def __irodsClient( self , user = None ):
global IRODS_USER
password = None
cfgPath = self.serviceInfoDict[ 'serviceSectionPath' ]
gLogger.debug( "cfgPath: %s" % cfgPath )
if not user:
credentials = self.getRemoteCredentials()
if credentials and ( "username" in credentials ):
IRODS_USER = credentials[ "username" ]
## TODO: should get user password somehow
elif user == "r":
IRODS_USER = gConfig.getValue( "%s/read" % cfgPath , IRODS_USER )
elif user == "w":
IRODS_USER = gConfig.getValue( "%s/write" % cfgPath , IRODS_USER )
if not IRODS_USER:
return False , "Failed to get iRods user"
gLogger.debug( "iRods user: %s" % IRODS_USER )
password = gConfig.getValue( "%s/%s" % ( cfgPath , IRODS_USER ) , password )
conn , errMsg = rcConnect( IRODS_HOST , IRODS_PORT , IRODS_USER , IRODS_ZONE )
status = clientLoginWithPassword( conn , password )
if not status == 0:
return False , "Failed to authenticate user '%s'" % IRODS_USER
return conn , errMsg
def create_irods_connection(username, password, rodsconfig):
from irods import (getRodsEnv, rcConnect, clientLoginWithPassword,
rodsErrorName)
err, rodsEnv = getRodsEnv() # Override all values later
rodsEnv.rodsUserName = username
rodsEnv.rodsHost = rodsconfig[0]
rodsEnv.rodsPort = rodsconfig[1]
rodsEnv.rodsZone = rodsconfig[2]
conn, err = rcConnect(rodsEnv.rodsHost,
rodsEnv.rodsPort,
rodsEnv.rodsUserName,
rodsEnv.rodsZone
)
if err.status != 0:
raise Exception('Connecting to iRODS failed %s'
% rodsErrorName(err.status)[0])
err = clientLoginWithPassword(conn, password)
if err != 0:
raise Exception('Authenticating to iRODS failed %s, user: %, pw: %s'
% rodsErrorName(err.status)[0], username, password)
return conn
def __irodsClient( self , user = None ):
""" Get the iRods client
"""
global IRODS_USER
userDict = {}
result = self.__getUserDetails()
if not result['OK']:
return False , "Failed to get iRods user info", userDict
userDict = result['Value']
IRODS_USER = userDict['iRodsUser']
if not IRODS_USER:
return False , "Failed to get iRods user", userDict
gLogger.debug( "iRods user: %s" % IRODS_USER )
password = userDict['iRodsPassword']
if not password:
return False , "Failed to get iRods user/password", userDict
conn , errMsg = rcConnect( IRODS_HOST , IRODS_PORT , IRODS_USER , IRODS_ZONE )
status = clientLoginWithPassword( conn , password )
if not status == 0:
return False , "Failed to authenticate user '%s'" % IRODS_USER, userDict
return conn , errMsg, userDict
def __init__(self, session, stream):
myEnv, status = irods.getRodsEnv()
conn, errMsg = irods.rcConnect(myEnv.getRodsHost(), myEnv.getRodsPort(),
myEnv.getRodsUserName(), myEnv.getRodsZone())
status = irods.clientLogin(conn)
if status:
raise ConfigFileException("Cannot connect to iRODS: (%s) %s" % (status, errMsg))
home = myEnv.getRodsHome()
c = irods.irodsCollection(conn, home)
self.cxn = conn
self.coll = c
instream = stream
# check if abs path to home dir
if stream.startswith(home):
stream = stream[len(home):]
if stream[0] == "/":
stream = stream[1:]
colls = stream.split('/')
for i, cln in enumerate(colls):
exit_status = c.openCollection(cln)
if exit_status < 0:
if (i < len(colls) - 1) or \
(cln not in [obj[0] for obj in c.getObjects()]):
raise IOError("When opening {0}: {1} does not exists in collection {2}".format(instream, cln, c.getCollName()))
def __irodsClient(self, user=None):
""" Get the iRods client
"""
global IRODS_USER
userDict = {}
result = self.__getUserDetails()
if not result['OK']:
return False, "Failed to get iRods user info", userDict
userDict = result['Value']
IRODS_USER = userDict['iRodsUser']
if not IRODS_USER:
return False, "Failed to get iRods user", userDict
gLogger.debug("iRods user: %s" % IRODS_USER)
password = userDict['iRodsPassword']
if not password:
return False, "Failed to get iRods user/password", userDict
conn, errMsg = rcConnect(IRODS_HOST, IRODS_PORT, IRODS_USER,
IRODS_ZONE)
status = clientLoginWithPassword(conn, password)
if not status == 0:
return False, "Failed to authenticate user '%s'" % IRODS_USER, userDict
return conn, errMsg, userDict
def __irodsClient(self, user=None):
global IRODS_USER
password = None
