def test_remove_project_node(self):
"""
Test removing of a node from a project.
"""
inserted_project, gid, gid_op = self._create_value_wrapper(self.test_user)
project_to_link = model.Project("Link", self.test_user.id, "descript")
project_to_link = dao.store_entity(project_to_link)
exact_data = dao.get_datatype_by_gid(gid)
dao.store_entity(model.Links(exact_data.id, project_to_link.id))
assert dao.get_datatype_by_gid(gid) is not None, "Initialization problem!"
operation_id = dao.get_generic_entity(model.Operation, gid_op, 'gid')[0].id
op_folder = self.structure_helper.get_project_folder("test_proj", str(operation_id))
assert os.path.exists(op_folder)
sub_files = os.listdir(op_folder)
assert 2 == len(sub_files)
### Validate that no more files are created than needed.
if(dao.get_system_user() is None):
dao.store_entity(model.User(TvbProfile.current.web.admin.SYSTEM_USER_NAME, None, None, True, None))
self.project_service._remove_project_node_files(inserted_project.id, gid)
sub_files = os.listdir(op_folder)
assert 1 == len(sub_files)
### operation.xml file should still be there
op_folder = self.structure_helper.get_project_folder("Link", str(operation_id + 1))
sub_files = os.listdir(op_folder)
assert 2 == len(sub_files)
assert dao.get_datatype_by_gid(gid) is not None, "Data should still be in DB, because of links"
self.project_service._remove_project_node_files(project_to_link.id, gid)
assert dao.get_datatype_by_gid(gid) is None
sub_files = os.listdir(op_folder)
assert 1 == len(sub_files)
def update():
"""
Update TVB code to SVN revision version 4455.
This update was done for release 1.0.2.
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start,
page_size=PAGE_SIZE)
for project in projects_page:
try:
user = dao.get_system_user()
adapter = ObjSurfaceImporter()
OperationService().fire_operation(adapter,
user,
project.id,
visible=False,
surface_type=EEG_CAP,
data_file=DATA_FILE_EEG_CAP)
adapter = ObjSurfaceImporter()
OperationService().fire_operation(adapter,
user,
project.id,
visible=False,
surface_type=FACE,
data_file=DATA_FILE_FACE)
except Exception as excep:
LOGGER.exception(excep)
TvbProfile.current.manager.add_entries_to_config_file(
{stored.KEY_MATLAB_EXECUTABLE: get_matlab_executable()})
def test_remove_project_node(self):
"""
Test removing of a node from a project.
"""
inserted_project, gid, op = TestFactory.create_value_wrapper(self.test_user)
project_to_link = model_project.Project("Link", self.test_user.id, "descript")
project_to_link = dao.store_entity(project_to_link)
exact_data = dao.get_datatype_by_gid(gid)
assert exact_data is not None, "Initialization problem!"
link = dao.store_entity(model_datatype.Links(exact_data.id, project_to_link.id))
vw_h5_path = h5.path_for_stored_index(exact_data)
assert os.path.exists(vw_h5_path)
if dao.get_system_user() is None:
dao.store_entity(model_operation.User(TvbProfile.current.web.admin.SYSTEM_USER_NAME,
TvbProfile.current.web.admin.SYSTEM_USER_NAME, None, None, True,
None))
self.project_service._remove_project_node_files(inserted_project.id, gid, [link])
assert not os.path.exists(vw_h5_path)
exact_data = dao.get_datatype_by_gid(gid)
assert exact_data is not None, "Data should still be in DB, because of links"
vw_h5_path_new = h5.path_for_stored_index(exact_data)
assert os.path.exists(vw_h5_path_new)
assert vw_h5_path_new != vw_h5_path
self.project_service._remove_project_node_files(project_to_link.id, gid, [])
assert dao.get_datatype_by_gid(gid) is None
def update():
"""
Update TVB code to SVN revision version 4455.
This update was done for release 1.0.2.
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start, page_size=PAGE_SIZE)
for project in projects_page:
try:
user = dao.get_system_user()
adapter = ObjSurfaceImporter()
FlowService().fire_operation(adapter, user, project.id, visible=False,
surface_type=EEG_CAP, data_file=DATA_FILE_EEG_CAP)
adapter = ObjSurfaceImporter()
FlowService().fire_operation(adapter, user, project.id, visible=False,
surface_type=FACE, data_file=DATA_FILE_FACE)
except Exception as excep:
LOGGER.exception(excep)
TvbProfile.current.manager.add_entries_to_config_file({stored.KEY_MATLAB_EXECUTABLE: get_matlab_executable()})
def update():
"""
Update TVB code to SVN revision version 4455.
This update was done for release 1.0.2.
