def transfer_toClient( self, fileID, token, fileHelper ):
""" Method to send files to clients.
fileID is the local file name in the SE.
token is used for access rights confirmation.
"""
conn , error = self.__irodsClient( "r" )
if not conn:
return S_ERROR( error )
file_path = self.__resolveFileID( fileID )
file_path = IRODS_HOME + file_path
gLogger.debug( "file_path to read: %s" % file_path )
fd = iRodsOpen( conn , file_path , "r" )
if not fd:
rcDisconnect( conn )
gLogger.error( "Failed to get file object" )
return S_ERROR( "Failed to get file object" )
result = fileHelper.FileToNetwork( fd )
fd.close()
rcDisconnect( conn )
if not result[ "OK" ]:
gLogger.error( "Failed to get file " + fileID )
return S_ERROR( "Failed to get file " + fileID )
else:
return result
def transfer_toClient(self, fileID, token, fileHelper):
""" Method to send files to clients.
fileID is the local file name in the SE.
token is used for access rights confirmation.
"""
conn, error = self.__irodsClient("r")
if not conn:
return S_ERROR(error)
file_path = self.__resolveFileID(fileID)
file_path = IRODS_HOME + file_path
gLogger.debug("file_path to read: %s" % file_path)
fd = iRodsOpen(conn, file_path, "r")
if not fd:
rcDisconnect(conn)
gLogger.error("Failed to get file object")
return S_ERROR("Failed to get file object")
result = fileHelper.FileToNetwork(fd)
fd.close()
rcDisconnect(conn)
if not result["OK"]:
gLogger.error("Failed to get file " + fileID)
return S_ERROR("Failed to get file " + fileID)
else:
return result
def irods_isfile(url, **kw):
chk_cache()
with IrodsConnection(url, **kw) as ic:
log.debug("irods_delete %s -> %s", url, ic.path)
f = irods.iRodsOpen(ic.conn, ic.path, 'r') # pylint: disable=no-member
if f:
f.close()
return True
return False
def irods_delete_file(url, **kw):
chk_cache()
ic = IrodsConnection(url, **kw)
log.debug("irods-path %s", ic.path)
localname = irods_cache_fetch(ic.path)
if localname is not None:
os.remove(localname)
with ic:
log.debug("irods_delete %s -> %s", url, ic.path)
f = irods.iRodsOpen(ic.conn, ic.path) # pylint: disable=no-member
if not f:
raise IrodsError("can't read from %s" % url)
f.close()
f.delete()
def irods_push_file(fileobj, url, savelocal=True, **kw):
chk_cache()
with IrodsConnection(url, **kw) as ic:
# Hmm .. if an irodsEnv exists then it is used over our login name provided above,
# meaning even though we have logged in as user X we may be the homedir of user Y (in .irodsEnv)
# irods.mkCollR(conn, basedir, os.path.dirname(path))
retcode = irods.mkCollR(ic.conn, '/', os.path.dirname(ic.path)) # pylint: disable=no-member
log.debug("irods-path %s", ic.path)
f = irods.iRodsOpen(ic.conn, ic.path, 'w') # pylint: disable=no-member
if f:
localname = irods_cache_save(fileobj, ic.path, f)
f.close()
return localname
raise IrodsError("can't write irods url %s" % url)
def irods_fetch_file(url, **kw):
chk_cache()
ic = IrodsConnection(url, **kw)
log.debug("irods-path %s", ic.path)
localname = irods_cache_fetch(ic.path)
if localname is None:
with ic:
log.debug("irods_fetching %s -> %s", url, ic.path)
f = irods.iRodsOpen(ic.conn, ic.path) # pylint: disable=no-member
if not f:
raise IrodsError("can't read from %s", url)
localname = irods_cache_save(f, ic.path)
f.close()
return localname
def getIrodsMetrics(self):
irodsMetrics = None
conn = self.mRods.getConnection()
if (conn is not None):
metricsFile = self.mRods.getMetricsFilePath() \
+ '/' + self.__class__.__name__ + '.json'
f = irods.iRodsOpen(conn, metricsFile, 'r')
if f is not None:
metricsStream = f.read()
irodsMetrics = json.loads(metricsStream)
f.close
self.mRods.disconnect()
return irodsMetrics
def import_collection_to_package(params, id):
"""
Import a collection to dataset. Does not import whole file data but
rather the metadata.
