:
        host_linux_distro: the linux distro of the host machine. For Example: redhat6, centos6.

    Returns:
        None
    """
    if len(host_linux_distro) == 7 and host_linux_distro[:6] in ["redhat", "centos"] and host_linux_distro[6] in ['5', '6', '7']:
        logging.debug("cctools provides the parrot binary needed for the host machine!")
    else:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("""cctools only provides the parrot binary for redhat[5-7] and centos[5-7]!
    To use the parrot execution mode on your machine, you need to install cctools:
        https://github.com/cooperative-computing-lab/cctools
    After installing cctools, run umbrella again with the --parrot_path option to specify the parrot path.""")

def parrotize_user_cmd(user_cmd, cwd_setting, cvmfs_http_proxy, parrot_mount_file, parrot_ldso_path, use_local_cvmfs, parrot_log):
    """Modify the user's command into `parrot_run + the user's command`.
    The cases when this function should be called: (1) sandbox_mode == parrot; (2) sandbox_mode != parrot and cvmfs is needed to deliver some dependencies not installed on the execution node.

    Args:
        user_cmd: the user's command.
        cwd_setting: the current working directory for the execution of the user's command.
        cvmfs_http_proxy: HTTP_PROXY environmetn variable used to access CVMFS by Parrot
        parrot_mount_file: the path of the mountfile for parrot
        parrot_ldso_path: the path of the ld.so file for parrot
        use_local_cvmfs: use the cvmfs on the host machine instead of using parrot_run to deliver cvmfs
        parrot_log: the path of the parrot debugging log

    Returns:
        None
    """
    # if parrot_namespace is used here, `--no-set-foreground` should be removed.
    parrot_options = ""
    if parrot_ldso_path == '':
        parrot_options = "-m %s --no-set-foreground" % parrot_mount_file
    else:
        parrot_options = "-m %s -l %s --no-set-foreground" % (parrot_mount_file, parrot_ldso_path)

    if use_local_cvmfs:
        parrot_options = "%s --disable-service cvmfs" % parrot_options

    if parrot_log:
        parrot_options = "%s -d all -o %s" % (parrot_options, parrot_log)

    if cvmfs_http_proxy and not use_local_cvmfs:
        user_cmd[0] = "export HTTP_PROXY=%s; export PARROT_ALLOW_SWITCHING_CVMFS_REPOSITORIES=yes; %s %s -- /bin/sh -c 'cd  %s; %s'" % (cvmfs_http_proxy, parrot_path, parrot_options, cwd_setting, user_cmd[0])
    else:
        user_cmd[0] = "%s %s -- /bin/sh -c 'cd  %s; %s'" % (parrot_path, parrot_options, cwd_setting, user_cmd[0])
    logging.debug("The parrotized user_cmd: %s" % user_cmd[0])

def chrootize_user_cmd(user_cmd, cwd_setting):
    """Modify the user's command when the sandbox_mode is chroot. This check should be done after `parrotize_user_cmd`.
    The cases when this function should be called: sandbox_mode == chroot

    Args:
        user_cmd: the user's command.
        cwd_setting: the current working directory for the execution of the user's command.

    Returns:
        the modified version of the user's cmd.
    """
    #By default, the directory of entering chroot is /. So before executing the user's command, first change the directory to the $PWD environment variable.
    user_cmd[0] = 'chroot / /bin/sh -c "cd %s; %s"' %(cwd_setting, user_cmd[0])
    return user_cmd

def software_install(mount_dict, env_para_dict, software_spec, meta_json, sandbox_dir, pac_install_destructive, osf_auth, name=None):
    """ Installation each software dependency specified in the software section of the specification.

    Args:
        mount_dict: a dict including each mounting item in the specification, whose key is the access path used by the user's task; whose value is the actual storage path.
        env_para_dict: the environment variables which need to be set for the execution of the user's command.
        software_spec: the software section of the specification
        meta_json: the json object including all the metadata of dependencies.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        pac_install_destructive: whether this is to install packages through package manager in destructive mode
        osf_auth: the osf authentication info including osf_username and osf_password.
        name: if name is specified, then only the specified item will be installed. All the other items in the software section will be ignored.

    Returns:
        None.
    """

    print("Installing software dependencies ...")

    for item in software_spec:
        if name and name != item:
            continue
        # always first check whether the attribute is set or not inside the umbrella specificiation file.
        id = ''
        if 'id' in software_spec[item].keys():
            id = software_spec[item]['id']
        mountpoint = ''
        if 'mountpoint' in software_spec[item].keys():
            mountpoint = software_spec[item]['mountpoint']
        mount_env = ''
        if 'mount_env' in software_spec[item].keys():
            mount_env = software_spec[item]['mount_env']
        action = 'unpack'
        if 'action' in software_spec[item].keys():
            action = software_spec[item]['action'].lower()

        if mount_env and not mountpoint:
            result = meta_search(meta_json, item, id)
            env_para_dict[mount_env] =attr_check(item, result, "source", 1)
        else:
            if mount_env and mountpoint:
                env_para_dict[mount_env] = mountpoint

            mount_value = dependency_process(item, id, action, meta_json, sandbox_dir, osf_auth)
            if len(mount_value) > 0:
                logging.debug("Add mountpoint (%s:%s) into mount_dict", mountpoint, mount_value)
                if pac_install_destructive:
                    parent_dir = os.path.dirname(mountpoint)
                    if not os.path.exists(parent_dir):
                        os.makedirs(parent_dir)
                    elif not os.path.isdir(parent_dir):
                        cleanup(tempfile_list, tempdir_list)
                        logging.critical("%s is not a directory!\n", parent_dir)
                        sys.exit("%s is not a directory!\n" % parent_dir)

                    if not os.path.exists(mountpoint):
                        cmd = "mv -f %s %s/" % (mount_value, parent_dir)
                        rc, stdout, stderr = func_call(cmd, ["mv"])
                        if rc != 0:
                            subprocess_error(cmd, rc, stdout, stderr)
                else:
                    mount_dict[mountpoint] = mount_value

                if 'mode' in software_spec[item].keys():
                    mode = int(software_spec[item]['mode'], 8)
                    os.chmod(mount_value, mode)
                    logging.debug("Change the file mode of `%s` to `%s`", mount_value, oct(mode))

def data_install(data_spec, meta_json, sandbox_dir, mount_dict, env_para_dict, osf_auth, cwd_setting, name=None):
    """Process data section of the specification.
    At the beginning of the function, mount_dict only includes items for software and os dependencies. After this function is done, all the items for data dependencies will be added into mount_dict.

    Args:
        data_spec: the data section of the specification.
        meta_json: the json object including all the metadata of dependencies.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        mount_dict: a dict including each mounting item in the specification, whose key is the access path used by the user's task; whose value is the actual storage path.
        env_para_dict: the environment variables which need to be set for the execution of the user's command.
        osf_auth: the osf authentication info including osf_username and osf_password.
        cwd_setting: the current working directory for the execution of the user's command.
        name: if name is specified, then only the specified item will be installed. All the other items in the software section will be ignored.

    Returns:
        None
    """
    print("Installing data dependencies ...")
    for item in data_spec:
        if name and name != item:
            continue
        id = ''
        if 'id' in data_spec[item].keys():
            id = data_spec[item]['id']
        mountpoint = ''
        if 'mountpoint' in data_spec[item].keys():
            mountpoint = data_spec[item]['mountpoint']
            if len(mountpoint) > 0 and mountpoint[0] != '/':
                mountpoint = cwd_setting + '/' + mountpoint
        mount_env = ''
        if 'mount_env' in data_spec[item].keys():
            mount_env = data_spec[item]['mount_env']
        action = 'unpack'
        if 'action' in data_spec[item].keys():
            action = data_spec[item]['action']

        if mount_env and not mountpoint:
            result = meta_search(meta_json, item, id)
            env_para_dict[mount_env] = attr_check(item, result, "source", 1)
        else:
            mount_value = data_dependency_process(item, id, meta_json, sandbox_dir, action, osf_auth)
            logging.debug("Add mountpoint (%s:%s) into mount_dict", mountpoint, mount_value)
            mount_dict[mountpoint] = mount_value
            if mount_env and mountpoint:
                env_para_dict[mount_env] = mountpoint

            if 'mode' in data_spec[item].keys():
                mode = int(data_spec[item]['mode'], 8)
                os.chmod(mount_value, mode)
                logging.debug("Change the file mode of `%s` to `%s`", mount_value, oct(mode))

def get_linker_path(hardware_platform, os_image_dir):
    """Return the path of ld-linux.so within the downloaded os image dependency

    Args:
        hardware_platform: the architecture of the required hardware platform (e.g., x86_64).
        os_image_dir: the path of the OS image inside the umbrella local cache.

    Returns:
        If the dynamic linker is found within the OS image, return its fullpath.
        Otherwise, returns None.
    """
    #env_list is directly under the directory of the downloaded os image dependency
    if hardware_platform == "x86_64":
        p = os_image_dir + "/lib64/ld-linux-x86-64.so.2"
        if os.path.exists(p):
            return p
        else:
            return None
    else:
        return None

def construct_docker_volume(input_dict, mount_dict, output_f_dict, output_d_dict):
    """Construct the docker volume parameters based on mount_dict.

    Args:
        input_dict: the setting of input files specified by the --inputs option.
        mount_dict: a dict including each mounting item in the specification, whose key is the access path used by the user's task; whose value is the actual storage path.

    Returns:
        volume_paras: all the `-v` options for the docker command.
    """
    if "/" in mount_dict:
        del mount_dict["/"] #remove "/" from the mount_dict to avoid messing the root directory of the host machine
    volume_paras = ""
    for key in mount_dict:
        volume_paras = volume_paras + " -v " + mount_dict[key] + ":" + key + " "

    for key in input_dict:
        volume_paras = volume_paras + " -v " + input_dict[key] + ":" + key + " "

    for key in output_f_dict:
        volume_paras = volume_paras + " -v " + output_f_dict[key] + ":" + key + " "

    for key in output_d_dict:
        volume_paras = volume_paras + " -v " + output_d_dict[key] + ":" + key + " "

    return volume_paras

def obtain_path(os_image_dir, sw_mount_dict):
    """Get the path environment variable from envfile and add the mountpoints of software dependencies into it
    the envfile here is named env_list under the OS image.

    Args:

        os_image_dir: the path of the OS image inside the umbrella local cache.
        sw_mount_dict: a dict only including all the software mounting items.

    Returns:
        path_env: the new value for PATH.
    """
    path_env = ''

    if os.path.exists(os_image_dir + "/env_list") and os.path.isfile(os_image_dir + "/env_list"):
        with open(os_image_dir + "/env_list", "rb") as f:
            for line in f:
                if line[:5] == 'PATH=':
                    path_env = line[5:-1]
                    break
    else:
        path_env = '.:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin'

    for key in sw_mount_dict:
        path_env = key + "/bin:" + path_env
    return path_env

def transfer_env_para_docker(env_para_dict):
    """Transfer the env_para_dict into the docker `-e` options.

    Args:
        env_para_dict: the environment variables which need to be set for the execution of the user's command.

    Returns:
        env_options: the docker `-e` options constructed from env_para_dict.
    """
    env_options = ''
    for key in env_para_dict:
        if key:
            env_options = env_options + ' -e "' + key + '=' + env_para_dict[key] + '" '
    return env_options

def collect_software_bin(sw_mount_dict):
    """Construct the path environment from the mountpoints of software dependencies.
    Each softare meta has a bin subdir containing all its executables.

    Args:
        sw_mount_dict: a dict only including all the software mounting items.

    Returns:
        extra_path: the paths which are extracted from sw_mount_dict and needed to be added into PATH.
    """
    extra_path = ""
    for key in sw_mount_dict:
        if key != '/':
            extra_path += '%s/bin:' % key
    return extra_path

def in_local_passwd():
    """Judge whether the current user exists in /etc/passwd.

    Returns:
        If the current user is inside /etc/passwd, returns 'yes'.
        Otherwise, returns 'no'.
    """
    user_name = getpass.getuser()
    with open('/etc/passwd') as f:
        for line in f:
            if line[:len(user_name)] == user_name:
                logging.debug("%s is included in /etc/passwd!", user_name)
                return 'yes'
    logging.debug("%s is not included in /etc/passwd!", user_name)
    return 'no'

def in_local_group():
    """Judge whether the current user's group exists in /etc/group.

    Returns:
        If the current user's group exists in /etc/group, returns 'yes'.
        Otherwise, returns 'no'.
    """
    group_name = grp.getgrgid(os.getgid())[0]
    with open('/etc/group') as f:
        for line in f:
            if line[:len(group_name)] == group_name:
                logging.debug("%s is included in /etc/group!", group_name)
                return 'yes'
    logging.debug("%s is not included in /etc/group!", group_name)
    return 'no'

def create_fake_mount(os_image_dir, sandbox_dir, mount_list, path):
    """For each ancestor dir B of path (including path iteself), check whether it exists in the rootfs and whether it exists in the mount_list and
    whether it exists in the fake_mount directory inside the sandbox.
    If B is inside the rootfs or the fake_mount dir, do nothing. Otherwise, create a fake directory inside the fake_mount.
    Reason: the reason why we need to guarantee any ancestor dir of a path exists somehow is that `cd` shell builtin does a syscall stat on each level of
    the ancestor dir of a path. Without creating the mountpoint for any ancestor dir, `cd` would fail.

    Args:
        os_image_dir: the path of the OS image inside the umbrella local cache.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        mount_list: a list of mountpoints which already been inside the parrot mountlist file.
        path: a dir path.

    Returns:
        mount_str: a string including the mount items which are needed to added into the parrot mount file.
    """
    mount_str = ''
    if not path: #if the path is NULL, directly return.
        return
    path_list = []
    tmp_path = path
    while tmp_path != '/':
        path_list.insert(0, tmp_path)
        tmp_path = remove_trailing_slashes(os.path.dirname(tmp_path))
    for item in path_list:
        logging.debug("Judge whether the following mountpoint exists: %s", item)
        fake_mount_path = '%s/fake_mount%s' % (sandbox_dir, item)
        #if item is under localdir, do nothing.
        if item in remove_trailing_slashes(os.path.dirname(sandbox_dir)):
            break
        if not os.path.exists(os_image_dir + item) and item not in mount_list and not os.path.exists(fake_mount_path):
            logging.debug("The mountpoint (%s) does not exist, create a fake mountpoint (%s) for it!", item, fake_mount_path)
            os.makedirs(fake_mount_path)
            mount_str += '%s %s\n' % (item, fake_mount_path)
        else:
            logging.debug("The mountpoint (%s) already exists, do nothing!", item)
    return mount_str

def remove_trailing_slashes(path):
    """Remove the trailing slashes of a string

    Args:
        path: a path, which can be any string.

    Returns:
        path: the new path without any trailing slashes.
    """
    while len(path) > 1 and path.endswith('/'):
        path = path[:-1]
    return path

def construct_mountfile_full(sandbox_dir, os_image_dir, mount_dict, input_dict, output_f_dict, output_d_dict, cvmfs_cms_siteconf_mountpoint, parrot_log):
    """Create the mountfile if parrot is used to create a sandbox for the application and a separate rootfs is needed.
    The trick here is the adding sequence does matter. The latter-added items will be checked first during the execution.

    Args:
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        os_image_dir: the path of the OS image inside the umbrella local cache.
        mount_dict: all the mount items extracted from the specification file and possible implicit dependencies like cctools.
        input_dict: the setting of input files specified by the --inputs option
        cvmfs_cms_siteconf_mountpoint: a string in the format of '/cvmfs/cms.cern.ch/SITECONF/local <SITEINFO dir in the umbrella local cache>/local'
        parrot_log: the path of the parrot debugging log

    Returns:
        the path of the mountfile.
    """
    mount_list = []
    mountfile_path = sandbox_dir + "/.__mountlist"
    with open(mountfile_path, "wb") as mountfile:
        new_root = mount_dict["/"]
        mountfile.write("/ " + new_root + "\n")
        mount_list.append('/')
        del mount_dict["/"]
        mountfile.write(new_root + " " + new_root + "\n")   #this one is needed to avoid recuisive path resolution.
        mount_list.append(new_root)

        mountfile.write("%s %s\n" % (os.path.dirname(sandbox_dir), os.path.dirname(sandbox_dir)))
        mount_list.append(os.path.dirname(sandbox_dir))

        # sandbox_dir should be added before the mount entry for entries under it.
        logging.debug("Add sandbox_dir(%s) into %s", sandbox_dir, mountfile_path)
        mountfile.write(sandbox_dir + ' ' + sandbox_dir + '\n')
        mount_list.append(sandbox_dir)

        logging.debug("Adding items from mount_dict into %s", mountfile_path)
        for key in mount_dict:
            #os.path.dirname('/a/b/') is '/a/b'. Therefore, before and after calling dirname, use remove_trailing_slashes to remove the trailing slashes.
            key = remove_trailing_slashes(key)
            mount_str = create_fake_mount(os_image_dir, sandbox_dir, mount_list, remove_trailing_slashes(os.path.dirname(key)))
            if mount_str:
                logging.debug("Adding fake mount items (%s) into %s", mount_str, mountfile_path)
                mountfile.write(mount_str)
            mount_list.append(key)
            mount_list.append(mount_dict[key])
            mountfile.write(key + " " + mount_dict[key] + "\n")
            mountfile.write(mount_dict[key] + " " + mount_dict[key] + "\n")

        for key in output_f_dict:
            mountfile.write(key + " " + output_f_dict[key] + "\n")

        for key in output_d_dict:
            mountfile.write(key + " " + output_d_dict[key] + "\n")

        #common-mountlist includes all the common mountpoint (/proc, /dev, /sys, /mnt, /disc, /selinux)
        if os.path.exists(os_image_dir + "/common-mountlist") and os.path.isfile(os_image_dir + "/common-mountlist"):
            logging.debug("Adding items from %s/common-mountlist into %s", os_image_dir, mountfile_path)
            with open(os_image_dir + "/common-mountlist", "rb") as f:
                for line in f:
                    tmplist = line.split(' ')
                    item = remove_trailing_slashes(tmplist[0])
                    mount_str = create_fake_mount(os_image_dir, sandbox_dir, mount_list, remove_trailing_slashes(os.path.dirname(item)))
                    if mount_str:
                        logging.debug("Adding fake mount items (%s) into %s", mount_str, mountfile_path)
                        mountfile.write(mount_str)
                    mount_list.append(tmplist[0])
                    mountfile.write(line)
        else:
            common_mounts = ["/proc", "/dev", "/sys", "/net", "/misc", "/selinux"]
            for mount in common_mounts:
                line = "%s %s\n" % (mount, mount)
                mount_str = create_fake_mount(os_image_dir, sandbox_dir, mount_list, remove_trailing_slashes(os.path.dirname(mount)))
                if mount_str:
                    logging.debug("Adding fake mount items (%s) into %s", mount_str, mountfile_path)
                    mountfile.write(mount_str)
                mount_list.append(mount)
                mountfile.write(line)

        logging.debug("Add /etc/hosts and /etc/resolv.conf into %s", mountfile_path)
        mount_str = create_fake_mount(os_image_dir, sandbox_dir, mount_list, '/etc')
        if mount_str:
            logging.debug("Adding fake mount items (%s) into %s", mount_str, mountfile_path)
            mountfile.write(mount_str)
        mountfile.write('/etc/hosts /etc/hosts\n')
        mount_list.append('/etc/hosts')
        mountfile.write('/etc/resolv.conf /etc/resolv.conf\n')
        mount_list.append('/etc/resolv.conf')