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start,
page_size=PAGE_SIZE)
for project in projects_page:
try:
user = dao.get_system_user()
adapter = ObjSurfaceImporter()
FlowService().fire_operation(adapter,
user,
project.id,
visible=False,
surface_type=EEG_CAP,
data_file=DATA_FILE_EEG_CAP)
adapter = ObjSurfaceImporter()
FlowService().fire_operation(adapter,
user,
project.id,
visible=False,
surface_type=FACE,
data_file=DATA_FILE_FACE)
except Exception, excep:
LOGGER.exception(excep)
def _remove_project_node_files(self,
project_id,
gid,
skip_validation=False):
"""
Delegate removal of a node in the structure of the project.
In case of a problem will THROW StructureException.
"""
try:
project = self.find_project(project_id)
datatype = dao.get_datatype_by_gid(gid)
links = dao.get_links_for_datatype(datatype.id)
if links:
was_link = False
for link in links:
# This means it's only a link and we need to remove it
if link.fk_from_datatype == datatype.id and link.fk_to_project == project.id:
dao.remove_entity(Links, link.id)
was_link = True
if not was_link:
# Create a clone of the operation
new_op = Operation(
dao.get_system_user().id, links[0].fk_to_project,
datatype.parent_operation.fk_from_algo,
datatype.parent_operation.parameters,
datatype.parent_operation.meta_data,
datatype.parent_operation.status,
datatype.parent_operation.start_date,
datatype.parent_operation.completion_date,
datatype.parent_operation.fk_operation_group,
datatype.parent_operation.additional_info,
datatype.parent_operation.user_group,
datatype.parent_operation.range_values)
new_op = dao.store_entity(new_op)
to_project = self.find_project(links[0].fk_to_project).name
new_op_loaded = dao.get_operation_by_id(new_op.id)
self.structure_helper.write_operation_metadata(
new_op_loaded)
full_path = h5.path_for_stored_index(datatype)
self.structure_helper.move_datatype(
datatype, to_project, str(new_op.id), full_path)
datatype.fk_from_operation = new_op.id
datatype.parent_operation = new_op
dao.store_entity(datatype)
dao.remove_entity(Links, links[0].id)
else:
specific_remover = get_remover(datatype.type)(datatype)
specific_remover.remove_datatype(skip_validation)
h5_path = h5.path_for_stored_index(datatype)
self.structure_helper.remove_datatype_file(h5_path)
except RemoveDataTypeException:
self.logger.exception("Could not execute operation Node Remove!")
raise
except FileStructureException:
self.logger.exception("Remove operation failed")
raise StructureException(
"Remove operation failed for unknown reasons.Please contact system administrator."
)
def _remove_project_node_files(self, project_id, gid, skip_validation=False):
"""
Delegate removal of a node in the structure of the project.
In case of a problem will THROW StructureException.
"""
try:
project = self.find_project(project_id)
datatype = dao.get_datatype_by_gid(gid)
links = dao.get_links_for_datatype(datatype.id)
if links:
was_link = False
for link in links:
#This means it's only a link and we need to remove it
if link.fk_from_datatype == datatype.id and link.fk_to_project == project.id:
dao.remove_entity(model.Links, link.id)
was_link = True
if not was_link:
# Create a clone of the operation
new_op = model.Operation(dao.get_system_user().id,
links[0].fk_to_project,
datatype.parent_operation.fk_from_algo,
datatype.parent_operation.parameters,
datatype.parent_operation.meta_data,
datatype.parent_operation.method_name,
datatype.parent_operation.status,
datatype.parent_operation.start_date,
datatype.parent_operation.completion_date,
datatype.parent_operation.fk_operation_group,
datatype.parent_operation.additional_info,
datatype.parent_operation.user_group,
datatype.parent_operation.range_values)
new_op = dao.store_entity(new_op)
to_project = self.find_project(links[0].fk_to_project).name
new_op_loaded = dao.get_operation_by_id(new_op.id)
self.structure_helper.write_operation_metadata(new_op_loaded)
self.structure_helper.move_datatype(datatype, to_project, str(new_op.id))
datatype.set_operation_id(new_op.id)
datatype.parent_operation = new_op
dao.store_entity(datatype)
dao.remove_entity(model.Links, links[0].id)
else:
specific_remover = get_remover(datatype.type)(datatype)
specific_remover.remove_datatype(skip_validation)
self.structure_helper.remove_datatype(datatype)
except RemoveDataTypeException:
self.logger.exception("Could not execute operation Node Remove!")
raise
except FileStructureException:
self.logger.exception("Remove operation failed")
raise StructureException("Remove operation failed for unknown reasons.Please contact system administrator.")
def test_initialize_startup(self):
"""
Test "reset_database" and "initialize_startup" calls.