cfgPath = self.serviceInfoDict['serviceSectionPath']
gLogger.debug("cfgPath: %s" % cfgPath)
if not user:
credentials = self.getRemoteCredentials()
if credentials and ("username" in credentials):
IRODS_USER = credentials["username"]
## TODO: should get user password somehow
elif user == "r":
IRODS_USER = gConfig.getValue("%s/read" % cfgPath, IRODS_USER)
elif user == "w":
IRODS_USER = gConfig.getValue("%s/write" % cfgPath, IRODS_USER)
if not IRODS_USER:
return False, "Failed to get iRods user"
gLogger.debug("iRods user: %s" % IRODS_USER)
password = gConfig.getValue("%s/%s" % (cfgPath, IRODS_USER), password)
conn, errMsg = rcConnect(IRODS_HOST, IRODS_PORT, IRODS_USER,
IRODS_ZONE)
status = clientLoginWithPassword(conn, password)
if not status == 0:
return False, "Failed to authenticate user '%s'" % IRODS_USER
return conn, errMsg
def connect_infos(self, host, port, user, zone):
"""Same as connect but with information on the server in parameters
port is an integer, host, user and zone are strings"""
conn, err_msg = irods.rcConnect(host, port, user, zone)
if not conn:
self.conn = None
return err_msg.status
self.conn = conn
return irods.clientLoginWithObfPassword(conn, self.cfg.password)
def _open(self, session):
if self.cxn == None:
# connect to iRODS
myEnv, status = irods.getRodsEnv()
host = self.host if self.host else myEnv.getRodsHost()
port = self.port if self.port else myEnv.getRodsPort()
user = self.user if self.user else myEnv.getRodsUserName()
zone = self.zone if self.zone else myEnv.getRodsZone()
conn, errMsg = irods.rcConnect(host, port, user, zone)
if self.passwd:
status = irods.clientLoginWithPassword(conn, self.passwd)
else:
status = irods.clientLogin(conn)
if status:
raise ConfigFileException("Cannot connect to iRODS: (%s) %s" % (status, errMsg.getMsg()))
self.cxn = conn
self.env = myEnv
resources = irods.getResources(self.cxn)
self.resourceHash = {}
for r in resources:
self.resourceHash[r.getName()] = r
if self.coll != None:
# already open, just skip
return None
c = irods.irodsCollection(self.cxn, self.env.getRodsHome())
self.coll = c
# move into cheshire3 section
path = self.get_path(session, 'irodsCollection', 'cheshire3')
dirs = c.getSubCollections()
if not path in dirs:
c.createCollection(path)
c.openCollection(path)
if self.get_setting(session, 'createSubDir', 1):
# now look for object's storage area
# maybe move into database collection
if (isinstance(self.parent, Database)):
sc = self.parent.id
dirs = c.getSubCollections()
if not sc in dirs:
c.createCollection(sc)
c.openCollection(sc)
# move into store collection
dirs = c.getSubCollections()
if not self.id in dirs:
c.createCollection(self.id)
c.openCollection(self.id)
def __init__(self, session, stream):
# Check for dependency
if irods is None:
raise MissingDependencyException(
'{0.__module__}.{0.__class__.__name__}'.format(self),
'irods (PyRods)'
)
# Check for URL
if stream.startswith(('irods://', 'rods://')):
myEnv = parse_irodsUrl(stream)
stream = myEnv.relpath
else:
# Get parameters from env
status, myEnv = irods.getRodsEnv()
try:
host = myEnv.getRodsHost()
port = myEnv.getRodsPort()
username = myEnv.getRodsUserName()
zone = myEnv.getRodsZone()
home = myEnv.getRodsHome()
except AttributeError:
host = myEnv.rodsHost
port = myEnv.rodsPort
username = myEnv.rodsUserName
zone = myEnv.rodsZone
home = myEnv.rodsHome
conn, errMsg = irods.rcConnect(host, port, username, zone)
status = irods.clientLogin(conn)
if status:
raise ConfigFileException("Cannot connect to iRODS: ({0}) {1}"
"".format(status, errMsg)
)
c = irods.irodsCollection(conn)
self.cxn = conn
self.coll = c
instream = stream
# Check if abs path to home dir
if stream.startswith(home):
stream = stream[len(home):]
if stream[0] == "/":
stream = stream[1:]
colls = stream.split('/')
for i, cln in enumerate(colls):
exit_status = c.openCollection(cln)
if exit_status < 0:
if (
(i < len(colls) - 1) or
(cln not in [obj[0] for obj in c.getObjects()])
):
raise IOError("When opening {0}: {1} does not exists in "
"collection {2}".format(instream,
cln,
c.getCollName()
)
)
def open_irodsUrl(url, mode='r'):
"""Open and return the file specified by an iRODS URL.