        #nd workstation uses NSCD (Name Service Cache Daemon) to deal with passwd, group, hosts services. Here first check whether the current uid and gid is in the /etc/passwd and /etc/group, if yes, use them. Otherwise, construct separate passwd and group files.
        #If the current user name and group can not be found in /etc/passwd and /etc/group, a fake passwd and group file will be constructed under sandbox_dir.
        existed_user = in_local_passwd()
        if existed_user == 'yes':
            logging.debug("Add /etc/passwd into %s", mountfile_path)
            mountfile.write('/etc/passwd /etc/passwd\n')
        else:
            logging.debug("Construct a fake passwd file: .passwd, add .passwd into %s", mountfile_path)
            with open('.passwd', 'w+') as f:
                f.write('%s:x:%d:%d:unknown:%s:%s\n' % (getpass.getuser(), os.getuid(), os.getgid(), sandbox_dir + '/' + getpass.getuser(), os.environ['SHELL']))
            mountfile.write('/etc/passwd %s/.passwd\n' % (sandbox_dir))

            logging.debug("Construct a fake acl file: .__acl, add .__acl into %s", mountfile_path)
            with open('.__acl', 'w+') as acl_file:
                acl_file.write('%s rwlax\n' % getpass.getuser())

        mount_list.append('/etc/passwd')
        #getpass.getuser() returns the login name of the user
        #os.makedirs(getpass.getuser()) #it is not really necessary to create this dir.

        existed_group = in_local_group()
        if existed_group == 'yes':
            logging.debug("Add /etc/group into %s", mountfile_path)
            mountfile.write('/etc/group /etc/group\n')
        else:
            logging.debug("Construct a fake group file: .group, add .group into %s", mountfile_path)
            with open('.group', 'w+') as f:
                f.write('%s:x:%d:%d\n' % (grp.getgrgid(os.getgid())[0], os.getgid(), os.getuid()))
            mountfile.write('/etc/group %s/.group\n' % (sandbox_dir))
        mount_list.append('/etc/group')

        #add /var/run/nscd/socket into mountlist
        mount_str = create_fake_mount(os_image_dir, sandbox_dir, mount_list, '/var/run/nscd')
        if mount_str:
            logging.debug("Adding fake mount items (%s) into %s", mount_str, mountfile_path)
            mountfile.write(mount_str)
        mountfile.write('/var/run/nscd/socket ENOENT\n')
        mount_list.append('/var/run/nscd/socket')

        if os.path.exists(os_image_dir + "/special_files") and os.path.isfile(os_image_dir + "/special_files"):
            logging.debug("Add %s/special_files into %s", os_image_dir, mountfile_path)
            with open(os_image_dir + "/special_files", "rb") as f:
                for line in f:
                    tmplist = line.split(' ')
                    item = remove_trailing_slashes(tmplist[0])
                    mount_str = create_fake_mount(os_image_dir, sandbox_dir, mount_list, remove_trailing_slashes(os.path.dirname(item)))
                    if mount_str:
                        logging.debug("Adding fake mount items (%s) into %s", mount_str, mountfile_path)
                        mountfile.write(mount_str)
                    mount_list.append(tmplist[0])
                    mountfile.write(line)

        #add the input_dict into mountflie
        logging.debug("Add items from input_dict into %s", mountfile_path)
        for key in input_dict:
            key = remove_trailing_slashes(key)
            mount_str = create_fake_mount(os_image_dir, sandbox_dir, mount_list, remove_trailing_slashes(os.path.dirname(key)))
            if mount_str:
                logging.debug("Adding fake mount items (%s) into %s", mount_str, mountfile_path)
                mountfile.write(mount_str)
            mountfile.write(key + " " + input_dict[key] + "\n")
            mount_list.append(key)

        if cvmfs_cms_siteconf_mountpoint == '':
            logging.debug('cvmfs_cms_siteconf_mountpoint is null')
        else:
            mountfile.write('/cvmfs /cvmfs\n')
            mountfile.write(cvmfs_cms_siteconf_mountpoint + '\n')
            logging.debug('cvmfs_cms_siteconf_mountpoint is not null: %s', cvmfs_cms_siteconf_mountpoint)

        if parrot_log:
            mountfile.write('%s %s\n' % (parrot_log, parrot_log))
            mount_list.append(parrot_log)

    return mountfile_path

def construct_mountfile_cvmfs_cms_siteconf(sandbox_dir, cvmfs_cms_siteconf_mountpoint, parrot_log):
    """ Create the mountfile if chroot and docker is used to execute a CMS application and the host machine does not have cvmfs installed.

    Args:
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        cvmfs_cms_siteconf_mountpoint: a string in the format of '/cvmfs/cms.cern.ch/SITECONF/local <SITEINFO dir in the umbrella local cache>/local'
        parrot_log: the path of the parrot debugging log

    Returns:
        the path of the mountfile.
    """
    mountfile_path = sandbox_dir + "/.__mountlist"
    with open(mountfile_path, "wb") as f:
        f.write(cvmfs_cms_siteconf_mountpoint + '\n')
        logging.debug('cvmfs_cms_siteconf_mountpoint is not null: %s', cvmfs_cms_siteconf_mountpoint)

        if parrot_log:
            mountfile.write('%s %s\n' % (parrot_log, parrot_log))
            mount_list.append(parrot_log)

    return mountfile_path

def construct_mountfile_easy(sandbox_dir, input_dict, output_f_dict, output_d_dict, mount_dict, cvmfs_cms_siteconf_mountpoint):
    """ Create the mountfile if parrot is used to create a sandbox for the application and a separate rootfs is not needed.
    The trick here is the adding sequence does matter. The latter-added items will be checked first during the execution.

    Args:
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        mount_dict: all the mount items extracted from the specification file and possible implicit dependencies like cctools.
        input_dict: the setting of input files specified by the --inputs option
        cvmfs_cms_siteconf_mountpoint: a string in the format of '/cvmfs/cms.cern.ch/SITECONF/local <SITEINFO dir in the umbrella local cache>/local'

    Returns:
        the path of the mountfile.
    """
    mountfile_path = sandbox_dir + "/.__mountlist"
    with open(mountfile_path, "wb") as f:
        for key in input_dict:
            f.write(key + " " + input_dict[key] + "\n")

        for key in output_f_dict:
            f.write(key + " " + output_f_dict[key] + "\n")

        for key in output_d_dict:
            f.write(key + " " + output_d_dict[key] + "\n")

        for key in mount_dict:
            f.write(key + " " + mount_dict[key] + "\n")
            f.write(mount_dict[key] + " " + mount_dict[key] + "\n")

        if cvmfs_cms_siteconf_mountpoint == '':
            logging.debug('cvmfs_cms_siteconf_mountpoint is null')
        else:
            f.write(cvmfs_cms_siteconf_mountpoint + '\n')
            logging.debug('cvmfs_cms_siteconf_mountpoint is not null: %s', cvmfs_cms_siteconf_mountpoint)

    return mountfile_path

def construct_env(sandbox_dir, os_image_dir):
    """ Read env_list inside an OS image and save all the environment variables into a dictionary.

    Args:
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        os_image_dir: the path of the OS image inside the umbrella local cache.

    Returns:
        env_dict: a dictionary which includes all the environment variables from env_list
    """
    if os.path.exists(os_image_dir + "/env_list") and os.path.isfile(os_image_dir + "/env_list"):
        with open(os_image_dir + "/env_list", "rb") as f:
            env_dict = {}
            for line in f:
                index = line.find("=")
                key = line[:index]
                value = line[(index+1):-1]
                env_dict[key] = value
            return env_dict
    return {}

def has_docker_image(hardware_platform, distro_name, distro_version, tag):
    """Check whether the required docker image exists on the local machine or not.

    Args:
        hardware_platform: the architecture of the required hardware platform (e.g., x86_64).
        distro_name: the name of the required OS (e.g., redhat).
        distro_version: the version of the required OS (e.g., 6.5).
        tag: the tag of the expected docker image. tag is os_id

    Returns:
        If the required docker image exists on the local machine, returns 'yes'.
        Otherwise, returns 'no'.
    """
    name = "%s-%s-%s" %(distro_name, distro_version, hardware_platform)
    cmd = "docker images %s | awk '{print $2}'" % (name)
    logging.debug("Start to run the command: %s", cmd)
    p = subprocess.Popen(cmd, stdout = subprocess.PIPE, shell = True)
    (stdout, stderr) = p.communicate()
    rc = p.returncode
    logging.debug("returncode: %d\nstdout: %s\nstderr: %s", rc, stdout, stderr)
    if rc != 0:
        subprocess_error(cmd, rc, stdout, stderr)
    #str = "\n%s\s+" % (name)
    if stdout.find(tag) == -1:
        return 'no'
    else:
        return 'yes'

def create_docker_image(sandbox_dir, hardware_platform, distro_name, distro_version, tag):
    """Create a docker image based on the cached os image directory.

    Args:
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        hardware_platform: the architecture of the required hardware platform (e.g., x86_64).
        distro_name: the name of the required OS (e.g., redhat).
        distro_version: the version of the required OS (e.g., 6.5).
        tag: the tag of the expected docker image. tag is os_id

    Returns:
        If the docker image is imported from the tarball successfully, returns None.
        Otherwise, directly exit.
    """
    name = "%s-%s-%s" %(distro_name, distro_version, hardware_platform)
    location = os.path.dirname(sandbox_dir) + '/cache/' + tag + '/' + name
    #docker container runs as root user, so use the owner option of tar command to set the owner of the docker image
    cmd = 'cd ' + location + '; tar --owner=root -c .|docker import - ' + name + ":" + tag + '; cd -'
    rc, stdout, stderr = func_call(cmd, ["cd", "tar", "docker"])
    if rc != 0:
        subprocess_error(cmd, rc, stdout, stderr)

def construct_chroot_mount_dict(sandbox_dir, output_dir, input_dict, need_separate_rootfs, os_image_dir, mount_dict):
    """Construct directory mount list and file mount list for chroot. chroot requires the target mountpoint must be created within the chroot jail.

    Args:
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        output_f_dict: the mappings of output files (key is the file path used by the application; value is the file path the user specifies.)
        output_d_dict: the mappings of output dirs (key is the dir path used by the application; value is the dir path the user specified.)
        input_dict: the setting of input files specified by the --inputs option.
        need_separate_rootfs: whether a separate rootfs is needed to execute the user's command.
        os_image_dir: the path of the OS image inside the umbrella local cache.
        mount_dict: a dict including each mounting item in the specification, whose key is the access path used by the user's task; whose value is the actual storage path.

    Returns:
        a tuple includes the directory mount list and the file mount list
    """
    dir_dict = {}
    file_dict = {}
    logging.debug("need_separate_rootfs: %d", need_separate_rootfs)
    if need_separate_rootfs == 1:
        logging.debug("Add %s into dir_dict of chroot", os_image_dir + "/common-mountlist")
        with open(os_image_dir + "/common-mountlist") as f:
            for line in f:
                index = line.find(' ')
                item = line[:index]
                dir_dict[item] = item

        #special_files includes all the paths of the files which includes all the file paths of special types (block, character, socket, pipe)
        logging.debug("Add %s into dir_dict of chroot", os_image_dir + "/special_files")
        with open(os_image_dir + "/special_files") as f:
            for line in f:
                index = line.find(' ')
                item = line[:index]
                if os.path.exists(item):
                    file_dict[item] = item

    logging.debug("Add sandbox_dir and output_dir into dir_dict of chroot")
    dir_dict[sandbox_dir] = sandbox_dir
    dir_dict[output_dir] = output_dir

    logging.debug("Add items from mount_dict into dir_dict of chroot")
    for key in mount_dict:
        if key != '/':
            value = mount_dict[key]
            mode = os.lstat(value).st_mode
            if S_ISDIR(mode):
                dir_dict[value] = key
            else:
                file_dict[value] = key

    logging.debug("Add /etc/passwd /etc/group /etc/hosts /etc/resolv.conf into file_dict of chroot")
    file_dict['/etc/passwd'] = '/etc/passwd'
    file_dict['/etc/group'] = '/etc/group'
    file_dict['/etc/hosts'] = '/etc/hosts'
    file_dict['/etc/resolv.conf'] = '/etc/resolv.conf'

    logging.debug("Add input_dict into file_dict of chroot")
    for key in input_dict:
        value = input_dict[key]
        mode = os.lstat(value).st_mode
        if S_ISDIR(mode):
            dir_dict[value] = key
        else:
            file_dict[value] = key

    logging.debug("dir_dict:")
    logging.debug(dir_dict)
    logging.debug("file_dict:")
    logging.debug(file_dict)
    return (dir_dict, file_dict)

def chroot_mount_bind(dir_dict, file_dict, sandbox_dir, need_separate_rootfs, hardware_platform, distro_name, distro_version):
    """Create each target mountpoint under the cached os image directory through `mount --bind`.

    Args:
        dir_dict: a dict including all the directory mountpoints needed to be created inside the OS image.
        file_dict: a dict including all the file mountpoints needed to be created inside the OS image.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        need_separate_rootfs: whether a separate rootfs is needed to execute the user's command.
        hardware_platform: the architecture of the required hardware platform (e.g., x86_64).
        distro_name: the name of the required OS (e.g., redhat).
        distro_version: the version of the required OS (e.g., 6.5).

    Returns:
        If no error happens, returns None.
        Otherwise, directly exit.
    """
    logging.debug("Use mount --bind to redirect mountpoints")
    if need_separate_rootfs == 1:
        os_image_name = "%s-%s-%s" %(distro_name, distro_version, hardware_platform)
        os_image_path = os.path.dirname(sandbox_dir) + '/cache/' + os_image_name
    else:
        os_image_path = '/'
    #mount --bind -o ro hostdir sandboxdir
    for key in dir_dict:
        jaildir = '%s%s' % (os_image_path, dir_dict[key])
        hostdir = key
        #if jaildir and hostdir are the same, there is no necessary to do mount.
        if jaildir != hostdir:
            if not os.path.exists(jaildir):
                os.makedirs(jaildir)
            cmd = 'mount --bind -o ro %s %s' % (hostdir, jaildir)
            rc, stdout, stderr = func_call(cmd, ["mount"])
            if rc != 0:
                subprocess_error(cmd, rc, stdout, stderr)

    for key in file_dict:
        jailfile = '%s%s' % (os_image_path, file_dict[key])
        hostfile = key
        if jailfile != hostfile:
            if not os.path.exists(jailfile):
                d = os.path.dirname(jailfile)
                if not os.path.exists(d):
                    os.makedirs(d)
                with open(jailfile, 'w+') as f:
                    pass
            cmd = 'mount --bind -o ro %s %s' % (hostfile, jailfile)
            rc, stdout, stderr = func_call(cmd, ["mount"])
            if rc != 0:
                subprocess_error(cmd, rc, stdout, stderr)

def chroot_post_process(dir_dict, file_dict, sandbox_dir, need_separate_rootfs, hardware_platform, distro_name, distro_version):
    """Remove all the created target mountpoints within the cached os image directory.
    It is not necessary to change the mode of the output dir, because only the root user can use the chroot method.

    Args:
        dir_dict: a dict including all the directory mountpoints needed to be created inside the OS image.
        file_dict: a dict including all the file mountpoints needed to be created inside the OS image.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        need_separate_rootfs: whether a separate rootfs is needed to execute the user's command.
        hardware_platform: the architecture of the required hardware platform (e.g., x86_64).
        distro_name: the name of the required OS (e.g., redhat).
        distro_version: the version of the required OS (e.g., 6.5).

    Returns:
        If no error happens, returns None.
        Otherwise, directly exit.
    """
    logging.debug("post process of chroot")
    if need_separate_rootfs == 1:
        os_image_name = "%s-%s-%s" %(distro_name, distro_version, hardware_platform)
        os_image_path = os.path.dirname(sandbox_dir) + '/cache/' + os_image_name
    else:
        os_image_path = '/'

    #file_dict must be processed ahead of dir_dict, because we can not umount a directory if there is another mountpoints created for files under it.
    for key in file_dict:
        jailfile = '%s%s' % (os_image_path, file_dict[key])
        hostfile = key
        if jailfile != hostfile:
            if os.path.exists(jailfile):
                cmd = 'umount -f %s' % (jailfile)
                rc, stdout, stderr = func_call(cmd, ["umount"])
                if rc != 0:
                    subprocess_error(cmd, rc, stdout, stderr)

    for key in dir_dict:
        jaildir = '%s%s' % (os_image_path, dir_dict[key])
        hostdir = key
        if jaildir != hostdir:
            if os.path.exists(jaildir):
                cmd = 'umount -f %s' % (jaildir)
                rc, stdout, stderr = func_call(cmd, ["umount"])
                if rc != 0:
                    subprocess_error(cmd, rc, stdout, stderr)

            #remove all the empty ancestor directory
                parent_dir = jaildir
                mode = os.lstat(parent_dir).st_mode
                if S_ISDIR(mode):
                    while len(os.listdir(parent_dir)) == 0:
                        os.rmdir(parent_dir)
                        parent_dir = os.path.dirname(parent_dir)

def workflow_repeat(cwd_setting, sandbox_dir, sandbox_mode, output_f_dict, output_d_dict, input_dict, env_para_dict, user_cmd, hardware_platform, host_linux_distro, distro_name, distro_version, need_separate_rootfs, os_image_dir, os_image_id, cvmfs_cms_siteconf_mountpoint, mount_dict, sw_mount_dict, meta_json, new_os_image_dir, cvmfs_http_proxy, needs_parrotize_user_cmd, use_local_cvmfs, parrot_log):
    """Run user's task with the help of the sandbox techniques, which currently inculde chroot, parrot, docker.

