/usr/bin/pegasus-create-dir is in pegasus-wms 4.0.1+dfsg-8.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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"""
Pegasus utility for creating directories for a set of protocols
Usage: pegasus-create-dir [options]
"""
##
# Copyright 2007-2011 University Of Southern California
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
##
import os
import re
import sys
import errno
import logging
import optparse
import tempfile
import subprocess
import signal
import string
import stat
import time
from collections import deque
__author__ = "Mats Rynge <rynge@isi.edu>"
# --- regular expressions -------------------------------------------------------------
re_parse_url = re.compile(r'([\w]+)://([\w\.\-:@]*)(/[\S]*)')
# --- classes -------------------------------------------------------------------------
class URL:
proto = ""
host = ""
path = ""
def set_url(self, url):
self.proto, self.host, self.path = self.parse_url(url)
def parse_url(self, url):
proto = ""
host = ""
path = ""
# default protocol is file://
if string.find(url, ":") == -1:
logger.debug("URL without protocol (" + url + ") - assuming file://")
url = "file://" + url
# file url is a special cases as it can contain relative paths and env vars
if string.find(url, "file:") == 0:
proto = "file"
# file urls can either start with file://[\w]*/ or file: (no //)
path = re.sub("^file:(//[\w\.\-:@]*)?", "", url)
path = expand_env_vars(path)
return proto, host, path
# other than file urls
r = re_parse_url.search(url)
if not r:
raise RuntimeError("Unable to parse URL: %s" % (url))
# Parse successful
proto = r.group(1)
host = r.group(2)
path = r.group(3)
# no double slashes in urls
path = re.sub('//+', '/', path)
return proto, host, path
def url(self):
return "%s://%s%s" % (self.proto, self.host, self.path)
def url_dirname(self):
dn = os.path.dirname(self.path)
return "%s://%s%s" % (self.proto, self.host, dn)
def parent_url(self):
parent = URL()
parent.proto = self.proto
parent.host = self.host
parent.path = os.path.dirname(self.path)
return parent
class Alarm(Exception):
pass
# --- global variables ----------------------------------------------------------------
prog_base = os.path.split(sys.argv[0])[1] # Name of this program
logger = logging.getLogger("my_logger")
# this is the map of what tool to use for a given protocol pair (src, dest)
tool_map = {}
tool_map['file' ] = 'mkdir'
tool_map['ftp' ] = 'gsiftp'
tool_map['gsiftp'] = 'gsiftp'
tool_map['irods' ] = 'irods'
tool_map['s3' ] = 's3'
tool_map['s3s' ] = 's3'
tool_map['scp' ] = 'scp'
tool_map['srm' ] = 'srm'
tool_info = {}
# --- functions -----------------------------------------------------------------------
def setup_logger(level_str):
# log to the console
console = logging.StreamHandler()
# default log level - make logger/console match
logger.setLevel(logging.INFO)
console.setLevel(logging.INFO)
# level - from the command line
level_str = level_str.lower()
if level_str == "debug":
logger.setLevel(logging.DEBUG)
console.setLevel(logging.DEBUG)
if level_str == "warning":
logger.setLevel(logging.WARNING)
console.setLevel(logging.WARNING)
if level_str == "error":
logger.setLevel(logging.ERROR)
console.setLevel(logging.ERROR)
# formatter
formatter = logging.Formatter("%(asctime)s %(levelname)7s: %(message)s")
console.setFormatter(formatter)
logger.addHandler(console)
logger.debug("Logger has been configured")
def prog_sigint_handler(signum, frame):
logger.warn("Exiting due to signal %d" % (signum))
myexit(1)
def alarm_handler(signum, frame):
raise Alarm
def expand_env_vars(s):
re_env_var = re.compile(r'\${?([a-zA-Z0-9_]+)}?')
s = re.sub(re_env_var, get_env_var, s)
return s
def get_env_var(match):
name = match.group(1)
value = ""
logger.debug("Looking up " + name)
if name in os.environ:
value = os.environ[name]
return value
def myexec(cmd_line, timeout_secs, should_log):
"""
executes shell commands with the ability to time out if the command hangs
"""
global delay_exit_code
if should_log or logger.isEnabledFor(logging.DEBUG):
logger.info(cmd_line)
sys.stdout.flush()
# set up signal handler for timeout
signal.signal(signal.SIGALRM, alarm_handler)
signal.alarm(timeout_secs)
p = subprocess.Popen(cmd_line + " 2>&1", shell=True)
try:
stdoutdata, stderrdata = p.communicate()
except Alarm:
if sys.version_info >= (2, 6):
p.terminate()
raise RuntimeError("Command '%s' timed out after %s seconds" % (cmd_line, timeout_secs))
rc = p.returncode
if rc != 0:
raise RuntimeError("Command '%s' failed with error code %s" % (cmd_line, rc))
def backticks(cmd_line):
"""
what would a python program be without some perl love?
