def test_tvb_export_of_simple_datatype_with_encryption(
self, dummy_datatype_index_factory):
"""
Test export of an encrypted data type which has no data stored on file system
"""
datatype = dummy_datatype_index_factory()
storage_interface = StorageInterface()
import_export_encryption_handler = StorageInterface.get_import_export_encryption_handler(
)
import_export_encryption_handler.generate_public_private_key_pair(
TvbProfile.current.TVB_TEMP_FOLDER)
_, file_path, _ = self.export_manager.export_data(
datatype, self.TVB_EXPORTER, self.test_project,
os.path.join(TvbProfile.current.TVB_TEMP_FOLDER,
import_export_encryption_handler.PUBLIC_KEY_NAME))
assert file_path is not None, "Export process should return path to export file"
assert os.path.exists(
file_path), "Could not find export file: %s on disk." % file_path
result = storage_interface.unpack_zip(
file_path, TvbProfile.current.TVB_TEMP_FOLDER)
encrypted_password_path = import_export_encryption_handler.extract_encrypted_password_from_list(
result)
decrypted_file_path = import_export_encryption_handler.decrypt_content(
encrypted_password_path, result,
os.path.join(TvbProfile.current.TVB_TEMP_FOLDER,
import_export_encryption_handler.PRIVATE_KEY_NAME))[0]
original_path = h5.path_for_stored_index(datatype)
self.compare_files(original_path, decrypted_file_path)
def launch(self, view_model):
# type: (TumorDatasetImporterModel) -> []
"""
Download the Tumor Dataset and then import its data
(currently only the connectivties and pearson coefficients are imported).
"""
storage_interface = StorageInterface()
folder = storage_interface.get_tumor_dataset_folder()
download_path = os.path.join(folder, self.TUMOR_ZIP_FILE_NAME)
import_path = os.path.join(os.path.dirname(download_path),
'TVB_brain_tumor', 'derivatives', 'TVB')
if not os.path.exists(import_path):
was_downloaded = self.__download_tumor_dataset(
0, download_path, self.MAXIMUM_DOWNLOAD_RETRIES,
view_model.tumor_dataset_url)
if was_downloaded is False:
return
storage_interface.unpack_zip(download_path,
os.path.dirname(download_path))
os.remove(download_path)
for patient in os.listdir(import_path):
patient_path = os.path.join(import_path, patient)
if os.path.isdir(patient_path):
user_tags = os.listdir(patient_path)
for user_tag in user_tags:
datatype_folder = os.path.join(patient_path, user_tag)
conn_gid = self.__import_tumor_connectivity(
datatype_folder, patient, user_tag)
# The Time Series are invisible in the UI and are imported
# just so we can link them with the Pearson Coefficients
ts_gid = self.__import_time_series_csv_datatype(
datatype_folder, conn_gid, patient, user_tag)
self.__import_pearson_coefficients_datatype(
datatype_folder, patient, user_tag, ts_gid)
self.logger.debug(
"Importing Tumor Dataset has been successfully completed!")
