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 __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(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 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 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
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 _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, 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