def __init__(self, manager, result=None):
self.manager = manager
if result:
self.id = result[Collection.id]
self.path = result[Collection.name]
self.name = irods_basename(result[Collection.name])
self._meta = None
def _download(self, obj, local_path, **options):
if os.path.isdir(local_path):
file = os.path.join(local_path, irods_basename(obj))
else:
file = local_path
# Check for force flag if file exists
if os.path.exists(file) and kw.FORCE_FLAG_KW not in options:
raise ex.OVERWRITE_WITHOUT_FORCE_FLAG
with open(file, 'wb') as f, self.open(obj, 'r', **options) as o:
for chunk in chunks(o, self.READ_BUFFER_SIZE):
f.write(chunk)
def _download(self, obj, local_path, **options):
if os.path.isdir(local_path):
file = os.path.join(local_path, irods_basename(obj))
else:
file = local_path
# Check for force flag if file exists
if os.path.exists(file) and kw.FORCE_FLAG_KW not in options:
raise ex.OVERWRITE_WITHOUT_FORCE_FLAG
with open(file, 'wb') as f, self.open(obj, 'r', **options) as o:
for chunk in chunks(o, self.READ_BUFFER_SIZE):
f.write(chunk)
def get(self, path, file=None, **options):
parent = self.sess.collections.get(irods_dirname(path))
# TODO: optimize
if file:
self._download(path, file, **options)
query = self.sess.query(DataObject)\
.filter(DataObject.name == irods_basename(path))\
.filter(DataObject.collection_id == parent.id)
results = query.all() # get up to max_rows replicas
if len(results) <= 0:
raise ex.DataObjectDoesNotExist()
return iRODSDataObject(self, parent, results)
def get(self, path, file=None, **options):
parent = self.sess.collections.get(irods_dirname(path))
# TODO: optimize
if file:
self._download(path, file, **options)
query = self.sess.query(DataObject)\
.filter(DataObject.name == irods_basename(path))\
.filter(DataObject.collection_id == parent.id)
results = query.all() # get up to max_rows replicas
if len(results) <= 0:
raise ex.DataObjectDoesNotExist()
return iRODSDataObject(self, parent, results)
def do_mkdir(self, line):
try:
opts, args = self.parse_command("mkdir", "", line)
except self._ConnectionError:
return
for arg in args:
path = self.get_path(arg)
try:
self.session.collections.create(path)
except CATALOG_ALREADY_HAS_ITEM_BY_THAT_NAME:
self.println(
"... mkdir: cannot create collection `{:}`:"
" Object exists", irods_basename(path))
break
def get(self, path, file=None, **options):
parent = self.sess.collections.get(irods_dirname(path))
# TODO: optimize
if file:
self._download(path, file, **options)
query = self.sess.query(DataObject)\
.filter(DataObject.name == irods_basename(path))\
.filter(DataObject.collection_id == parent.id)\
.add_keyword(kw.ZONE_KW, path.split('/')[1])
results = query.all() # get up to max_rows replicas
if len(results) <= 0:
raise ex.DataObjectDoesNotExist()
# workaround incompatibility of irodsclient-0.8.2 and iRODS server 3.x
for r in results:
if DataObject.resc_hier not in r:
r[DataObject.resc_hier] = None
return iRODSDataObject(self, parent, results)
def do_cd(self, line):
"""Change the current irods collection
"""
# Parse the new path
try:
opts, args = self.parse_command("cd", "", line, noargs=True)
except self._ConnectionError:
return
if not args:
path = HOME
else:
path = self.get_path(args[0])
# Fetch the corresponding irods collection
try:
self.cursor = self.session.collections.get(path)
except CollectionDoesNotExist:
self.println("... path `{:}` does not exist", args[0])
else:
# Update the prompt
current = irods_basename(self.cursor.path)
self.prompt = "[trirods@ccirods {:}]$ ".format(current)
def get(self,
path,
local_path=None,
num_threads=DEFAULT_NUMBER_OF_THREADS,
**options):
parent = self.sess.collections.get(irods_dirname(path))
# TODO: optimize
if local_path:
self._download(path,
local_path,
num_threads=num_threads,
**options)
query = self.sess.query(DataObject)\
.filter(DataObject.name == irods_basename(path))\
.filter(DataObject.collection_id == parent.id)\
.add_keyword(kw.ZONE_KW, path.split('/')[1])
results = query.all() # get up to max_rows replicas
if len(results) <= 0:
raise ex.DataObjectDoesNotExist()
return iRODSDataObject(self, parent, results)
def _download(self, obj, local_path, num_threads, **options):
if os.path.isdir(local_path):
local_file = os.path.join(local_path, irods_basename(obj))
else:
local_file = local_path
# Check for force flag if local_file exists
if os.path.exists(local_file) and kw.FORCE_FLAG_KW not in options:
raise ex.OVERWRITE_WITHOUT_FORCE_FLAG
with open(local_file, 'wb') as f, self.open(obj, 'r', **options) as o:
if self.should_parallelize_transfer(num_threads, o):
f.close()
if not self.parallel_get(
(obj, o),
local_path,
num_threads=num_threads,
target_resource_name=options.get(kw.RESC_NAME_KW, '')):
raise RuntimeError("parallel get failed")
else:
for chunk in chunks(o, self.READ_BUFFER_SIZE):
f.write(chunk)
def data_access_query(self, path):
cn = irods_dirname(path)
dn = irods_basename(path)
return self.sess.query(DataObject,
DataAccess).filter(Collection.name == cn,
DataObject.name == dn)
def get_collection_tree(self, base, path, sessions_cleanup=True):
"""
Lists the folders and files attributes at the input 'path'
Parameters
----------
base : str
The base path to validate ; eg. P000000001/C000000001
path : str
The collection's id; eg. P000000001/C000000001/SubFolder1/Experiment1/
sessions_cleanup: bool
If true, the session will be closed after retrieving the values.
Returns
-------
dict
The folders and files attributes at the requested path
"""
output = []
base_path = "/nlmumc/projects/" + base
absolute_path = "/nlmumc/projects/" + path
if not is_safe_path(base_path, absolute_path):
raise CAT_NO_ACCESS_PERMISSION
collection = self.session.collections.get(absolute_path)
for coll in collection.subcollections:
# query extra collection info: ctime
query = self.session.query(iRODSCollection).filter(
iRODSCollection.id == coll.id)
try:
result = query.one()
except NoResultFound:
raise CollectionDoesNotExist()
name = irods_basename(result[iRODSCollection.name])
ctime = result[iRODSCollection.create_time]
relative_path = path + "/" + name
folder_node = {
"name": name,
"path": relative_path,
"type": "folder",
"size": "--",
"rescname": "--",
"ctime": ctime.strftime("%Y-%m-%d %H:%M:%S"),
}
output.append(folder_node)
for data in collection.data_objects:
# query extra data info: ctime
query = self.session.query(DataObject).filter(
DataObject.id == data.id)
try:
result = query.first()
except NoResultFound:
raise DataObjectDoesNotExist()
ctime = result[DataObject.create_time]
relative_path = path + "/" + data.name
data_node = {
"name": data.name,
"path": relative_path,
"type": "file",
"size": data.size,
"rescname": data.resource_name,
"offlineResource": data.resource_name == "arcRescSURF01",
"ctime": ctime.strftime("%Y-%m-%d %H:%M:%S"),
}
output.append(data_node)
if sessions_cleanup:
self.session.cleanup()
return output