def launch(self, data_file):
"""
Execute import operations: unpack ZIP, build and store generic DataType objects.
:param data_file: an archive (ZIP / HDF5) containing the `DataType`
:raises LaunchException: when data_file is None, nonexistent, or invalid \
(e.g. incomplete meta-data, not in ZIP / HDF5 format etc. )
"""
if data_file is None:
raise LaunchException(
"Please select file which contains data to import")
if os.path.exists(data_file):
if zipfile.is_zipfile(data_file):
current_op = dao.get_operation_by_id(self.operation_id)
# Creates a new TMP folder where to extract data
tmp_folder = os.path.join(self.storage_path, "tmp_import")
FilesHelper().unpack_zip(data_file, tmp_folder)
operations = ImportService().import_project_operations(
current_op.project, self.storage_path)
shutil.rmtree(tmp_folder)
self.nr_of_datatypes += len(operations)
else:
# upgrade file if necessary
file_update_manager = FilesUpdateManager()
file_update_manager.upgrade_file(data_file)
folder, h5file = os.path.split(data_file)
manager = HDF5StorageManager(folder, h5file)
if manager.is_valid_hdf5_file():
datatype = None
try:
service = ImportService()
datatype = service.load_datatype_from_file(
folder,
h5file,
self.operation_id,
final_storage=self.storage_path)
service.store_datatype(datatype)
self.nr_of_datatypes += 1
except Exception as excep:
# If import operation failed delete file from disk.
if datatype is not None and os.path.exists(
datatype.get_storage_file_path()):
os.remove(datatype.get_storage_file_path())
self.log.exception(excep)
raise LaunchException(
"Invalid file received as input. Most probably incomplete "
"meta-data ... " + str(excep))
else:
raise LaunchException(
"Uploaded file: %s is neither in ZIP or HDF5 format" %
data_file)
else:
raise LaunchException("File: %s to import does not exists." %
data_file)
def setup_method(self):
"""
Reset the database before each test.
"""
self.import_service = ImportService()
self.project_service = ProjectService()
self.zip_path = None
def load_burst_from_json(self, **data):
"""Upload Burst from previously exported JSON file"""
self.logger.debug("Uploading ..." + str(data))
try:
upload_param = "uploadedfile"
if upload_param in data and data[upload_param]:
upload_param = data[upload_param]
if isinstance(upload_param, FieldStorage) or isinstance(
upload_param, Part):
if not upload_param.file:
raise BurstServiceException(
"Please select a valid JSON file.")
upload_param = upload_param.file.read()
upload_param = json.loads(upload_param)
prj_id = common.get_current_project().id
importer = ImportService()
burst_entity = importer.load_burst_entity(upload_param, prj_id)
common.add2session(common.KEY_BURST_CONFIG, burst_entity)
except Exception as excep:
self.logger.warning(excep.message)
common.set_error_message(excep.message)
raise cherrypy.HTTPRedirect('/burst/')
def launch_simulation_workflow(json_path, prj_id):
"""
:param json_path: Path towards a local JSON file exported from GUI
:param prj_id: This ID of a project needs to exists in DB, and it can be taken from the WebInterface
"""
project = dao.get_project_by_id(prj_id)
with open(json_path, 'rb') as input_file:
simulation_json = input_file.read()
simulation_json = json.loads(simulation_json)
LOG.info("Simulation JSON loaded from file '%s': \n %s", json_path,
simulation_json)
importer = ImportService()
simulation_config = importer.load_burst_entity(simulation_json, prj_id)
LOG.info("Simulation Workflow configuration object loaded: \n %s",
simulation_config)
flow_service = FlowService()
stored_adapter = flow_service.get_algorithm_by_module_and_class(
SIMULATOR_MODULE, SIMULATOR_CLASS)
LOG.info("Found Simulation algorithm in local DB: \n %s",
stored_adapter)
burst_service = BurstService()
burst_service.launch_burst(simulation_config, 0, stored_adapter.id,
project.administrator.id, LAUNCH_NEW)
LOG.info(
"Check in the web GUI for your operation. It should be starting now ..."