    Args:
        cwd_setting: the current working directory for the execution of the user's command.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        sandbox_mode: the execution engine.
        output_f_dict: the mappings of output files (key is the file path used by the application; value is the file path the user specifies.)
        output_d_dict: the mappings of output dirs (key is the dir path used by the application; value is the dir path the user specified.)
        input_dict: the setting of input files specified by the --inputs option.
        env_para_dict: the environment variables which need to be set for the execution of the user's command.
        user_cmd: the user's command.
        hardware_platform: the architecture of the required hardware platform (e.g., x86_64).
        distro_name: the name of the required OS (e.g., redhat).
        distro_version: the version of the required OS (e.g., 6.5).
        need_separate_rootfs: whether a separate rootfs is needed to execute the user's command.
        os_image_dir: the path of the OS image inside the umbrella local cache.
        os_image_id: the id of the OS image.
        cvmfs_cms_siteconf_mountpoint: a string in the format of '/cvmfs/cms.cern.ch/SITECONF/local <SITEINFO dir in the umbrella local cache>/local'
        mount_dict: a dict including each mounting item in the specification, whose key is the access path used by the user's task; whose value is the actual storage path.
        sw_mount_dict: a dict only including all the software mounting items.
        meta_json: the json object including all the metadata of dependencies.
        new_os_image_dir: the path of the newly created OS image with all the packages installed by package manager.
        cvmfs_http_proxy: HTTP_PROXY environment variable used to access CVMFS by Parrot
        needs_parrotize_user_cmd: whether the user cmd needs to be wrapped inside parrot.
        use_local_cvmfs: use the cvmfs on the host machine instead of using parrot_run to deliver cvmfs
        parrot_log: the path of the parrot debugging log

    Returns:
        return_code: the return code of executing the user command
        If critical errors happen, directly exit.
    """
    #sandbox_dir will be the home directory of the sandbox
    print('Executing the application ....')
    return_code = 0
    if not os.path.exists(sandbox_dir):
        os.makedirs(sandbox_dir)
    logging.debug("chdir(%s)", sandbox_dir)
    os.chdir(sandbox_dir) #here, we indeed want to chdir to sandbox_dir, not cwd_setting, to do preparation work like create mountlist file for Parrot.
    #at this point, all the software should be under the cache dir, all the mountpoint of the software should be in mount_dict
    print("Execution engine: %s" % sandbox_mode)
    logging.debug("execution engine: %s", sandbox_mode)
    logging.debug("need_separate_rootfs: %d", need_separate_rootfs)
    if sandbox_mode == "destructive":
        env_dict = os.environ

        if cvmfs_cms_siteconf_mountpoint:
            logging.debug("Create a parrot mountfile for the siteconf meta ...")
            env_dict['PARROT_MOUNT_FILE'] = construct_mountfile_cvmfs_cms_siteconf(sandbox_dir, cvmfs_cms_siteconf_mountpoint)

        logging.debug("Add env_para_dict into environment variables")
        for key in env_para_dict:
            env_dict[key] = env_para_dict[key]

        logging.debug("Add software binary into PATH")
        extra_path = collect_software_bin(sw_mount_dict)
        if "PATH" not in env_dict:
            env_dict['PATH'] = ""
        env_dict['PATH'] = '%s:%s' % (env_dict['PATH'], extra_path[:-1])

        #move software and data into the location
        for key in mount_dict:
            parent_dir = os.path.dirname(key)
            if not os.path.exists(parent_dir):
                os.makedirs(parent_dir)
            elif not os.path.isdir(parent_dir):
                cleanup(tempfile_list, tempdir_list)
                logging.critical("%s is not a directory!\n", parent_dir)
                sys.exit("%s is not a directory!\n" % parent_dir)

            if not os.path.exists(key):
                cmd = "mv -f %s %s/" % (mount_dict[key], parent_dir)
                rc, stdout, stderr = func_call_withenv(cmd, env_dict, ["mv"])
                if rc != 0:
                    subprocess_error(cmd, rc, stdout, stderr)

        print("Start executing the user's task: %s" % user_cmd[0])
        cmd = "cd %s; %s" % (cwd_setting, user_cmd[0])
        rc, stdout, stderr = func_call_withenv(cmd, env_dict, ["cd"])
        if rc != 0:
            subprocess_error(cmd, rc, stdout, stderr)
        return_code = rc

        logging.debug("Moving the outputs to the expected locations ...")
        print("Moving the outputs to the expected locations ...")
        for key in output_f_dict:
            cmd = "mv -f %s %s" % (key, output_f_dict[key])
            rc, stdout, stderr = func_call_withenv(cmd, env_dict, ["mv"])
            if rc != 0:
                subprocess_error(cmd, rc, stdout, stderr)

        for key in output_d_dict:
            cmd = "mv -f %s %s" % (key, output_d_dict[key])
            rc, stdout, stderr = func_call_withenv(cmd, env_dict, ["mv"])
            if rc != 0:
                subprocess_error(cmd, rc, stdout, stderr)

    elif sandbox_mode == "docker":
        if need_separate_rootfs == 1:
            if has_docker_image(hardware_platform, distro_name, distro_version, os_image_id) == 'no':
                logging.debug("Start to construct a docker image from the os image")
                create_docker_image(sandbox_dir, hardware_platform, distro_name, distro_version, os_image_id)
                logging.debug("Finish constructing a docker image from the os image")

            if cvmfs_cms_siteconf_mountpoint:
                item = cvmfs_cms_siteconf_mountpoint.split(' ')[1]
                logging.debug("Adding the siteconf meta (%s) into mount_dict", item)
                mount_dict[item] = item
                logging.debug("Create a parrot mountfile for the siteconf meta (%s)", item)
                env_para_dict['PARROT_MOUNT_FILE'] = construct_mountfile_cvmfs_cms_siteconf(sandbox_dir, cvmfs_cms_siteconf_mountpoint)

            # if the new os image has been ready, do not build the image again.
            if len(new_os_image_dir) > 0:
                os_tar = new_os_image_dir + ".tar"
                if os.path.exists(os_tar):
                    return 0

            logging.debug("Add a volume item (%s:%s) for the sandbox_dir", sandbox_dir, sandbox_dir)
            #-v /home/hmeng/umbrella_test/output:/home/hmeng/umbrella_test/output
            volume_output = " -v %s:%s " % (sandbox_dir, sandbox_dir)
            #-v /home/hmeng/umbrella_test/cache/git-x86_64-redhat5:/software/git-x86_64-redhat5/
            logging.debug("Start to construct other volumes from input_dict")
            volume_parameters = construct_docker_volume(input_dict, mount_dict, output_f_dict, output_d_dict)

            #-e "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/software/git-x86_64-redhat5/bin"
            logging.debug("Set the environment variables ....")
            path_env = obtain_path(os_image_dir, sw_mount_dict)
            other_envs = transfer_env_para_docker(env_para_dict)

            docker_image_name = "%s-%s-%s" %(distro_name, distro_version, hardware_platform)

            #by default, docker executes user_cmd as the root user, `chown` is used to change the owner of the output dir to be the user who calls `umbrella`
            chown_cmd = 'chown -R %d:%d %s %s %s' % (os.getuid(), os.getgid(), sandbox_dir, ' '.join(output_f_dict), ' '.join(output_d_dict))

            #to count the post processing time, this cmd is split into two commands
            container_name = "umbrella_%s_%s_%s" % (docker_image_name, os_image_id, os.path.basename(sandbox_dir))

            #do not enable `-i` and `-t` option of Docker, it will fail when condor execution engine is chosen.
            #to allow the exit code of user_cmd to be transferred back, seperate the user_cmd and the chown command.
            cmd = 'docker run --name %s %s %s -e "PATH=%s" %s %s:%s /bin/sh -c "cd %s; %s"' % (container_name, volume_output, volume_parameters, path_env, other_envs, docker_image_name, os_image_id, cwd_setting, user_cmd[0])
            print("Start executing the user's task: %s" % cmd)
            return_code, stdout, stderr = func_call(cmd, ["docker", "sh", "cd"])

            print("\n********** STDOUT of the command **********")
            print(stdout)

            print("\n********** STDERR of the command **********")
            print(stderr)

            #docker export container_name > tarball
            if len(new_os_image_dir) > 0:
                if not os.path.exists(new_os_image_dir):
                    os.makedirs(new_os_image_dir)
                os_tar = new_os_image_dir + ".tar"

                cmd = "docker export %s > %s" % (container_name, os_tar)
                rc, stdout, stderr = func_call(cmd, ["docker"])
                if rc != 0:
                    subprocess_error(cmd, rc, stdout, stderr)

                #uncompress the tarball
                cmd = "tar xf %s -C %s" % (os_tar, new_os_image_dir)
                extract_tar(os_tar, new_os_image_dir, ["tar"])

            #docker rm container_name
            cmd = "docker rm %s" % (container_name)
            rc, stdout, stderr = func_call(cmd, ["docker"])
            if rc != 0:
                subprocess_error(cmd, rc, stdout, stderr)

            cmd1 = 'docker run --rm %s %s -e "PATH=%s" %s %s:%s %s' % (volume_output, volume_parameters, path_env, other_envs, docker_image_name, os_image_id, chown_cmd)
            rc, stdout, stderr = func_call(cmd1)
            if rc != 0:
                subprocess_error(cmd, rc, stdout, stderr)

        else:
            #if a separate rootfs is not needed to execute the user's cmd, should forcely use other execution engine to run the user cmd.
            cleanup(tempfile_list, tempdir_list)
            logging.debug("Docker execution engine can only be used when a separate rootfs is needed.")
            sys.exit("Docker execution engine can only be used when a separate rootfs is needed.\n")
    elif sandbox_mode == "parrot":
        if need_separate_rootfs == 1:
            logging.debug("Construct environment variables ....")
            env_dict = construct_env(sandbox_dir, os_image_dir)
            env_dict['PWD'] = cwd_setting
            logging.debug("Construct mounfile ....")
            parrot_mount_file = construct_mountfile_full(sandbox_dir, os_image_dir, mount_dict, input_dict, output_f_dict, output_d_dict, cvmfs_cms_siteconf_mountpoint, parrot_log)
            with open(parrot_mount_file, 'r') as f:
                logging.debug("the parrot mountlist is:\n%s\n", f.read())

            for key in env_para_dict:
                env_dict[key] = env_para_dict[key]

            #here, setting the linker will cause strange errors.
            logging.debug("Construct dynamic linker path ....")
            result = get_linker_path(hardware_platform, os_image_dir)
            if not result:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("Can not find the dynamic linker inside the os image (%s)!", os_image_dir)
                sys.exit("Can not find the dynamic linker inside the os image (%s)!\n" % os_image_dir)

            parrot_ldso_path = result
            env_dict['USER'] = getpass.getuser()
            #env_dict['HOME'] = sandbox_dir + '/' + getpass.getuser()

            logging.debug("Add software binary into PATH")
            extra_path = collect_software_bin(sw_mount_dict)
            if "PATH" not in env_dict:
                env_dict['PATH'] = '.:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin'
            env_dict['PATH'] = '%s%s' % (extra_path, env_dict['PATH'])

            if needs_parrotize_user_cmd:
                parrotize_user_cmd(user_cmd, cwd_setting, cvmfs_http_proxy, parrot_mount_file, parrot_ldso_path, use_local_cvmfs, parrot_log)

            print("Start executing the user's task: %s" % user_cmd[0])
            return_code, stdout, stderr = func_call_withenv(user_cmd[0], env_dict, ["sh"])

            print("\n********** STDOUT of the command **********")
            print(stdout)

            print("\n********** STDERR of the command **********")
            print(stderr)

        else:
            env_dict = os.environ
            parrot_mount_file = construct_mountfile_easy(sandbox_dir, input_dict, output_f_dict, output_d_dict, mount_dict, cvmfs_cms_siteconf_mountpoint, parrot_log)
            with open(parrot_mount_file, 'r') as f:
                logging.debug("the parrot mountlist is:\n%s\n", f.read())

            for key in env_para_dict:
                env_dict[key] = env_para_dict[key]

            if 'PATH' not in env_dict: #if we run umbrella on Condor, Condor will not set PATH by default.
                env_dict['PATH'] = '.:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin'
                logging.debug("PATH is empty, forcely set it to be %s", env_dict['PATH'])
            else:
                env_dict['PATH'] = '.' + env_dict['PATH']
                logging.debug("Forcely add '.' into PATH")

            logging.debug("Add software binary into PATH")
            extra_path = collect_software_bin(sw_mount_dict)
            env_dict['PATH'] = '%s%s' % (extra_path, env_dict['PATH'])

            if needs_parrotize_user_cmd:
                parrotize_user_cmd(user_cmd, cwd_setting, cvmfs_http_proxy, parrot_mount_file, '', use_local_cvmfs, parrot_log)

            print("Start executing the user's task: %s" % user_cmd[0])
            return_code, stdout, stderr = func_call_withenv(user_cmd[0], env_dict, ["sh"])

            print("\n********** STDOUT of the command **********")
            print(stdout)

            print("\n********** STDERR of the command **********")
            print(stderr)

#       logging.debug("Removing the parrot mountlist file and the parrot submit file from the sandbox")
#       if os.path.exists(env_dict['PARROT_MOUNT_FILE']):
#           os.remove(env_dict['PARROT_MOUNT_FILE'])

    else:
        pass

    return return_code

def condor_process(spec_path, spec_json, spec_path_basename, meta_path, sandbox_dir, output_dir, input_list_origin, user_cmd, cwd_setting, condorlog_path, cvmfs_http_proxy):
    """Process the specification when condor execution engine is chosen

    Args:
        spec_path: the absolute path of the specification.
        spec_json: the json object including the specification.
        spec_path_basename: the file name of the specification.
        meta_path: the path of the json file including all the metadata information.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        output_dir: the output directory.
        input_list_origin: the list of input file paths.
        user_cmd: the user's command.
        cwd_setting: the current working directory for the execution of the user's command.
        condorlog_path: the path of the umbrella log executed on the remote condor execution node.
        cvmfs_http_proxy: HTTP_PROXY environment variable used to access CVMFS by Parrot

    Returns:
        If no errors happen, return None;
        Otherwise, directly exit.
    """
    if not os.path.exists(sandbox_dir):
        os.makedirs(sandbox_dir)

    print("Checking the validity of the umbrella specification ...")
    if "hardware" in spec_json.keys() and spec_json["hardware"] and "kernel" in spec_json.keys() and spec_json["kernel"] and spec_json.has_key("os") and spec_json["os"]:
        logging.debug("Setting the environment parameters (hardware, kernel and os) according to the specification file ....")
        (hardware_platform, cpu_cores, memory_size, disk_size, kernel_name, kernel_version, linux_distro, distro_name, distro_version, os_id) = env_parameter_init(spec_json["hardware"], spec_json["kernel"], spec_json["os"])
    else:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("this specification is not complete! You must have a hardware section, a kernel section and a os section!")
        sys.exit("this spec has no hardware section\n")

    condor_submit_path = sandbox_dir + "/condor_task.submit"

    print("Constructing Condor submission file according to the umbrella specification ...")
    transfer_inputs = ''
    new_input_options = ''
    logging.debug("Transform input_list_origin into condor attributes ....")
    for item in input_list_origin:
        index_equal = item.find('=')
        access_path = item[:index_equal]
        actual_path = item[(index_equal+1):]
        transfer_inputs += ',%s' % (actual_path)
        new_input_options += '%s=%s,' % (access_path, os.path.basename(actual_path))
    if new_input_options[-1] == ',':
        new_input_options = new_input_options[:-1]
    logging.debug("transfer_input_files: %s, %s", spec_path, transfer_inputs)
    logging.debug("The new_input_options of Umbrella: %s", new_input_options)

    condor_output_dir = tempfile.mkdtemp(dir=".")
    condor_output_dir = os.path.abspath(condor_output_dir)
    condor_log_path = sandbox_dir + '/condor_task.log'

    umbrella_fullpath = which_exec("umbrella")
    if umbrella_fullpath == None:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("Failed to find the executable umbrella. Please modify your $PATH.")
        sys.exit("Failed to find the executable umbrella. Please modify your $PATH.\n")

    logging.debug("The full path of umbrella is: %s" % umbrella_fullpath)

    condor_submit_file = open(condor_submit_path, "w+")
    condor_submit_file.write('universe = vanilla\n')
    condor_submit_file.write('executable = %s\n' % '/usr/bin/python')
    if cvmfs_http_proxy:
        condor_submit_file.write('arguments = "./umbrella -s local --spec %s --cvmfs_http_proxy %s --meta %s -l condor_umbrella -i \'%s\' -o %s --log condor_umbrella.log run \'%s\'"\n' % (spec_path_basename, cvmfs_http_proxy, os.path.basename(meta_path), new_input_options, os.path.basename(condor_output_dir), user_cmd[0]))
    else:
        condor_submit_file.write('arguments = "./umbrella -s local --spec %s --meta %s -l condor_umbrella -i \'%s\' -o %s --log condor_umbrella.log run \'%s\'"\n' % (spec_path_basename, os.path.basename(meta_path), new_input_options, os.path.basename(condor_output_dir), user_cmd[0]))
#   condor_submit_file.write('PostCmd = "echo"\n')
#   condor_submit_file.write('PostArguments = "$?>%s/condor_rc"\n' % os.path.basename(condor_output_dir))
    condor_submit_file.write('transfer_input_files = %s, %s, %s%s\n' % (umbrella_fullpath, meta_path, spec_path, transfer_inputs))
    condor_submit_file.write('transfer_output_files = %s, condor_umbrella.log\n' % os.path.basename(condor_output_dir))
    condor_submit_file.write('transfer_output_remaps = "condor_umbrella.log=%s"\n' % condorlog_path)

    #the python on the redhat5 machines in the ND condor pool is 2.4. However, umbrella requires python 2.6.* or 2.7*.
    if linux_distro == "redhat5":
        condor_submit_file.write('requirements = TARGET.Arch == "%s" && TARGET.OpSys == "%s" && TARGET.OpSysAndVer == "redhat6"\n' % (hardware_platform, kernel_name))
    else:
        #condor_submit_file.write('requirements = TARGET.Arch == "%s" && TARGET.OpSys == "%s" && TARGET.OpSysAndVer == "%s" && TARGET.has_docker == true\n' % (hardware_platform, kernel_name, linux_distro))
        condor_submit_file.write('requirements = TARGET.Arch == "%s" && TARGET.OpSys == "%s" && TARGET.OpSysAndVer == "%s"\n' % (hardware_platform, kernel_name, linux_distro))
    condor_submit_file.write('environment = PATH=.:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin\n')

    condor_submit_file.write('output = %s/condor_stdout\n' % sandbox_dir)
    condor_submit_file.write('error = %s/condor_stderr\n' % sandbox_dir)
    condor_submit_file.write('log = %s\n' % condor_log_path)

    condor_submit_file.write('should_transfer_files = yes\n')
    condor_submit_file.write('when_to_transfer_output = on_exit\n')
    condor_submit_file.write('queue\n')
    condor_submit_file.close()

    #submit condor job
    print("Submitting the Condor job ...")
    cmd = 'condor_submit ' + condor_submit_path
    rc, stdout, stderr = func_call(cmd, ["condor_submit"])
    if rc != 0:
        subprocess_error(cmd, rc, stdout, stderr)
    #keep tracking whether condor job is done
    print("Waiting for the job is done ...")
    logging.debug("Waiting for the job is done ...")
    cmd = 'condor_wait %s' % condor_log_path
    rc, stdout, stderr = func_call(cmd, ["condor_wait"])
    if rc != 0:
        subprocess_error(cmd, rc, stdout, stderr)

    #check the content of condor log file to figure out the exit code of the remote executed umbrella
    remote_rc = 500
    with open(condor_log_path, 'rb') as f:
        content = f.read()
        str = "Normal termination (return value "
        index1 = content.rfind(str)
        index2 = content.find(')', index1)
        remote_rc = int(content[(index1 + len(str)):index2])

    print("The exit code of the remote executed umbrella found in the condor log file (%s) is %d!" % (condor_log_path, remote_rc))
    logging.debug("The exit code of the remote executed umbrella found in the condor log file (%s) is %d!", condor_log_path, remote_rc)

    if remote_rc == 500:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("Can not find the exit code of the remote executed umbrella inside the condor log file (%s)!", condor_log_path)
        sys.exit("Can not find the exit code of the remote executed umbrella inside the condor log file (%s)!" % condor_log_path)
    elif remote_rc != 0:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("The remote umbrella fails and the exit code is %d.", remote_rc)
        sys.exit("The remote umbrella fails and the exit code is %d." % remote_rc)

    logging.debug("the condor jos is done, put the output back into the output directory!")
    print("the condor jobs is done, put the output back into the output directory!")
    #check until the condor job is done, post-processing (put the output back into the output directory)
    #the semantics of condor_output_files only supports transferring a dir from the execution node back to the current working dir (here it is condor_output_dir).
    os.rename(condor_output_dir, output_dir)

    print("move condor_stdout, condor_stderr and condor_task.log from sandbox_dir to output_dir.")
    logging.debug("move condor_stdout, condor_stderr and condor_task.log from sandbox_dir to output_dir.")
    os.rename(sandbox_dir + '/condor_stdout', output_dir + '/condor_stdout')
    os.rename(sandbox_dir + '/condor_stderr', output_dir + '/condor_stderr')
    os.rename(sandbox_dir + '/condor_task.log', output_dir + '/condor_task.log')

    print("Remove the sandbox dir")
    logging.debug("Remove the sandbox_dir.")
    shutil.rmtree(sandbox_dir)

    print("The output has been put into the output dir: %s" % output_dir)

def decide_instance_type(cpu_cores, memory_size, disk_size, instances):
    """ Compare the required hardware configurations with each instance type, and return the first matched instance type, return 'no' if no matched instance type exist.
    We can rank each instance type in the future, so that in the case of multiple matches exit, the closest matched instance type is returned.