def test_tvb_linked_export_of_simple_datatype_with_encryption(
self, connectivity_index_factory, surface_index_factory,
region_mapping_index_factory):
"""
Test export of an encrypted data type and its linked data types which have no data stored on file system
"""
conn = connectivity_index_factory()
surface_idx, surface = surface_index_factory(cortical=True)
region_mapping_index = region_mapping_index_factory(
conn_gid=conn.gid, surface_gid=surface.gid.hex)
storage_interface = StorageInterface()
import_export_encryption_handler = StorageInterface.get_import_export_encryption_handler(
)
import_export_encryption_handler.generate_public_private_key_pair(
TvbProfile.current.TVB_TEMP_FOLDER)
_, file_path, _ = self.export_manager.export_data(
region_mapping_index, self.TVB_LINKED_EXPORTER, self.test_project,
os.path.join(TvbProfile.current.TVB_TEMP_FOLDER,
import_export_encryption_handler.PUBLIC_KEY_NAME))
assert file_path is not None, "Export process should return path to export file"
assert os.path.exists(
file_path), "Could not find export file;: %s on disk." % file_path
result = storage_interface.unpack_zip(
file_path, TvbProfile.current.TVB_TEMP_FOLDER)
encrypted_password = import_export_encryption_handler.extract_encrypted_password_from_list(
result)
decrypted_file_paths = import_export_encryption_handler.decrypt_content(
encrypted_password, result,
os.path.join(TvbProfile.current.TVB_TEMP_FOLDER,
import_export_encryption_handler.PRIVATE_KEY_NAME))
original_conn_path = h5.path_for_stored_index(conn)
decrypted_conn_path, idx = (decrypted_file_paths[0], 0) if 'Connectivity' in decrypted_file_paths[0] else \
(decrypted_file_paths[1], 1) if 'Connectivity' in decrypted_file_paths[1] else (decrypted_file_paths[2], 2)
self.compare_files(original_conn_path, decrypted_conn_path)
original_surface_path = h5.path_for_stored_index(surface_idx)
del decrypted_file_paths[idx]
decrypted_surface_path, idx = (decrypted_file_paths[0], 0) if 'Surface' in decrypted_file_paths[0] else \
(decrypted_file_paths[1], 1)
self.compare_files(original_surface_path, decrypted_surface_path)
original_rm_path = h5.path_for_stored_index(region_mapping_index)
del decrypted_file_paths[idx]
self.compare_files(original_rm_path, decrypted_file_paths[0])
def test_tvb_export_for_encrypted_datatype_group_with_links(
self, datatype_group_factory):
"""
This method checks export of an encrypted data type group
"""
ts_datatype_group, dm_datatype_group = datatype_group_factory(
project=self.test_project, store_vm=True)
storage_interface = StorageInterface()
import_export_encryption_handler = StorageInterface.get_import_export_encryption_handler(
)
import_export_encryption_handler.generate_public_private_key_pair(
TvbProfile.current.TVB_TEMP_FOLDER)
file_name, file_path, _ = self.export_manager.export_data(
dm_datatype_group, self.TVB_EXPORTER, self.test_project,
os.path.join(TvbProfile.current.TVB_TEMP_FOLDER,
import_export_encryption_handler.PUBLIC_KEY_NAME))
assert file_name is not None, "Export process should return a file name"
assert file_path is not None, "Export process should return path to export file"
assert os.path.exists(
file_path), "Could not find export file: %s on disk." % file_path
# Now check if the generated file is a correct ZIP file
assert zipfile.is_zipfile(
file_path), "Generated file is not a valid ZIP file"
result = storage_interface.unpack_zip(
file_path, TvbProfile.current.TVB_TEMP_FOLDER)
encrypted_password = import_export_encryption_handler.extract_encrypted_password_from_list(
result)
decrypted_file_paths = import_export_encryption_handler.decrypt_content(
encrypted_password, result,
os.path.join(TvbProfile.current.TVB_TEMP_FOLDER,
import_export_encryption_handler.PRIVATE_KEY_NAME))
# Here we only test if the length of decrypted_file_paths is the one expected
assert len(decrypted_file_paths) == len(
result
), "Number of decrypted data type group files is not correct!"
class ImportService(object):
"""
Service for importing TVB entities into system.
It supports TVB exported H5 files as input, but it should also handle H5 files
generated outside of TVB, as long as they respect the same structure.
"""
def __init__(self):
self.logger = get_logger(__name__)
self.user_id = None
self.storage_interface = StorageInterface()
self.created_projects = []
self.view_model2adapter = self._populate_view_model2adapter()
def _download_and_unpack_project_zip(self, uploaded, uq_file_name,
temp_folder):
if isinstance(uploaded, (FieldStorage, Part)):
if not uploaded.file:
raise ImportException(
"Please select the archive which contains the project structure."
)
with open(uq_file_name, 'wb') as file_obj:
self.storage_interface.copy_file(uploaded.file, file_obj)
else:
shutil.copy2(uploaded, uq_file_name)
try:
self.storage_interface.unpack_zip(uq_file_name, temp_folder)
except FileStructureException as excep:
self.logger.exception(excep)
raise ImportException(
"Bad ZIP archive provided. A TVB exported project is expected!"
