def retrieve_raw_files_metadata_by_metadata(cls,
search_criteria_list: List[
Tuple],
zone=None):
search_criteria_objs = []
for k, v in search_criteria_list:
search_criterion = SearchCriterion(k, v)
search_criteria_objs.append(search_criterion)
# Getting metadata from iRODS:
try:
connection = connect_to_irods_with_baton(
config.BATON_BIN
) # skip_baton_binaries_validation=True) # type: Connection
list_of_data_objs_and_metadata = connection.data_object.get_by_metadata(
search_criteria_objs, zone=zone)
except RuntimeError as e:
if str(e).find('KRB_ERROR_ACQUIRING_CREDS') != -1:
raise OSError(
"ERROR: you need to log into iRODS and aquire the KERBEROS credentials."
) from None
else:
raise e from None
raw_meta_objects = [
IrodsRawFileMetadata.from_baton_wrapper(data_obj)
for data_obj in list_of_data_objs_and_metadata
]
return raw_meta_objects
def test_from_baton_wrapper_file_replicas(self):
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc"),
baton_models.DataObjectReplica(number=2, checksum="abc"),]
data_obj = baton_models.DataObject(path='/humgen/projects/helic/123.bam', replicas=replicas)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(len(raw_meta.file_replicas), 2)
def test_from_baton_wrapper_missing_bits(self):
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc", host='hgi-dev', resource_name='irods-s1', up_to_date=True)]
metadata = baton_coll.IrodsMetadata({'study': set(['BLUEPRINT'])})
data_obj = baton_models.DataObject(path='/somepath/file.txt', metadata=metadata, replicas=replicas)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(len(raw_meta.file_replicas), 1)
self.assertEqual(len(raw_meta.acls), 0)
def test_from_baton_wrapper_acls(self):
user = "******"
acl = [baton_models.AccessControl(user, level=baton_models.AccessControl.Level.WRITE)]
data_obj = baton_models.DataObject(path='/somepath/file.txt', access_controls=acl)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(len(raw_meta.acls), 1)
self.assertEqual(raw_meta.acls[0].access_group, 'hgi')
self.assertEqual(raw_meta.acls[0].permission, IrodsPermission.WRITE)
self.assertEqual(raw_meta.acls[0].zone, 'Sanger1')
def test_from_baton_wrapper_all_ok(self):
user = "******"
acl = [baton_models.AccessControl(user, level=baton_models.AccessControl.Level.OWN)]
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc", host='hgi-dev', resource_name='irods-s1', up_to_date=True)]
data_obj = baton_models.DataObject(path='/somepath/file.txt', access_controls=acl, replicas=replicas)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(raw_meta.fpath, '/somepath/file.txt')
self.assertEqual(len(raw_meta.file_replicas), 1)
self.assertEqual(len(raw_meta.acls), 1)
self.assertEqual(raw_meta.acls[0].zone, 'humgen')
self.assertEqual(raw_meta.acls[0].access_group, 'serapis')
def test_from_baton_wrapper_full_obj(self):
user = "******"
acl = [baton_models.AccessControl(user, level=baton_models.AccessControl.Level.OWN)]
replicas = [
baton_models.DataObjectReplica(number=1, checksum="123abc", host='hgi-dev', resource_name='irods-s1', up_to_date=True),
baton_models.DataObjectReplica(number=2, checksum="abc", host='hgi-dev-wow', resource_name='irods-s2', up_to_date=True),]
metadata = baton_coll.IrodsMetadata({'study': set(['BLUEPRINT'])})
data_obj = baton_models.DataObject(path='/somepath/file.txt', access_controls=acl, metadata=metadata, replicas=replicas)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(raw_meta.fpath, '/somepath/file.txt')
self.assertEqual(len(raw_meta.file_replicas), 2)
self.assertEqual(len(raw_meta.acls), 1)
self.assertEqual(raw_meta.acls[0].zone, 'humgen')
self.assertEqual(raw_meta.acls[0].access_group, 'hgi')
def fetch_raw_file_metadata_by_path(cls, fpath):
try:
connection = connect_to_irods_with_baton(config.BATON_BIN)#, skip_baton_binaries_validation=True)
data_object = connection.data_object.get_by_path(fpath)
except Exception as e:
if str(e).find('KRB_ERROR_ACQUIRING_CREDS') != -1:
raise OSError("ERROR: you need to log into iRODS and aquire the KERBEROS credentials.") from None
else:
raise e from None
else:
if data_object:
raw_metadata = IrodsRawFileMetadata.from_baton_wrapper(data_object)
return raw_metadata
return None
def retrieve_raw_files_metadata_by_metadata(cls, search_criteria_list: List[Tuple], zone=None):
search_criteria_objs = []
for k, v in search_criteria_list:
search_criterion = SearchCriterion(k, v)
search_criteria_objs.append(search_criterion)
# Getting metadata from iRODS:
try:
connection = connect_to_irods_with_baton(config.BATON_BIN) # skip_baton_binaries_validation=True) # type: Connection
list_of_data_objs_and_metadata = connection.data_object.get_by_metadata(search_criteria_objs, zone=zone)
except RuntimeError as e:
if str(e).find('KRB_ERROR_ACQUIRING_CREDS') != -1:
raise OSError("ERROR: you need to log into iRODS and aquire the KERBEROS credentials.") from None
else:
raise e from None
raw_meta_objects = [IrodsRawFileMetadata.from_baton_wrapper(data_obj) for data_obj in list_of_data_objs_and_metadata]
return raw_meta_objects
def fetch_raw_file_metadata_by_path(cls, fpath):
try:
connection = connect_to_irods_with_baton(
config.BATON_BIN) #, skip_baton_binaries_validation=True)
data_object = connection.data_object.get_by_path(fpath)
except Exception as e:
if str(e).find('KRB_ERROR_ACQUIRING_CREDS') != -1:
raise OSError(
"ERROR: you need to log into iRODS and aquire the KERBEROS credentials."
) from None
else:
raise e from None
else:
if data_object:
raw_metadata = IrodsRawFileMetadata.from_baton_wrapper(
data_object)
return raw_metadata
return None
def test_from_baton_wrapper_fpath_2(self):
data_obj = baton_models.DataObject(path='/humgen/projects/helic/123.bam')
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(raw_meta.fpath, '/humgen/projects/helic/123.bam')
def test_from_baton_wrapper_fpath_1(self):
data_obj = baton_models.DataObject(path='/seq/123/123.bam.bai')
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(raw_meta.fpath, '/seq/123/123.bam.bai')
def test_from_baton_wrapper_metadata(self):
metadata = baton_coll.IrodsMetadata({'study': set(['BLUEPRINT']), 'sample': set(['123sam'])})
data_obj = baton_models.DataObject(path='/somepath/file.txt', metadata=metadata)
raw_meta = IrodsRawFileMetadata.from_baton_wrapper(data_obj)
self.assertEqual(raw_meta.get_values_for_attribute('study'), set(['BLUEPRINT']))