"""
reset_database()
# Table USERS should not exist:
self.assertRaises(Exception, dao.get_all_users)
initialize_startup()
# Table exists, but no rows
self.assertEqual(0, len(dao.get_all_users()))
self.assertEqual(None, dao.get_system_user())
# DB revisions folder should exist:
self.assertTrue(os.path.exists(TvbProfile.current.db.DB_VERSIONING_REPO))
def test_initialize_startup(self):
"""
Test "reset_database" and "initialize_startup" calls.
"""
reset_database()
# Table USERS should not exist:
self.assertRaises(Exception, dao.get_all_users)
initialize_startup()
# Table exists, but no rows
self.assertEqual(0, len(dao.get_all_users()))
self.assertEqual(None, dao.get_system_user())
# DB revisions folder should exist:
self.assertTrue(os.path.exists(TvbProfile.current.db.DB_VERSIONING_REPO))
def update():
"""
Update TVB code to SVN revision version 4770.
This update was done for release 1.0.5
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start, page_size=PAGE_SIZE)
for project in projects_page:
try:
handle_event(EVENT_FILE_IDENTIFIER, dao.get_system_user(), project)
except Exception, excep:
LOGGER.exception(excep)
def test_initialize_startup(self):
"""
Test "reset_database" and "initialize_startup" calls.
"""
reset_database()
# Table USERS should not exist:
with pytest.raises(Exception):
dao.get_all_users()
initialize_startup()
# Table exists, but no rows
assert 0 == len(dao.get_all_users())
assert None == dao.get_system_user()
# DB revisions folder should exist:
assert os.path.exists(TvbProfile.current.db.DB_VERSIONING_REPO)
def update():
"""
Update TVB code to SVN revision version 6093.
This update was done for release 1.1.5.
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start, page_size=PAGE_SIZE)
for project in projects_page:
try:
handle_event(EVENT_FILE_IDENTIFIER, dao.get_system_user(), project)
except Exception:
LOGGER.exception("could not migrate project id: %s, name %s" % (project.id, project.name))
def update():
"""
Update TVB code to SVN revision version 4770.
This update was done for release 1.0.5
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start, page_size=PAGE_SIZE)
for project in projects_page:
try:
adapter = SensorsImporter()
FlowService().fire_operation(adapter, dao.get_system_user(), project.id, visible=False,
sensors_file=DATA_FILE, sensors_type=SensorsImporter.INTERNAL_SENSORS)
except Exception as excep:
LOGGER.exception(excep)
def update():
"""
Update TVB code to SVN revision version 4770.
This update was done for release 1.0.5
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start, page_size=PAGE_SIZE)
for project in projects_page:
try:
adapter = Sensors_Importer()
FlowService().fire_operation(adapter, dao.get_system_user(), project.id, visible=False,
sensors_file=DATA_FILE, sensors_type=Sensors_Importer.INTERNAL_SENSORS)
except Exception, excep:
LOGGER.exception(excep)
def update():
"""
Update TVB code to SVN revision version 6093.
This update was done for release 1.1.5.
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start, page_size=PAGE_SIZE)
for project in projects_page:
try:
user = dao.get_system_user()
adapter = ObjSurfaceImporter()
FlowService().fire_operation(adapter, user, project.id, visible=False,
surface_type=FACE, data_file=DATA_FILE_FACE)
except Exception:
LOGGER.exception("could not migrate project id: %s, name %s" % (project.id, project.name))
def update():
"""
Update TVB code to SVN revision version 6093.
This update was done for release 1.1.5.