)
@staticmethod
def _compute_unpack_path():
"""
:return: the name of the folder where to expand uploaded zip
"""
now = datetime.now()
date_str = "%d-%d-%d_%d-%d-%d_%d" % (now.year, now.month, now.day,
now.hour, now.minute, now.second,
now.microsecond)
uq_name = "%s-ImportProject" % date_str
return os.path.join(TvbProfile.current.TVB_TEMP_FOLDER, uq_name)
@transactional
def import_project_structure(self, uploaded, user_id):
"""
Execute import operations:
1. check if ZIP or folder
2. find all project nodes
3. for each project node:
- create project
- create all operations and groups
- import all images
- create all dataTypes
"""
self.user_id = user_id
self.created_projects = []
# Now compute the name of the folder where to explode uploaded ZIP file
temp_folder = self._compute_unpack_path()
uq_file_name = temp_folder + ".zip"
try:
self._download_and_unpack_project_zip(uploaded, uq_file_name,
temp_folder)
self._import_project_from_folder(temp_folder)
except Exception as excep:
self.logger.exception(
"Error encountered during import. Deleting projects created during this operation."
)
# Remove project folders created so far.
# Note that using the project service to remove the projects will not work,
# because we do not have support for nested transaction.
# Removing from DB is not necessary because in transactional env a simple exception throw
# will erase everything to be inserted.
for project in self.created_projects:
self.storage_interface.remove_project(project)
raise ImportException(str(excep))
finally:
# Now delete uploaded file and temporary folder where uploaded ZIP was exploded.
self.storage_interface.remove_files([uq_file_name, temp_folder])
def _import_project_from_folder(self, temp_folder):
"""
Process each project from the uploaded pack, to extract names.
"""
temp_project_path = None
for root, _, files in os.walk(temp_folder):
if StorageInterface.TVB_PROJECT_FILE in files:
temp_project_path = root
break
if temp_project_path is not None:
update_manager = ProjectUpdateManager(temp_project_path)
if update_manager.checked_version < 3:
raise ImportException(
'Importing projects with versions older than 3 is not supported in TVB 2! '
'Please import the project in TVB 1.5.8 and then launch the current version of '
'TVB in order to upgrade this project!')
update_manager.run_all_updates()
project = self.__populate_project(temp_project_path)
# Populate the internal list of create projects so far, for cleaning up folders, in case of failure
self.created_projects.append(project)
# Ensure project final folder exists on disk
project_path = self.storage_interface.get_project_folder(
project.name)
shutil.move(
os.path.join(temp_project_path,
StorageInterface.TVB_PROJECT_FILE), project_path)
# Now import project operations with their results
self.import_list_of_operations(project, temp_project_path)
# Import images and move them from temp into target
self._store_imported_images(project, temp_project_path,
project.name)
if StorageInterface.encryption_enabled():
self.storage_interface.remove_project(project, True)
def _load_datatypes_from_operation_folder(self, src_op_path,
operation_entity,
datatype_group):
"""
Loads datatypes from operation folder
:returns: Datatype entities as dict {original_path: Dt instance}
"""
all_datatypes = {}
for file_name in os.listdir(src_op_path):
if self.storage_interface.ends_with_tvb_storage_file_extension(
file_name):
h5_file = os.path.join(src_op_path, file_name)
try:
file_update_manager = FilesUpdateManager()
file_update_manager.upgrade_file(h5_file)
datatype = self.load_datatype_from_file(
h5_file, operation_entity.id, datatype_group,
operation_entity.fk_launched_in)
all_datatypes[h5_file] = datatype
except IncompatibleFileManagerException:
os.remove(h5_file)
self.logger.warning(
"Incompatible H5 file will be ignored: %s" % h5_file)
self.logger.exception("Incompatibility details ...")