Returns a file-like object - ``irods.IrodsFile``
"""
if irods is None:
raise MissingDependencyException("open_irodsUrl()", 'irods (PyRods)')
parsed = parse_irodsUrl(url)
conn, errMsg = irods.rcConnect(parsed.rodsHost, parsed.rodsPort,
parsed.rodsUserName, parsed.rodsZone)
status = irods.clientLogin(conn)
return irods.irodsOpen(conn, parsed.path, mode)
def __init__(self): self.status, self.myEnv = irods.getRodsEnv() self.conn, self.errMsg = irods.rcConnect(self.myEnv.rodsHost, self.myEnv.rodsPort, self.myEnv.rodsUserName, self.myEnv.rodsZone) self.status = irods.clientLogin(self.conn) self.path = makePath(self.myEnv.rodsHome, FOLDER) # addSlash(self.myEnv.rodsHome, reduce(addSlash, FOLDER)) self.coll = irods.irodsCollection(self.conn, self.path) self.popen_opt = dict(shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
def getConnection(self):
err = None
logging.debug('connecting to iRODS: host=%s port=%d login=%s zone=%s' \
% (self.host, self.port, self.user, self.zone))
# now connect
self.conn, err = irods.rcConnect(self.host, self.port, self.user, self.zone)
if self.conn is None:
logging.info('cannot connect to iRODS - Is server up?')
else:
irods.clientLoginWithPassword(self.conn, self.password)
return self.conn
def connect_to_irods(host, port, username, password, zone):
conn, err = rcConnect(host, port, username, zone)
if err.status != 0:
print 'ERROR: Unable to connect to iRODS@%s' % config['RODSHOST']
return None
if conn is None:
return conn
err = clientLoginWithPassword(conn, password)
if err != 0:
return conn
print 'Connection successful'
return conn
def get_connection_from_params(params):
"""
Create a iRODS data connection from POST parameters.
"""
conn = None
username = params['uname']
password = params['pw']
host = params['server']
port = params['port']
zone = params['zone']
if (host and port and username and zone):
from irods import rcConnect, clientLoginWithPassword
conn, _ = rcConnect(host, int(port), username, zone)
clientLoginWithPassword(conn, password)
return conn
def open_irodsUrl(url, mode='r'):
"""Open and return the file specified by an iRODS URL.
Returns a file-like object - ``irods.IrodsFile``
"""
if irods is None:
raise MissingDependencyException("open_irodsUrl()", 'irods (PyRods)')
parsed = parse_irodsUrl(url)
conn, errMsg = irods.rcConnect(parsed.rodsHost,
parsed.rodsPort,
parsed.rodsUserName,
parsed.rodsZone
)
status = irods.clientLogin(conn)
return irods.irodsOpen(conn, parsed.path, mode)
def get_connection_from_params(params):
"""
Create a iRODS data connection from POST parameters.
"""
conn = None
username = params['uname']
password = params['pw']
host = params['server']
port = params['port']
zone = params['zone']
if (host and port and username and zone):
from irods import rcConnect, clientLoginWithPassword
conn, _ = rcConnect(host, int(port), username, zone)
clientLoginWithPassword(conn, password)
return conn
def rods_connect():
"""
A basic iRODS connection mechanism that connects using the current iRODS
environment
"""
status, env = irods.getRodsEnv()
assert status == 0, 'connect(): getRodsEnv() failed (%s): %s' % ( status, irods.strerror( status ) )
conn, err = irods.rcConnect( env.rodsHost,
env.rodsPort,
env.rodsUserName,
env.rodsZone )
assert err.status == 0, 'connect(): rcConnect() failed (%s): %s' % ( err.status, err.msg )
status, pw = irods.obfGetPw()
assert status == 0, 'connect(): getting password with obfGetPw() failed (%s): %s' % ( status, irods.strerror( status ) )
status = irods.clientLoginWithObfPassword( conn, pw )
assert status == 0, 'connect(): logging in with clientLoginWithObfPassword() failed (%s): %s' % ( status, irods.strerror( status ) )
return env, conn
def rods_connect():
"""
A basic iRODS connection mechanism that connects using the current iRODS
environment
"""
status, env = irods.getRodsEnv()
assert status == 0, 'connect(): getRodsEnv() failed (%s): %s' % ( status, irods.strerror( status ) )
conn, err = irods.rcConnect( env.rodsHost,
env.rodsPort,
env.rodsUserName,
env.rodsZone )
assert err.status == 0, 'connect(): rcConnect() failed (%s): %s' % ( err.status, err.msg )
status, pw = irods.obfGetPw()