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start, page_size=PAGE_SIZE)
for project in projects_page:
try:
user = dao.get_system_user()
adapter = ObjSurfaceImporter()
OperationService().fire_operation(adapter, user, project.id, visible=False,
surface_type=SurfaceTypesEnum.FACE_SURFACE.value,
data_file=DATA_FILE_FACE)
except Exception:
LOGGER.exception("could not migrate project id: %s, name %s" % (project.id, project.name))
def __copy_linked_datatype_before_delete(self, op, datatype, project, fk_to_project):
new_op = Operation(op.view_model_gid,
dao.get_system_user().id,
fk_to_project,
datatype.parent_operation.fk_from_algo,
datatype.parent_operation.status,
datatype.parent_operation.start_date,
datatype.parent_operation.completion_date,
datatype.parent_operation.fk_operation_group,
datatype.parent_operation.additional_info,
datatype.parent_operation.user_group,
datatype.parent_operation.range_values)
new_op.visible = datatype.parent_operation.visible
new_op = dao.store_entity(new_op)
to_project = self.find_project(fk_to_project)
to_project_path = self.storage_interface.get_project_folder(to_project.name)
full_path = h5.path_for_stored_index(datatype)
old_folder = self.storage_interface.get_project_folder(project.name, str(op.id))
file_paths = h5.gather_references_of_view_model(op.view_model_gid, old_folder, only_view_models=True)[0]
file_paths.append(full_path)
# The BurstConfiguration h5 file has to be moved only when we handle the time series which has the operation
# folder containing the file
if datatype.is_ts and datatype.fk_parent_burst is not None:
bc_path = h5.path_for(datatype.parent_operation.id, BurstConfigurationH5, datatype.fk_parent_burst,
project.name)
if os.path.exists(bc_path):
file_paths.append(bc_path)
bc = dao.get_burst_for_operation_id(op.id)
bc.fk_simulation = new_op.id
dao.store_entity(bc)
# Move all files to the new operation folder
self.storage_interface.move_datatype_with_sync(to_project, to_project_path, new_op.id, file_paths)
datatype.fk_from_operation = new_op.id
datatype.parent_operation = new_op
dao.store_entity(datatype)
return new_op
def update():
"""
Update TVB code to SVN revision version 4455.
This update was done for release 1.0.2.
"""
projects_count = dao.get_all_projects(is_count=True)
for page_start in range(0, projects_count, PAGE_SIZE):
projects_page = dao.get_all_projects(page_start=page_start, page_size=PAGE_SIZE)
for project in projects_page:
try:
user = dao.get_system_user()
adapter = ObjSurfaceImporter()
FlowService().fire_operation(adapter, user, project.id, visible=False,
surface_type=EEG_CAP, data_file=DATA_FILE_EEG_CAP)
adapter = ObjSurfaceImporter()
FlowService().fire_operation(adapter, user, project.id, visible=False,
surface_type=FACE, data_file=DATA_FILE_FACE)
except Exception, excep:
LOGGER.exception(excep)
def _remove_project_node_files(self, project_id, gid, skip_validation=False):
"""
Delegate removal of a node in the structure of the project.
In case of a problem will THROW StructureException.
"""
try:
project = self.find_project(project_id)
datatype = dao.get_datatype_by_gid(gid)
links = dao.get_links_for_datatype(datatype.id)
op = dao.get_operation_by_id(datatype.fk_from_operation)
adapter = ABCAdapter.build_adapter(op.algorithm)
if links:
was_link = False
for link in links:
# This means it's only a link and we need to remove it
if link.fk_from_datatype == datatype.id and link.fk_to_project == project.id:
dao.remove_entity(Links, link.id)
was_link = True
if not was_link:
# Create a clone of the operation
# There is no view_model so the view_model_gid is None
new_op = Operation(op.view_model_gid,
dao.get_system_user().id,
links[0].fk_to_project,
datatype.parent_operation.fk_from_algo,
datatype.parent_operation.status,
datatype.parent_operation.start_date,
datatype.parent_operation.completion_date,
datatype.parent_operation.fk_operation_group,
datatype.parent_operation.additional_info,
datatype.parent_operation.user_group,
datatype.parent_operation.range_values)
new_op = dao.store_entity(new_op)
to_project = self.find_project(links[0].fk_to_project)
to_project_path = self.structure_helper.get_project_folder(to_project)
encryption_handler.set_project_active(to_project)
encryption_handler.sync_folders(to_project_path)
to_project_name = to_project.name
full_path = h5.path_for_stored_index(datatype)
self.structure_helper.move_datatype(datatype, to_project_name, str(new_op.id), full_path)
# Move also the ViewModel H5
old_folder = self.structure_helper.get_project_folder(project, str(op.id))
view_model = adapter.load_view_model(op)
vm_full_path = h5.determine_filepath(op.view_model_gid, old_folder)
self.structure_helper.move_datatype(view_model, to_project_name, str(new_op.id), vm_full_path)
encryption_handler.sync_folders(to_project_path)
encryption_handler.set_project_inactive(to_project)
datatype.fk_from_operation = new_op.id
datatype.parent_operation = new_op
dao.store_entity(datatype)
dao.remove_entity(Links, links[0].id)
else:
specific_remover = get_remover(datatype.type)(datatype)
specific_remover.remove_datatype(skip_validation)
h5_path = h5.path_for_stored_index(datatype)
self.structure_helper.remove_datatype_file(h5_path)
encryption_handler.push_folder_to_sync(self.structure_helper.get_project_folder_from_h5(h5_path))
except RemoveDataTypeException:
self.logger.exception("Could not execute operation Node Remove!")
raise
except FileStructureException:
self.logger.exception("Remove operation failed")
raise StructureException("Remove operation failed for unknown reasons.Please contact system administrator.")