"""
return subprocess.Popen(cmd_line, shell=True, stdout=subprocess.PIPE).communicate()[0]
def check_tool(executable, version_arg, version_regex):
# initialize the global tool info for this executable
tool_info[executable] = {}
tool_info[executable]['full_path'] = None
tool_info[executable]['version'] = None
tool_info[executable]['version_major'] = None
tool_info[executable]['version_minor'] = None
tool_info[executable]['version_patch'] = None
# figure out the full path to the executable
full_path = backticks("which " + executable + " 2>/dev/null")
full_path = full_path.rstrip('\n')
if full_path == "":
logger.info("Command '%s' not found in the current environment" %(executable))
return
tool_info[executable]['full_path'] = full_path
# version
if version_regex == None:
version = "N/A"
else:
version = backticks(executable + " " + version_arg + " 2>&1")
version = version.replace('\n', "")
re_version = re.compile(version_regex)
result = re_version.search(version)
if result:
version = result.group(1)
tool_info[executable]['version'] = version
# if possible, break up version into major, minor, patch
re_version = re.compile("([0-9]+)\.([0-9]+)(\.([0-9]+)){0,1}")
result = re_version.search(version)
if result:
tool_info[executable]['version_major'] = int(result.group(1))
tool_info[executable]['version_minor'] = int(result.group(2))
tool_info[executable]['version_patch'] = result.group(4)
if tool_info[executable]['version_patch'] == None or tool_info[executable]['version_patch'] == "":
tool_info[executable]['version_patch'] = None
else:
tool_info[executable]['version_patch'] = int(tool_info[executable]['version_patch'])
logger.info(" %-18s Version: %-7s Path: %s" % (executable, version, full_path))
def check_env_and_tools():
# PATH setup
path = "/usr/bin:/bin"
if "PATH" in os.environ:
path = os.environ['PATH']
path_entries = path.split(':')
# is /usr/bin in the path?
if not("/usr/bin" in path_entries):
path_entries.append("/usr/bin")
path_entries.append("/bin")
# fink on macos x
if os.path.exists("/sw/bin") and not("/sw/bin" in path_entries):
path_entries.append("/sw/bin")
# need LD_LIBRARY_PATH for Globus tools
ld_library_path = ""
if "LD_LIBRARY_PATH" in os.environ:
ld_library_path = os.environ['LD_LIBRARY_PATH']
ld_library_path_entries = ld_library_path.split(':')
# if PEGASUS_HOME is set, prepend it to the PATH (we want it early to override other cruft)
if "PEGASUS_HOME" in os.environ:
try:
path_entries.remove(os.environ['PEGASUS_HOME'] + "/bin")
except Exception:
pass
path_entries.insert(0, os.environ['PEGASUS_HOME'] + "/bin")
# if GLOBUS_LOCATION is set, prepend it to the PATH and LD_LIBRARY_PATH
# (we want it early to override other cruft)
if "GLOBUS_LOCATION" in os.environ:
try:
path_entries.remove(os.environ['GLOBUS_LOCATION'] + "/bin")
except Exception:
pass
path_entries.insert(0, os.environ['GLOBUS_LOCATION'] + "/bin")
try:
ld_library_path_entries.remove(os.environ['GLOBUS_LOCATION'] + "/lib")
except Exception:
pass
ld_library_path_entries.insert(0, os.environ['GLOBUS_LOCATION'] + "/lib")
os.environ['PATH'] = ":".join(path_entries)
os.environ['LD_LIBRARY_PATH'] = ":".join(ld_library_path_entries)
os.environ['DYLD_LIBRARY_PATH'] = ":".join(ld_library_path_entries)
logger.info("PATH=" + os.environ['PATH'])
logger.info("LD_LIBRARY_PATH=" + os.environ['LD_LIBRARY_PATH'])
# irods requires a password hash file
os.environ['irodsAuthFileName'] = os.getcwd() + "/.irodsA"
def mkdir(url):
"""
creates a directory on a mounted file system
"""
path = url.path
if not(os.path.exists(path)):
logger.debug("Creating local directory " + path)
try:
os.makedirs(path, 0755)
except os.error, err:
# if dir already exists, ignore the error
if not(os.path.isdir(path)):
raise RuntimeError(err)
def scp(url):
"""
creates a directory using ssh
"""
cmd = "/usr/bin/ssh"
if "SSH_PRIVATE_KEY" in os.environ:
cmd += " -i " + os.environ['SSH_PRIVATE_KEY']
cmd += " -o PasswordAuthentication=no"
cmd += " -o StrictHostKeyChecking=no"
cmd += " " + url.host
cmd += " '/bin/mkdir -p " + url.path + "'"
myexec(cmd, 60, True)
def gsiftp(url):
"""
create directories on gridftp servers
"""
if tool_info['globus-url-copy']['full_path'] == None:
raise RuntimeError("Unable to do gsiftp mkdir becuase globus-url-copy could not be found")
# build command line for globus-url-copy
cmd = tool_info['globus-url-copy']['full_path']
# make output from guc match our current log level
if logger.isEnabledFor(logging.DEBUG):
cmd += " -dbg"
cmd += " -create-dest"
cmd += " -no-third-party-transfers -no-data-channel-authentication"
cmd += " file:///dev/null " + url.url() + "/.empty"
