def fetch_metadata(self, session, id, mType):
""" Open irodsFile and get metadata from it. """
if (self.idNormalizer is not None):
id = self.idNormalizer.process_string(session, id)
elif type(id) == unicode:
id = id.encode('utf-8')
else:
id = str(id)
self._open(session)
upwards = 0
if id.find('/') > -1 and self.allowStoreSubDirs:
idp = id.split('/')
id = idp.pop()
while idp:
dn = idp.pop(0)
if not dn in self.coll.getSubCollections():
for x in range(upwards):
self.coll.upCollection()
raise ObjectDoesNotExistException(id)
self.coll.openCollection(dn)
upwards += 1
else:
id = id.replace('/', '--')
collPath = self.coll.getCollName()
# This is much more efficient than getting the file as it's simply
# interacting with iCAT
umd = irods.getFileUserMetadata(self.cxn,
'{0}/{1}'.format(collPath, id)
)
# if self.resource:
# f = self.coll.open(id, rescName=self.resource)
# else:
# f = self.coll.open(id)
#
# if not f:
# for x in range(upwards):
# self.coll.upCollection()
# return None
# umd = f.getUserMetadata()
# f.close()
val = None
for x in umd:
if x[0] == mType:
val = icatValToPy(x[1], x[2])
break
for x in range(upwards):
self.coll.upCollection()
return val
def find_documents(self, session, cache=0):
# Given a location in irods, go there and descend looking for files
c = self.coll
files = c.getObjects()
files.sort()
fList = [x[0] for x in files]
for i, f in enumerate(self._processFiles(session, fList)):
md = {}
irodsFilePath = '{0}/{1}'.format(c.getCollName(), f.filename)
for x in irods.getFileUserMetadata(self.cxn, irodsFilePath):
md[x[0]] = icatValToPy(x[1], x[2])
if len(md):
f.metadata['iRODS'] = md
# Delete the file on its resource
c.delete(files[i][0], files[i][1])
yield f
dirs = c.getSubCollections()
while dirs:
d = dirs.pop(0)
upColls = 0
for dx in d.split('/'):
c.openCollection(dx)
upColls += 1
files = c.getObjects()
files.sort()
fList = [x[0] for x in files]
for i, f in enumerate(self._processFiles(session, fList)):
md = {}
irodsFilePath = '{0}/{1}'.format(c.getCollName(), f.filename)
for x in irods.getFileUserMetadata(self.cxn, irodsFilePath):
md[x[0]] = icatValToPy(x[1], x[2])
if len(md):
f.metadata['iRODS'] = md
# Delete the file on its resource
c.delete(files[i][0], files[i][1])
yield f
ndirs = c.getSubCollections()
dirs.extend(["%s/%s" % (d, x) for x in ndirs])
for x in range(upColls):
c.upCollection()
def find_documents(self, session, cache=0):
# Given a location in irods, go there and descend looking for files
c = self.coll
files = c.getObjects()
files.sort()
fList = [x[0] for x in files]
for i, f in enumerate(self._processFiles(session, fList)):
md = {}
irodsFilePath = '{0}/{1}'.format(c.getCollName(), f.filename)
for x in irods.getFileUserMetadata(self.cxn, irodsFilePath):
md[x[0]] = icatValToPy(x[1], x[2])
if len(md):
f.metadata['iRODS'] = md
# Delete the file on its resource
c.delete(files[i][0], files[i][1])
yield f
dirs = c.getSubCollections()
while dirs:
d = dirs.pop(0)
upColls = 0
for dx in d.split('/'):
c.openCollection(dx)
upColls += 1
files = c.getObjects()
files.sort()
fList = [x[0] for x in files]
for i, f in enumerate(self._processFiles(session, fList)):
md = {}
irodsFilePath = '{0}/{1}'.format(c.getCollName(), f.filename)
for x in irods.getFileUserMetadata(self.cxn, irodsFilePath):
md[x[0]] = icatValToPy(x[1], x[2])
if len(md):
f.metadata['iRODS'] = md
# Delete the file on its resource
c.delete(files[i][0], files[i][1])
yield f
ndirs = c.getSubCollections()