return all_datatypes
@staticmethod
def check_import_references(file_path, datatype):
h5_class = H5File.h5_class_from_file(file_path)
reference_list = h5_class(file_path).gather_references()
for _, reference_gid in reference_list:
if not reference_gid:
continue
ref_index = load.load_entity_by_gid(reference_gid)
if ref_index is None:
os.remove(file_path)
dao.remove_entity(datatype.__class__, datatype.id)
raise MissingReferenceException(
'Imported file depends on datatypes that do not exist. Please upload '
'those first!')
def _store_or_link_burst_config(self, burst_config, bc_path, project_id):
bc_already_in_tvb = dao.get_generic_entity(BurstConfiguration,
burst_config.gid, 'gid')
if len(bc_already_in_tvb) == 0:
self.store_datatype(burst_config, bc_path)
return 1
return 0
def store_or_link_datatype(self, datatype, dt_path, project_id):
self.check_import_references(dt_path, datatype)
stored_dt_count = 0
datatype_already_in_tvb = load.load_entity_by_gid(datatype.gid)
if not datatype_already_in_tvb:
self.store_datatype(datatype, dt_path)
stored_dt_count = 1
elif datatype_already_in_tvb.parent_operation.project.id != project_id:
AlgorithmService.create_link(datatype_already_in_tvb.id,
project_id)
if datatype_already_in_tvb.fk_datatype_group:
AlgorithmService.create_link(
datatype_already_in_tvb.fk_datatype_group, project_id)
return stored_dt_count
def _store_imported_datatypes_in_db(self, project, all_datatypes):
# type: (Project, dict) -> int
sorted_dts = sorted(
all_datatypes.items(),
key=lambda dt_item: dt_item[1].create_date or datetime.now())
count = 0
for dt_path, datatype in sorted_dts:
count += self.store_or_link_datatype(datatype, dt_path, project.id)
return count
def _store_imported_images(self, project, temp_project_path, project_name):
"""
Import all images from project
"""
images_root = os.path.join(temp_project_path,
StorageInterface.IMAGES_FOLDER)
target_images_path = self.storage_interface.get_images_folder(
project_name)
for root, _, files in os.walk(images_root):
for metadata_file in files:
if self.storage_interface.ends_with_tvb_file_extension(
metadata_file):
self._import_image(root, metadata_file, project.id,
target_images_path)
@staticmethod
def _populate_view_model2adapter():
if len(VIEW_MODEL2ADAPTER) > 0:
return VIEW_MODEL2ADAPTER
view_model2adapter = {}
algos = dao.get_all_algorithms()
for algo in algos:
adapter = ABCAdapter.build_adapter(algo)
view_model_class = adapter.get_view_model_class()
view_model2adapter[view_model_class] = algo
return view_model2adapter
def _retrieve_operations_in_order(self,
project,
import_path,
importer_operation_id=None):
# type: (Project, str, int) -> list[Operation2ImportData]
retrieved_operations = []
for root, _, files in os.walk(import_path):
if OPERATION_XML in files:
# Previous Operation format for uploading previous versions of projects
operation_file_path = os.path.join(root, OPERATION_XML)
operation, operation_xml_parameters, _ = self.build_operation_from_file(
project, operation_file_path)
operation.import_file = operation_file_path
self.logger.debug("Found operation in old XML format: " +
str(operation))
retrieved_operations.append(
Operation2ImportData(
operation,
root,
info_from_xml=operation_xml_parameters))
else:
# We strive for the new format with ViewModelH5
main_view_model = None
dt_paths = []
all_view_model_files = []
for file in files:
if self.storage_interface.ends_with_tvb_storage_file_extension(
file):
h5_file = os.path.join(root, file)
try:
h5_class = H5File.h5_class_from_file(h5_file)
if h5_class is ViewModelH5:
all_view_model_files.append(h5_file)
if not main_view_model:
view_model = h5.load_view_model_from_file(
h5_file)
if type(
view_model
) in self.view_model2adapter.keys():
main_view_model = view_model
else:
file_update_manager = FilesUpdateManager()
file_update_manager.upgrade_file(h5_file)
dt_paths.append(h5_file)
except Exception:
self.logger.warning(
"Unreadable H5 file will be ignored: %s" %
h5_file)
if main_view_model is not None:
alg = self.view_model2adapter[type(main_view_model)]
op_group_id = None
if main_view_model.operation_group_gid:
op_group = dao.get_operationgroup_by_gid(
main_view_model.operation_group_gid.hex)
if not op_group:
op_group = OperationGroup(
project.id,
ranges=json.loads(main_view_model.ranges),
gid=main_view_model.operation_group_gid.hex)
op_group = dao.store_entity(op_group)
op_group_id = op_group.id
operation = Operation(
main_view_model.gid.hex,
project.fk_admin,
project.id,
alg.id,
status=STATUS_FINISHED,
user_group=main_view_model.generic_attributes.