    Args:
        cpu_cores: the number of required  cpus (e.g., 1).
        memory_size: the memory size requirement (e.g., 2GB). Not case sensitive.
        disk_size: the disk size requirement (e.g., 2GB). Not case sensitive.
        instances: the instances section of the ec2 json file.

    Returns:
        If there is no matched instance type, return 'no'.
        Otherwise, returns the first matched instance type.
    """
    cpu_cores = int(cpu_cores)
    memory_size = int(memory_size[:-2])
    disk_size = int(disk_size[:-2])
    for item in instances:
        j = instances[item]
        inst_mem = int(float((j["memory"][:-2])))
        inst_disk = int(j["disk"][:-2])
        if cpu_cores <= int(j["cores"]) and memory_size <= inst_mem and disk_size <= inst_disk:
            return item
    return 'no'

def ec2_process(spec_path, spec_json, meta_option, meta_path, ssh_key, ec2_key_pair, ec2_security_group, ec2_instance_type, sandbox_dir, output_option, output_f_dict, output_d_dict, sandbox_mode, input_list, input_list_origin, env_option, env_para_dict, user_cmd, cwd_setting, ec2log_path, cvmfs_http_proxy):
    """
    Args:
        spec_path: the path of the specification.
        spec_json: the json object including the specification.
        meta_option: the --meta option.
        meta_path: the path of the json file including all the metadata information.
        ssh_key: the name the private key file to use when connecting to an instance.
        ec2_key_pair: the path of the key-pair to use when launching an instance.
        ec2_security_group: the security group id within which the EC2 instance should be run.
        ec2_instance_type: the type of an Amazone ec2 instance
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        output_f_dict: the mappings of output files (key is the file path used by the application; value is the file path the user specifies.)
        output_d_dict: the mappings of output dirs (key is the dir path used by the application; value is the dir path the user specified.)
        sandbox_mode: the execution engine.
        input_list: a list including all the absolute path of the input files on the local machine.
        input_list_origin: the list of input file paths.
        env_para_dict: the environment variables which need to be set for the execution of the user's command.
        user_cmd: the user's command.
        cwd_setting: the current working directory for the execution of the user's command.
        ec2log_path: the path of the umbrella log executed on the remote EC2 execution node.
        cvmfs_http_proxy: HTTP_PROXY environment variable used to access CVMFS by Parrot

    Returns:
        If no errors happen, return None;
        Otherwise, directly exit.
    """
    print("Checking the validity of the umbrella specification ...")
    if "hardware" in spec_json.keys() and spec_json["hardware"] and "kernel" in spec_json.keys() and spec_json["kernel"] and spec_json.has_key("os") and spec_json["os"]:
        (hardware_platform, cpu_cores, memory_size, disk_size, kernel_name, kernel_version, linux_distro, distro_name, distro_version, os_id) = env_parameter_init(spec_json["hardware"], spec_json["kernel"], spec_json["os"])
    else:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("this spec has no hardware section!\n")

    # the instance types provided by the Amazon EC2 keep changing. So, the instance type will be provided by the user.
    # The AMI will be provided by the author of the Umbrella spec.
    print("Obtaining the AMI info from the umbrella specification ...")
    name = '%s-%s-%s' % (distro_name, distro_version, hardware_platform)

    if not "ec2" in spec_json["os"].keys():
        logging.debug("To use ec2 execution engine, the os section should have a ec2 subsection providing the AMI, region and user info!")
        sys.exit("To use ec2 execution engine, the os section should have a ec2 subsection providing the AMI, region and user info!")

    ec2 = spec_json["os"]["ec2"]

    ami = attr_check('', ec2, "ami")
    user_name = attr_check('', ec2, "user")
    region = attr_check('', ec2, "region")

    #here we should judge the os type, yum is used by Fedora, CentOS, and REHL.
    if distro_name not in ["fedora", "centos", "redhat"]:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("Currently the supported Linux distributions are redhat, centos and fedora.\n")
            sys.exit("Currently the supported Linux distributions are redhat, centos and fedora.\n")

    #start the instance and obtain the instance id
    print("Starting an Amazon EC2 instance ...")
    instance = launch_ec2_instance(ami, region, ec2_instance_type, ec2_key_pair, ec2_security_group)
    logging.debug("Start the instance and obtain the instance id: %s", instance)

    #get the public DNS of the instance
    public_ip = instance.public_ip_address
    logging.debug("Get the public IP of the instance: %s", public_ip)

    #install wget on the instance
    print("Installing wget on the EC2 instance ...")
    logging.debug("Install wget on the instance")
    #ssh exit code 255: the remote node is down or unavailable
    rc = 300
    while rc != 0:
        #without `-t` option of ssh, if the username is not root, `ssh + sudo` will get the following error: sudo: sorry, you must have a tty to run sudo.
        cmd = 'ssh -t -o ConnectionAttempts=5 -o StrictHostKeyChecking=no -o ConnectTimeout=60 -i %s %s@%s \'sudo yum -y install wget\'' % (ssh_key, user_name, public_ip)
        rc, stdout, stderr = func_call(cmd, ["ssh"])
        if rc != 0:
            logging.debug("`%s` fails with the return code of %d, \nstdout: %s, \nstderr: %s" % (cmd, rc, stdout, stderr))
            time.sleep(5)

    #python, the python is needed to execute umbrella itself
    print("Installing python 2.6.9 on the instance ...")
    logging.debug("Install python 2.6.9 on the instance.")
    python_name = 'python-2.6.9-%s-%s' % (linux_distro, hardware_platform)
    python_url = "http://ccl.cse.nd.edu/research/data/hep-case-study/python-2.6.9-%s-%s.tar.gz" % (linux_distro, hardware_platform)
    scheme, netloc, path, query, fragment = urlsplit(python_url)
    python_url_filename = os.path.basename(path)
    cmd = 'ssh -t -o ConnectionAttempts=5 -o StrictHostKeyChecking=no -o ConnectTimeout=60 -i %s %s@%s \'sudo wget %s && sudo tar zxvf %s\'' % (ssh_key, user_name, public_ip, python_url, python_url_filename)
    rc, stdout, stderr = func_call(cmd, ["ssh"])
    if rc != 0:
        terminate_instance(instance)
        subprocess_error(cmd, rc, stdout, stderr)

    #scp umbrella, meta.json and input files to the instance
    print("Sending the umbrella task to the EC2 instance ...")
    logging.debug("scp relevant files into the HOME dir of the instance.")
    input_file_string = ''
    for input_file in input_list:
        input_file_string += input_file + ' '

    #here meta_path may start with http so need a special treatement
    umbrella_fullpath = which_exec("umbrella")
    if umbrella_fullpath == None:
        cleanup(tempfile_list, tempdir_list)
        terminate_instance(instance)
        logging.critical("Failed to find the executable umbrella. Please modify your $PATH.")
        sys.exit("Failed to find the executable umbrella. Please modify your $PATH.\n")

    logging.debug("The full path of umbrella is: %s" % umbrella_fullpath)

    if meta_option:
        meta_option = " --meta ~%s/%s " % (user_name, os.path.basename(meta_path))
        cmd = 'scp -i %s %s %s %s %s %s@%s:' % (ssh_key, umbrella_fullpath, spec_path, meta_path, input_file_string, user_name, public_ip)
    else:
        meta_option = ""
        cmd = 'scp -i %s %s %s %s %s@%s:' % (ssh_key, umbrella_fullpath, spec_path, input_file_string, user_name, public_ip)

    rc, stdout, stderr = func_call(cmd, ["scp"])
    if rc != 0:
        terminate_instance(instance)
        subprocess_error(cmd, rc, stdout, stderr)

    #change the --inputs option to put all the inputs directory in the home dir of the instance
    new_input_options = ''
    if len(input_list_origin) > 0:
        logging.debug("change the --inputs option to put all the inputs directory in the home dir of the instance")
        logging.debug("Transform input_list_origin ....")
        new_input_options = " -i '"
        for item in input_list_origin:
            index_equal = item.find('=')
            access_path = item[:index_equal]
            actual_path = item[(index_equal+1):]
            new_input_options += '%s=%s,' % (access_path, os.path.basename(actual_path))
        if new_input_options[-1] == ',':
            new_input_options = new_input_options[:-1]
        new_input_options += "'"
        logging.debug("The new_input_options of Umbrella: %s", new_input_options) #--inputs option

    #cvmfs_http_proxy
    cvmfs_http_proxy_option = ''
    if cvmfs_http_proxy:
        cvmfs_http_proxy_option = '--cvmfs_http_proxy %s' % cvmfs_http_proxy

    #execute the command on the instance
    print("Executing the user's task on the EC2 instance ...")
    logging.debug("Execute the command on the instance ...")

    ec2_output_option = ""
    if output_option:
        ec2_output_option = " -o '%s'" % output_option

    if not env_option:
        env_option = ''

    cmd = 'ssh -t -o ConnectionAttempts=5 -o StrictHostKeyChecking=no -o ConnectTimeout=60 -i %s %s@%s "sudo %s/bin/python ~%s/umbrella %s -s destructive --spec ~%s/%s %s --log ~%s/ec2_umbrella.log -l ec2_umbrella %s %s %s run \'%s\'"' % (ssh_key, user_name, public_ip, python_name, user_name, cvmfs_http_proxy_option, user_name, os.path.basename(spec_path), meta_option, user_name, ec2_output_option, new_input_options, env_option, user_cmd[0])
    rc, stdout, stderr = func_call(cmd, ["ssh"])
    if rc != 0:
        terminate_instance(instance)
        subprocess_error(cmd, rc, stdout, stderr)

    print("\n********** STDOUT of the command **********")
    print(stdout)

    print("\n********** STDERR of the command **********")
    print(stderr)

    #postprocessing
    print("Transferring the output of the user's task from the EC2 instance back to the local machine ...")
    logging.debug("Create a tarball for the output dir on the instance.")

    output = '%s %s' % (' '.join(output_f_dict.values()), ' '.join(output_d_dict.values()))
    cmd = 'ssh -t -o ConnectionAttempts=5 -o StrictHostKeyChecking=no -o ConnectTimeout=60 -i %s %s@%s \'sudo tar cvzf ~%s/output.tar.gz %s && sudo chown %s:%s ~%s/output.tar.gz ~%s/ec2_umbrella.log\'' % (ssh_key, user_name, public_ip, user_name, output, user_name, user_name, user_name, user_name)
    rc, stdout, stderr = func_call(cmd, ["ssh"])
    if rc != 0:
        terminate_instance(instance)
        subprocess_error(cmd, rc, stdout, stderr)

    logging.debug("The instance returns the output.tar.gz to the local machine.")
    cmd = 'scp -i %s %s@%s:output.tar.gz %s/' % (ssh_key, user_name, public_ip, sandbox_dir)
    rc, stdout, stderr = func_call(cmd, ["scp"])
    if rc != 0:
        terminate_instance(instance)
        subprocess_error(cmd, rc, stdout, stderr)

    logging.debug("The instance returns the remote umbrella log file to the local machine.")
    cmd = 'scp -i %s %s@%s:ec2_umbrella.log %s' % (ssh_key, user_name, public_ip, ec2log_path)
    rc, stdout, stderr = func_call(cmd, ["scp"])
    if rc != 0:
        terminate_instance(instance)
        subprocess_error(cmd, rc, stdout, stderr)

    cmd = 'tar zxvf %s/output.tar.gz -C /' % (sandbox_dir)
    rc, stdout, stderr = func_call(cmd, ["tar"])
    if rc != 0:
        terminate_instance(instance)
        subprocess_error(cmd, rc, stdout, stderr)

    print("Terminating the EC2 instance ...")
    terminate_instance(instance)

def obtain_package(spec_json):
    """Check whether this spec includes a package_manager section, which in turn includes a list attr.

    Args:
        spec_json: the json object including the specification.

    Returns:
        if a package list is specified in the spec_json, return the package manager name and a list of the required package name.
        Otherwise, return None
    """
    if "package_manager" in spec_json.keys() and spec_json["package_manager"]:
        if "name" in spec_json["package_manager"].keys() and spec_json["package_manager"].has_key("list"):
            pac_name = spec_json["package_manager"]["name"]
            pac_str = spec_json["package_manager"]["list"]
            pac_list = pac_str.split()
            pac_list.sort()
            if len(pac_list) > 0:
                if len(pac_name) == 0:
                    logging.critical("The spec does not specify which package manager to use\n")
                    sys.exit("The spec does not specify which package manager to use\n")
                else:
                    return (pac_name, pac_list)
    return (None, None)

def cal_new_os_id(sec, old_os_id, pac_list):
    """Calculate the id of the new OS based on the old_os_id and the package_manager section

    Args:
        sec: the json object including the package_manager section.
        old_os_id: the id of the original os image without any info about package manager.
        pac_list: a list of the required package name.

    Returns:
        md5_value: the md5 value of the string constructed from binding old_os_id and information from the package_manager section.
        install_cmd: the package install cmd, such as: yum -y install python
    """
    pm_name = attr_check("os", sec, "name")
    cmd = pm_name + " " + pac_manager[pm_name][0] + " " + ' '.join(pac_list)
    install_cmd = []
    install_cmd.append(cmd)
    pac_str = ''.join(pac_list)

    config_str = ''
    if "config" in sec.keys() and sec["config"]:
        l = []
        for item in sec["config"]:
            id_attr = sec["config"][item]["id"]
            l.append(id_attr)
        l.sort()
        config_str = ''.join(l)

    data = old_os_id + pm_name + pac_str + config_str
    md5 = hashlib.md5()
    md5.update(data)
    md5_value = md5.hexdigest()
    return (md5_value, install_cmd)

def specification_process(spec_json, sandbox_dir, behavior, meta_json, sandbox_mode, output_f_dict, output_d_dict, input_dict, env_para_dict, user_cmd, cwd_setting, cvmfs_http_proxy, osf_auth, use_local_cvmfs, parrot_log):
    """ Create the execution environment specified in the specification file and run the task on it.

    Args:
        spec_json: the json object including the specification.
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        behavior: the umbrella behavior, such as `run`.
        meta_json: the json object including all the metadata of dependencies.
        sandbox_mode: the execution engine.
        output_f_dict: the mappings of output files (key is the file path used by the application; value is the file path the user specifies.)
        output_d_dict: the mappings of output dirs (key is the dir path used by the application; value is the dir path the user specified.)
        input_dict: the setting of input files specified by the --inputs option.
        env_para_dict: the environment variables which need to be set for the execution of the user's command.
        user_cmd: the user's command.
        cwd_setting: the current working directory for the execution of the user's command.
        cvmfs_http_proxy: HTTP_PROXY environmetn variable used to access CVMFS by Parrot
        osf_auth: the osf authentication info including osf_username and osf_password.
        use_local_cvmfs: use the cvmfs on the host machine instead of using parrot_run to deliver cvmfs
        parrot_log: the path of the parrot debugging log

    Returns:
        None.
    """
    print("Checking the validity of the umbrella specification ...")
    if "hardware" in spec_json.keys() and spec_json["hardware"] and "kernel" in spec_json.keys() and spec_json["kernel"] and spec_json.has_key("os") and spec_json["os"]:
        logging.debug("Setting the environment parameters (hardware, kernel and os) according to the specification file ....")
        (hardware_platform, cpu_cores, memory_size, disk_size, kernel_name, kernel_version, linux_distro, distro_name, distro_version, os_id) = env_parameter_init(spec_json["hardware"], spec_json["kernel"], spec_json["os"])
    else:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("this specification is not complete! You must have a hardware section, a kernel section and a os section!")
        sys.exit("this specification is not complete! You must have a hardware section, a kernel section and a os section!\n")

    host_linux_distro =  env_check(sandbox_dir, sandbox_mode, hardware_platform, cpu_cores, memory_size, disk_size, kernel_name, kernel_version)

    #check os
    need_separate_rootfs = 0
    os_image_dir = ''
    if os_id == "":
        if sandbox_mode in ["docker"]:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("the specification does not provide a concrete OS image, but docker execution engine needs a specific OS image!")
            sys.exit("the specification does not provide a concrete OS image, but docker execution engine needs a specific OS image!\n")

        if linux_distro != host_linux_distro:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("the specification does not provide a concrete OS image, and the OS image of the local machine does not matching the requirement!")
            sys.exit("the specification does not provide a concrete OS image, and the OS image of the local machine does not matching the requirement!\n")
        else:
            logging.debug("the specification does not provide a concrete OS image, but the OS image of the local machine matches the requirement!")
            print("the specification does not provide a concrete OS image, but the OS image of the local machine matches the requirement!\n")
    else:
        need_separate_rootfs = 1

    #check for dependencies which need to be installed by package managers
    (pac_name, pac_list) = obtain_package(spec_json)
    if pac_list:
        logging.debug("The spec needs to use %s install packages.", pac_name)
        print("The spec needs to use %s install packages." % pac_name)
        if sandbox_mode in ["parrot"]:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("Installing packages through package managers requires the root authority! Please choose a different sandbox mode (docker or destructive)!")
            sys.exit("Installing packages through package managers requires the root authority! Please choose a different sandbox mode(docker or destructive)!")

    mount_dict = {}
    cvmfs_cms_siteconf_mountpoint = ''

    needs_parrotize_user_cmd = False
    if sandbox_mode in ["parrot"]:
        if not parrot_path:
            logging.debug("To use parrot sandbox mode, cctools binary is needed")
            cctools_download(sandbox_dir, hardware_platform, host_linux_distro, 'unpack')
        needs_parrotize_user_cmd = True

    item = '%s-%s-%s' % (distro_name, distro_version, hardware_platform) #example of item here: redhat-6.5-x86_64
    if need_separate_rootfs and sandbox_mode not in ["destructive"]:
        #download the os dependency into the local
        os_image_dir = "%s/cache/%s/%s" % (os.path.dirname(sandbox_dir), os_id, item)
        logging.debug("A separate OS (%s) is needed!", os_image_dir)
        mountpoint = '/'
        action = 'unpack'
        r3 = dependency_process(item, os_id, action, meta_json, sandbox_dir, osf_auth)
        logging.debug("Add mountpoint (%s:%s) into mount_dict for /.", mountpoint, r3)
        mount_dict[mountpoint] = r3

    #check for cvmfs dependency
    is_cms_cvmfs_app = 0

    cvmfs_path = ""
    cvmfs_mountpoint = ""
    result = needCVMFS(spec_json, meta_json)
    if result:
        (cvmfs_path, cvmfs_mountpoint) = result

    if cvmfs_path:
        logging.debug("cvmfs is needed! (%s)", cvmfs_path)
        print("cvmfs is needed! (%s)" % cvmfs_path)

        cvmfs_ready = False
        if need_separate_rootfs:
            os_cvmfs_path = "%s%s" % (os_image_dir, cvmfs_mountpoint)
            if os.path.exists(os_cvmfs_path) and os.path.isdir(os_cvmfs_path):
                cvmfs_ready = True
                logging.debug("The os image has /cvmfs/cms.cern.ch!")
                print("The os image has /cvmfs/cms.cern.ch!")

        if not cvmfs_ready:
            if use_local_cvmfs:
                logging.debug("Use the cvmfs intalled on the local host")
                print("Use the cvmfs intalled on the local host")
                mount_dict[cvmfs_mountpoint] = cvmfs_mountpoint
            else:
                logging.debug("Parrot will be used to deliver cvmfs")
                print("Parrot will be used to deliver cvmfs")

                if cvmfs_path.find("cms.cern.ch") != -1:
                    is_cms_cvmfs_app = 1 #cvmfs is needed to deliver cms.cern.ch repo, and the local host has no cvmfs installed.

                    if not cvmfs_http_proxy or len(cvmfs_http_proxy) == 0:
                        cvmfs_http_proxy = "':;DIRECT'"