assert status == 0, 'connect(): getting password with obfGetPw() failed (%s): %s' % ( status, irods.strerror( status ) )
status = irods.clientLoginWithObfPassword( conn, pw )
assert status == 0, 'connect(): logging in with clientLoginWithObfPassword() failed (%s): %s' % ( status, irods.strerror( status ) )
return env, conn
def _openIrods(self, session):
if self.cxn is None:
# connect to iRODS
myEnv, status = irods.getRodsEnv()
conn, errMsg = irods.rcConnect(myEnv.getRodsHost(),
myEnv.getRodsPort(),
myEnv.getRodsUserName(),
myEnv.getRodsZone()
)
status = irods.clientLogin(conn)
if status:
raise ConfigFileException("Cannot connect to iRODS: (%s) %s"
"" % (status, errMsg))
self.cxn = conn
self.env = myEnv
if self.coll is not None:
# already open, just skip
return None
c = irods.irodsCollection(self.cxn, self.env.getRodsHome())
self.coll = c
# move into cheshire3 section
path = self.get_path(session, 'irodsCollection', 'cheshire3')
dirs = c.getSubCollections()
if not path in dirs:
c.createCollection(path)
c.openCollection(path)
# now look for object's storage area
# maybe move into database collection
if (isinstance(self.parent, Database)):
sc = self.parent.id
dirs = c.getSubCollections()
if not sc in dirs:
c.createCollection(sc)
c.openCollection(sc)
# move into store collection
dirs = c.getSubCollections()
if not self.id in dirs:
c.createCollection(self.id)
c.openCollection(self.id)
def open(self):
# pylint: disable=no-member
conn, _err = irods.rcConnect(self.host, self.port, self.user,
self.zone)
if conn is None:
raise IrodsError("Can't create connection to %s:%s " %
(self.host, _err))
if self.password:
irods.clientLoginWithPassword(conn, self.password)
else:
irods.clientLogin(conn)
coll = irods.irodsCollection(conn)
nm = coll.getCollName()
self.irods_url = urlparse.urlunparse(
list(self.irods_url)[:2] + [''] * 4)
if self.path in ['', '/']:
self.path = nm
self.conn = conn
self.base_dir = nm
return self
# Copyright (c) 2013, University of Liverpool
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
#
# Author : Jerome Fuselier
#
from irods import *
import irods
if __name__ == "__main__":
conn, errMsg = irods.rcConnect(u"localhost", 1247, u"rods", u"tempZone", 0)
print conn, errMsg
status = clientLogin(conn)
print status
print getUserInfo(conn, u"rods//??")
conn.disconnect()
def _open(self, session):
if self.cxn == None:
# connect to iRODS
myEnv, status = irods.getRodsEnv()
host = self.host if self.host else myEnv.getRodsHost()
port = self.port if self.port else myEnv.getRodsPort()
user = self.user if self.user else myEnv.getRodsUserName()
zone = self.zone if self.zone else myEnv.getRodsZone()
conn, errMsg = irods.rcConnect(host, port, user, zone)
if self.passwd:
status = irods.clientLoginWithPassword(conn, self.passwd)
else:
status = irods.clientLogin(conn)
if status:
raise ConfigFileException("Cannot connect to iRODS: (%s) %s" % (status, errMsg))
self.cxn = conn
self.env = myEnv
resources = irods.getResources(self.cxn)
self.resourceHash = {}
for r in resources:
self.resourceHash[r.getName()] = r
if self.coll != None:
# already open, just skip
return None
c = irods.irodsCollection(self.cxn, self.env.getRodsHome())
self.coll = c
# move into cheshire3 section
path = self.get_path(session, 'irodsCollection', 'cheshire3')
dirs = c.getSubCollections()
if not path in dirs:
c.createCollection(path)
c.openCollection(path)
if self.get_setting(session, 'createSubDir', 1):
# now look for object's storage area
# maybe move into database collection
if (isinstance(self.parent, Database)):
sc = self.parent.id
dirs = c.getSubCollections()
if not sc in dirs:
c.createCollection(sc)
c.openCollection(sc)
# move into store collection
dirs = c.getSubCollections()
if not self.id in dirs:
c.createCollection(self.id)
c.openCollection(self.id)
# Fetch user metadata
myMetadata = self.get_metadataTypes(session)
umd = c.getUserMetadata()
umdHash = {}
for u in umd:
umdHash[u[0]] = icatValToPy(*u[1:])
for md in myMetadata:
try:
setattr(self, md, umdHash[md])
except KeyError:
# hasn't been set yet
pass
if self.totalItems != 0:
self.meanWordCount = self.totalWordCount / self.totalItems
self.meanByteCount = self.totalByteCount / self.totalItems
else:
self.meanWordCount = 1
self.meanByteCount = 1