operation_tag,
start_date=datetime.now(),
completion_date=datetime.now(),
op_group_id=op_group_id,
range_values=main_view_model.range_values)
operation.create_date = main_view_model.create_date
operation.visible = main_view_model.generic_attributes.visible
self.logger.debug(
"Found main ViewModel to create operation for it: " +
str(operation))
retrieved_operations.append(
Operation2ImportData(operation, root, main_view_model,
dt_paths, all_view_model_files))
elif len(dt_paths) > 0:
alg = dao.get_algorithm_by_module(TVB_IMPORTER_MODULE,
TVB_IMPORTER_CLASS)
default_adapter = ABCAdapter.build_adapter(alg)
view_model = default_adapter.get_view_model_class()()
view_model.data_file = dt_paths[0]
vm_path = h5.store_view_model(view_model, root)
all_view_model_files.append(vm_path)
operation = Operation(view_model.gid.hex,
project.fk_admin,
project.id,
alg.id,
status=STATUS_FINISHED,
start_date=datetime.now(),
completion_date=datetime.now())
operation.create_date = datetime.min
self.logger.debug(
"Found no ViewModel in folder, so we default to " +
str(operation))
if importer_operation_id:
operation.id = importer_operation_id
retrieved_operations.append(
Operation2ImportData(operation, root, view_model,
dt_paths, all_view_model_files,
True))
return sorted(retrieved_operations,
key=lambda op_data: op_data.order_field)
def create_view_model(self,
operation_entity,
operation_data,
new_op_folder,
generic_attributes=None,
add_params=None):
view_model = self._get_new_form_view_model(
operation_entity, operation_data.info_from_xml)
if add_params is not None:
for element in add_params:
key_attr = getattr(view_model, element[0])
setattr(key_attr, element[1], element[2])
view_model.range_values = operation_entity.range_values
op_group = dao.get_operationgroup_by_id(
operation_entity.fk_operation_group)
if op_group:
view_model.operation_group_gid = uuid.UUID(op_group.gid)
view_model.ranges = json.dumps(op_group.range_references)
view_model.is_metric_operation = 'DatatypeMeasure' in op_group.name
if generic_attributes is not None:
view_model.generic_attributes = generic_attributes
view_model.generic_attributes.operation_tag = operation_entity.user_group
h5.store_view_model(view_model, new_op_folder)
view_model_disk_size = StorageInterface.compute_recursive_h5_disk_usage(
new_op_folder)
operation_entity.view_model_disk_size = view_model_disk_size
operation_entity.view_model_gid = view_model.gid.hex
dao.store_entity(operation_entity)
return view_model
def import_list_of_operations(self,
project,
import_path,
is_group=False,
importer_operation_id=None):
"""
This method scans provided folder and identify all operations that needs to be imported
"""
all_dts_count = 0
all_stored_dts_count = 0
imported_operations = []
ordered_operations = self._retrieve_operations_in_order(
project, import_path, None if is_group else importer_operation_id)
if is_group and len(ordered_operations) > 0:
first_op = dao.get_operation_by_id(importer_operation_id)
vm_path = h5.determine_filepath(first_op.view_model_gid,
os.path.dirname(import_path))
os.remove(vm_path)
ordered_operations[0].operation.id = importer_operation_id
for operation_data in ordered_operations:
if operation_data.is_old_form:
operation_entity, datatype_group = self.import_operation(
operation_data.operation)
new_op_folder = self.storage_interface.get_project_folder(
project.name, str(operation_entity.id))
try:
operation_datatypes = self._load_datatypes_from_operation_folder(
operation_data.operation_folder, operation_entity,
datatype_group)
# Create and store view_model from operation
self.create_view_model(operation_entity, operation_data,
new_op_folder)