                    #currently, if the logic reaches here, only parrot execution engine is allowed.
                    cvmfs_cms_siteconf_mountpoint = set_cvmfs_cms_siteconf(sandbox_dir)
                    #add cvmfs SITEINFO into mount_dict

                    if sandbox_mode == "docker":
                        list1 = cvmfs_cms_siteconf_mountpoint.split(' ')
                        logging.debug("Add mountpoint (%s:%s) into mount_dict for cvmfs SITEINFO", list1[0], list1[1])
                        mount_dict[list1[0]] = list1[1]

                    if sandbox_mode != "parrot":
                        if not parrot_path:
                            logging.debug("To use parrot to access cvmfs, cctools binary is needed")
                            cctools_download(sandbox_dir, hardware_platform, linux_distro, 'unpack')
                        needs_parrotize_user_cmd = True

    if parrot_path:
        logging.debug("Add mountpoint (%s:%s) into mount_dict", parrot_path, parrot_path)
        mount_dict[parrot_path] = parrot_path

    if need_separate_rootfs:
        new_os_image_dir = ""
        #if some packages from package managers are needed, ceate a intermediate os image with all the packages ready.
        if pac_list:
            new_sw_sec = spec_json["package_manager"]["config"]
            (new_os_id, pm_cmd) = cal_new_os_id(spec_json["package_manager"], os_id, pac_list)
            new_os_image_dir = "%s/cache/%s/%s" % (os.path.dirname(sandbox_dir), new_os_id, item)

            logging.debug("Installing the package into the image (%s), and create a new image: %s ...", os_image_dir, new_os_image_dir)
            print("Installing the package into the image (%s), and create a new image: %s ..." % (os_image_dir, new_os_image_dir))
            if os.path.exists(new_os_image_dir) and os.path.isdir(new_os_image_dir):
                logging.debug("the new os image already exists!")
                print("the new os image already exists!")
                #use the intermidate os image which has all the dependencies from package manager ready as the os image
                os_image_dir = new_os_image_dir
                os_id = new_os_id
                pass
            else:
                logging.debug("the new os image does not exist!")
                print("the new os image does not exist!")
                new_env_para_dict = {}

                #install dependency specified in the spec_json["package_manager"]["config"] section
                logging.debug('Install dependency specified in the spec_json["package_manager"]["config"] section.')
                print('Install dependency specified in the spec_json["package_manager"]["config"] section.')
                if sandbox_mode == "destructive":
                    software_install(mount_dict, new_env_para_dict, new_sw_sec, meta_json, sandbox_dir, 1, osf_auth)

                    #install dependencies through package managers
                    rc, stdout, stderr = func_call(pm_cmd)
                    if rc != 0:
                        subprocess_error(cmd, rc, stdout, stderr)
                else:
                    software_install(mount_dict, new_env_para_dict, new_sw_sec, meta_json, sandbox_dir, 0, osf_auth)

                    #install dependencies through package managers
                    logging.debug("Create an intermediate OS image with all the dependencies from package managers ready!")
                    print("Create an intermediate OS image with all the dependencies from package managers ready!")
                    if workflow_repeat(cwd_setting, sandbox_dir, sandbox_mode, output_f_dict, output_d_dict, input_dict, env_para_dict, pm_cmd, hardware_platform, host_linux_distro, distro_name, distro_version, need_separate_rootfs, os_image_dir, os_id, cvmfs_cms_siteconf_mountpoint, mount_dict, mount_dict, meta_json, new_os_image_dir, cvmfs_http_proxy, needs_parrotize_user_cmd, use_local_cvmfs, parrot_log) != 0:
                        logging.critical("Fails to construct the intermediate OS image!")
                        sys.exit("Fails to construct the intermediate OS image!")
                    logging.debug("Finishing creating the intermediate OS image!")
                    print("Finishing creating the intermediate OS image!")

                    #use the intermidate os image which has all the dependencies from package manager ready as the os image
                    os_image_dir = new_os_image_dir
                    os_id = new_os_id

    if "software" in spec_json.keys() and spec_json["software"]:
        software_install(mount_dict, env_para_dict, spec_json["software"], meta_json, sandbox_dir, 0, osf_auth)
    else:
        logging.debug("this spec does not have software section!")
        software_install(mount_dict, env_para_dict, "", meta_json, sandbox_dir, 0, osf_auth)

    sw_mount_dict = dict(mount_dict) #sw_mount_dict will be used later to config the $PATH
    if parrot_path:
	    del sw_mount_dict[parrot_path]

    if "data" in spec_json.keys() and spec_json["data"]:
        data_install(spec_json["data"], meta_json, sandbox_dir, mount_dict, env_para_dict, osf_auth, cwd_setting)
    else:
        logging.debug("this spec does not have data section!")

    return workflow_repeat(cwd_setting, sandbox_dir, sandbox_mode, output_f_dict, output_d_dict, input_dict, env_para_dict, user_cmd, hardware_platform, host_linux_distro, distro_name, distro_version, need_separate_rootfs, os_image_dir, os_id, cvmfs_cms_siteconf_mountpoint, mount_dict, sw_mount_dict, meta_json, "", cvmfs_http_proxy, needs_parrotize_user_cmd, use_local_cvmfs, parrot_log)

def dependency_check(item):
    """Check whether an executable exists or not.

    Args:
        item: the name of the executable to be found.

    Returns:
        If the executable can be found through $PATH, return 0;
        Otherwise, return -1.
    """
    logging.debug("dependency check -- %s", item)
    result = which_exec(item)
    if result == None:
        logging.debug("Failed to find the executable `%s` through $PATH.", item)
        print("Failed to find the executable `%s` through $PATH." % item)
        return -1
    else:
        logging.debug("Find the executable `%s` through $PATH.", item)
        return 0

def dependency_check_list(item_list):
    """Check whether any executable in the item_list does not exist.

    Args:
        item_list: a list of executables.

    Returns:
        If all the executables in the item_list can be found through $PATH, return 0;
        Otherwise, return -1.
    """
    if item_list is None:
        return 0

    for item in item_list:
        if dependency_check(item) == -1:
            return -1
    return 0

def launch_ec2_instance(image_id, region, instance_type, ec2_key_pair, ec2_security_group):
    """ Start one VM instance through Amazon EC2 command line interface and return the instance id.

    Args:
        image_id: the Amazon Image Identifier.
        region: the AWS region where the AMI specified by image_id belongs to. The instance will be launched within the same region.
        instance_type: the Amazon EC2 instance type used for the task.
        ec2_key_pair: the path of the key-pair to use when launching an instance.
        ec2_security_group: the security group id within which the EC2 instance should be run.

    Returns:
        If no error happens, returns an EC2.Instance object.
        Otherwise, directly exit.
    """
    # check the current user can access the region
    client = boto3.client('ec2')
    regions = (client.describe_regions())["Regions"]
    region_avail = False
    for i in regions:
        if region == i["RegionName"]:
            region_avail = True
            break

    if not region_avail:
        logging.critical("The AMI locates at the %s region, which is not available to your AWS account!", region)
        sys.exit("The AMI locates at the %s region, which is not available to your AWS account!" % region)

    session = boto3.session.Session(region_name=region)
    ec2 = session.resource("ec2")

    if ec2_security_group and ec2_security_group != '':
        instances = ec2.create_instances(ImageId=image_id, MinCount=1, MaxCount=1, KeyName=ec2_key_pair, SecurityGroupIds=[ec2_security_group], InstanceType=instance_type)
    else:
        instances = ec2.create_instances(ImageId=image_id, MinCount=1, MaxCount=1, KeyName=ec2_key_pair, InstanceType=instance_type)

    if len(instances) <= 0:
        logging.critical("No instance was launched!")
        sys.exit("No instance was launched!")

    instance = instances[0]
    instance.wait_until_running()

    # Calls EC2.Client.describe_instances() to update the attributes of the Instance resource
    instance.load()

    return instance

def terminate_instance(instance):
    """Terminate an instance.

    Args:
        instance_id: an ec2.Instance object

    Returns:
        None.
    """
    logging.debug("Terminate the ec2 instance:")
    instance.terminate()
    instance.wait_until_terminated()

def add2spec(item, source_dict, target_dict):
    """Abstract the metadata information (source format checksum size uncompressed_size) from source_dict (metadata database) and add these information into target_dict (umbrella spec).
    For any piece of metadata information, if it already exists in target_dict, do nothing; otherwise, add it into the umbrella spec.

    Args:
        item: the name of a dependency
        source_dict: fragment of an Umbrella metadata database
        target_dict: fragement of an Umbrella specficiation

    Returns:
        None
    """
    #item must exist inside target_dict.
    ident = None
    if "checksum" in source_dict.keys():
        checksum = source_dict["checksum"].lower()
        ident = checksum
        if not "id" in target_dict.keys():
            target_dict["id"] = ident
        if not checksum in target_dict.keys():
            target_dict["checksum"] = source_dict["checksum"].lower()

    if "source" in source_dict.keys():
        if len(source_dict["source"]) == 0:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("the source attribute of %s can not be empty!" % item)
            sys.exit("the source attribute of %s can not be empty!" % item)
        else:
            source = source_dict["source"][0]

        #if checksum is not provided in source_dict, the first url in the source section will be set to the ident.
        if not ident and not "id" in target_dict.keys():
            target_dict["id"] = source

        if not "source" in target_dict.keys():
            target_dict["source"] = list(source_dict["source"])

    else:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("%s does not have source attribute in the umbrella metadata database!", item)
        sys.exit("%s does not have source attribute in the umbrella metadata database!" % item)

    if "format" in source_dict.keys() and not "format" in target_dict.keys():
        target_dict["format"] = source_dict["format"]

    if "size" in source_dict.keys() and not "size" in target_dict.keys():
        target_dict["size"] = source_dict["size"]

    if "uncompressed_size" in source_dict.keys() and not "uncompressed_size" in target_dict.keys():
        target_dict["uncompressed_size"] = source_dict["uncompressed_size"]

def add2db(item, source_dict, target_dict):
    """Add the metadata information (source format checksum size uncompressed_size) about item from source_dict (umbrella specification) to target_dict (metadata database).
    The item can be identified through two mechanisms: checksum attribute or one source location, which is used when checksum is not applicable for this item.
    If the item has been in the metadata database, do nothing; otherwise, add it, together with its metadata, into the metadata database.

    Args:
        item: the name of a dependency
        source_dict: fragment of an Umbrella specification
        target_dict: fragement of an Umbrella metadata database

    Returns:
        None
    """
    if not item in target_dict:
        target_dict[item] = {}

    ident = None
    if "checksum" in source_dict.keys():
        checksum = source_dict["checksum"].lower()
        if checksum in target_dict[item].keys():
            logging.debug("%s has been inside the metadata database!", item)
            return
        ident = checksum
        target_dict[item][ident] = {}
        target_dict[item][ident]["checksum"] = source_dict["checksum"].lower()

    if "source" in source_dict.keys():
        if len(source_dict["source"]) == 0:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("the source attribute of %s can not be empty!" % item)
            sys.exit("the source attribute of %s can not be empty!" % item)
        else:
            source = source_dict["source"][0]

        if source in target_dict[item].keys():
            logging.debug("%s has been inside the metadata database!", item)
            return

        #if checksum is not provided in source_dict, the first url in the source section will be set to the ident.
        if not ident:
            ident = source
            target_dict[item][ident] = {}

        target_dict[item][ident]["source"] = list(source_dict["source"])
    else:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("%s does not have source attribute in the umbrella specification!", item)
        sys.exit("%s does not have source attribute in the umbrella specification!" % item)

    if "format" in source_dict.keys():
        target_dict[item][ident]["format"] = source_dict["format"]

    if "size" in source_dict.keys():
        target_dict[item][ident]["size"] = source_dict["size"]

    if "uncompressed_size" in source_dict.keys():
        target_dict[item][ident]["uncompressed_size"] = source_dict["uncompressed_size"]

def prune_attr(dict_item, attr_list):
    """Remove certain attributes from a dict.
    If a specific ttribute does not exist, pass.

    Args:
        dict_item: a dict
        attr_list: a list of attributes which will be removed from the dict.

    Returns:
        None
    """
    for item in attr_list:
        if item in dict_item.keys():
            del dict_item[item]

def prune_spec(json_object):
    """Remove the metadata information from a json file (which represents an umbrella specification).
    Note: the original json file will not be changed by this function.

    Args:
        json_object: a json file representing an umbrella specification

    Returns:
        temp_json: a new json file without metadata information
    """
    logging.debug("Remove the metadata information from %s.\n", json_object)
    temp_json = dict(json_object)

    attr_list = ["source", "checksum", "format", "size", "uncompressed_size"]
    if "os" in temp_json.keys():
        os_sec = temp_json["os"]
        if os_sec:
            prune_attr(os_sec, attr_list)

    if "package_manager" in temp_json.keys() and temp_json["package_manager"] \
        and "config" in temp_json["package_manager"].keys() and temp_json["package_manager"]["config"]:
        pm_config_sec = temp_json["package_manager"]["config"]
        if pm_config_sec:
            for item in pm_config_sec:
                prune_attr(pm_config_sec[item], attr_list)

    if "software" in temp_json.keys():
        software_sec = temp_json["software"]
        if software_sec:
            for item in software_sec:
                prune_attr(software_sec[item], attr_list)

    if "data" in temp_json.keys():
        data_sec = temp_json["data"]
        if data_sec:
            for item in data_sec:
                prune_attr(data_sec[item], attr_list)
    return temp_json

def abstract_metadata(spec_json, meta_path):
    """Abstract metadata information from a self-contained umbrella spec into a metadata database.

    Args:
        spec_json: a dict including the contents from a json file
        meta_path: the path of the metadata database.

    Returns:
        If the umbrella spec is not complete, exit directly.
        Otherwise, return None.
    """
    hardware_sec = attr_check("hardware", spec_json, "hardware")
    hardware_arch = attr_check("hardware", hardware_sec, "arch")

    metadata = {}
    os_sec = attr_check("os", spec_json, "os")
    os_name = attr_check("os", os_sec, "name")
    os_version = attr_check("os", os_sec, "version")
    os_item = "%s-%s-%s" % (os_name, os_version, hardware_arch)
    os_item = os_item.lower()
    add2db(os_item, os_sec, metadata)

    if "package_manager" in spec_json.keys() and spec_json["package_manager"] \
        and "config" in spec_json["package_manager"].keys() and spec_json["package_manager"]["config"]:
        pm_config_sec = spec_json["package_manager"]["config"]
        if pm_config_sec:
            for item in pm_config_sec:
                add2db(item, pm_config_sec[item], metadata)

    if "software" in spec_json.keys():
        software_sec = spec_json["software"]
        if software_sec:
            for item in software_sec:
                add2db(item, software_sec[item], metadata)

    if "data" in spec_json.keys():
        data_sec = spec_json["data"]
        if data_sec:
            for item in data_sec:
                add2db(item, data_sec[item], metadata)

    with open(meta_path, 'w') as f:
        json.dump(metadata, f, indent=4)
        logging.debug("dump the metadata information from the umbrella spec to %s" % meta_path)
        print("dump the metadata information from the umbrella spec to %s" % meta_path)

def needCVMFS(spec_json, meta_json):
    """For each dependency in the spec_json, check whether cvmfs is needed to deliver it.

    Args:
        spec_json: the json object including the specification.
        meta_json: the json object including all the metadata of dependencies.

    Returns:
        if cvmfs is needed, return the cvmfs url. Otherwise, return None
    """
    for sec_name in ["software", "data", "package_manager"]:
        if sec_name in spec_json.keys() and spec_json[sec_name]:
            sec = spec_json[sec_name]
            if sec_name == "package_manager":
                if "config" in sec.keys() and sec["config"]:
                    sec = sec["config"]
                else:
                    logging.debug("%s does not have config attribute!", sec_name)
                    break

            for item in sec:
                item_id = ""
                if "id" in sec[item].keys() and len(sec[item]["id"]) > 0:
                    item_id = sec[item]["id"]

                mountpoint = sec[item]["mountpoint"]

                result = meta_search(meta_json, item, item_id)
                if "source" in result.keys() and len(result["source"]) > 0:
                    url = result["source"][0]
                    if url[:5] == "cvmfs":
                        return (url, mountpoint)
    return None

def cleanup(filelist, dirlist):
    """Cleanup the temporary files and dirs created by umbrella

    Args:
        filelist: a list including file paths
        dirlist: a list including dir paths

    Returns:
        None
    """
    #cleanup the temporary files
    for item in filelist:
        if os.path.exists(item):
            logging.debug("cleanup temporary file: %s", item)
            print("cleanup temporary file: ", item)
            os.remove(item)

    #cleanup the temporary dirs
    for item in dirlist:
        if os.path.exists(item):
            logging.debug("cleanup temporary dir: %s", item)
            print("cleanup temporary dir: ", item)
            shutil.rmtree(item)

def separatize_spec(spec_json, meta_json, target_type):
    """Given an umbrella specification and an umbrella metadata database, generate a self-contained umbrella specification or a metadata database only including the informationnecessary for the umbrella spec.
    If the target_type is spec, then generate a self-contained umbrella specification.
    If the target_type is db, then generate a metadata database only including the information necessary for the umbrella spec.

    Args:
        spec_json: the json object including the specification.
        meta_json: the json object including all the metadata of dependencies.
        target_type: the type of the target json file, which can be an umbrella spec or an umbrella metadata db.

    Returns:
        metadata: a json object
    """
    #pull the metadata information of the spec from the meatadata db to the spec
    if target_type == "spec":
        metadata = dict(spec_json)

    #pull the metadata information of the spec from the metadata db into a separate db
    if target_type == "meta":
        metadata = {}


    hardware_sec = attr_check("hardware", spec_json, "hardware")
    hardware_arch = attr_check("hardware", hardware_sec, "arch")

    os_sec = attr_check("os", spec_json, "os")
    os_name = attr_check("os", os_sec, "name")
    os_version = attr_check("os", os_sec, "version")
    os_item = "%s-%s-%s" % (os_name, os_version, hardware_arch)
    os_item = os_item.lower()
    ident = None
    if "id" in os_sec.keys():
        ident = os_sec["id"]
    source = meta_search(meta_json, os_item, ident)

    if target_type == "spec":
        add2spec(os_item, source, metadata["os"])
    if target_type == "meta":
        add2db(os_item, source, metadata)

    if "package_manager" in spec_json.keys() and spec_json["package_manager"] \
        and "config" in spec_json["package_manager"].keys() and spec_json["package_manager"]["config"]:
        pm_config_sec = spec_json["package_manager"]["config"]
        if pm_config_sec:
            for item in pm_config_sec:
                ident = None
                if "id" in pm_config_sec[item].keys():
                    ident = pm_config_sec[item]["id"]
                source = meta_search(meta_json, item, ident)
                if target_type == "spec":
                    add2spec(os_item, source, metadata["package_manager"]["config"][item])
                if target_type == "meta":
                    add2db(item, source, metadata)

    if "software" in spec_json.keys():
        software_sec = spec_json["software"]
        if software_sec:
            for item in software_sec:
                ident = None
                if "id" in software_sec[item].keys():
                    ident = software_sec[item]["id"]
                source = meta_search(meta_json, item, ident)
                if target_type == "spec":
                    add2spec(os_item, source, metadata["software"][item])
                if target_type == "meta":
                    add2db(item, source, metadata)

    if "data" in spec_json.keys():
        data_sec = spec_json["data"]
        if data_sec:
            for item in data_sec:
                ident = None
                if "id" in data_sec[item].keys():
                    ident = data_sec[item]["id"]
                source = meta_search(meta_json, item, ident)
                if target_type == "spec":
                    add2spec(os_item, source, metadata["data"][item])
                if target_type == "meta":
                    add2db(item, source, metadata)

    return metadata

def json2file(filepath, json_item):
    """Write a json object into a file

    Args:
        filepath: a file path
        json_item: a dict representing a json object

    Returns:
        None
    """
    with open(filepath, 'w') as f:
        json.dump(json_item, f, indent=4)
        logging.debug("dump a json object from the umbrella spec to %s" % filepath)
        print("dump a json object from the umbrella spec to %s" % filepath)

def path_exists(filepath):
    """Check the validity and existence of a file path.