myexec(cmd, 60, True)
def irods_login():
"""
log in to irods by using the iinit command - if the file already exists,
we are already logged in
"""
f = os.environ['irodsAuthFileName']
if os.path.exists(f):
return
# read password from env file
if not "irodsEnvFile" in os.environ:
raise RuntimeError("Missing irodsEnvFile - unable to do irods transfers")
password = None
h = open(os.environ['irodsEnvFile'], 'r')
for line in h:
items = line.split(" ", 2)
if items[0].lower() == "irodspassword":
password = items[1].strip(" \t'\"\r\n")
h.close()
if password == None:
raise RuntimeError("No irodsPassword specified in irods env file")
h = open(".irodsAc", "w")
h.write(password + "\n")
h.close()
cmd = "cat .irodsAc | iinit"
myexec(cmd, 60*60, True)
os.unlink(".irodsAc")
def irods(url):
"""
irods - use the icommands to interact with irods
"""
if len(transfers) == 0:
return
if tool_info['imkdir']['full_path'] == None:
raise RuntimeError("Unable to do irods create dir because imkdir could not be found in the current path")
# log in to irods
try:
irods_login()
except Exception, loginErr:
logger.error(loginErr)
raise RuntimError("Unable to log into irods")
cmd = "imkdir -p " + os.path.dirname(url.path)
myexec(cmd, 60, True)
def srm(url):
"""
implements recursive mkdir as srm-mkdir can not handle it
"""
if tool_info['srm-mkdir']['full_path'] == None:
raise RuntimeError("Unable to do srm mkdir becuase srm-mkdir could not be found")
# if the directory exists, just return
cmd = "srm-ls %s >/dev/null" %(url.url())
try:
myexec(cmd, 60, True)
return
except Exception, err:
logger.info("Directory %s does not exist yet" % (url.path))
# back down to a directory which exists
one_up = url.parent_url()
if one_up.path != "/":
srm(one_up)
cmd = "srm-mkdir %s" %(url.url())
try:
myexec(cmd, 60, True)
except Exception, err:
if check_error:
raise err
def s3(url):
"""
s3 - uses pegasus-s3 to interact with Amazon S3
"""
if tool_info['pegasus-s3']['full_path'] == None:
raise RuntimeError("Unable to do S3 mkdir becuase pegasus-s3 could not be found")
# extract the bucket part
re_bucket = re.compile(r'(s3(s){0,1}://\w+@\w+/+[\w]+)')
bucket = url.url()
r = re_bucket.search(bucket)
if r:
bucket = r.group(1)
else:
raise RuntimeError("Unable to parse bucket: %s" % (bucket))
# first ensure that the bucket exists
cmd = "pegasus-s3 mkdir %s" %(bucket)
myexec(cmd, 60, True)
def create_dir(url):
"""
handles the creation of a directory
"""
try:
if tool_map.has_key(url.proto):
tool = tool_map[url.proto]
if tool == "mkdir":
mkdir(url)
elif tool == "scp":
scp(url)
elif tool == "gsiftp":
check_tool("globus-url-copy", "-version", "([0-9]+\.[0-9]+)")
check_tool("uberftp", "-version", "([0-9]+\.[0-9]+)")
gsiftp(url)
elif tool == "irods":
check_tool("imkdir", "-h", "Version[ \t]+([\.0-9a-zA-Z]+)")
irods(url)
elif tool == "srm":
check_tool("srm-mkdir", "-version", "srm-mkdir[ \t]+([\.0-9a-zA-Z]+)")
srm(url)
elif tool == "s3":
check_tool("pegasus-s3", "help", None)
s3(url)
else:
logger.critical("Error: No mapping for the tool '%s'" %(tool))
myexit(1)
else:
logger.critical("Error: This tool does not know how to create a directory for %s://" % (url.proto))
myexit(1)
except RuntimeError, err:
logger.critical(err)
myexit(1)
def myexit(rc):
"""
system exit without a stack trace - silly python
"""
try:
sys.exit(rc)
except SystemExit:
sys.exit(rc)
# --- main ----------------------------------------------------------------------------
# dup stderr onto stdout
sys.stderr = sys.stdout
# Configure command line option parser
prog_usage = "usage: %s [options]" % (prog_base)
parser = optparse.OptionParser(usage=prog_usage)
parser.add_option("-l", "--loglevel", action = "store", dest = "log_level",
help = "Log level. Valid levels are: debug,info,warning,error, Default is info.")
parser.add_option("-u", "--url", action = "store", dest = "url",
help = "URL for the directory to create")
# Parse command line options
(options, args) = parser.parse_args()
if options.log_level == None:
options.log_level = "info"
setup_logger(options.log_level)
if options.url == None:
logger.critical("Please specify the URL for the directory to create")
myexit(1)
# Die nicely when asked to (Ctrl+C, system shutdown)
signal.signal(signal.SIGINT, prog_sigint_handler)
# check environment and tools
try:
check_env_and_tools()
except Exception, err:
logger.critical(err)
myexit(1)
url = URL()
url.set_url(options.url)
try:
create_dir(url)
except Exception, err:
logger.critical(err)
logger.critical("Directory not created!")
myexit(1)
logger.info("Directory created")
myexit(0)
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