self._store_imported_datatypes_in_db(
project, operation_datatypes)
imported_operations.append(operation_entity)
except MissingReferenceException:
operation_entity.status = STATUS_ERROR
dao.store_entity(operation_entity)
elif operation_data.main_view_model is not None:
operation_data.operation.create_date = datetime.now()
operation_data.operation.start_date = datetime.now()
operation_data.operation.completion_date = datetime.now()
do_merge = False
if importer_operation_id:
do_merge = True
operation_entity = dao.store_entity(operation_data.operation,
merge=do_merge)
dt_group = None
op_group = dao.get_operationgroup_by_id(
operation_entity.fk_operation_group)
if op_group:
dt_group = dao.get_datatypegroup_by_op_group_id(
op_group.id)
if not dt_group:
first_op = dao.get_operations_in_group(
op_group.id, only_first_operation=True)
dt_group = DataTypeGroup(
op_group,
operation_id=first_op.id,
state=DEFAULTDATASTATE_INTERMEDIATE)
dt_group = dao.store_entity(dt_group)
# Store the DataTypes in db
dts = {}
all_dts_count += len(operation_data.dt_paths)
for dt_path in operation_data.dt_paths:
dt = self.load_datatype_from_file(dt_path,
operation_entity.id,
dt_group, project.id)
if isinstance(dt, BurstConfiguration):
if op_group:
dt.fk_operation_group = op_group.id
all_stored_dts_count += self._store_or_link_burst_config(
dt, dt_path, project.id)
else:
dts[dt_path] = dt
if op_group:
op_group.fill_operationgroup_name(dt.type)
dao.store_entity(op_group)
try:
stored_dts_count = self._store_imported_datatypes_in_db(
project, dts)
all_stored_dts_count += stored_dts_count
if operation_data.main_view_model.is_metric_operation:
self._update_burst_metric(operation_entity)
imported_operations.append(operation_entity)
new_op_folder = self.storage_interface.get_project_folder(
project.name, str(operation_entity.id))
view_model_disk_size = 0
for h5_file in operation_data.all_view_model_files:
view_model_disk_size += StorageInterface.compute_size_on_disk(
h5_file)
shutil.move(h5_file, new_op_folder)
operation_entity.view_model_disk_size = view_model_disk_size
dao.store_entity(operation_entity)
except MissingReferenceException as excep:
self.storage_interface.remove_operation_data(
project.name, operation_entity.id)
operation_entity.fk_operation_group = None
dao.store_entity(operation_entity)
dao.remove_entity(DataTypeGroup, dt_group.id)
raise excep
else:
self.logger.warning(
"Folder %s will be ignored, as we could not find a serialized "
"operation or DTs inside!" %
operation_data.operation_folder)
# We want importer_operation_id to be kept just for the first operation (the first iteration)
if is_group:
importer_operation_id = None
self._update_dt_groups(project.id)
self._update_burst_configurations(project.id)
return imported_operations, all_dts_count, all_stored_dts_count
@staticmethod
def _get_new_form_view_model(operation, xml_parameters):
# type (Operation) -> ViewModel
algo = dao.get_algorithm_by_id(operation.fk_from_algo)
ad = ABCAdapter.build_adapter(algo)
view_model = ad.get_view_model_class()()
if xml_parameters:
declarative_attrs = type(view_model).declarative_attrs
if isinstance(xml_parameters, str):
xml_parameters = json.loads(xml_parameters)
for param in xml_parameters:
new_param_name = param
if param != '' and param[0] == "_":
new_param_name = param[1:]
new_param_name = new_param_name.lower()
if new_param_name in declarative_attrs:
try:
setattr(view_model, new_param_name,
xml_parameters[param])
except (TraitTypeError, TraitAttributeError):
pass
return view_model
def _import_image(self, src_folder, metadata_file, project_id,
target_images_path):
"""
Create and store a image entity.