    Args:
        filepath: a file path

    Returns:
        Exit directly if any error happens.
        Otherwise, returns None.
    """
    logging.debug("Checking file path: %s", filepath)
    if os.path.exists(filepath):
        cleanup(tempfile_list, tempdir_list)
        logging.debug("The file (%s) already exists, please specify a new path!", filepath)
        sys.exit("The file (%s) already exists, please specify a new path!" % filepath)

def dir_create(filepath):
    """Create the directory for it if necessary. If the file already exists, exit directly.

    Args:
        filepath: a file path

    Returns:
        Exit directly if any error happens.
        Otherwise, returns None.
    """
    dirpath = os.path.dirname(filepath)

    if not os.path.exists(dirpath):
        os.makedirs(dirpath)
    else:
        if not os.path.isdir(dirpath):
            cleanup(tempfile_list, tempdir_list)
            logging.debug("The basename of the file (%s) is not a directory!\n", dirpath)
            sys.exit("The basename of the file (%s) is not a directory!\n" % dirpath)

def validate_meta(meta_json):
    """Validate a metadata db.
    The current standard for a valid metadata db is: for each item, the "source" attribute must exist and not be not empty.

    Args:
        meta_json: a dict object representing a metadata db.

    Returns:
        If error happens, return directly with the error info.
        Otherwise, None.
    """
    logging.debug("Starting validating the metadata db ....\n")
    print("Starting validating the metadata db ....")

    for name in meta_json:
        for ident in meta_json[name]:
            logging.debug("check for %s with the id of %s ...", name, ident)
            print("check for %s with the id of %s ..." % (name, ident))
            attr_check(name, meta_json[name][ident], "source", 1)

    logging.debug("Finish validating the metadata db ....\n")
    print("Finish validating the metadata db successfully!")

def validate_spec(spec_json, meta_json = None):
    """Validate a spec_json.

    Args:
        spec_json: a dict object representing a specification.
        meta_json: a dict object representing a metadata db.

    Returns:
        If error happens, return directly with the error info.
        Otherwise, None.
    """
    logging.debug("Starting validating the spec file ....\n")
    print("Starting validating the spec file ....")

    #validate the following three sections: hardware, kernel and os.
    env_parameter_init(spec_json["hardware"], spec_json["kernel"], spec_json["os"])

    for sec_name in ["software", "data", "package_manager"]:
        if sec_name in spec_json.keys() and spec_json[sec_name]:
            sec = spec_json[sec_name]
            if sec_name == "package_manager":
                if "config" in sec.keys() and sec["config"]:
                    sec = sec["config"]
                else:
                    logging.debug("%s does not have config attribute!", sec_name)
                    break
            for item in sec:
                if ("mountpoint" in sec[item].keys() and sec[item]["mountpoint"]) \
                        or ("mount_env" in sec[item].keys() and sec[item]["mount_env"]):
                    pass
                else:
                    cleanup(tempfile_list, tempdir_list)
                    logging.critical("%s in the %s section should have either <mountpoint> or <mount_env>!\n", item, sec_name)
                    sys.exit("%s in the %s section should have either <mountpoint> or <mount_env>!\n" % (item, sec_name))

                if "source" in sec[item].keys() and len(sec[item]["source"]) > 0:
                    pass
                else:
                    if meta_json:
                        ident = None
                        if "id" in sec[item].keys():
                            ident = sec[item]["id"]
                        result = meta_search(meta_json, item, ident)
                        if "source" in result.keys() and len(result["source"]) > 0:
                            pass
                        else:
                            cleanup(tempfile_list, tempdir_list)
                            logging.critical("%s in the metadata db should have <source> attr!\n", item)
                            sys.exit("%s in the metadata db should have <source> attr!\n", item)
                    else:
                        cleanup(tempfile_list, tempdir_list)
                        logging.critical("%s in the %s section should have <source> attr!\n", item, sec_name)
                        sys.exit("%s in the %s section should have <source> attr!\n" % (item, sec_name))
    logging.debug("Finish validating the spec file ....\n")
    print("Finish validating the spec file successfully!")

def osf_create(username, password, user_id, proj_name, is_public):
    """Create an OSF project, and return the project id.

    Args:
        username: an OSF username
        password: an OSF password
        user_id: the id of an OSF user
        proj_name: the name of the OSF project
        is_public: set to 1 if the project is public; set to 0 if the project is private.

    Returns:
        the id of the OSF project
    """
    #first check whether the user already has an existing OSF project having the same name
    url="https://api.osf.io:443/v2/users/%s/nodes/" % user_id
    nodes=set()

    #the response results are splitted into pages, and each page has 10 items.
    while url:
        r=requests.get(url)
        if r.status_code != 200:
            cleanup(tempfile_list, tempdir_list)
            sys.exit("Fails to check the projects contributed by the user (%d): %s!" % (r.status_code, r.reason))
        for data in r.json()['data']:
            nodes.add(data['attributes']['title'])

        url=r.json()['links']['next']

    if proj_name in nodes:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("The project name (%s) already exists!" % proj_name)

    #create the new project
    auth = (username, password)

    payload = {
        "type": "nodes",
        "title": proj_name,
        "category": "project",
        "public": is_public
    }

    url="https://api.osf.io:443/v2/nodes/"
    r=requests.post(url, auth=auth, data=payload)

    if r.status_code != 201:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("Fails to create the new project (%d): %s!" % (r.status_code, r.reason))

    proj_id = r.json()['data']['id']
    return proj_id

def osf_upload(username, password, proj_id, source):
    """upload a file from source into the OSF project identified by proj_id.

    Args:
        username: an OSF username
        password: an OSF password
        proj_id: the id of the OSF project
        source: a file path

    Returns:
        the OSF download url of the uploaded file
    """
    print("Upload %s to OSF ..." % source)
    logging.debug("Upload %s to OSF ...",source)
    url="https://files.osf.io/v1/resources/%s/providers/osfstorage/" % proj_id
    payload = {"kind":"file", "name":os.path.basename(source)}
    auth = (username, password)
    f=open(source, 'rb')
    r=requests.put(url, params=payload, auth = auth, data=f)

    if r.status_code != 201 and r.status_code != 200:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("Fails to upload the file %s to OSF(%d): %s!" % (source, r.status_code, r.reason))

    return r.json()['data']['links']['download']

def osf_download(username, password, osf_url, dest):
    """download a file pointed by an OSF url to dest.

    Args:
        username: an OSF username
        password: an OSF password
        osf_url: the OSF download url
        dest: the destination of the OSF file

    Returns:
        If the osf_url is downloaded successfully, return None;
        Otherwise, directly exit.
    """
    if not found_requests:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("\nDownloading private stuff from OSF requires a python package - requests. Please check the installation page of requests:\n\n\thttp://docs.python-requests.org/en/latest/user/install/\n")
        sys.exit("\nDownloading private stuff from OSF requires a python package - requests. Please check the installation page of requests:\n\n\thttp://docs.python-requests.org/en/latest/user/install/\n")

    print("Download %s from OSF to %s" % (osf_url, dest))
    logging.debug("Download %s from OSF to %s", osf_url, dest)
    word = 'resources'
    proj_id = osf_url[(osf_url.index(word) + len(word) + 1):(osf_url.index(word) + len(word) + 6)]
    url="https://api.osf.io:443/v2/nodes/%s/" % proj_id
    r=requests.get(url)

    r2 = None
    if r.status_code == 401:
        if username == None or password == None:
            cleanup(tempfile_list, tempdir_list)
            sys.exit("The OSF resource (%s) is private (%d): %s! To use the OSF resource, you need to provide a legal OSF username and password." % (url, r.status_code, r.reason))

        auth = (username, password)
        r1=requests.get(url, auth=auth)
        if r1.status_code != 200:
            cleanup(tempfile_list, tempdir_list)
            sys.exit("The OSF resource (%s) is private (%d): %s! The username or password is incorrect!" % (url, r1.status_code, r1.reason))
        else:
            r2=requests.get(osf_url, auth=auth, stream=True)
    else:
        r2=requests.get(osf_url, stream=True)

    if r2.status_code != 200:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("Fails to download the osf resource: %s (%d): %s!" % (r2.status_code, r2.reason))

    chunk_size=10240
    if not os.path.exists(os.path.dirname(dest)):
        os.makedirs(os.path.dirname(dest))
    with open(dest, 'wb') as fd:
        for chunk in r2.iter_content(chunk_size):
            fd.write(chunk)

def s3_create(bucket_name, acl):
    """Create a s3 bucket

    Args:
        bucket_name: the bucket name
        acl: the access control, which can be: private, public-read

    Returns:
        bucket: an S3.Bucket instance
    """
    #create the connection with s3
    s3 = boto3.resource('s3')

    #list all the bucket names
    buckets = set()
    try:
        for bucket in s3.buckets.all():
            buckets.add(bucket.name)
    except botocore.exceptions.ClientError as e:
        cleanup(tempfile_list, tempdir_list)
        sys.exit(e.message)
    except Exception as e:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("Fails to list all the current buckets: %s!" % e)

    #check whether the bucket name already exists
    if bucket_name in buckets:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("The bucket name (%s) already exists!" % bucket_name)

    #create a new bucket
    try:
        s3.create_bucket(Bucket=bucket_name)
    except Exception as e:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("Fails to create the new bucket (%s): %s!" % (bucket_name, e))

    #obtain the created bucket
    bucket = s3.Bucket(bucket_name)

    #set access control
    #ACL totally can be one of these options: 'private'|'public-read'|'public-read-write'|'authenticated-read'
    #for now, when an user uses Umbrella to upload to s3, the acl can only be private, public-read.
    try:
        bucket.Acl().put(ACL=acl)
    except botocore.exceptions.ClientError as e:
        cleanup(tempfile_list, tempdir_list)
        sys.exit(e.message)
    except Exception as e:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("Fails to list all the current buckets: %s!" % e)

    return bucket

def s3_upload(bucket, source, acl):
    """Upload a local file to s3

    Args:
        bucket: an S3.Bucket instance
        source: the local file path
        acl: the access control, which can be: private, public-read

    Returns:
        link: the link of a s3 object
    """
    print("Upload %s to S3 ..." % source)
    logging.debug("Upload %s to S3 ...", source)

    key = os.path.basename(source)
    data = open(source, 'rb')

    try:
        #acl on the bucket does not automatically apply to all the objects in it. Acl must be set on each object.
        bucket.put_object(ACL=acl, Key=key, Body=data) #https://s3.amazonaws.com/testhmeng/s3
    except botocore.exceptions.ClientError as e:
        cleanup(tempfile_list, tempdir_list)
        sys.exit(e.message)
    except Exception as e:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("Fails to upload the file (%s) to S3: %s!" % (source, e))

    return "%s/%s/%s" % (s3_url, bucket.name, key)

def s3_download(link, dest):
    """Download a s3 file to dest

    Args:
        link: the link of a s3 object. e.g., https://s3.amazonaws.com/testhmeng/s3
        dest: a local file path

    Returns:
        None
    """
    if not found_boto3 or not found_botocore:
        cleanup(tempfile_list, tempdir_list)
        logging.critical("\nUploading umbrella spec dependencies to s3 requires a python package - boto3. Please check the installation page of boto3:\n\n\thttps://boto3.readthedocs.org/en/latest/guide/quickstart.html#installation\n")
        sys.exit("\nUploading umbrella spec dependencies to s3 requires a python package - boto3. Please check the installation page of boto3:\n\n\thttps://boto3.readthedocs.org/en/latest/guide/quickstart.html#installation\n")

    print("Download %s from S3 to %s" % (link, dest))
    logging.debug("Download %s from S3 to %s", link, dest)
    s3 = boto3.resource('s3')

    if (len(s3_url)+1) >= len(link):
        cleanup(tempfile_list, tempdir_list)
        sys.exit("The s3 object link (%s) is invalid! The correct format shoulde be <%s>/<bucket_name>/<key>!" % (link, s3_url))

    m = link[(len(s3_url)+1):] #m format: <bucket_name>/<key>

    i = m.find('/')
    if i == -1:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("The s3 object link (%s) is invalid! The correct format shoulde be <%s>/<bucket_name>/<key>!" % (link, s3_url))

    bucket_name = m[:i]

    if (i+1) >= len(m):
        cleanup(tempfile_list, tempdir_list)
        sys.exit("The s3 object link (%s) is invalid! The correct format shoulde be <%s>/<bucket_name>/<key>!" % (link, s3_url))

    key = m[(i+1):]

    if not os.path.exists(os.path.dirname(dest)):
        os.makedirs(os.path.dirname(dest))

    #the download url can be automatically combined through bucket name and key
    try:
        s3.Object(bucket_name, key).download_file(dest)
    except botocore.exceptions.ClientError as e:
        cleanup(tempfile_list, tempdir_list)
        sys.exit(e.message)
    except Exception as e:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("Fails to download the object (%s) from the bucket(%s):! Please ensure you have the right permission to download these s3 objects: %s!" % (key, bucket_name, e))

def has_source(sources, target):
    """Check whether the sources includes a url from the specific target.

    Args:
        sources: a list of url
        target: the specific resource url. For example, s3, osf.

    Returns:
        If a url from the specific target exists, return True.
        Otherwise, return False.
    """
    if not sources or len(sources) == 0:
        return False

    n = len(target)
    for source in sources:
        if len(source) > n and source[:n] == target:
            return True
    return False

def spec_upload(spec_json, meta_json, target_info, sandbox_dir, cwd_setting, osf_auth=None, s3_bucket=None):
    """Upload each dependency in an umbrella spec to the target (OSF or s3), and add the new target download url into the umbrella spec.

    The source of the dependencies can be anywhere supported by umbrella: http
    https git local s3 osf. Umbrella always first downloads each dependency into
    its local cache, then upload the dep from its local cache to the target.

    Args:
        spec_json: the json object including the specification.
        meta_json: the json object including all the metadata of dependencies.
        target_info: the info necessary to communicate with the remote target (i.e., OSF, s3)
        sandbox_dir: the sandbox dir for temporary files like Parrot mountlist file.
        cwd_setting: the current working directory for the execution of the user's command.
        osf_auth: the osf authentication info including osf_username and osf_password.
        s3_bucket: an S3.Bucket instance

    Returns:
        None
    """
    mount_dict = {}
    env_para_dict = {}
    global upload_count

    print("Upload the dependencies from the umbrella spec to %s ..." % target_info[0])
    logging.debug("Upload the dependencies from the umbrella spec to %s ...", target_info[0])
    if "os" in spec_json.keys() and spec_json["os"] and "id" in spec_json["os"].keys() and spec_json["os"]["id"]:
        os_id = spec_json["os"]["id"]

        if "hardware" in spec_json.keys() and spec_json["hardware"] and "kernel" in spec_json.keys() and spec_json["kernel"] and spec_json.has_key("os") and spec_json["os"]:
            logging.debug("Setting the environment parameters (hardware, kernel and os) according to the specification file ....")
            (hardware_platform, cpu_cores, memory_size, disk_size, kernel_name, kernel_version, linux_distro, distro_name, distro_version, os_id) = env_parameter_init(spec_json["hardware"], spec_json["kernel"], spec_json["os"])
        item = '%s-%s-%s' % (distro_name, distro_version, hardware_platform) #example of item here: redhat-6.5-x86_64
        os_image_dir = "%s/cache/%s/%s" % (os.path.dirname(sandbox_dir), os_id, item)
        logging.debug("A separate OS (%s) is needed!", os_image_dir)
        mountpoint = '/'
        action = 'unpack'

        if not "upload" in spec_json["os"].keys() or spec_json["os"]["upload"] == True:
            if "source" in spec_json["os"].keys() or attr_check(item, meta_search(meta_json, item, os_id), "source", 1):
                if "source" in spec_json["os"].keys():
                    sources = spec_json["os"]["source"]
                else:
                    sources = meta_search(meta_json, item, os_id)["source"]

                if has_source(sources, target_info[0]):
                    logging.debug("The os section already has a url from %s!", target_info[0])
                    print("The os section already has a url from %s!" % target_info[0])
                else:
                    upload_count += 1
                    r3 = dependency_process(item, os_id, action, meta_json, sandbox_dir, osf_auth)
                    logging.debug("Add mountpoint (%s:%s) into mount_dict for /.", mountpoint, r3)
                    mount_dict[mountpoint] = r3
                    if target_info[0] == "osf":
                        osf_url = osf_upload(target_info[1], target_info[2], target_info[3], os_image_dir + ".tar.gz")
                        spec_json["os"]["source"].append("osf+" + osf_url)
                    elif target_info[0] == "s3":
                        s3_url = s3_upload(s3_bucket, os_image_dir + ".tar.gz", target_info[1])
                        spec_json["os"]["source"].append("s3+" + s3_url)
            else:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("the os section does not has source attr!")
                sys.exit("the os section does not has source attr!")
        else:
            logging.debug("the os section has its upload field set to false, ignore uploading it")

    for sec_name in ["data"]:
        if sec_name in spec_json.keys() and spec_json[sec_name]:
            sec = spec_json[sec_name]
            for item in sec:
                if "upload" in sec[item].keys() and sec[item]["upload"] == False:
                    logging.debug("ignore upload %s becuase its upload field is set to false", item)
                    continue

                if "source" in sec[item].keys() or attr_check(item, meta_search(meta_json, item, id), "source", 1):
                    if "source" in sec[item].keys():
                        sources = sec[item]["source"]
                    else:
                        sources = meta_search(meta_json, item, id)["source"]

                    if has_source(sources, target_info[0]):
                        logging.debug("%s already has a url from %s!", item, target_info[0])
                        print("%s already has a url from %s!" % (item, target_info[0]))
                        continue
                else:
                    cleanup(tempfile_list, tempdir_list)
                    logging.critical("%s does not has the source attr!", item)
                    sys.exit("%s does not has the source attr!" % item)

                upload_count += 1
                data_install(sec, meta_json, sandbox_dir, mount_dict, env_para_dict, osf_auth, cwd_setting, item)

                if sec[item]["format"] == "tgz":
                    source_url = mount_dict[sec[item]["mountpoint"]] + ".tar.gz"
                else:
                    source_url = mount_dict[sec[item]["mountpoint"]]

                if target_info[0] == "osf":
                    osf_url = osf_upload(target_info[1], target_info[2], target_info[3], source_url)
                    sec[item]["source"].append("osf+" + osf_url)
                elif target_info[0] == "s3":
                    s3_url = s3_upload(s3_bucket, source_url, target_info[1])
                    sec[item]["source"].append("s3+" + s3_url)

    for sec_name in ["software", "package_manager"]:
        if sec_name in spec_json.keys() and spec_json[sec_name]:
            sec = spec_json[sec_name]
            if sec_name == "package_manager":
                if "config" in sec.keys() and sec["config"]:
                    sec = sec["config"]
                else:
                    logging.debug("%s does not have config attribute!", sec_name)
                    break

            for item in sec:
                if "upload" in sec[item].keys() and sec[item]["upload"] == False:
                    logging.debug("ignore upload %s becuase its upload field is set to false", item)
                    continue

                if "source" in sec[item].keys() or attr_check(item, meta_search(meta_json, item, id), "source", 1):
                    if "source" in sec[item].keys():
                        sources = sec[item]["source"]
                    else:
                        sources = meta_search(meta_json, item, id)["source"]

                    if has_source(sources, target_info[0]):
                        logging.debug("%s already has a url from %s!", item, target_info[0])
                        print("%s already has a url from %s!" % (item, target_info[0]))
                        continue
                else:
                    cleanup(tempfile_list, tempdir_list)
                    logging.critical("%s does not has the source attr!", item)
                    sys.exit("%s does not has the source attr!" % item)

                upload_count += 1
                software_install(mount_dict, env_para_dict, sec, meta_json, sandbox_dir, 0, osf_auth, item)
                #ignore upload resouces from cvmfs
                if (not "mountpoint" in sec[item].keys()) or (not sec[item]["mountpoint"] in mount_dict.keys()) or mount_dict[sec[item]["mountpoint"]] == "":
                    continue

                if sec[item]["format"] == "tgz":
                    source_url = mount_dict[sec[item]["mountpoint"]] + ".tar.gz"
                else:
                    source_url = mount_dict[sec[item]["mountpoint"]]
                if target_info[0] == "osf":
                    osf_url = osf_upload(target_info[1], target_info[2], target_info[3], source_url)
                    sec[item]["source"].append("osf+" + osf_url)
                elif target_info[0] == "s3":
                    s3_url = s3_upload(s3_bucket, source_url, target_info[1])
                    sec[item]["source"].append("s3+" + s3_url)

def dep_build(d, name):
    """Build the metadata info of a dependency.