)
def load_simulator_configuration_from_zip(self, **data):
"""Upload Simulator from previously exported ZIP file"""
self.logger.debug("Uploading ..." + str(data))
last_loaded_form_url = SimulatorWizzardURLs.SETUP_PSE_URL
try:
upload_param = "uploadedfile"
if upload_param in data and data[upload_param]:
simulator, burst_config, sim_folder = self.burst_service.load_simulation_from_zip(
data[upload_param], self.context.project)
dts_folder = os.path.join(
sim_folder, StorageInterface.EXPORTED_SIMULATION_DTS_DIR)
ImportService().import_project_operations(
self.context.project, dts_folder, False, None)
self.monitors_handler.build_list_of_monitors_from_view_models(
simulator)
if burst_config.is_pse_burst():
last_loaded_form_url = SimulatorWizzardURLs.LAUNCH_PSE_URL
self.context.init_session_at_sim_config_from_zip(
burst_config, simulator, last_loaded_form_url)
except IOError as ioexcep:
self.logger.exception(ioexcep)
self.context.set_warning_message(
"This ZIP does not contain a complete simulator configuration")
except ServicesBaseException as excep:
self.logger.warning(excep.message)
self.context.set_warning_message(excep.message)
raise cherrypy.HTTPRedirect('/burst/')
def create_user(self,
username=None,
password=None,
password2=None,
role=None,
email=None,
comment=None,
email_msg=None,
validated=False):
"""
Service Layer for creating a new user.
"""
#Basic fields validation.
if (username is None) or len(username) < 1:
raise UsernameException("Empty UserName!")
if (password is None) or len(password) < 1:
raise UsernameException("Empty password!")
if password2 is None:
password2 = password
if password != password2:
raise UsernameException("Passwords do not match!")
try:
user_validated = (role == 'ADMINISTRATOR') or validated
user = model.User(username, password, email, user_validated, role)
if email_msg is None:
email_msg = 'Hello ' + username + TEXT_CREATE
admin_msg = (TEXT_CREATE_TO_ADMIN + username + ' :\n ' +
TvbProfile.current.web.BASE_URL + 'user/validate/' +
username + '\n\n"' + str(comment) + '"')
self.logger.info("Registering user " + username + " !")
if role != 'ADMINISTRATOR' and email is not None:
admins = UserService.get_administrators()
admin = admins[randint(0, len(admins) - 1)]
if admin.email is not None and (
admin.email !=
TvbProfile.current.web.admin.DEFAULT_ADMIN_EMAIL):
# Do not send validation email in case default admin email remained unchanged
email_sender.send(FROM_ADDRESS, admin.email,
SUBJECT_REGISTER, admin_msg)
self.logger.debug("Email sent to:" + admin.email +
" for validating user:"******" !")
email_sender.send(FROM_ADDRESS, email, SUBJECT_REGISTER,
email_msg)
self.logger.debug("Email sent to:" + email +
" for notifying new user:"******" !")
user = dao.store_entity(user)
if role == model.ROLE_ADMINISTRATOR:
uploaded = os.path.join(os.path.dirname(tvb_data.__file__),
"Default_Project.zip")
ImportService().import_project_structure(uploaded, user.id)
else:
handle_event(
".".join([self.__class__.__name__,
stack()[0][3]]), user)
return TEXT_DISPLAY
except Exception, excep:
self.logger.exception("Could not create user!")
raise UsernameException(str(excep))
def update(input_file, burst_match_dict=None):
"""
:param input_file: the file that needs to be converted to a newer file storage version.
"""
if not os.path.isfile(input_file):
raise IncompatibleFileManagerException("The input path %s received for upgrading from 3 -> 4 is not a "
"valid file on the disk." % input_file)
folder, file_name = os.path.split(input_file)
storage_manager = HDF5StorageManager(folder, file_name)
root_metadata = storage_manager.get_metadata()
if DataTypeMetaData.KEY_CLASS_NAME not in root_metadata:
raise IncompatibleFileManagerException("File %s received for upgrading 3 -> 4 is not valid, due to missing "
"metadata: %s" % (input_file, DataTypeMetaData.KEY_CLASS_NAME))
class_name = root_metadata[DataTypeMetaData.KEY_CLASS_NAME]
class_name = str(class_name, 'utf-8')
if "ProjectionSurface" in class_name and FIELD_PROJECTION_TYPE not in root_metadata:
LOGGER.info("Updating ProjectionSurface %s from %s" % (file_name, folder))
projection_type = ProjectionsType.EEG.value
if "SEEG" in class_name:
projection_type = ProjectionsType.SEEG.value
elif "MEG" in class_name:
projection_type = ProjectionsType.MEG.value
root_metadata[FIELD_PROJECTION_TYPE] = json.dumps(projection_type)
LOGGER.debug("Setting %s = %s" % (FIELD_PROJECTION_TYPE, projection_type))
elif "TimeSeries" in class_name:
LOGGER.info("Updating TS %s from %s" % (file_name, folder))
service = ImportService()
try:
operation_id = int(os.path.split(folder)[1])
dt = service.load_datatype_from_file(os.path.join(folder, file_name), operation_id)
dt_db = dao.get_datatype_by_gid(dt.gid)
except ValueError:
dt_db = None
if dt_db is not None:
# DT already in DB (update of own storage, by making sure all fields are being correctly populated)
dt_db.configure()
dt_db.persist_full_metadata()
try:
# restore in DB, in case TVB 1.4 had wrongly imported flags
dao.store_entity(dt_db)
except Exception:
LOGGER.exception("Could not update flags in DB, but we continue with the update!")