"""
figure_dict = StorageInterface().read_metadata_from_xml(
os.path.join(src_folder, metadata_file))
actual_figure = os.path.join(
src_folder,
os.path.split(figure_dict['file_path'])[1])
if not os.path.exists(actual_figure):
self.logger.warning("Expected to find image path %s .Skipping" %
actual_figure)
return
figure_dict['fk_user_id'] = self.user_id
figure_dict['fk_project_id'] = project_id
figure_entity = manager_of_class(ResultFigure).new_instance()
figure_entity = figure_entity.from_dict(figure_dict)
stored_entity = dao.store_entity(figure_entity)
# Update image meta-data with the new details after import
figure = dao.load_figure(stored_entity.id)
shutil.move(actual_figure, target_images_path)
self.logger.debug("Store imported figure")
_, meta_data = figure.to_dict()
self.storage_interface.write_image_metadata(figure, meta_data)
def load_datatype_from_file(self,
current_file,
op_id,
datatype_group=None,
current_project_id=None):
# type: (str, int, DataTypeGroup, int) -> HasTraitsIndex
"""
Creates an instance of datatype from storage / H5 file
:returns: DatatypeIndex
"""
self.logger.debug("Loading DataType from file: %s" % current_file)
h5_class = H5File.h5_class_from_file(current_file)
if h5_class is BurstConfigurationH5:
if current_project_id is None:
op_entity = dao.get_operationgroup_by_id(op_id)
current_project_id = op_entity.fk_launched_in
h5_file = BurstConfigurationH5(current_file)
burst = BurstConfiguration(current_project_id)
burst.fk_simulation = op_id
h5_file.load_into(burst)
result = burst
else:
datatype, generic_attributes = h5.load_with_links(current_file)
already_existing_datatype = h5.load_entity_by_gid(datatype.gid)
if datatype_group is not None and already_existing_datatype is not None:
raise DatatypeGroupImportException(
"The datatype group that you are trying to import"
" already exists!")
index_class = h5.REGISTRY.get_index_for_datatype(
datatype.__class__)
datatype_index = index_class()
datatype_index.fill_from_has_traits(datatype)
datatype_index.fill_from_generic_attributes(generic_attributes)
if datatype_group is not None and hasattr(datatype_index, 'fk_source_gid') and \
datatype_index.fk_source_gid is not None:
ts = h5.load_entity_by_gid(datatype_index.fk_source_gid)
if ts is None:
op = dao.get_operations_in_group(
datatype_group.fk_operation_group,
only_first_operation=True)
op.fk_operation_group = None
dao.store_entity(op)
dao.remove_entity(OperationGroup,
datatype_group.fk_operation_group)
dao.remove_entity(DataTypeGroup, datatype_group.id)
raise DatatypeGroupImportException(
"Please import the time series group before importing the"
" datatype measure group!")
# Add all the required attributes
if datatype_group:
datatype_index.fk_datatype_group = datatype_group.id
if len(datatype_group.subject) == 0:
datatype_group.subject = datatype_index.subject
dao.store_entity(datatype_group)
datatype_index.fk_from_operation = op_id
associated_file = h5.path_for_stored_index(datatype_index)
if os.path.exists(associated_file):
datatype_index.disk_size = StorageInterface.compute_size_on_disk(
associated_file)
result = datatype_index
return result
def store_datatype(self, datatype, current_file=None):
"""This method stores data type into DB"""
try:
self.logger.debug("Store datatype: %s with Gid: %s" %
(datatype.__class__.__name__, datatype.gid))
# Now move storage file into correct folder if necessary
if current_file is not None:
final_path = h5.path_for_stored_index(datatype)
if final_path != current_file:
shutil.move(current_file, final_path)
stored_entry = load.load_entity_by_gid(datatype.gid)
if not stored_entry:
stored_entry = dao.store_entity(datatype)
return stored_entry
except MissingDataSetException as e:
self.logger.exception(e)
error_msg = "Datatype %s has missing data and could not be imported properly." % (
datatype, )
raise ImportException(error_msg)
except IntegrityError as excep:
self.logger.exception(excep)
error_msg = "Could not import data with gid: %s. There is already a one with " \
"the same name or gid." % datatype.gid
raise ImportException(error_msg)
def __populate_project(self, project_path):
"""
Create and store a Project entity.