    Args:
        d: a dependency object
        name: the name of the dependency

    Returns:
        If the dependency comes from a local path, return 1 denoting this dependency has been built up.
        Otherwise, return 0 denoting nothing is built up.
    """
    #check the validity of the 'source' attr
    source = attr_check(name, d, "source", 1)

    if source == '':
        cleanup(tempfile_list, tempdir_list)
        sys.exit("The source of %s is empty!" % name)

    if source[0] != '/':
        logging.debug("The source of %s is not a local path (%s)!" % (name, source))
        return 0

    #check the validity of the 'format' attr
    formats = ['plain', 'tgz']
    form = attr_check(name, d, "format")
    if not form in formats:
        cleanup(tempfile_list, tempdir_list)
        sys.exit("The format attr can only be: %s!\n", ' or '.join(formats))

    #set the file size
    size = os.stat(source).st_size
    d["size"] = str(size)

    #set the uncompressed size of tgz file
    if form == "tgz":
        full_size = get_tgz_size(source)
        d["uncompressed_size"] = str(full_size)

    #set the 'checksum' and 'id' attrs
    checksum = md5_cal(source)
    d["id"] = checksum
    d["checksum"] = checksum

    return 1

def get_tgz_size(path):
    """Get the uncompressed size of a tgz file

    Args:
        path: a tgz file path

    Returns:
        size: the uncompressed size of a tgz file
    """
    size = 0
    f = gzip.open(path, 'rb')
    try:
        while True:
            c = f.read(1024*1024)
            if not c:
                break
            else:
                size += len(c)
    finally:
        f.close()

    return size

def spec_build(spec_json):
    """Build the metadata information of an umbrella spec

    Args:
        spec_json: the json object including the specification.

    Returns:
        count: the count of dependencies whose metadata have been built.
    """
    count = 0
    if "os" in spec_json.keys() and spec_json["os"]:
        count += dep_build(spec_json["os"], "os")

    for sec_name in ["data", "software", "package_manager"]:
        if sec_name in spec_json.keys() and spec_json[sec_name]:
            sec = spec_json[sec_name]
            if sec_name == "package_manager":
                if "config" in sec.keys() and sec["config"]:
                    sec = sec["config"]
                else:
                    logging.debug("%s does not have config attribute!", sec_name)
                    break
            for item in sec:
                count += dep_build(sec[item], item)
    return count

def trim_list(origin, s):
    """Trim the strings in the set s from the origin list.

    Args:
        origin: a list of string
        s: a set of string

    Returns:
        final: a new list of string
    """
    final = []
    for a in origin:
        if a not in s:
            final.append(a)
    return final

help_info = {
"build": '''Build up the metadata info of dependencies inside an umbrella spec, and write the built-up version into a new file.

A good use case of build is when you have some dependencies from the local filesystem. In this case, umbrella will calculate the metadata info about these dependencies.
The source spec should specify the following info of each local dependency: source, action, mountpoint, format.
The format of local dependencies can be plain (a file which will be used directly) or tgz file (a *.tar.gz file which will be uncompressed inside the sandbox).
When the local dependency is a .tar.gz file, the following metadata info will be put into the target spec: id, checksum, size, uncompressed size.
When the local dependency is a plain file, the following metadata info will be put into the target spec: id, checksum, size.

Umbrella build can not be used together with the --meta option!

For more info about how to compose an umbrella spec, please check the following link:
    http://ccl.cse.nd.edu/software/manuals/umbrella.html#create_spec

usage: umbrella [options] build target

    required options: --spec

    target      an non-existing file path on your local filesystem where the built-up version of the umbrella spec will be wrotten into
''',
"expand": '''Expand an umbrella spec file into a self-contained umbrella spec

Add the dependency metadata information (source format checksum size uncompressed_size) from the metadata database into the umbrella specfication.
If the metadata information has been in the the umbrella specification, do nothing.

The source umbrella spec should be specified through the --spec option; the metadata db should be specified through the --meta option.
For each dependency in the source umbrella spec, the following info will be extracted from the metadata db: source, size, format, checksum.
Finally, the expanded umbrella sepc will be wrotten into a new file.

usage: umbrella [options] expand target

    required options: --spec, --meta

    target      an non-existing file path on your local filesystem where the expanded version of the umbrella spec will be wrotten into
''',
"filter": '''Filter the metadata info for an umbrella spec file from a huge metadata db into a separate metadata database.

Filter the dependency metadata information (source format checksum size uncompressed_size) into a separate metadata database.

The source umbrella spec should be specified through the --spec option; the metadata db should be specified through the --meta option.
The source umbrella spec should NOT be self-contained.
For each dependency specified in the source umbrella spec, its metadata info will be extracted from the huge metadata db, and written into the target path.

usage: umbrella [options] filter target

    required options: --spec, --meta

    target      an non-existing file path on your local filesystem where the metadata info of all the dependencies in the umbrella spec will be wrotten into
''',
"run": '''Run your application through umbrella

Note for ec2 sandbox mode: the EC2 AMIs, security groups, key pairs are all regional resources ( http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/resources.html ).
Therefore, please check the region setting of the desired AMI in the umbrella spec file, and provide security group, key pairs, ssh keys in the same region.
The security group used should allow incoming ssh traffic.

usage: umbrella [options] run [command]

    required options: --spec, --meta (if the --spec option is not self-contained), --localdir, --sandbox_mode, --output (if output is needed)
    additional reqired options for ec2 sandbox_mode: --ec2_sshkey, --ec2_key, --ec2_instance_type, --ec2_log, --ec2_group (if a non-default security group is needed).

    command     command to run, the command can also be set inside the umbrella spec. By default: /bin/sh
''',
"split": '''Split a self-contained umbrella spec file into an umbrella spec and a metadata db

The dependency metadata information (source format checksum size uncompressed_size) will be put into a separate metadata database.
The remaining information will be put into a new umbrella spec.

The source umbrella spec should be specified through the --spec option; The --meta option will be ignored.
The source umbrella spec should be self-contained.

usage: umbrella [options] split newspec newdb

    required options: --spec

    newspec     an non-existing file path on your local filesystem where the new umbrella spec will be wrotten into
    newdb       an non-existing file path on your local filesystem where the metadata info corresponding to newspec will be wrotten into
''',
"upload": '''Upload the dependencies in an umbrella spec into remote archives (OSF, Amazon S3)

Umbrella will upload all the dependencies to the target archive, and add the new resource location into the source section of each dependency.
Finally, the new umbrella spec will be written into a new file.
When the source of a dependency has already include one url from the target archive, the dependency will be ignored.

Currently, the supported target includes: OSF, the Amazon S3.

usage of upload osf: umbrella [options] upload osf proj acl target

    required options: --spec, --meta (if the --spec option is not self-contained), --localdir, --osf_user, --osf_pass, --osf_userid

    proj        the osf project name
    acl     the access permission of the uploaded data. Options: public, private
    target      an non-existing file path on your local filesystem where the new umbrella spec will be wrotten into

usage of upload s3: umbrella [options] upload s3 bucket acl target

    required options: --spec, --meta (if the --spec option is not self-contained), --localdir

    bucket      the s3 bucket name
    acl     the access permission of the uploaded data. Options: public-read, private
    target      an non-existing file path on your local filesystem where the new umbrella spec will be wrotten into
''',
"validate": '''Validate an umbrella spec file

This validation process does the following checkings:
    whether all the required attributes in the hardware, kernel, and os sections are set;
    whether each dependency has a source attr;
    whether each dependency at least has one of the following two attributes (mountpoint, mount_env).

The source umbrella spec should be specified through the --spec option; the metadata db should be specified through the --meta option.

usage: umbrella [options] validate

    required options: --spec, --meta (if the --spec option is not self-contained)
'''
}

def main():
    parser = OptionParser(description="Umbrella is a portable environment creator for reproducible computing on clusters, clouds, and grids.",
usage="""usage: %prog [options] run|expand|filter|split|validate|upload|build ...

Currently, umbrella supports the following behaviors:
    build\t\tbuild up the metadata info of dependencies inside an umbrella spec
    expand\t\texpand an umbrella spec file into a self-contained umbrella spec
    filter\t\tfilter the metadata info for an umbrella spec file from a huge metadata db
    run\t\trun your application through umbrella
    split\t\tsplit a self-contained umbrella spec file into an umbrella spec and a metadata db
    upload\t\tupload the dependencies in an umbrella spec into remote archives (OSF, Amazon S3)
    validate\tvalidate an umbrella spec file

To check the help doc for a specific behavoir, use: %prog <behavior> help""",
                        version="%prog CCTOOLS_VERSION")
    parser.add_option("--spec",
                    action="store",
                    help="The specification json file.",)
    parser.add_option("--meta",
                    action="store",
                    help="The source of meta information, which can be a local file relative or absolute path (e.g., /tmp/meta.json) or url (e.g., http://...).\nIf this option is not provided, the specification will be treated a self-contained specification.",)
    parser.add_option("-l", "--localdir",
                    action="store",
                    help="The path of directory used for all the cached data and all the sandboxes, the directory can be an existing dir.",)
    parser.add_option("-o", "--output",
                    action="store",
                    help="The mappings of outputs in the format of <container_path>=<local_path>[=<output_type>]. Multiple mappings should be separated by comma.\ncontainer_path is a path inside the sandbox and should be exposed in the output section of an umbrella spec.\nlocal_path should be a non-existing path on your local filessytem where you want the output from container_path to be put into.\noutput_type marks the output type, which can be 'f' for files, or 'd' for dirs.",)
    parser.add_option("-s", "--sandbox_mode",
                    action="store",
                    choices=['parrot', 'destructive', 'docker', 'ec2', 'local'],
                    help="sandbox mode, which can be parrot, destructive, docker, ec2, local.",)
    parser.add_option("-i", "--inputs",
                    action="store",
                    help="The path of input files in the format of <container_path>=<local_path>. Multiple mappings should be separated by comma. Please refer to the --output option for the settings of local_path and container_path.",)
    parser.add_option("-e", "--env",
                    action="store",
                    help="The environment variables in the format of <variable_name>=<variable_value>. Multiple settings should be separated by comma. I.e., -e 'PWD=/tmp'.")
    parser.add_option("--log",
                    action="store",
                    default="./umbrella.log",
                    help="The path of umbrella log file. (By default: ./umbrella.log)",)
    parser.add_option("--cvmfs_http_proxy",
                    action="store",
                    help="HTTP_PROXY to access cvmfs (Used by Parrot)",)
    parser.add_option("--ec2",
                    action="store",
                    help="The source of ec2 information.",)
    parser.add_option("--condor_log",
                    action="store",
                    help="The path of the condor umbrella log file. Required for condor execution engines.",)
    parser.add_option("--ec2_log",
                    action="store",
                    help="The path of the ec2 umbrella log file. Required for ec2 execution engines.",)
    parser.add_option("-g", "--ec2_group",
                    action="store",
                    help="the security group id within which an Amazon EC2 instance should be run, the security group should should support incoming ssh traffic. (only for ec2)",)
    parser.add_option("-k", "--ec2_key",
                    action="store",
                    help="the name of the key pair to use when launching an Amazon EC2 instance. (only for ec2)",)
    parser.add_option("--ec2_sshkey",
                    action="store",
                    help="the name of the private key file to use when connecting to an Amazon EC2 instance. (only for ec2)",)
    parser.add_option("--ec2_instance_type",
                    action="store",
                    help="the type of an Amazon EC2 instance. (only for ec2)",)
    parser.add_option("--osf_user",
                    action="store",
                    help="the OSF username (required in two cases: uploading to osf; downloading private osf resources.)",)
    parser.add_option("--osf_pass",
                    action="store",
                    help="the OSF password (required in two cases: uploading to osf; downloading private osf resources.)",)
    parser.add_option("--osf_userid",
                    action="store",
                    help="the OSF user id (required in two cases: uploading to osf; downloading private osf resources.)",)
    parser.add_option("--use_local_cvmfs",
                    action="store_true",
                    default=False,
                    help="Use the cvmfs on the host machine.",)
    parser.add_option("--parrot_log",
                    action="store",
                    help="the path of the parrot debugging log",)
    parser.add_option("--parrot_path",
                    action="store",
                    help="the path of parrot_run on the host machine",)
    parser.add_option("--cms_siteconf",
                    action="store",
                    help="a tar.gz local file path (e.g., /tmp/1.tar.gz) or url path (e.g., http://.../1.tar.gz) pointing to the site configuration files for cms applications, the SITECONF dir should be organized following the suggestions at https://twiki.cern.ch/twiki/bin/view/CMSPublic/SiteConfInGitlab",)

    (options, args) = parser.parse_args()

    #sys.stdout = os.fdopen(sys.stdout.fileno(), 'wb', 0)

    logfilename = options.log
    if os.path.exists(logfilename) and not os.path.isfile(logfilename):
        sys.exit("The --log option <%s> is not a file!" % logfilename)

    parrot_log = None
    if options.parrot_log:
        if os.path.exists(options.parrot_log) and not os.path.isfile(options.parrot_log):
            sys.exit("the --parrot_log option <%s> is not a file!" % options.parrot_log)
        parrot_log = os.path.abspath(options.parrot_log)

    if options.cms_siteconf:
        global cms_siteconf_url
        cms_siteconf_url = options.cms_siteconf

    global tempfile_list
    global tempdir_list
    global upload_count

    """
    disable_warnings function is used here to disable the SNIMissingWarning and InsecurePlatformWarning from /afs/crc.nd.edu/user/h/hmeng/.local/lib/python2.6/site-packages/requests-2.9.1-py2.6.egg/requests/packages/urllib3/util/ssl_.py.
    "Requests 2.6 introduced this warning for users of Python prior to Python 2.7.9 with only stock SSL modules available."
    """
    if found_requests:
        requests.packages.urllib3.disable_warnings()

    logging.basicConfig(filename=logfilename, level=logging.DEBUG,
        format='%(asctime)s.%(msecs)d %(levelname)s %(module)s - %(funcName)s: %(message)s', datefmt="%Y-%m-%d %H:%M:%S")

    logging.debug("*******Welcome to Umbrella*******")
    logging.debug("Arguments: ")
    logging.debug(sys.argv)

    start = datetime.datetime.now()
    logging.debug("Start time: %s", start)

    logging.debug("Check the validity of the command ....")
    if not args:
        logging.critical("You must provide the behavior and the command!")
        print("You must provide the behavior and the command!\n")
        parser.print_help()
        sys.exit(1)

    user_cmd = []

    behavior = args[0]
    logging.debug("Check the validity of the behavior: %s", behavior)
    behavior_list = ["run", "expand", "filter", "split", "validate", "upload", "build"]
    if behavior not in behavior_list:
        logging.critical("%s is not supported by umbrella!", behavior)
        print(behavior + " is not supported by umbrella!\n")
        parser.print_help()
        sys.exit(1)

    if len(args) > 1 and args[1] in ['help']:
        print(help_info[behavior])
        sys.exit(0)

    logging.debug("the FQDN of the node: %s", socket.getfqdn())
    if behavior in ["run", "upload"]:
        #get the absolute path of the localdir directory, which will cache all the data, and store all the sandboxes.
        #to allow the reuse the local cache, the localdir can be a dir which already exists.
        localdir = options.localdir
        localdir = os.path.abspath(localdir)
        logging.debug("Check the localdir option: %s", localdir)

        if not os.path.exists(localdir):
            logging.debug("create the localdir: %s", localdir)
            os.makedirs(localdir)

        sandbox_dir = tempfile.mkdtemp(dir=localdir)
        logging.debug("Create the sandbox_dir: %s", sandbox_dir)

        #add sandbox_dir into tempdir_list
        tempdir_list.append(sandbox_dir)

    osf_auth = []
    #osf_auth info
    osf_user = options.osf_user
    osf_pass = options.osf_pass
    if osf_user or osf_pass:
        osf_auth.append(osf_user)
        osf_auth.append(osf_pass)


    if behavior in ["run"]:
        sandbox_mode = options.sandbox_mode
        logging.debug("Check the sandbox_mode option: %s", sandbox_mode)
        if sandbox_mode in ["destructive"]:
            if getpass.getuser() != 'root':
                cleanup(tempfile_list, tempdir_list)
                logging.critical("You must be root to use the %s sandbox mode.", sandbox_mode)
                print('You must be root to use the %s sandbox mode.\n' % (sandbox_mode))
                parser.print_help()
                sys.exit(1)

        #transfer options.env into a dictionary, env_para_dict
        env_para = options.env
        env_para_dict = {}
        if (not env_para) or env_para == '':
            logging.debug("The env option is null")
            env_para_list = ''
            env_para_dict = {}
        else:
            logging.debug("Process the env option: %s", env_para)
            env_para = re.sub('\s+', '', env_para).strip()
            env_para_list = env_para.split(',')
            for item in env_para_list:
                index = item.find('=')
                name = item[:index]
                value = item[(index+1):]
                env_para_dict[name] = value
            logging.debug("the dictionary format of the env options (env_para_dict):")
            logging.debug(env_para_dict)

        #get the cvmfs HTTP_PROXY
        cvmfs_http_proxy = options.cvmfs_http_proxy

    if behavior in ["run", "expand", "filter", "split", "validate", "upload", "build"]:
        spec_path = options.spec
        if spec_path == None:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("The --spec option is missing!")
            sys.exit("The --spec option is missing!")

        spec_path_basename = os.path.basename(spec_path)
        logging.debug("Start to read the specification file: %s", spec_path)
        if not os.path.isfile(spec_path):
            cleanup(tempfile_list, tempdir_list)
            logging.critical("The specification json file (%s) does not exist! Please refer the -c option.", spec_path)
            print("The specification json file does not exist! Please refer the -c option.\n")
            parser.print_help()
            sys.exit(1)

        with open(spec_path) as f: #python 2.4 does not support this syntax: with open () as
            spec_json = json.load(f)
            if behavior in ["run"]:
                user_cmd = args[1:]
                if len(user_cmd) == 0:
                    if "cmd" in spec_json.keys() and len(spec_json["cmd"]) > 0:
                        user_cmd.append(spec_json["cmd"])
                    else:
                        user_cmd.append("/bin/sh") #set the user_cmd to be default: /bin/sh

                logging.debug("The user's command is: %s", user_cmd)