dirs.extend(["%s/%s" % (d, x) for x in ndirs])
for x in range(upColls):
c.upCollection()
def find_documents(self, session, cache=0):
# given a location in irods, go there and descend looking for files
c = self.coll
files = c.getObjects()
files = [x[0] for x in files]
files.sort()
for f in self._processFiles(session, files):
md = {}
for x in irods.getFileUserMetadata(self.cxn, '{0}/{1}'.format(c.getCollName(), f.filename)):
md[x[0]] = icatValToPy(x[1], x[2])
if len(md):
f.metadata['iRODS'] = md
yield f
dirs = c.getSubCollections()
while dirs:
d = dirs.pop(0)
upColls = 0
for dx in d.split('/'):
c.openCollection(dx)
upColls += 1
files = c.getObjects()
files = [x[0] for x in files]
files.sort()
for f in self._processFiles(session, files):
md = {}
for x in irods.getFileUserMetadata(self.cxn, '{0}/{1}'.format(c.getCollName(), f.filename)):
md[x[0]] = icatValToPy(x[1], x[2])
if len(md):
f.metadata['iRODS'] = md
yield f
ndirs = c.getSubCollections()
dirs.extend(["%s/%s" % (d, x) for x in ndirs])
for x in range(upColls):
c.upCollection()
def sync_irods(params, id):
"""
Fetches a resource from database with the same path as user specified and
that matches an existing resource in CKAN.
"""
from irods import getFileUserMetadata, rcModAccessControl
rev = model.repo.new_revision()
conn = get_connection_from_params(params)
resource = Resource.get(id)
path = params['path']
extras = {}
# Lets handle only resources with file names
if resource.name:
fname = "%s/%s" % (path, resource.name.split('/')[-1])
log.debug(fname)
i = 0
access = rcModAccessControl()
log.debug(access.getPath())
if conn:
for met in getFileUserMetadata(conn, fname):
i += 1
key, value, _ = met
extras[key] = value
resource.extras = extras
Session.add(resource)
conn.disconnect()
model.repo.commit()
rev.message = "Update from iRODS, matched file %s" % fname
h.flash_success(
"iRODS import to resource OK! Imported %s metadatas" % i)
else:
h.flash_error("Could not connect to iRODS!")
else:
h.flash_error("Resource is an URL, cannot import!")
h.redirect_to(controller='package', action='resource_read', \
id=resource.resource_group.package.name, \
resource_id=resource.id)
def sync_irods(params, id):
"""
Fetches a resource from database with the same path as user specified and
that matches an existing resource in CKAN.
"""
from irods import getFileUserMetadata, rcModAccessControl
rev = model.repo.new_revision()
conn = get_connection_from_params(params)
resource = Resource.get(id)
path = params['path']
extras = {}
# Lets handle only resources with file names
if resource.name:
fname = "%s/%s" % (path, resource.name.split('/')[-1])
log.debug(fname)
i = 0
access = rcModAccessControl()
log.debug(access.getPath())
if conn:
for met in getFileUserMetadata(conn, fname):
i += 1
key, value, _ = met
extras[key] = value
resource.extras = extras
Session.add(resource)
conn.disconnect()
model.repo.commit()
rev.message = "Update from iRODS, matched file %s" % fname
h.flash_success("iRODS import to resource OK! Imported %s metadatas" % i)
else:
h.flash_error("Could not connect to iRODS!")
else:
h.flash_error("Resource is an URL, cannot import!")
h.redirect_to(controller='package', action='resource_read', \
id=resource.resource_group.package.name, \
resource_id=resource.id)
def get_file_metadatas(self, irods_path):
"""Get a list of metadatas for a file
a metadata is a tuple (name, value, units)"""
return irods.getFileUserMetadata(self.conn, irods_path)