"""
from irods import irodsCollection
path = params['path']
pkg = Package.get(id)
conn = get_connection_from_params(params)
if (conn):
coll = irodsCollection(conn, path)
from irods import iRodsOpen
rev = model.repo.new_revision()
i = 0
for obj in coll.getObjects():
extras = {}
fname, _ = obj
fpath = "%s/%s" % (coll.getCollName(), fname)
f = iRodsOpen(conn, fpath, 'r')
if f:
i += 1
res = Resource.by_name(fname)
if not res:
res = Resource(url = '', name=fname, extras=extras, \
resource_type='file')
for met in f.getUserMetadata():
key, value, _ = met
extras[key] = value
res.extras = extras
resgrp = pkg.resource_groups[0]
resgrp.resources.append(res)
Session.add(res)
Session.add(resgrp)
rev.message = "Update from iRODS, matched file %s" % fname
for met in coll.getUserMetadata():
key, value, _ = met
pkg.extras[key] = value
Session.add(pkg)
model.repo.commit()
conn.disconnect()
h.flash_success("iRODS import to dataset OK! Imported %s resources." %
i)
else:
h.flash_error("Could not connect to iRODS!")
h.redirect_to(controller='package', action='read', id=id)
def import_collection_to_package(params, id):
"""
Import a collection to dataset. Does not import whole file data but
rather the metadata.
"""
from irods import irodsCollection
path = params['path']
pkg = Package.get(id)
conn = get_connection_from_params(params)
if (conn):
coll = irodsCollection(conn, path)
from irods import iRodsOpen
rev = model.repo.new_revision()
i = 0
for obj in coll.getObjects():
extras = {}
fname, _ = obj
fpath = "%s/%s" % (coll.getCollName(), fname)
f = iRodsOpen(conn, fpath, 'r')
if f:
i += 1
res = Resource.by_name(fname)
if not res:
res = Resource(url = '', name=fname, extras=extras, \
resource_type='file')
for met in f.getUserMetadata():
key, value, _ = met
extras[key] = value
res.extras = extras
resgrp = pkg.resource_groups[0]
resgrp.resources.append(res)
Session.add(res)
Session.add(resgrp)
rev.message = "Update from iRODS, matched file %s" % fname
for met in coll.getUserMetadata():
key, value, _ = met
pkg.extras[key] = value
Session.add(pkg)
model.repo.commit()
conn.disconnect()
h.flash_success("iRODS import to dataset OK! Imported %s resources." % i)
else:
h.flash_error("Could not connect to iRODS!")
h.redirect_to(controller='package', action='read', id=id)
def setIrodsMetrics(self, metrics):
if (metrics is None):
return
irodsMetricsList = list()
# retrieve list of metrics passed in
tmpMetricsList = metrics[self.__class__.__name__]
# first see if irods metrics already exist
irodsMetrics = self.getIrodsMetrics()
if irodsMetrics is not None:
irodsMetricsList = \
irodsMetrics[self.__class__.__name__]
# now add my new metrics to these metrics
irodsMetricsList += tmpMetricsList
metrics[self.__class__.__name__] = irodsMetricsList
# finally save as a json file to iRODS
conn = self.mRods.getConnection()
if (conn is not None):
# create the guinan collection in iRODS if it does not already exist
metricsCollection = self.mRods.getMetricsFilePath()
self.createGuinanCollection()
metricsFile = metricsCollection \
+ '/' + self.__class__.__name__ + '.json'
f = irods.iRodsOpen(conn, metricsFile, 'w')
if f is not None:
metricsJson = json.dumps(metrics)
f.write(metricsJson)
f.close()
logging.debug('Saved updated metrics to iRODS')
self.mRods.disconnect()