elif FIELD_SURFACE_MAPPING not in root_metadata:
# Have default values, to avoid the full project not being imported
root_metadata[FIELD_SURFACE_MAPPING] = json.dumps(False)
root_metadata[FIELD_VOLUME_MAPPING] = json.dumps(False)
root_metadata[TvbProfile.current.version.DATA_VERSION_ATTRIBUTE] = TvbProfile.current.version.DATA_VERSION
storage_manager.set_metadata(root_metadata)
def import_default_project(admin_user=None):
if not admin_user:
admin_user = TestFactory.create_user()
project_path = os.path.join(os.path.dirname(os.path.dirname(cff_dataset.__file__)), 'Default_Project.zip')
import_service = ImportService()
import_service.import_project_structure(project_path, admin_user.id)
return import_service.created_projects[0]
def create_user(self, username=None, display_name=None, password=None, password2=None,
role=None, email=None, comment=None, email_msg=None, validated=False, skip_import=False,
gid=None, skip_sending_email=False):
"""
Service Layer for creating a new user.
"""
if (username is None) or len(username) < 1:
raise UsernameException("Empty UserName!")
if (display_name is None) or len(display_name) < 1:
raise UsernameException("Empty display name!")
if (password is None) or len(password) < 1:
raise UsernameException("Empty password!")
if password2 is None:
password2 = password
if password != password2:
raise UsernameException("Passwords do not match!")
try:
user_validated = (role == ROLE_ADMINISTRATOR) or validated
user = User(username, display_name, password, email, user_validated, role, gid)
if email_msg is None:
email_msg = 'Hello ' + username + TEXT_CREATE
admin_msg = (TEXT_CREATE_TO_ADMIN + username + ' :\n ' + TvbProfile.current.web.BASE_URL +
'/user/validate/' + username + '\n\n"' + str(comment) + '"')
self.logger.info("Registering user " + username + " !")
if role != ROLE_ADMINISTRATOR and email is not None and not skip_sending_email:
admins = UserService.get_administrators()
admin = admins[random.randint(0, len(admins) - 1)]
if admin.email is not None and (admin.email != TvbProfile.current.web.admin.DEFAULT_ADMIN_EMAIL):
# Do not send validation email in case default admin email remained unchanged
email_sender.send(FROM_ADDRESS, admin.email, SUBJECT_REGISTER, admin_msg)
self.logger.debug("Email sent to:" + admin.email + " for validating user:"******" !")
email_sender.send(FROM_ADDRESS, email, SUBJECT_REGISTER, email_msg)
self.logger.debug("Email sent to:" + email + " for notifying new user:"******" !")
user = dao.store_entity(user)
if role == ROLE_ADMINISTRATOR and not skip_import:
to_upload = os.path.join(os.path.dirname(tvb_data.__file__), "Default_Project.zip")
if not os.path.exists(to_upload):
self.logger.warning("Could not find DEFAULT PROJECT at path %s. You might want to import it "
"yourself. See TVB documentation about where to find it!" % to_upload)
return TEXT_DISPLAY
ImportService().import_project_structure(to_upload, user.id)
else:
try:
default_prj_id = dao.get_project_by_gid(DEFAULT_PROJECT_GID).id
dao.add_members_to_project(default_prj_id, [user.id])
except Exception:
self.logger.warning(
"Could not link user_id: %d with project_gid: %s " % (user.id, DEFAULT_PROJECT_GID))
return TEXT_DISPLAY
except Exception as excep:
self.logger.exception("Could not create user!")
raise UsernameException(str(excep))
def launch(self, view_model):
# type: (TVBImporterModel) -> []
"""
Execute import operations: unpack ZIP, build and store generic DataType objects.
:raises LaunchException: when data_file is None, nonexistent, or invalid \
(e.g. incomplete meta-data, not in ZIP / HDF5 format etc. )
"""
if view_model.data_file is None:
raise LaunchException(
"Please select file which contains data to import")
service = ImportService()
if os.path.exists(view_model.data_file):
if zipfile.is_zipfile(view_model.data_file):
current_op = dao.get_operation_by_id(self.operation_id)
# Creates a new TMP folder where to extract data
tmp_folder = os.path.join(self.storage_path, "tmp_import")
FilesHelper().unpack_zip(view_model.data_file, tmp_folder)
operations = service.import_project_operations(
current_op.project, tmp_folder)
shutil.rmtree(tmp_folder)
self.nr_of_datatypes += len(operations)
else:
# upgrade file if necessary
file_update_manager = FilesUpdateManager()
file_update_manager.upgrade_file(view_model.data_file)
folder, h5file = os.path.split(view_model.data_file)
manager = HDF5StorageManager(folder, h5file)
if manager.is_valid_hdf5_file():
datatype = None
try:
datatype = service.load_datatype_from_file(
view_model.data_file, self.operation_id)
service.check_import_references(
view_model.data_file, datatype)
service.store_datatype(datatype, view_model.data_file)
self.nr_of_datatypes += 1
except ImportException as excep:
self.log.exception(excep)
if datatype is not None:
target_path = h5.path_for_stored_index(datatype)
if os.path.exists(target_path):
os.remove(target_path)
raise LaunchException(
"Invalid file received as input. " + str(excep))
else:
raise LaunchException(
"Uploaded file: %s is neither in ZIP or HDF5 format" %
view_model.data_file)
else:
raise LaunchException("File: %s to import does not exists." %
view_model.data_file)
def projectupload(self, **data):
"""Upload Project from TVB ZIP."""
self.logger.debug("Uploading ..." + str(data))
try:
upload_param = "uploadedfile"
if upload_param in data and data[upload_param]:
import_service = ImportService()
import_service.import_project_structure(data[upload_param], common.get_logged_user().id)
except ServicesBaseException, excep:
self.logger.warning(excep.message)
common.set_error_message(excep.message)
def _update_localconnectivity_metadata(folder, file_name):
service = ImportService()
operation_id = int(os.path.split(folder)[1])
dt = service.load_datatype_from_file(folder,
file_name,
operation_id,
move=False)
info_dict = SparseMatrix.extract_sparse_matrix_metadata(dt.matrix)
dt.set_metadata(info_dict, '', True, SparseMatrix.ROOT_PATH + 'matrix')
def update():
"""
Try to import Default_Project, so that new users created with the latest code can share this project.
"""
try:
admins = dao.get_administrators()
service = ImportService()
service.import_project_structure(DATA_FILE, admins[0].id)
except Exception:
LOGGER.exception("Could import DefaultProject!")
def update_localconnectivity_metadata(folder, file_name):
service = ImportService()
operation_id = int(os.path.split(folder)[1])
dt = service.load_datatype_from_file(os.path.join(folder, file_name), operation_id)
info_dict = {"dtype": dt.matrix.dtype.str,
"format": dt.matrix.format,
"Shape": str(dt.matrix.shape),
"Maximum": dt.matrix.data.max(),
"Minimum": dt.matrix.data.min(),
"Mean": dt.matrix.mean()}
dt.set_metadata(info_dict, '', True, '/matrix')
def load_simulation_from_zip(self, zip_file, project):
import_service = ImportService()
simulator_folder = import_service.import_simulator_configuration_zip(zip_file)
simulator_h5_filename = DirLoader(simulator_folder, None).find_file_for_has_traits_type(SimulatorAdapterModel)
simulator_h5_filepath = os.path.join(simulator_folder, simulator_h5_filename)
simulator = h5.load_view_model_from_file(simulator_h5_filepath)
burst_config = self.load_burst_configuration_from_folder(simulator_folder, project)
burst_config_copy = burst_config.clone()
simulator.generic_attributes.parent_burst = burst_config_copy.gid
return simulator, burst_config_copy, simulator_folder
def update(input_file):
"""
:param input_file: the file that needs to be converted to a newer file storage version.
"""
if not os.path.isfile(input_file):
raise FileVersioningException("The input path %s received for upgrading from 3 -> 4 is not a "
"valid file on the disk." % input_file)
folder, file_name = os.path.split(input_file)
storage_manager = HDF5StorageManager(folder, file_name)
root_metadata = storage_manager.get_metadata()
class_name = root_metadata[DataTypeMetaData.KEY_CLASS_NAME]
if "ProjectionSurface" in class_name and FIELD_PROJECTION_TYPE not in root_metadata:
LOGGER.info("Updating ProjectionSurface %s from %s" % (file_name, folder))
projection_type = projections_data.EEG_POLYMORPHIC_IDENTITY
if "SEEG" in class_name:
projection_type = projections_data.SEEG_POLYMORPHIC_IDENTITY
elif "MEG" in class_name:
projection_type = projections_data.MEG_POLYMORPHIC_IDENTITY
root_metadata[FIELD_PROJECTION_TYPE] = json.dumps(projection_type)
LOGGER.debug("Setting %s = %s" % (FIELD_PROJECTION_TYPE, projection_type))
elif "TimeSeries" in class_name:
LOGGER.info("Updating TS %s from %s" % (file_name, folder))
service = ImportService()
operation_id = int(os.path.split(folder)[1])
dt = service.load_datatype_from_file(folder, file_name, operation_id, move=False)
dt_db = dao.get_datatype_by_gid(dt.gid)
if dt_db is not None:
# DT already in DB (update of own storage, by making sure all fields are being correctly populated)
dt_db.configure()
dt_db.persist_full_metadata()
# restore in DB, in case TVB 1.4 had wrongly imported flags
dao.store_entity(dt_db)
elif FIELD_SURFACE_MAPPING not in root_metadata:
# Have default values, to avoid the full project not being imported
root_metadata[FIELD_SURFACE_MAPPING] = json.dumps(False)
root_metadata[FIELD_VOLUME_MAPPING] = json.dumps(False)
root_metadata[TvbProfile.current.version.DATA_VERSION_ATTRIBUTE] = TvbProfile.current.version.DATA_VERSION
storage_manager.set_metadata(root_metadata)
def load_from_zip(self, zip_file, project):
import_service = ImportService()
simulator_folder = import_service.import_simulator_configuration_zip(
zip_file)
simulator_h5_filename = DirLoader(
simulator_folder, None).find_file_for_has_traits_type(Simulator)
with SimulatorH5(os.path.join(simulator_folder,
simulator_h5_filename)) as sim_h5:
simulator_gid = sim_h5.gid.load()
simulator = SimulatorSerializer.deserialize_simulator(
simulator_gid, simulator_folder)
burst_config = self.burst_service.load_burst_configuration_from_folder(
simulator_folder, project)
return simulator, burst_config
def transactional_setup_method(self):
"""
Reset the database before each test.
"""
self.import_service = ImportService()
self.flow_service = FlowService()
self.project_service = ProjectService()
self.test_user = TestFactory.create_user()
self.test_project = TestFactory.create_project(self.test_user,
name="GeneratedProject",
description="test_desc")
self.operation = TestFactory.create_operation(
test_user=self.test_user, test_project=self.test_project)
self.adapter_instance = TestFactory.create_adapter()
TestFactory.import_cff(test_user=self.test_user,
test_project=self.test_project)
self.zip_path = None
def transactional_setup_method(self):
"""
Prepare the database before each test.
"""
self.import_service = ImportService()
self.flow_service = FlowService()
self.project_service = ProjectService()
self.test_user = TestFactory.create_user()
self.delete_project_folders()
result = self.count_all_entities(DataType)
assert 0 == result, "There should be no data type in DB"
result = self.count_all_entities(Project)
assert 0 == result
self.test_project = TestFactory.import_default_project(self.test_user)
self.operation = TestFactory.create_operation(
test_user=self.test_user, test_project=self.test_project)
def setUp(self):
"""
Prepare the database before each test.
"""
self.import_service = ImportService()
self.flow_service = FlowService()
self.project_service = ProjectService()
self.test_user = TestFactory.create_user()
self.delete_project_folders()
result = self.count_all_entities(DataType)
self.assertEqual(0, result, "There should be no data type in DB")
result = self.count_all_entities(Project)
self.assertEqual(0, result)
self.test_project = TestFactory.import_default_project(self.test_user)
self.operation = TestFactory.create_operation(test_user=self.test_user, test_project=self.test_project)
self.adapter_instance = TestFactory.create_adapter(test_project=self.test_project)
def read_h5(full_paths):
# We need to load the DataType in the context of an operation, and a project
all_projects = dao.get_all_projects()
all_operations = dao.get_generic_entity(Operation, all_projects[0].id,
"fk_launched_in")
service = ImportService()
results = []
for full_path in full_paths:
# The actual read of H5:
datatype = service.load_datatype_from_file(full_path,
all_operations[0].id)
print("We've build DataType: [%s]" % datatype.__class__.__name__,
datatype)
results.append(datatype)
return results
def transactional_setup_method(self):
"""
Reset the database before each test.
"""
self.import_service = ImportService()
self.flow_service = FlowService()
self.project_service = ProjectService()
self.test_user = TestFactory.create_user()
self.test_project = TestFactory.create_project(self.test_user,
name="GeneratedProject",
description="test_desc")
self.operation = TestFactory.create_operation(
test_user=self.test_user, test_project=self.test_project)
self.adapter_instance = TestFactory.create_adapter()
zip_path = os.path.join(os.path.dirname(tvb_data.__file__),
'connectivity', 'connectivity_66.zip')
TestFactory.import_zip_connectivity(self.test_user, self.test_project,
zip_path)
self.zip_path = None
def run_import(project_path):
## If we would know a UserID to have as admin, next step would not be necessary.
## Make sure at least one user exists in TVB DB:
user_service = UserService()
admins = user_service.get_administrators()
if admins:
admin = admins[0]
else:
## No Admin user was found, we will create one
user_service.create_user("admin", "pass", role=model.ROLE_ADMINISTRATOR,
email="*****@*****.**", validated=True, skip_import=True)
admin = user_service.get_administrators()[0]
## Do the actual import of a project from ZIP:
import_service = ImportService()
import_service.import_project_structure(project_path, admin.id)
print("Project imported successfully. Check the Web UI!")
def _import(self, export_file, user_id):
""" import a project zip for a user """
# instantiated for every use because it is stateful
import_service = ImportService()
import_service.import_project_structure(export_file, user_id)
return import_service.created_projects[0].id
def launch(self, view_model):
# type: (TVBImporterModel) -> []
"""
Execute import operations: unpack ZIP, build and store generic DataType objects.
:raises LaunchException: when data_file is None, nonexistent, or invalid \
(e.g. incomplete meta-data, not in ZIP / HDF5 format etc. )
"""
if view_model.data_file is None:
raise LaunchException(
"Please select file which contains data to import")
service = ImportService()
if os.path.exists(view_model.data_file):
current_op = dao.get_operation_by_id(self.operation_id)
if zipfile.is_zipfile(view_model.data_file):
# Creates a new TMP folder where to extract data
tmp_folder = os.path.join(self.storage_path, "tmp_import")
self.storage_interface.unpack_zip(view_model.data_file,
tmp_folder)
is_group = False
current_op_id = current_op.id
for file in os.listdir(tmp_folder):
# In case we import a DatatypeGroup, we want the default import flow
if os.path.isdir(os.path.join(tmp_folder, file)):
current_op_id = None
is_group = True
break
try:
operations, all_dts, stored_dts_count = service.import_project_operations(
current_op.project, tmp_folder, is_group,
current_op_id)
self.nr_of_datatypes += stored_dts_count
if stored_dts_count == 0:
current_op.additional_info = 'All chosen datatypes already exist!'
dao.store_entity(current_op)
elif stored_dts_count < all_dts:
current_op.additional_info = 'Part of the chosen datatypes already exist!'
dao.store_entity(current_op)
except ImportException as excep:
self.log.exception(excep)
current_op.additional_info = excep.message
current_op.status = STATUS_ERROR
raise LaunchException("Invalid file received as input. " +
str(excep))
finally:
shutil.rmtree(tmp_folder)
else:
# upgrade file if necessary
file_update_manager = FilesUpdateManager()
file_update_manager.upgrade_file(view_model.data_file)
if self.storage_interface.get_storage_manager(
view_model.data_file).is_valid_tvb_file():
datatype = None
try:
datatype = service.load_datatype_from_file(
view_model.data_file, self.operation_id)
stored_new_dt = service.store_or_link_datatype(
datatype, view_model.data_file,
current_op.project.id)
if stored_new_dt == 0:
current_op.additional_info = 'The chosen datatype already exists!'
dao.store_entity(current_op)
self.nr_of_datatypes += stored_new_dt
except ImportException as excep:
self.log.exception(excep)
if datatype is not None:
target_path = h5.path_for_stored_index(datatype)
if os.path.exists(target_path):
os.remove(target_path)
raise LaunchException(
"Invalid file received as input. " + str(excep))
else:
raise LaunchException(
"Uploaded file: %s is neither in ZIP or HDF5 format" %
view_model.data_file)
else:
raise LaunchException("File: %s to import does not exists." %
view_model.data_file)