"""
self.logger.debug("Creating project from path: %s" % project_path)
project_dict = self.storage_interface.read_project_metadata(
project_path)
project_entity = manager_of_class(Project).new_instance()
project_entity = project_entity.from_dict(project_dict, self.user_id)
try:
self.logger.debug("Storing imported project")
return dao.store_entity(project_entity)
except IntegrityError as excep:
self.logger.exception(excep)
error_msg = (
"Could not import project: %s with gid: %s. There is already a "
"project with the same name or gid.") % (project_entity.name,
project_entity.gid)
raise ImportException(error_msg)
def build_operation_from_file(self, project, operation_file):
"""
Create Operation entity from metadata file.
"""
operation_dict = StorageInterface().read_metadata_from_xml(
operation_file)
operation_entity = manager_of_class(Operation).new_instance()
return operation_entity.from_dict(operation_dict, dao, self.user_id,
project.gid)
@staticmethod
def import_operation(operation_entity, migration=False):
"""
Store a Operation entity.
"""
do_merge = False
if operation_entity.id:
do_merge = True
operation_entity = dao.store_entity(operation_entity, merge=do_merge)
operation_group_id = operation_entity.fk_operation_group
datatype_group = None
if operation_group_id is not None:
datatype_group = dao.get_datatypegroup_by_op_group_id(
operation_group_id)
if datatype_group is None and migration is False:
# If no dataType group present for current op. group, create it.
operation_group = dao.get_operationgroup_by_id(
operation_group_id)
datatype_group = DataTypeGroup(
operation_group, operation_id=operation_entity.id)
datatype_group.state = UploadAlgorithmCategoryConfig.defaultdatastate
datatype_group = dao.store_entity(datatype_group)
return operation_entity, datatype_group
def import_simulator_configuration_zip(self, zip_file):
# Now compute the name of the folder where to explode uploaded ZIP file
temp_folder = self._compute_unpack_path()
uq_file_name = temp_folder + ".zip"
if isinstance(zip_file, (FieldStorage, Part)):
if not zip_file.file:
raise ServicesBaseException(
"Could not process the given ZIP file...")
with open(uq_file_name, 'wb') as file_obj:
self.storage_interface.copy_file(zip_file.file, file_obj)
else:
shutil.copy2(zip_file, uq_file_name)
try:
self.storage_interface.unpack_zip(uq_file_name, temp_folder)
return temp_folder
except FileStructureException as excep:
raise ServicesBaseException(
"Could not process the given ZIP file..." + str(excep))
@staticmethod
def _update_burst_metric(operation_entity):
burst_config = dao.get_burst_for_operation_id(operation_entity.id)
if burst_config and burst_config.ranges:
if burst_config.fk_metric_operation_group is None:
burst_config.fk_metric_operation_group = operation_entity.fk_operation_group
dao.store_entity(burst_config)
@staticmethod
def _update_dt_groups(project_id):
dt_groups = dao.get_datatypegroup_for_project(project_id)
for dt_group in dt_groups:
dt_group.count_results = dao.count_datatypes_in_group(dt_group.id)
dts_in_group = dao.get_datatypes_from_datatype_group(dt_group.id)
if dts_in_group:
dt_group.fk_parent_burst = dts_in_group[0].fk_parent_burst
dao.store_entity(dt_group)
@staticmethod
def _update_burst_configurations(project_id):
burst_configs = dao.get_bursts_for_project(project_id)
for burst_config in burst_configs:
burst_config.datatypes_number = dao.count_datatypes_in_burst(
burst_config.gid)
dao.store_entity(burst_config)