                #if the spec file has environ seciton, merge the variables defined in it into env_para_dict
                if "environ" in spec_json.keys() and spec_json["environ"]:
                    logging.debug("The specification file has environ section, update env_para_dict ....")
                    spec_env = spec_json["environ"]
                    for key in spec_env:
                        env_para_dict[key] = spec_env[key]
                    logging.debug("env_para_dict:")
                    logging.debug(env_para_dict)

    meta_json = None
    meta_path = options.meta

    if behavior in ["build"]:
        if meta_path:
            logging.critical("umbrella build can not be used together with the --meta option!")
            sys.exit("umbrella build can not be used together with the --meta option!")

        if len(args) != 2:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("The syntax for umbrella build is: umbrella ... build <dest.umbrella>\n")
            sys.exit("The syntax for umbrella build is: umbrella ... build <dest.umbrella>\n")

        if os.path.exists(args[1]):
            cleanup(tempfile_list, tempdir_list)
            logging.critical("<dest.umbrella> (%s) should be a non-existing file!\n", args[1])
            sys.exit("<dest.umbrella> (%s) should be a non-existing file!\n" % args[1])

        args[1] = os.path.abspath(args[1])
        if not os.path.exists(os.path.dirname(args[1])):
            print(os.path.dirname(args[1]))
            try:
                os.makedirs(os.path.dirname(args[1]))
            except Exception as e:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("Fails to create the directory for the <dest.umbrella> (%s): %s!", args[1], e)
                sys.exit("Fails to create the directory for the <dest.umbrella> (%s)!" % (args[1], e))

        if spec_build(spec_json) == 0:
            print("There is no local dependencies whose metadata info needs to built!")
        else:
            json2file(args[1], spec_json)
        sys.exit(0)

    output_fileset = set()
    output_dirset = set()
    if behavior in ["run"]:
        if not meta_path:
            print("Trying to build the metadata info for local dependencies ...")
            spec_build(spec_json)

        if 'PWD' in env_para_dict:
            cwd_setting = env_para_dict['PWD']
            logging.debug("PWD environment variable is set explicitly: %s", cwd_setting)
        else:
            cwd_setting = sandbox_dir
            env_para_dict['PWD'] = cwd_setting
            logging.debug("PWD is not set explicitly, use sandbox_dir (%s) as PWD", cwd_setting)

        #get the absolute path of each input file
        input_files = options.inputs

        input_list = []
        input_dict = {}

        if (not input_files) or input_files == '':
            input_list_origin = ''
            input_list = []
            input_dict = {}
            logging.debug("the inputs options is null")
        else:
            input_files = re.sub( '\s+', '', input_files).strip() #remove all the whitespaces within the inputs option
            logging.debug("The inputs option: %s", input_files)
            input_list_origin = input_files.split(',')
            for item in input_list_origin:
                if item == '':
                    continue
                index = item.find('=')
                access_path = item[:index]
                actual_path = item[(index+1):]
                if access_path[0] != '/':
                    access_path = os.path.join(cwd_setting, access_path)
                actual_path = os.path.abspath(actual_path)
                input_dict[access_path] = actual_path
                input_list.append(actual_path) #get the absolute path of each input file and add it into input_list
            logging.debug("The list version of the inputs option: ")
            logging.debug(input_list)
            logging.debug("The dict version of the inputs option: ")
            logging.debug(input_dict)

        #get the absolute path of each output file
        output_dir = options.output
        output_dict = {}
        output_f_dict = {}
        output_d_dict = {}
        if output_dir and len(output_dir) > 0:
            output_dir = re.sub( '\s+', '', output_dir).strip() #remove all the whitespaces within the inputs option
            if output_dir == "":
                logging.debug("the output option is null!")
            else:
                logging.debug("the output option: %s", output_dir)
                outputs = output_dir.split(',')
                for item in outputs:
                    if item == '':
                        continue
                    index = item.find('=')
                    access_path = item[:index]
                    if access_path[0] != '/':
                        access_path = os.path.join(cwd_setting, access_path)

                    remain_path = item[(index+1):]

                    index = remain_path.find(':')
                    actual_path = ''
                    output_type = ''
                    if index == -1:
                        actual_path = remain_path
                    else:
                        actual_path = remain_path[:index]
                        output_type = remain_path[(index+1):]

                    actual_path = os.path.abspath(actual_path)

                    if output_type == '':
                        output_dict[access_path] = actual_path
                    elif output_type == 'f':
                        output_f_dict[access_path] = actual_path
                    elif output_type == 'd':
                        output_d_dict[access_path] = actual_path
                    else:
                        cleanup(tempfile_list, tempdir_list)
                        logging.critical("the output type can only be 'f' or 'd'!")
                        sys.exit("the output type can only be 'f' or 'd'!")

        if len(output_dict) > 0:
            if "output" in spec_json.keys():
                files = []
                dirs = []
                if "files" in spec_json["output"].keys():
                    files = spec_json["output"]["files"]

                if "dirs" in spec_json["output"].keys():
                    dirs = spec_json["output"]["dirs"]

                for key in output_dict.keys():
                    if key in files:
                        output_f_dict[key] = output_dict[key]
                    elif key in dirs:
                        output_d_dict[key] = output_dict[key]

        del output_dict

        for f in output_f_dict.values():
            if not os.path.exists(f):
                logging.debug("create the output file: %s", f)
                d = os.path.dirname(f)
                if not os.path.exists(d):
                    os.makedirs(d)
                    tempdir_list.append(d)
                    output_dirset.add(d)
                elif not os.path.isdir(d):
                    cleanup(tempfile_list, tempdir_list)
                    logging.critical("the parent path of the output file (%s) is not a directory!", f)
                    sys.exit("the parent path of the output file (%s) is not a directory!" % f)
                else:
                    pass
                new_file = open(f, 'a')
                new_file.close()
                tempfile_list.append(f)
                output_fileset.add(f)
            elif len(f) != 0:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("the output file (%s) already exists!", f)
                sys.exit("the output file (%s) already exists!\n" % f)
            else:
                pass

        for d in output_d_dict.values():
            if not os.path.exists(d):
                logging.debug("create the output dir: %s", d)
                os.makedirs(d)
                tempdir_list.append(d)
                output_dirset.add(d)
            elif len(d) != 0:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("the output dir (%s) already exists!", d)
                sys.exit("the output dir(%s) already exists!" % d)
            else:
                pass

    if behavior in ["run", "expand", "filter", "validate"]:
        """
        meta_path is optional. If set, it provides the metadata information for the dependencies.
        If not set, the umbrella specification is treated as a self-contained specification.
        meta_path can be in either a local filepath (relative or absolute) or a http/https url like http:/ccl.cse.nd.edu/.... Otherwise, it is treated as a local path.
        """
        if meta_path:
            if meta_path[:1] == "/":
                meta_path = os.path.abspath(meta_path)
                logging.debug("Check the metatdata database file: %s", meta_path)
                if not os.path.exists(meta_path):
                    cleanup(tempfile_list, tempdir_list)
                    logging.critical("the metatdata database file (%s) does not exist!", meta_path)
                    sys.exit("the metatdata database file (%s) does not exist!" % meta_path)
            elif meta_path[:7] == "http://" or meta_path[:8] == "https://":
                url = meta_path
                if behavior in ["run"]:
                    meta_path = '%s/meta.json' % (sandbox_dir)
                if behavior in ["expand", "filter", "validate"]:
                    #create a tempfile under /tmp
                    (fd, meta_path) = tempfile.mkstemp()
                    tempfile_list.append(meta_path)
                    os.close(fd)
                    logging.debug("Creating a temporary file (%s) to hold the metadata file specified by the --meta options!", meta_path)
                logging.debug("Download metadata database from %s into %s", url, meta_path)
                print("Download metadata database from %s into %s" % (url, meta_path))
                url_download(url, meta_path)
            else:
                logging.debug("Check the metatdata database file: %s", meta_path)
                if not os.path.exists(meta_path):
                    cleanup(tempfile_list, tempdir_list)
                    logging.critical("the metatdata database file (%s) does not exist!", meta_path)
                    sys.exit("the metatdata database file (%s) does not exist!" % meta_path)
        else:
            if behavior in ["run"]:
                #the provided specification should be self-contained.
                # One solution is to change all the current implementation of Umbrella to check whether the metadata information is included in the specification.
                # Another solution is to extract all the metadata information into a separate metadata database file. (This solution is currently used).
                meta_path = '%s/meta.json' % (sandbox_dir)
                abstract_metadata(spec_json, meta_path)
            elif behavior in ["expand", "filter"]:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("The --meta option should be provided for the umbrella %s behavior!\n", behavior)
                sys.exit("The --meta option should be provided for the umbrella %s behavior!\n" % behavior)

        if meta_path:
            with open(meta_path) as f: #python 2.4 does not support this syntax: with open () as
                meta_json = json.load(f)

    if behavior in ["upload"]:
        #the provided specification should be self-contained.
        # One solution is to change all the current implementation of Umbrella to check whether the metadata information is included in the specification.
        # Another solution is to extract all the metadata information into a separate metadata database file. (This solution is currently used).
        meta_path = '%s/meta.json' % (sandbox_dir)
        abstract_metadata(spec_json, meta_path)

        with open(meta_path) as f: #python 2.4 does not support this syntax: with open () as
            meta_json = json.load(f)

    if behavior in ["run", "validate", "split", "filter", "expand", "upload"]:
        #for validate, if only --spec is provided, then check whether this spec is self-contained.
        #for validate, if only --meta is provided, then check whether each item in the metadata db is well archived (for now, well-archived means the source attr is not null).
        #for validate, if both --spec and --meta are provided, then check whether the dependencies of the spec file is well archived.
        if spec_json == None:
            if meta_json == None:
                pass
            else:
                validate_meta(meta_json)
        else:
            if meta_json == None:
                validate_spec(spec_json)
            else:
                validate_spec(spec_json, meta_json)

    if behavior in ["run"]:
        # set parrot_path
        global parrot_path
        parrot_path = options.parrot_path
        if parrot_path:
            if not os.path.exists(parrot_path):
                cleanup(tempfile_list, tempdir_list)
                sys.exit("parrot_path <%s> does not exist!" % parrot_path)
            elif not os.path.isfile(parrot_path):
                cleanup(tempfile_list, tempdir_list)
                sys.exit("parrot_path <%s> should be a file!" % parrot_path)
            parrot_path = os.path.abspath(parrot_path)

#       user_name = 'root' #username who can access the VM instances from Amazon EC2
#       ssh_key = 'hmeng_key_1018.pem' #the pem key file used to access the VM instances from Amazon EC2
        if sandbox_mode == "ec2":
            ec2log_path = options.ec2_log
            ec2log_path = os.path.abspath(ec2log_path)
            if os.path.exists(ec2log_path):
                cleanup(tempfile_list, tempdir_list)
                sys.exit("The ec2_log option <%s> already exists!" % ec2log_path)

            ssh_key = os.path.abspath(options.ec2_sshkey)
            if not os.path.exists(ssh_key):
                cleanup(tempfile_list, tempdir_list)
                logging.critical("The ssh key file (%s) does not exists!", ssh_key)
                sys.exit("The ssh key file (%s) does not exists!\n" % ssh_key)

            if not found_boto3 or not found_botocore:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("\nUsing the Amazon EC2 resources requires a python package - boto3. Please check the installation page of boto3:\n\n\thttps://boto3.readthedocs.org/en/latest/guide/quickstart.html#installation\n")
                sys.exit("\nUsing the Amazon EC2 resources requires a python package - boto3. Please check the installation page of boto3:\n\n\thttps://boto3.readthedocs.org/en/latest/guide/quickstart.html#installation\n")

            # Here the security group id, instead of the security group name, is used to allow an instance to be launched into a nondefault VPC.
            # the security group name can only be used to launch an instance into EC2-Classic or default VPC.
            ec2_security_group = options.ec2_group
            ec2_key_pair = options.ec2_key
            ec2_instance_type = options.ec2_instance_type

            ec2_process(spec_path, spec_json, options.meta, meta_path, ssh_key, ec2_key_pair, ec2_security_group, ec2_instance_type, sandbox_dir, output_dir, output_f_dict, output_d_dict, sandbox_mode, input_list, input_list_origin, env_para, env_para_dict, user_cmd, cwd_setting, ec2log_path, cvmfs_http_proxy)

        elif sandbox_mode == "condor":
            condorlog_path = options.condor_log
            condorlog_path = os.path.abspath(condorlog_path)
            if os.path.exists(condorlog_path):
                cleanup(tempfile_list, tempdir_list)
                sys.exit("The condor_log option <%s> already exists!" % condorlog_path)
            condor_process(spec_path, spec_json, spec_path_basename, meta_path, sandbox_dir, output_dir, input_list_origin, user_cmd, cwd_setting, condorlog_path, cvmfs_http_proxy)

        elif sandbox_mode == "local":
            #first check whether Docker exists, if yes, use docker execution engine; if not, use parrot execution engine.
            if dependency_check('docker') == 0:
                logging.debug('docker exists, use docker execution engine')
                rc = specification_process(spec_json, sandbox_dir, behavior, meta_json, 'docker', output_f_dict, output_d_dict, input_dict, env_para_dict, user_cmd, cwd_setting, cvmfs_http_proxy, osf_auth, options.use_local_cvmfs, parrot_log)
                if rc != 0:
                    cleanup(tempfile_list, tempdir_list)
                    sys.exit("The return code of the task is: %d" % rc)
            else:
                logging.debug('docker does not exist, use parrot execution engine')
                rc = specification_process(spec_json, sandbox_dir, behavior, meta_json, 'parrot', output_f_dict, output_d_dict, input_dict, env_para_dict, user_cmd, cwd_setting, cvmfs_http_proxy, osf_auth, options.use_local_cvmfs, parrot_log)
                if rc != 0:
                    cleanup(tempfile_list, tempdir_list)
                    sys.exit("The return code of the task is: %d" % rc)
        else:
            if sandbox_mode == 'docker' and dependency_check('docker') != 0:
                cleanup(tempfile_list, tempdir_list)
                logging.critical('Docker is not installed on the host machine, please try other execution engines!')
                sys.exit('Docker is not installed on the host machine, please try other execution engines!')

            rc = specification_process(spec_json, sandbox_dir, behavior, meta_json, sandbox_mode, output_f_dict, output_d_dict, input_dict, env_para_dict, user_cmd, cwd_setting, cvmfs_http_proxy, osf_auth, options.use_local_cvmfs, parrot_log)
            if rc != 0:
                cleanup(tempfile_list, tempdir_list)
                sys.exit("The return code of the task is: %d" % rc)

    if behavior in ["expand", "filter"]:
        if len(args) != 2:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("The syntax for umbrella %s is: umbrella ... %s <filepath>.\n", behavior, behavior)
            sys.exit("The syntax for umbrella %s is: umbrella ... %s <filepath>.\n" % (behavior, behavior))
        target_specpath = os.path.abspath(args[1])
        path_exists(target_specpath)
        dir_create(target_specpath)
        if behavior == "expand":
            new_json = separatize_spec(spec_json, meta_json, "spec")
        else:
            new_json = separatize_spec(spec_json, meta_json, "meta")
        #write new_json into the file specified by the user.
        json2file(target_specpath, new_json)

    if behavior in ["split"]:
        if len(args) != 3:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("The syntax for umbrella split is: umbrella ... split <spec_filepath> <meta_filepath>.\n")
            sys.exit("The syntax for umbrella split is: umbrella ... split <spec_filepath> <meata_filepath>.\n")

        new_spec_path = os.path.abspath(args[1])
        db_path = os.path.abspath(args[2])
        path_exists(new_spec_path)
        dir_create(new_spec_path)
        path_exists(db_path)
        dir_create(db_path)
        abstract_metadata(spec_json, db_path)
        new_json = prune_spec(spec_json)
        json2file(new_spec_path, new_json)

    if behavior in ["upload"]:
        target = ["osf", "s3"]
        if len(args) < 2 or args[1] not in target:
            cleanup(tempfile_list, tempdir_list)
            logging.critical("The syntax for umbrella upload is: umbrella ... upload <target> ... (target can be: %s)\n", " or ".join(target))
            sys.exit("The syntax for umbrella upload is: umbrella ... upload <target> ... (target can be: %s)\n" % " or ".join(target))
        if args[1] == "osf":

            if not found_requests:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("\nUploading umbrella spec dependencies to OSF requires a python package - requests. Please check the installation page of requests:\n\n\thttp://docs.python-requests.org/en/latest/user/install/\n")
                sys.exit("\nUploading umbrella spec dependencies to OSF requires a python package - requests. Please check the installation page of requests:\n\n\thttp://docs.python-requests.org/en/latest/user/install/\n")

            if len(args) != 5:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("The syntax for umbrella upload osf is: umbrella ... upload osf <osf_project_name> <public_or_private> <target_specpath>\n")
                sys.exit("The syntax for umbrella upload osf is: umbrella ... upload osf <osf_project_name> <public_or_private> <target_specpath>\n")

            acl = ["private", "public"]
            if args[3] not in acl:
                cleanup(tempfile_list, tempdir_list)
                sys.exit("The access control for s3 bucket and object can only be: %s" % " or ".join(acl))

            target_specpath = os.path.abspath(args[4])
            path_exists(target_specpath)
            dir_create(target_specpath)

            osf_info = []
            osf_info.append("osf")
            osf_info += [options.osf_user, options.osf_pass]
            osf_proj_id = osf_create(options.osf_user, options.osf_pass, options.osf_userid, args[2], args[3] == "public")
            osf_info.append(osf_proj_id)
            spec_upload(spec_json, meta_json, osf_info, sandbox_dir, cwd_setting, osf_auth)
            if upload_count > 0:
                json2file(target_specpath, spec_json)
                osf_upload(options.osf_user, options.osf_pass, osf_proj_id, target_specpath)
            else:
                logging.debug("All the dependencies has been already inside OSF!")
                print("All the dependencies has been already inside OSF!")

        elif args[1] == "s3":
            if not found_boto3 or not found_botocore:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("\nUploading umbrella spec dependencies to s3 requires a python package - boto3. Please check the installation page of boto3:\n\n\thttps://boto3.readthedocs.org/en/latest/guide/quickstart.html#installation\n")
                sys.exit("\nUploading umbrella spec dependencies to s3 requires a python package - boto3. Please check the installation page of boto3:\n\n\thttps://boto3.readthedocs.org/en/latest/guide/quickstart.html#installation\n")

            if len(args) != 5:
                cleanup(tempfile_list, tempdir_list)
                logging.critical("The syntax for umbrella upload s3 is: umbrella ... upload s3 <bucket_name> <access_control> <target_specpath>\n")
                sys.exit("The syntax for umbrella upload s3 is: umbrella ... upload s3 <bucket_name> <access_control> <target_specpath>\n")

            acl = ["private", "public-read"]
            if args[3] not in acl:
                cleanup(tempfile_list, tempdir_list)
                sys.exit("The access control for s3 bucket and object can only be: %s" % " or ".join(acl))

            target_specpath = os.path.abspath(args[4])
            path_exists(target_specpath)
            dir_create(target_specpath)

            s3_info = []
            s3_info.append("s3")
            s3_info.append(args[3])
            bucket = s3_create(args[2], args[3])
            spec_upload(spec_json, meta_json, s3_info, sandbox_dir, cwd_setting, s3_bucket=bucket)
            if upload_count > 0:
                json2file(target_specpath, spec_json)
                s3_upload(bucket, target_specpath, args[3])
            else:
                logging.debug("All the dependencies has been already inside S3!")
                print("All the dependencies has been already inside S3!")

    cleanup(trim_list(tempfile_list, output_fileset), trim_list(tempdir_list, output_dirset))
    end = datetime.datetime.now()
    diff = end - start
    logging.debug("End time: %s", end)
    logging.debug("execution time: %d seconds", diff.seconds)


if __name__ == "__main__":
    main()

#vim: set sts=4 sw=4 ts=4 expandtab ft=python:
