def reset_password(self, **data):
"""
Service Layer for resetting a password.
"""
if (KEY_USERNAME not in data) or len(data[KEY_USERNAME]) < 1:
raise UsernameException("Empty UserName!")
if (KEY_EMAIL not in data) or len(data[KEY_EMAIL]) < 1:
raise UsernameException("Empty Email!")
old_pass, user = None, None
try:
user_name = data[KEY_USERNAME]
email = data[KEY_EMAIL]
user = dao.get_user_by_name_email(user_name, email)
if user is None:
raise UsernameException("Given credentials don't match!")
old_pass = user.password
new_pass = ''.join(chr(randint(48, 122)) for _ in range(DEFAULT_PASS_LENGTH))
user.password = md5(new_pass).hexdigest()
self.edit_user(user, old_pass)
self.logger.info("Setting new password for user " + user_name + " !")
email_sender.send(FROM_ADDRESS, email, SUBJECT_RECOVERY, TEXT_RECOVERY % (new_pass,))
return TEXT_DISPLAY
except Exception, excep:
if old_pass and len(old_pass) > 1 and user:
user.password = old_pass
dao.store_entity(user)
self.logger.error("Could not change user password!")
self.logger.exception(excep)
raise UsernameException(excep.message)
def test_get_users_for_project(self):
"""
Get all members of a project except the current user.
"""
user_1 = model.User("test_user1", "test_pass", "*****@*****.**", False, "user")
dao.store_entity(user_1)
user_2 = model.User("test_user2", "test_pass", "*****@*****.**", False, "user")
dao.store_entity(user_2)
user_3 = model.User("test_user3", "test_pass", "*****@*****.**", False, "user")
dao.store_entity(user_3)
user_4 = model.User("test_user4", "test_pass", "*****@*****.**", False, "user")
dao.store_entity(user_4)
user_5 = model.User("test_user5", "test_pass", "*****@*****.**", False, "user")
dao.store_entity(user_5)
admin = dao.get_user_by_name("test_user1")
member1 = dao.get_user_by_name("test_user2")
member2 = dao.get_user_by_name("test_user5")
data = dict(name="test_proj", description="test_desc", users=[member1.id, member2.id])
project = ProjectService().store_project(admin, True, None, **data)
all_users, members, pag = self.user_service.get_users_for_project(admin.username, project.id)
assert len(members) == 2, "More members than there should be."
assert len(all_users) == 5, "Admin should not be viewed as member. " \
"Neither should users that were not part of the project's users list."
assert pag == 1, "Invalid total pages number."
for user in all_users:
assert user.username != admin.username, "Admin is in members!"
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))
self.assertTrue(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))
self.assertTrue(os.path.exists(op_folder))
sub_files = os.listdir(op_folder)
self.assertEqual(2, len(sub_files))
### Validate that no more files are created than needed.
self.project_service._remove_project_node_files(inserted_project.id, gid)
sub_files = os.listdir(op_folder)
self.assertEqual(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)
self.assertEqual(2, len(sub_files))
self.assertTrue(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)
self.assertTrue(dao.get_datatype_by_gid(gid) is None)
sub_files = os.listdir(op_folder)
self.assertEqual(1, len(sub_files))
def create_operation(algorithm=None, test_user=None, test_project=None,
operation_status=model.STATUS_FINISHED, parameters="test params"):
"""
Create persisted operation.
:param algorithm: When not None, introspect TVB and TVB_TEST for adapters.
:return: Operation entity after persistence.
"""
if algorithm is None:
algorithm = dao.get_algorithm_by_module('tvb.tests.framework.adapters.ndimensionarrayadapter',
'NDimensionArrayAdapter')
if test_user is None:
test_user = TestFactory.create_user()
if test_project is None:
test_project = TestFactory.create_project(test_user)
meta = {DataTypeMetaData.KEY_SUBJECT: "John Doe",
DataTypeMetaData.KEY_STATE: "RAW_DATA"}
operation = model.Operation(test_user.id, test_project.id, algorithm.id, parameters, meta=json.dumps(meta),
status=operation_status)
dao.store_entity(operation)
### Make sure lazy attributes are correctly loaded.
return dao.get_operation_by_id(operation.id)
def submit(self, dynamic_gid, dynamic_name):
if dao.get_dynamic_by_name(dynamic_name):
return {'saved': False, 'msg': 'There is another configuration with the same name'}
dynamic = self.get_cached_dynamic(dynamic_gid)
model = dynamic.model
integrator = dynamic.integrator
model_parameters = []
for name in model.ui_configurable_parameters:
value = getattr(model, name)[0]
model_parameters.append((name, value))
entity = tvb.core.entities.model.Dynamic(
dynamic_name,
common.get_logged_user().id,
model.__class__.__name__,
json.dumps(model_parameters),
integrator.__class__.__name__,
None
# todo: serialize integrator parameters
# json.dumps(integrator.raw_ui_integrator_parameters)
)
dao.store_entity(entity)
return {'saved': True}
def reset_password(self, **data):
"""
Service Layer for resetting a password.
"""
if (KEY_EMAIL not in data) or len(data[KEY_EMAIL]) < 1:
raise UsernameException("Empty Email!")
old_pass, user = None, None
try:
email = data[KEY_EMAIL]
name_hint = data[KEY_USERNAME]
user = dao.get_user_by_email(email, name_hint)
if user is None:
raise UsernameException("No singular user could be found for the given data!")
old_pass = user.password
new_pass = ''.join(chr(randint(48, 122)) for _ in range(DEFAULT_PASS_LENGTH))
user.password = md5(new_pass).hexdigest()
self.edit_user(user, old_pass)
self.logger.info("Resetting password for email : " + email)
email_sender.send(FROM_ADDRESS, email, SUBJECT_RECOVERY, TEXT_RECOVERY % (user.username, new_pass))
return TEXT_DISPLAY
except Exception, excep:
if old_pass and len(old_pass) > 1 and user:
user.password = old_pass
dao.store_entity(user)
self.logger.exception("Could not change user password!")
raise UsernameException(excep.message)
def upgrade_file(self, input_file_name, datatype=None):
"""
Upgrades the given file to the latest data version. The file will be upgraded
sequentially, up until the current version from tvb.basic.config.settings.VersionSettings.DB_STRUCTURE_VERSION
:param input_file_name the path to the file which needs to be upgraded
:return True, when update was needed and running it was successful.
False, the the file is already up to date.
"""
if self.is_file_up_to_date(input_file_name):
# Avoid running the DB update of size, when H5 is not being changed, to speed-up
return False
file_version = self.get_file_data_version(input_file_name)
self.log.info("Updating from version %s , file: %s " % (file_version, input_file_name))
for script_name in self.get_update_scripts(file_version):
self.run_update_script(script_name, input_file=input_file_name)
if datatype:
# Compute and update the disk_size attribute of the DataType in DB:
datatype.disk_size = self.files_helper.compute_size_on_disk(input_file_name)
dao.store_entity(datatype)
return True
def test_validate_user_non_existent(self):
"""
Flow for trying to validate a user that doesn't exist in the database.
"""
user = model.User("test_user", "test_pass", "*****@*****.**", True, "user")
dao.store_entity(user)
assert not self.user_service.validate_user("test_user2"), "Validation done even tho user is non-existent"
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 _run_cluster_job(operation_identifier, user_name_label, adapter_instance):
"""
Threaded Popen
It is the function called by the ClusterSchedulerClient in a Thread.
This function starts a new process.
"""
# Load operation so we can estimate the execution time
operation = dao.get_operation_by_id(operation_identifier)
kwargs = parse_json_parameters(operation.parameters)
kwargs = adapter_instance.prepare_ui_inputs(kwargs)
time_estimate = int(adapter_instance.get_execution_time_approximation(**kwargs))
hours = int(time_estimate / 3600)
minutes = (int(time_estimate) % 3600) / 60
seconds = int(time_estimate) % 60
# Anything lower than 5 hours just use default walltime
if hours < 5:
walltime = "05:00:00"
else:
if hours < 10:
hours = "0%d" % hours
else:
hours = str(hours)
walltime = "%s:%s:%s" % (hours, str(minutes), str(seconds))
call_arg = TvbProfile.current.cluster.SCHEDULE_COMMAND % (operation_identifier, user_name_label, walltime)
LOGGER.info(call_arg)
process_ = Popen([call_arg], stdout=PIPE, shell=True)
job_id = process_.stdout.read().replace('\n', '').split(TvbProfile.current.cluster.JOB_ID_STRING)[-1]
LOGGER.debug("Got jobIdentifier = %s for CLUSTER operationID = %s" % (operation_identifier, job_id))
operation_identifier = model.OperationProcessIdentifier(operation_identifier, job_id=job_id)
dao.store_entity(operation_identifier)
def remove_datatype(self, skip_validation=False):
"""
Called when a Connectivity is to be removed.
"""
if not skip_validation:
associated_ts = dao.get_generic_entity(TimeSeriesRegion, self.handled_datatype.gid, '_connectivity')
associated_rm = dao.get_generic_entity(RegionMapping, self.handled_datatype.gid, '_connectivity')
associated_stim = dao.get_generic_entity(StimuliRegion, self.handled_datatype.gid, '_connectivity')
associated_mes = dao.get_generic_entity(ConnectivityMeasure, self.handled_datatype.gid, '_connectivity')
msg = "Connectivity cannot be removed as it is used by at least one "
if len(associated_ts) > 0:
raise RemoveDataTypeException(msg + " TimeSeriesRegion.")
if len(associated_rm) > 0:
raise RemoveDataTypeException(msg + " RegionMapping.")
if len(associated_stim) > 0:
raise RemoveDataTypeException(msg + " StimuliRegion.")
if len(associated_mes) > 0:
raise RemoveDataTypeException(msg + " ConnectivityMeasure.")
#### Update child Connectivities, if any.
child_conns = dao.get_generic_entity(Connectivity, self.handled_datatype.gid, '_parent_connectivity')
if len(child_conns) > 0:
for one_conn in child_conns[1:]:
one_conn.parent_connectivity = child_conns[0].gid
if child_conns and child_conns[0]:
child_conns[0].parent_connectivity = self.handled_datatype.parent_connectivity
for one_child in child_conns:
dao.store_entity(one_child)
ABCRemover.remove_datatype(self, skip_validation)
def _run_cluster_job(operation_identifier, user_name_label, adapter_instance):
"""
Threaded Popen
It is the function called by the ClusterSchedulerClient in a Thread.
This function starts a new process.
"""
# Load operation so we can estimate the execution time
operation = dao.get_operation_by_id(operation_identifier)
kwargs = parse_json_parameters(operation.parameters)
time_estimate = int(adapter_instance.get_execution_time_approximation(**kwargs))
hours = int(time_estimate / 3600)
minutes = (int(time_estimate) % 3600) / 60
seconds = int(time_estimate) % 60
# Anything lower than 2 hours just use default walltime
if hours < 2:
walltime = "02:00:00"
elif hours > 23:
walltime = "23:59:59"
else:
walltime = datetime.time(hours, minutes, seconds)
walltime = walltime.strftime("%H:%M:%S")
call_arg = config.CLUSTER_SCHEDULE_COMMAND % (walltime, operation_identifier, user_name_label)
LOGGER.info(call_arg)
process_ = Popen([call_arg], stdout=PIPE, shell=True)
job_id = process_.stdout.read().replace('\n', '').split('OAR_JOB_ID=')[-1]
LOGGER.debug("Got jobIdentifier = %s for CLUSTER operationID = %s" % (operation_identifier, job_id))
operation_identifier = model.OperationProcessIdentifier(operation_identifier, job_id=job_id)
dao.store_entity(operation_identifier)
def generate_users(nr_users, nr_projects):
"""
The generate_users method will create a clean state db with
:param nr_users: number of users to be generated (with random roles between
CLINICIAN and RESEARCHER and random validated state)
:param nr_projects: maximum number of projects to be generated for each user
"""
users = []
for i in range(nr_users):
coin_flip = random.randint(0, 1)
role = 'CLINICIAN' if coin_flip == 1 else 'RESEARCHER'
password = md5("test").hexdigest()
new_user = model.User("gen" + str(i), password, "*****@*****.**", True, role)
dao.store_entity(new_user)
new_user = dao.get_user_by_name("gen" + str(i))
ExtremeTestFactory.VALIDATION_DICT[new_user.id] = 0
users.append(new_user)
for i in range(nr_users):
current_user = dao.get_user_by_name("gen" + str(i))
projects_for_user = random.randint(0, nr_projects)
for j in range(projects_for_user):
data = dict(name='GeneratedProject' + str(i) + '_' + str(j),
description='test_desc',
users=ExtremeTestFactory.get_users_ids(random.randint(0, nr_users - 3),
nr_users, current_user.id, users))
ProjectService().store_project(current_user, True, None, **data)
ExtremeTestFactory.VALIDATION_DICT[current_user.id] += 1
def update():
"""
Move images previously stored in TVB operation folders, in a single folder/project.
"""
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_end=min(page_start + PAGE_SIZE, projects_count))
for project in projects_page:
figures = _figures_in_project(project.id)
for figure in figures:
figure.file_path = "%s-%s" % (figure.operation.id, figure.file_path)
dao.store_entities(figures)
project_path = FilesHelper().get_project_folder(project)
update_manager = ProjectUpdateManager(project_path)
update_manager.run_all_updates()
project.version = TvbProfile.current.version.PROJECT_VERSION
dao.store_entity(project)
def stop_operation(operation_id):
"""
Stop a thread for a given operation id
"""
operation = dao.get_operation_by_id(operation_id)
if not operation or operation.status != model.STATUS_STARTED:
LOGGER.warning("Operation already stopped or not found is given to stop job: %s" % operation_id)
return True
LOGGER.debug("Stopping operation: %s" % str(operation_id))
## Set the thread stop flag to true
for thread in CURRENT_ACTIVE_THREADS:
if int(thread.operation_id) == operation_id:
thread.stop()
LOGGER.debug("Found running thread for operation: %d" % operation_id)
## Kill Thread
stopped = True
operation_process = dao.get_operation_process_for_operation(operation_id)
if operation_process is not None:
## Now try to kill the operation if it exists
stopped = OperationExecutor.stop_pid(operation_process.pid)
if not stopped:
LOGGER.debug("Operation %d was probably killed from it's specific thread." % operation_id)
else:
LOGGER.debug("Stopped OperationExecutor process for %d" % operation_id)
## Mark operation as canceled in DB.
operation.mark_cancelled()
dao.store_entity(operation)
return stopped
def test_launch_operation_HDD_full_space_started_ops(self):
"""
Test the actual operation flow by executing a test adapter.
"""
space_taken_by_started = 100
module = "tvb.tests.framework.adapters.testadapter3"
class_name = "TestAdapterHDDRequired"
group = dao.find_group(module, class_name)
started_operation = model.Operation(
self.test_user.id,
self.test_project.id,
group.id,
"",
status=model.STATUS_STARTED,
estimated_disk_size=space_taken_by_started,
)
dao.store_entity(started_operation)
adapter = FlowService().build_adapter_instance(group)
data = {"test": 100}
TvbProfile.current.MAX_DISK_SPACE = float(adapter.get_required_disk_size(**data) + space_taken_by_started - 1)
tmp_folder = FilesHelper().get_project_folder(self.test_project, "TEMP")
self.assertRaises(
NoMemoryAvailableException,
self.operation_service.initiate_operation,
self.test_user,
self.test_project.id,
adapter,
tmp_folder,
**data
)
self._assert_no_dt2()
def save_project_to_user(user_id, project_id):
"""
Mark for current user that the given project is the last one selected.
"""
user = dao.get_user_by_id(user_id)
user.selected_project = project_id
dao.store_entity(user)
def remove_datatype(self, skip_validation = False):
"""
Called when a TimeSeries is removed.
"""
associated_cv = dao.get_generic_entity(Covariance, self.handled_datatype.gid, '_source')
associated_pca = dao.get_generic_entity(PrincipalComponents, self.handled_datatype.gid, '_source')
associated_is = dao.get_generic_entity(IndependentComponents, self.handled_datatype.gid, '_source')
associated_cc = dao.get_generic_entity(CrossCorrelation, self.handled_datatype.gid, '_source')
associated_fr = dao.get_generic_entity(FourierSpectrum, self.handled_datatype.gid, '_source')
associated_wv = dao.get_generic_entity(WaveletCoefficients, self.handled_datatype.gid, '_source')
associated_cs = dao.get_generic_entity(CoherenceSpectrum, self.handled_datatype.gid, '_source')
associated_dm = dao.get_generic_entity(DatatypeMeasure, self.handled_datatype.gid, '_analyzed_datatype')
for datatype_measure in associated_dm:
datatype_measure._analyed_datatype = None
dao.store_entity(datatype_measure)
msg = "TimeSeries cannot be removed as it is used by at least one "
if not skip_validation:
if len(associated_cv) > 0:
raise RemoveDataTypeException(msg + " Covariance.")
if len(associated_pca) > 0:
raise RemoveDataTypeException(msg + " PrincipalComponents.")
if len(associated_is) > 0:
raise RemoveDataTypeException(msg + " IndependentComponents.")
if len(associated_cc) > 0:
raise RemoveDataTypeException(msg + " CrossCorrelation.")
if len(associated_fr) > 0:
raise RemoveDataTypeException(msg + " FourierSpectrum.")
if len(associated_wv) > 0:
raise RemoveDataTypeException(msg + " WaveletCoefficients.")
if len(associated_cs) > 0:
raise RemoveDataTypeException(msg + " CoherenceSpectrum.")
ABCRemover.remove_datatype(self, skip_validation)
def add_operation_additional_info(self, message):
"""
Adds additional info on the operation to be displayed in the UI. Usually a warning message.
"""
current_op = dao.get_operation_by_id(self.operation_id)
current_op.additional_info = message
dao.store_entity(current_op)
def test_validate_user_validated(self):
"""
Flow for trying to validate a user that was already validated.
"""
user = model.User("test_user", "test_pass", "*****@*****.**", True, "user")
dao.store_entity(user)
assert not self.user_service.validate_user("test_user"), "Validation invalid."
def __upgrade_datatype_list(self, datatypes):
"""
Upgrade a list of DataTypes to the current version.
:param datatypes: The list of DataTypes that should be upgraded.
:returns: (nr_of_dts_upgraded_fine, nr_of_dts_upgraded_fault) a two-tuple of integers representing
the number of DataTypes for which the upgrade worked fine, and the number of DataTypes for which
some kind of fault occurred
"""
nr_of_dts_upgraded_fine = 0
nr_of_dts_upgraded_fault = 0
for datatype in datatypes:
specific_datatype = dao.get_datatype_by_gid(datatype.gid)
if isinstance(specific_datatype, MappedType):
try:
self.upgrade_file(specific_datatype.get_storage_file_path())
nr_of_dts_upgraded_fine += 1
except (MissingDataFileException, FileVersioningException) as ex:
# The file is missing for some reason. Just mark the DataType as invalid.
datatype.invalid = True
dao.store_entity(datatype)
nr_of_dts_upgraded_fault += 1
self.log.exception(ex)
return nr_of_dts_upgraded_fine, nr_of_dts_upgraded_fault
def test_validate_user_happy_flow(self):
"""
Standard flow for a validate user action.
"""
user = model.User("test_user", "test_pass", "*****@*****.**", False, "user")
dao.store_entity(user)
assert self.user_service.validate_user("test_user"), "Validation failed when it shouldn't have."
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
meta.bind = migrate_engine
table = meta.tables['DATA_TYPES_GROUPS']
create_column(COL_RANGES_1, table)
create_column(COL_RANGES_2, table)
try:
## Iterate DataTypeGroups from previous code-versions and try to update value for the new column.
previous_groups = dao.get_generic_entity(model.DataTypeGroup, "0", "no_of_ranges")
for group in previous_groups:
operation_group = dao.get_operationgroup_by_id(group.fk_operation_group)
#group.only_numeric_ranges = operation_group.has_only_numeric_ranges
if operation_group.range3 is not None:
group.no_of_ranges = 3
elif operation_group.range2 is not None:
group.no_of_ranges = 2
elif operation_group.range1 is not None:
group.no_of_ranges = 1
else:
group.no_of_ranges = 0
dao.store_entity(group)
except Exception, excep:
## we can live with a column only having default value. We will not stop the startup.
logger = get_logger(__name__)
logger.exception(excep)
def clean_database(self, delete_folders=True):
"""
Deletes data from all tables
"""
self.cancel_all_operations()
LOGGER.warning("Your Database content will be deleted.")
try:
session = SessionMaker()
for table in reversed(model.Base.metadata.sorted_tables):
# We don't delete data from some tables, because those are
# imported only during introspection which is done one time
if table.name not in self.EXCLUDE_TABLES:
try:
session.open_session()
con = session.connection()
LOGGER.debug("Executing Delete From Table " + table.name)
con.execute(table.delete())
session.commit()
except Exception as e:
# We cache exception here, in case some table does not exists and
# to allow the others to be deleted
LOGGER.warning(e)
session.rollback()
finally:
session.close_session()
LOGGER.info("Database was cleanup!")
except Exception as excep:
LOGGER.warning(excep)
raise
# Now if the database is clean we can delete also project folders on disk
if delete_folders:
self.delete_project_folders()
dao.store_entity(model.User(TvbProfile.current.web.admin.SYSTEM_USER_NAME, None, None, True, None))
def __init__(self):
micro_postfix = "_%d" % int(time.time() * 1000000)
# Here create all structures needed later for data types creation
self.files_helper = FilesHelper()
# First create user
user = model.User("datatype_factory_user" + micro_postfix, "test_pass",
"*****@*****.**" + micro_postfix, True, "user")
self.user = dao.store_entity(user)
# Now create a project
project_service = ProjectService()
data = dict(name='DatatypesFactoryProject' + micro_postfix, description='test_desc', users=[])
self.project = project_service.store_project(self.user, True, None, **data)
# Create algorithm
alg_category = model.AlgorithmCategory('one', True)
dao.store_entity(alg_category)
ad = model.Algorithm(SIMULATOR_MODULE, SIMULATOR_CLASS, alg_category.id)
self.algorithm = dao.get_algorithm_by_module(SIMULATOR_MODULE, SIMULATOR_CLASS)
if self.algorithm is None:
self.algorithm = dao.store_entity(ad)
# Create an operation
self.meta = {DataTypeMetaData.KEY_SUBJECT: self.USER_FULL_NAME,
DataTypeMetaData.KEY_STATE: self.DATATYPE_STATE}
operation = model.Operation(self.user.id, self.project.id, self.algorithm.id, 'test parameters',
meta=json.dumps(self.meta), status=model.STATUS_FINISHED)
self.operation = dao.store_entity(operation)
def update_dt(dt_id, new_create_date):
dt = dao.get_datatype_by_id(dt_id)
dt.create_date = new_create_date
dao.store_entity(dt)
# Update MetaData in H5 as well.
dt = dao.get_datatype_by_gid(dt.gid)
dt.persist_full_metadata()
def create_link(data_ids, project_id):
"""
For a list of dataType IDs and a project id create all the required links.
"""
for data in data_ids:
link = model.Links(data, project_id)
dao.store_entity(link)
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
meta.bind = migrate_engine
table = meta.tables['DATA_TYPES_GROUPS']
create_column(COL_RANGES_1, table)
create_column(COL_RANGES_2, table)
try:
## Iterate DataTypeGroups from previous code-versions and try to update value for the new column.
previous_groups = dao.get_generic_entity(model.DataTypeGroup, "0", "no_of_ranges")
for group in previous_groups:
operation_group = dao.get_operationgroup_by_id(group.fk_operation_group)
#group.only_numeric_ranges = operation_group.has_only_numeric_ranges
if operation_group.range3 is not None:
group.no_of_ranges = 3
elif operation_group.range2 is not None:
group.no_of_ranges = 2
elif operation_group.range1 is not None:
group.no_of_ranges = 1
else:
group.no_of_ranges = 0
dao.store_entity(group)
except Exception as excep:
## we can live with a column only having default value. We will not stop the startup.
logger = get_logger(__name__)
logger.exception(excep)
session = SA_SESSIONMAKER()
session.execute(text("""UPDATE "OPERATIONS"
SET status =
CASE
WHEN status = 'FINISHED' THEN '4-FINISHED'
WHEN status = 'STARTED' THEN '3-STARTED'
WHEN status = 'CANCELED' THEN '2-CANCELED'
ELSE '1-ERROR'
END
WHERE status IN ('FINISHED', 'CANCELED', 'STARTED', 'ERROR');"""))
session.commit()
session.close()
try:
session = SA_SESSIONMAKER()
for sim_state in session.query(SimulationState).filter(SimulationState.fk_datatype_group is not None).all():
session.delete(sim_state)
session.commit()
session.close()
except Exception as excep:
## It might happen that SimulationState table is not yet created, e.g. if user has version 1.0.2
logger = get_logger(__name__)
logger.exception(excep)
def __init_algorithmn(self):
"""
Insert some starting data in the database.
"""
categ1 = model.AlgorithmCategory('one', True)
self.categ1 = dao.store_entity(categ1)
ad = model.Algorithm(TEST_ADAPTER_VALID_MODULE, TEST_ADAPTER_VALID_CLASS, categ1.id)
self.algo_inst = dao.store_entity(ad)
def rename_burst(burst_id, new_name):
"""
Rename the burst given by burst_id, setting it's new name to
burst_name.
"""
burst = dao.get_burst_by_id(burst_id)
burst.name = new_name
dao.store_entity(burst)
def test_prepare_name(self):
"""
Test prepare burst name
"""
stored_burst = TestFactory.store_burst(self.test_project.id)
simulation_tuple = self.burst_service.prepare_simulation_name(
stored_burst, self.test_project.id)
assert simulation_tuple[0] == 'simulation_' + str(dao.get_number_of_bursts(self.test_project.id) + 1), \
"The default simulation name is not the defined one"
busrt_test_name = "Burst Test Name"
stored_burst.name = busrt_test_name
stored_burst = dao.store_entity(stored_burst)
simulation_tuple = self.burst_service.prepare_simulation_name(
stored_burst, self.test_project.id)
assert simulation_tuple[
0] == busrt_test_name, "The burst name is not the given one"
def test_adapter_launch(self, connectivity_factory, region_mapping_factory,
time_series_region_index_factory):
"""
Test that the adapters launches and successfully generates a datatype measure entry.
"""
meta = {
DataTypeMetaData.KEY_SUBJECT: "John Doe",
DataTypeMetaData.KEY_STATE: "RAW_DATA"
}
algo = FlowService().get_algorithm_by_module_and_class(
IntrospectionRegistry.SIMULATOR_MODULE,
IntrospectionRegistry.SIMULATOR_CLASS)
self.operation = model_operation.Operation(
self.test_user.id,
self.test_project.id,
algo.id,
json.dumps(''),
meta=json.dumps(meta),
status=model_operation.STATUS_STARTED)
self.operation = dao.store_entity(self.operation)
# Get connectivity, region_mapping and a dummy time_series_region
connectivity = connectivity_factory()
region_mapping = region_mapping_factory()
dummy_time_series_index = time_series_region_index_factory(
connectivity=connectivity, region_mapping=region_mapping)
dummy_time_series_index.start_time = 0.0
dummy_time_series_index.sample_period = 1.0
dummy_time_series_index = \
dao.get_generic_entity(dummy_time_series_index.__class__, dummy_time_series_index.gid, 'gid')[0]
ts_metric_adapter = TimeseriesMetricsAdapter()
form = TimeseriesMetricsAdapterForm()
view_model = form.get_view_model()()
view_model.time_series = UUID(dummy_time_series_index.gid)
form.fill_trait(view_model)
ts_metric_adapter.submit_form(form)
resulted_metric = ts_metric_adapter.launch(view_model)
assert isinstance(
resulted_metric,
DatatypeMeasureIndex), "Result should be a datatype measure."
assert len(resulted_metric.metrics) >= len(list(ts_metric_adapter.get_form().algorithms.choices)), \
"At least a result should have been generated for every metric."
for metric_value in json.loads(resulted_metric.metrics).values():
assert isinstance(metric_value, (float, int))
def _import_bursts(project_entity, bursts_dict):
"""
Re-create old bursts, but keep a mapping between the id it has here and the old-id it had
in the project where they were exported, so we can re-add the datatypes to them.
"""
burst_ids_mapping = {}
for old_burst_id in bursts_dict:
burst_information = BurstInformation.load_from_dict(
bursts_dict[old_burst_id])
burst_entity = model.BurstConfiguration(project_entity.id)
burst_entity.from_dict(burst_information.data)
burst_entity = dao.store_entity(burst_entity)
burst_ids_mapping[int(old_burst_id)] = burst_entity.id
# We don't need the data in dictionary form anymore, so update it with new BurstInformation object
bursts_dict[old_burst_id] = burst_information
return burst_ids_mapping
def prepare_operation(self, user_id, project_id, algorithm, view_model_gid,
op_group=None, ranges=None, visible=True):
op_group_id = None
if op_group:
op_group_id = op_group.id
if isinstance(view_model_gid, uuid.UUID):
view_model_gid = view_model_gid.hex
operation = Operation(user_id, project_id, algorithm.id, json.dumps({'gid': view_model_gid}),
op_group_id=op_group_id, range_values=ranges)
self.logger.debug("Saving Operation(userId=" + str(user_id) + ",projectId=" + str(project_id) +
",algorithmId=" + str(algorithm.id) + ", ops_group= " + str(op_group_id) + ")")
operation.visible = visible
operation = dao.store_entity(operation)
return operation
def persist_operation_state(self, operation, operation_status, message=None):
"""
Update Operation instance state. Store it in DB and on HDD/
:param operation: Operation instance
:param operation_status: new status
:param message: message in case of error
:return: operation instance changed
"""
operation.mark_complete(operation_status, message)
operation.queue_full = False
operation = dao.store_entity(operation)
# update burst also
burst_config = self.get_burst_for_operation_id(operation.id)
if burst_config is not None:
burst_status = STATUS_FOR_OPERATION.get(operation_status)
self.mark_burst_finished(burst_config, burst_status, message)
return operation
def test_read_write_arrays(self):
"""
Test the filter function when retrieving dataTypes with a filter
after a column from a class specific table (e.g. DATA_arraywrapper).
"""
test_array = numpy.array(range(16))
shapes = [test_array.shape, (2, 8), (2, 2, 4), (2, 2, 2, 2)]
storage_path = self.flow_service.file_helper.get_project_folder(
self.operation.project, str(self.operation.id))
for i in range(4):
datatype_inst = MappedArray(title="dim_" + str(i + 1),
d_type="MappedArray",
storage_path=storage_path,
module="tvb.datatypes.arrays",
subject="John Doe",
state="RAW",
operation_id=self.operation.id)
datatype_inst.array_data = test_array.reshape(shapes[i])
result = dao.store_entity(datatype_inst)
result.array_data = None
inserted_data = self.flow_service.get_available_datatypes(
self.test_project.id, "tvb.datatypes.arrays.MappedArray")[0]
assert len(inserted_data) == 4, "Found " + str(len(inserted_data))
for i in range(4):
## inserted_data will be retrieved in the opposite order than the insert order
actual_datatype = dao.get_generic_entity(MappedArray,
inserted_data[3 - i][2],
'gid')[0]
assert actual_datatype.length_1d, shapes[i][0]
if i > 0:
assert actual_datatype.length_2d == shapes[i][1]
expected_arr = test_array.reshape(shapes[i])
assert numpy.equal(actual_datatype.array_data, expected_arr).all(),\
str(i + 1) + "D Data not read correctly"
actual_datatype.array_data = None
### Check that meta-data are also written for Array attributes.
metadata = actual_datatype.get_metadata('array_data')
assert actual_datatype.METADATA_ARRAY_MAX in metadata
assert metadata[actual_datatype.METADATA_ARRAY_MAX] == 15
assert actual_datatype.METADATA_ARRAY_MIN in metadata
assert metadata[actual_datatype.METADATA_ARRAY_MIN] == 0
assert actual_datatype.METADATA_ARRAY_MEAN in metadata
assert metadata[actual_datatype.METADATA_ARRAY_MEAN] == 7.5
def create_value_wrapper(test_user, test_project=None):
"""
Creates a ValueWrapper dataType, and the associated parent Operation.
This is also used in ProjectStructureTest.
"""
if test_project is None:
test_project = TestFactory.create_project(test_user, 'test_proj')
operation = TestFactory.create_operation(test_user=test_user,
test_project=test_project)
value_wrapper = ValueWrapper(data_value="5.0",
data_name="my_value",
data_type="float")
op_dir = FilesHelper().get_project_folder(test_project,
str(operation.id))
vw_idx = h5.store_complete(value_wrapper, op_dir)
vw_idx.fk_from_operation = operation.id
vw_idx = dao.store_entity(vw_idx)
return test_project, vw_idx.gid, operation
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.files_helper.read_project_metadata(project_path)
project_entity = manager_of_class(model.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, 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 ProjectImportException(error_msg)
def build(data=None, op=None):
ts = time_series_factory(data)
if op is None:
op = operation_factory()
ts_db = TimeSeriesIndex()
ts_db.fk_from_operation = op.id
ts_db.fill_from_has_traits(ts)
ts_h5_path = h5.path_for_stored_index(ts_db)
with TimeSeriesH5(ts_h5_path) as f:
f.store(ts)
f.sample_rate.store(ts.sample_rate)
f.nr_dimensions.store(ts.data.ndim)
ts_db = dao.store_entity(ts_db)
return ts_db
def store_datatype(self, datatype):
"""This method stores data type into DB"""
try:
self.logger.debug("Store datatype: %s with Gid: %s" %
(datatype.__class__.__name__, datatype.gid))
return dao.store_entity(datatype)
except MissingDataSetException:
self.logger.error(
"Datatype %s has missing data and could not be imported properly."
% (datatype, ))
os.remove(datatype.get_storage_file_path())
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
# Delete file if can't be imported
os.remove(datatype.get_storage_file_path())
raise ProjectImportException(error_msg)
def build(row1=None, row2=None, project=None, operation=None, subject=None, state=None):
data_type = DummyDataType()
data_type.row1 = row1
data_type.row2 = row2
if operation is None:
operation = operation_factory(test_project=project)
data_type_index = DummyDataTypeIndex(subject=subject, state=state)
data_type_index.fk_from_operation = operation.id
data_type_index.fill_from_has_traits(data_type)
data_type_h5_path = h5.path_for_stored_index(data_type_index)
with DummyDataTypeH5(data_type_h5_path) as f:
f.store(data_type)
data_type_index = dao.store_entity(data_type_index)
return data_type_index
def _remove_project_node_files(self, project_id, gid, links, 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)
if links:
op = dao.get_operation_by_id(datatype.fk_from_operation)
# Instead of deleting, we copy the datatype to the linked project
# We also clone the operation
new_operation = self.__copy_linked_datatype_before_delete(op, datatype, project,
links[0].fk_to_project)
# If there is a datatype group and operation group and they were not moved yet to the linked project,
# then do it
if datatype.fk_datatype_group is not None:
dt_group_op = dao.get_operation_by_id(datatype.fk_from_operation)
op_group = dao.get_operationgroup_by_id(dt_group_op.fk_operation_group)
op_group.fk_launched_in = links[0].fk_to_project
dao.store_entity(op_group)
burst = dao.get_burst_for_operation_id(op.id)
if burst is not None:
burst.fk_project = links[0].fk_to_project
dao.store_entity(burst)
dt_group = dao.get_datatypegroup_by_op_group_id(op_group.id)
dt_group.parent_operation = new_operation
dt_group.fk_from_operation = new_operation.id
dao.store_entity(dt_group)
else:
# There is no link for this datatype so it has to be deleted
specific_remover = get_remover(datatype.type)(datatype)
specific_remover.remove_datatype(skip_validation)
# Remove burst if dt has one and it still exists
if datatype.fk_parent_burst is not None and datatype.is_ts:
burst = dao.get_burst_for_operation_id(datatype.fk_from_operation)
if burst is not None:
dao.remove_entity(BurstConfiguration, burst.id)
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 __init__(self):
now = datetime.now()
micro_postfix = "_%d" % now.microsecond
# Here create all structures needed later for data types creation
self.files_helper = FilesHelper()
# First create user
user = model.User("datatype_factory_user" + micro_postfix, "test_pass",
"*****@*****.**" + micro_postfix, True, "user")
self.user = dao.store_entity(user)
# Now create a project
project_service = ProjectService()
data = dict(name='DatatypesFactoryProject' + micro_postfix,
description='test_desc',
users=[])
self.project = project_service.store_project(self.user, True, None,
**data)
# Create algorithm
alg_category = model.AlgorithmCategory('one', True)
dao.store_entity(alg_category)
alg_group = model.AlgorithmGroup("test_module1", "classname1",
alg_category.id)
dao.store_entity(alg_group)
algorithm = model.Algorithm(alg_group.id,
'id',
name='',
req_data='',
param_name='',
output='')
self.algorithm = dao.store_entity(algorithm)
#Create an operation
self.meta = {
DataTypeMetaData.KEY_SUBJECT: self.USER_FULL_NAME,
DataTypeMetaData.KEY_STATE: self.DATATYPE_STATE
}
operation = model.Operation(self.user.id,
self.project.id,
self.algorithm.id,
'test parameters',
meta=json.dumps(self.meta),
status="FINISHED",
method_name=ABCAdapter.LAUNCH_METHOD)
self.operation = dao.store_entity(operation)
def build():
time_series_index = time_series_index_factory()
time_series = h5.load_from_index(time_series_index)
data = numpy.random.random((10, 10, 10, 10, 10))
cross_correlation = temporal_correlations.CrossCorrelation(source=time_series, array_data=data)
op = operation_factory()
cross_correlation_index = CrossCorrelationIndex()
cross_correlation_index.fk_from_operation = op.id
cross_correlation_index.fill_from_has_traits(cross_correlation)
cross_correlation_h5_path = h5.path_for_stored_index(cross_correlation_index)
with CrossCorrelationH5(cross_correlation_h5_path) as f:
f.store(cross_correlation)
cross_correlation_index = dao.store_entity(cross_correlation_index)
return cross_correlation_index
def _prepare_group(self, project_id, existing_dt_group, kwargs):
"""
Create and store OperationGroup entity, or return None
"""
# Standard ranges as accepted from UI
range1_values = self.get_range_values(kwargs, self._range_name(1))
range2_values = self.get_range_values(kwargs, self._range_name(2))
available_args = self.__expand_arguments([(kwargs, None)],
range1_values,
self._range_name(1))
available_args = self.__expand_arguments(available_args, range2_values,
self._range_name(2))
is_group = False
ranges = []
if self._range_name(1) in kwargs and range1_values is not None:
is_group = True
ranges.append(
json.dumps((kwargs[self._range_name(1)], range1_values)))
if self._range_name(2) in kwargs and range2_values is not None:
is_group = True
ranges.append(
json.dumps((kwargs[self._range_name(2)], range2_values)))
# Now for additional ranges which might be the case for the 'model exploration'
last_range_idx = 3
ranger_name = self._range_name(last_range_idx)
while ranger_name in kwargs:
values_for_range = self.get_range_values(kwargs, ranger_name)
available_args = self.__expand_arguments(available_args,
values_for_range,
ranger_name)
last_range_idx += 1
ranger_name = self._range_name(last_range_idx)
if last_range_idx > 3:
ranges = [
] # Since we only have 3 fields in db for this just hide it
if not is_group:
group = None
elif existing_dt_group is None:
group = OperationGroup(project_id=project_id, ranges=ranges)
group = dao.store_entity(group)
else:
group = existing_dt_group.parent_operation_group
return available_args, group
def test_get_inputs_for_op_group(self):
"""
Tests method get_datatypes_inputs_for_operation_group.
The DataType inputs will be from a DataType group.
"""
project, dt_group_id, first_dt, second_dt = self._create_datatype_group()
first_dt.visible = False
dao.store_entity(first_dt)
second_dt.visible = False
dao.store_entity(second_dt)
op_group = model.OperationGroup(project.id, "group", "range1[1..2]")
op_group = dao.store_entity(op_group)
params_1 = json.dumps({"param_5": "1", "param_1": first_dt.gid, "param_6": "2"})
params_2 = json.dumps({"param_5": "1", "param_4": second_dt.gid, "param_6": "5"})
algo_group = dao.find_group('tvb.tests.framework.adapters.testadapter3', 'TestAdapter3')
algo = dao.get_algorithm_by_group(algo_group.id)
op1 = model.Operation(self.test_user.id, project.id, algo.id, params_1, op_group_id=op_group.id)
op2 = model.Operation(self.test_user.id, project.id, algo.id, params_2, op_group_id=op_group.id)
dao.store_entities([op1, op2])
inputs = self.project_service.get_datatypes_inputs_for_operation_group(op_group.id, self.relevant_filter)
self.assertEqual(len(inputs), 0)
inputs = self.project_service.get_datatypes_inputs_for_operation_group(op_group.id, self.full_filter)
self.assertEqual(len(inputs), 1, "Incorrect number of dataTypes.")
self.assertFalse(first_dt.id == inputs[0].id, "Retrieved wrong dataType.")
self.assertFalse(second_dt.id == inputs[0].id, "Retrieved wrong dataType.")
self.assertTrue(dt_group_id == inputs[0].id, "Retrieved wrong dataType.")
first_dt.visible = True
dao.store_entity(first_dt)
inputs = self.project_service.get_datatypes_inputs_for_operation_group(op_group.id, self.relevant_filter)
self.assertEqual(len(inputs), 1, "Incorrect number of dataTypes.")
self.assertFalse(first_dt.id == inputs[0].id, "Retrieved wrong dataType.")
self.assertFalse(second_dt.id == inputs[0].id, "Retrieved wrong dataType.")
self.assertTrue(dt_group_id == inputs[0].id, "Retrieved wrong dataType.")
inputs = self.project_service.get_datatypes_inputs_for_operation_group(op_group.id, self.full_filter)
self.assertEqual(len(inputs), 1, "Incorrect number of dataTypes.")
self.assertFalse(first_dt.id == inputs[0].id, "Retrieved wrong dataType.")
self.assertFalse(second_dt.id == inputs[0].id, "Retrieved wrong dataType.")
self.assertTrue(dt_group_id == inputs[0].id, "Retrieved wrong dataType.")
def prepare_operations_for_workflowsteps(self, workflow_step_list, workflows, user_id, burst_id,
project_id, group, sim_operations):
"""
Create and store Operation entities from a list of Workflow Steps.
Will be generated workflows x workflow_step_list Operations.
For every step in workflow_step_list one OperationGroup and one DataTypeGroup will be created
(in case of PSE).
"""
for step in workflow_step_list:
operation_group = None
if (group is not None) and not isinstance(step, model.WorkflowStepView):
operation_group = model.OperationGroup(project_id=project_id, ranges=group.range_references)
operation_group = dao.store_entity(operation_group)
operation = None
metadata = {DataTypeMetaData.KEY_BURST: burst_id}
algo_category = dao.get_algorithm_by_id(step.fk_algorithm)
if algo_category is not None:
algo_category = algo_category.algorithm_category
for wf_idx, workflow in enumerate(workflows):
cloned_w_step = step.clone()
cloned_w_step.fk_workflow = workflow.id
dynamic_params = cloned_w_step.dynamic_param
op_params = cloned_w_step.static_param
op_params.update(dynamic_params)
range_values = None
group_id = None
if operation_group is not None:
group_id = operation_group.id
range_values = sim_operations[wf_idx].range_values
if not isinstance(step, model.WorkflowStepView):
## For visualization steps, do not create operations, as those are not really needed.
metadata, user_group = self._prepare_metadata(metadata, algo_category, operation_group, op_params)
operation = model.Operation(user_id, project_id, step.fk_algorithm,
json.dumps(op_params, cls=MapAsJson.MapAsJsonEncoder),
meta=json.dumps(metadata),
op_group_id=group_id, range_values=range_values, user_group=user_group)
operation.visible = step.step_visible
operation = dao.store_entity(operation)
cloned_w_step.fk_operation = operation.id
dao.store_entity(cloned_w_step)
if operation_group is not None and operation is not None:
datatype_group = model.DataTypeGroup(operation_group, operation_id=operation.id,
fk_parent_burst=burst_id,
state=metadata[DataTypeMetaData.KEY_STATE])
dao.store_entity(datatype_group)
def test_get_inputs_for_operation(self):
"""
Tests method get_datatype_and_datatypegroup_inputs_for_operation.
Verifies filters' influence over results is as expected
"""
algo_group = dao.find_group('tvb.tests.framework.adapters.testadapter3', 'TestAdapter3')
algo = dao.get_algorithm_by_group(algo_group.id)
array_wrappers = self._create_mapped_arrays(self.test_project.id)
ids = []
for datatype in array_wrappers:
ids.append(datatype[0])
datatype = dao.get_datatype_by_id(ids[0])
datatype.visible = False
dao.store_entity(datatype)
parameters = json.dumps({"param_5": "1", "param_1": array_wrappers[0][2],
"param_2": array_wrappers[1][2], "param_3": array_wrappers[2][2], "param_6": "0"})
operation = model.Operation(self.test_user.id, self.test_project.id, algo.id, parameters)
operation = dao.store_entity(operation)
inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(operation.gid,
self.relevant_filter)
self.assertEqual(len(inputs), 2)
self.assertTrue(ids[1] in [inputs[0].id, inputs[1].id], "Retrieved wrong dataType.")
self.assertTrue(ids[2] in [inputs[0].id, inputs[1].id], "Retrieved wrong dataType.")
self.assertFalse(ids[0] in [inputs[0].id, inputs[1].id], "Retrieved wrong dataType.")
inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(operation.gid,
self.full_filter)
self.assertEqual(len(inputs), 3, "Incorrect number of operations.")
self.assertTrue(ids[0] in [inputs[0].id, inputs[1].id, inputs[2].id], "Retrieved wrong dataType.")
self.assertTrue(ids[1] in [inputs[0].id, inputs[1].id, inputs[2].id], "Retrieved wrong dataType.")
self.assertTrue(ids[2] in [inputs[0].id, inputs[1].id, inputs[2].id], "Retrieved wrong dataType.")
project, dt_group_id, first_dt, _ = self._create_datatype_group()
first_dt.visible = False
dao.store_entity(first_dt)
parameters = json.dumps({"other_param": "_", "param_1": first_dt.gid})
operation = model.Operation(self.test_user.id, project.id, algo.id, parameters)
operation = dao.store_entity(operation)
inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(operation.gid,
self.relevant_filter)
self.assertEqual(len(inputs), 0, "Incorrect number of dataTypes.")
inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(operation.gid,
self.full_filter)
self.assertEqual(len(inputs), 1, "Incorrect number of dataTypes.")
self.assertEqual(inputs[0].id, dt_group_id, "Wrong dataType.")
self.assertTrue(inputs[0].id != first_dt.id, "Wrong dataType.")
def _populate_algorithm_categories(algo_category):
algo_category_instance = dao.filter_category(
algo_category.category_name, algo_category.rawinput,
algo_category.display, algo_category.launchable,
algo_category.order_nr)
if algo_category_instance is not None:
algo_category_instance.last_introspection_check = datetime.datetime.now(
)
algo_category_instance.removed = False
else:
algo_category_instance = AlgorithmCategory(
algo_category.category_name, algo_category.launchable,
algo_category.rawinput, algo_category.display,
algo_category.defaultdatastate, algo_category.order_nr,
datetime.datetime.now())
algo_category_instance = dao.store_entity(algo_category_instance)
return algo_category_instance.id
def _populate_algorithms(self, algo_category_class, algo_category_id):
for adapter_class in self.introspection_registry.ADAPTERS[
algo_category_class]:
try:
if not adapter_class.can_be_active():
self.logger.warning(
"Skipped Adapter(probably because MATLAB not found):" +
str(adapter_class))
stored_adapter = Algorithm(
adapter_class.__module__, adapter_class.__name__,
algo_category_id, adapter_class.get_group_name(),
adapter_class.get_group_description(),
adapter_class.get_ui_name(),
adapter_class.get_ui_description(),
adapter_class.get_ui_subsection(), datetime.datetime.now())
adapter_inst = adapter_class()
adapter_form = adapter_inst.get_form()
required_datatype = adapter_form.get_required_datatype()
if required_datatype is not None:
required_datatype = required_datatype.__name__
filters = adapter_form.get_filters()
if filters is not None:
filters = filters.to_json()
stored_adapter.required_datatype = required_datatype
stored_adapter.datatype_filter = filters
stored_adapter.parameter_name = adapter_form.get_input_name()
stored_adapter.outputlist = str(adapter_inst.get_output())
inst_from_db = dao.get_algorithm_by_module(
adapter_class.__module__, adapter_class.__name__)
if inst_from_db is not None:
stored_adapter.id = inst_from_db.id
stored_adapter = dao.store_entity(stored_adapter, inst_from_db
is not None)
adapter_class.stored_adapter = stored_adapter
except Exception:
self.logger.exception("Could not introspect Adapters file:" +
adapter_class.__module__)
def _prepare_metric_operation(self, sim_operation):
# type: (Operation) -> Operation
metric_algo = dao.get_algorithm_by_module(MEASURE_METRICS_MODULE,
MEASURE_METRICS_CLASS)
datatype_index = h5.REGISTRY.get_index_for_datatype(TimeSeries)
time_series_index = dao.get_generic_entity(datatype_index,
sim_operation.id,
'fk_from_operation')[0]
view_model = get_class_by_name("{}.{}".format(
MEASURE_METRICS_MODULE, MEASURE_METRICS_MODEL_CLASS))()
view_model.time_series = time_series_index.gid
view_model.algorithms = tuple(choices.values())
range_values = sim_operation.range_values
metadata = {
DataTypeMetaData.KEY_BURST: time_series_index.fk_parent_burst
}
metadata, user_group = self._prepare_metadata(
metadata, metric_algo.algorithm_category, None, {})
meta_str = json.dumps(metadata)
parent_burst = dao.get_generic_entity(
BurstConfiguration, time_series_index.fk_parent_burst, 'id')[0]
metric_operation_group_id = parent_burst.fk_metric_operation_group
metric_operation = Operation(sim_operation.fk_launched_by,
sim_operation.fk_launched_in,
metric_algo.id,
json.dumps({'gid': view_model.gid.hex}),
meta_str,
op_group_id=metric_operation_group_id,
range_values=range_values)
metric_operation.visible = False
stored_metric_operation = dao.store_entity(metric_operation)
metrics_datatype_group = dao.get_generic_entity(
DataTypeGroup, metric_operation_group_id, 'fk_operation_group')[0]
if metrics_datatype_group.fk_from_operation is None:
metrics_datatype_group.fk_from_operation = metric_operation.id
self._store_view_model(stored_metric_operation, sim_operation.project,
view_model)
return stored_metric_operation
def _create_operation(self, project_id, algorithm_id):
"""
dummy operation
:param project_id: the project in which the operation is created
:param algorithm_id: the algorithm to be run for the operation
:return: a dummy `Operation` with the given specifications
"""
algorithm = dao.get_algorithm_by_id(algorithm_id)
meta = {
DataTypeMetaData.KEY_SUBJECT: "John Doe",
DataTypeMetaData.KEY_STATE: "RAW_DATA"
}
operation = Operation(self.test_user.id,
project_id,
algorithm.id,
'test params',
meta=json.dumps(meta),
status=STATUS_FINISHED)
return dao.store_entity(operation)
def test_get_upload_operations(self):
"""
Test get_all when filter is for Upload category.
"""
self.__init_algorithmn()
upload_algo = self._create_algo_for_upload()
project = model.Project("test_proj_2", self.test_user.id, "desc")
project = dao.store_entity(project)
op1 = model.Operation(self.test_user.id, self.test_project.id,
self.algo_inst.id, "")
op2 = model.Operation(self.test_user.id,
project.id,
upload_algo.id,
"",
status=model.STATUS_FINISHED)
op3 = model.Operation(self.test_user.id, self.test_project.id,
upload_algo.id, "")
op4 = model.Operation(self.test_user.id,
self.test_project.id,
upload_algo.id,
"",
status=model.STATUS_FINISHED)
op5 = model.Operation(self.test_user.id,
self.test_project.id,
upload_algo.id,
"",
status=model.STATUS_FINISHED)
operations = dao.store_entities([op1, op2, op3, op4, op5])
upload_operations = self.project_service.get_all_operations_for_uploaders(
self.test_project.id)
self.assertEqual(2, len(upload_operations),
"Wrong number of upload operations.")
upload_ids = [operation.id for operation in upload_operations]
for i in [3, 4]:
self.assertTrue(operations[i].id in upload_ids,
"The operation should be an upload operation.")
for i in [0, 1, 2]:
self.assertFalse(
operations[i].id in upload_ids,
"The operation should not be an upload operation.")
def build(connectivity, region_mapping, ts=None, test_user=None, test_project=None, op=None):
if ts is None:
ts = time_series_region_factory(connectivity, region_mapping)
if not op:
op = operation_factory(test_user=test_user, test_project=test_project)
ts_db = TimeSeriesRegionIndex()
ts_db.fk_from_operation = op.id
ts_db.fill_from_has_traits(ts)
ts_h5_path = h5.path_for_stored_index(ts_db)
with TimeSeriesRegionH5(ts_h5_path) as f:
f.store(ts)
f.sample_rate.store(ts.sample_rate)
f.nr_dimensions.store(ts.data.ndim)
ts_db = dao.store_entity(ts_db)
return ts_db
def build():
time_series_index = time_series_index_factory()
time_series = h5.load_from_index(time_series_index)
data = numpy.random.random((10, 10))
covariance = graph.Covariance(source=time_series, array_data=data)
op = operation_factory()
covariance_index = CovarianceIndex()
covariance_index.fk_from_operation = op.id
covariance_index.fill_from_has_traits(covariance)
covariance_h5_path = h5.path_for_stored_index(covariance_index)
with CovarianceH5(covariance_h5_path) as f:
f.store(covariance)
covariance_index = dao.store_entity(covariance_index)
return covariance_index
def test_load_burst_history(self):
burst_config1 = BurstConfiguration(self.test_project.id)
burst_config2 = BurstConfiguration(self.test_project.id)
burst_config3 = BurstConfiguration(self.test_project.id)
dao.store_entity(burst_config1)
dao.store_entity(burst_config2)
dao.store_entity(burst_config3)
with patch('cherrypy.session', self.sess_mock, create=True):
common.add2session(common.KEY_BURST_CONFIG, burst_config1)
burst_parameters = self.simulator_controller.load_burst_history()
assert len(burst_parameters['burst_list']) == 3, "The burst configurations where not stored."
def test_get_upload_operations(self):
"""
Test get_all when filter is for Upload category.
"""
self.__init_algorithmn()
upload_algo = self._create_algo_for_upload()
project = Project("test_proj_2", self.test_user.id, "desc")
project = dao.store_entity(project)
op1 = Operation(None, self.test_user.id, self.test_project.id,
self.algo_inst.id)
op2 = Operation(None,
self.test_user.id,
project.id,
upload_algo.id,
status=STATUS_FINISHED)
op3 = Operation(None, self.test_user.id, self.test_project.id,
upload_algo.id)
op4 = Operation(None,
self.test_user.id,
self.test_project.id,
upload_algo.id,
status=STATUS_FINISHED)
op5 = Operation(None,
self.test_user.id,
self.test_project.id,
upload_algo.id,
status=STATUS_FINISHED)
operations = dao.store_entities([op1, op2, op3, op4, op5])
upload_operations = self.project_service.get_all_operations_for_uploaders(
self.test_project.id)
assert 2 == len(
upload_operations), "Wrong number of upload operations."
upload_ids = [operation.id for operation in upload_operations]
for i in [3, 4]:
assert operations[i].id in upload_ids, \
"The operation should be an upload operation."
for i in [0, 1, 2]:
assert not operations[i].id in upload_ids, \
"The operation should not be an upload operation."
def test_get_members_pages(self):
"""
Create many users (more than one page of members.
Create a project and asign all Users as members.
Test that 2 pages or Project Members are retrieved.
Now remove extra users, to have only one page of members for the project.
"""
user_ids = []
for i in range(MEMBERS_PAGE_SIZE + 3):
user = model_project.User("test_user_no" + str(i),
"test_user_no" + str(i), "pass",
"*****@*****.**")
user = dao.store_entity(user)
user_ids.append(user.id)
admin = dao.get_user_by_name("test_user_no1")
data = dict(name='test_proj', description='test_desc', users=user_ids)
project = ProjectService().store_project(admin, True, None, **data)
page_users, all_users, pag = self.user_service.get_users_for_project(
admin.username, project.id, 2)
assert len(page_users) == (MEMBERS_PAGE_SIZE + 3) % MEMBERS_PAGE_SIZE
assert len(
all_users) == MEMBERS_PAGE_SIZE + 3, 'Not all members returned'
assert pag == 2, 'Invalid page number returned'
for i in range(3):
user = dao.get_user_by_name("test_user_no" + str(i + 2))
self.user_service.delete_user(user.id)
page_users, all_users, pag = self.user_service.get_users_for_project(
"test_user_no1", project.id, 2)
assert len(page_users) == 0, 'Paging not working properly'
assert len(all_users) == MEMBERS_PAGE_SIZE, 'Not all members returned'
assert pag == 1, 'Invalid page number returned'
page_users, all_users, pag = self.user_service.get_users_for_project(
"test_user_no1", project.id, 1)
assert len(
page_users) == MEMBERS_PAGE_SIZE, 'Paging not working properly'
assert len(all_users) == MEMBERS_PAGE_SIZE, 'Not all members returned'
assert pag == 1, 'Invalid page number returned'
def _prepare_metric_operation(self, sim_operation):
# type: (Operation) -> None
metric_algo = dao.get_algorithm_by_module(
TimeseriesMetricsAdapter.__module__,
TimeseriesMetricsAdapter.__name__)
time_series_index = dao.get_generic_entity(TimeSeriesIndex,
sim_operation.id,
'fk_from_operation')[0]
view_model = TimeseriesMetricsAdapterModel()
view_model.time_series = time_series_index.gid
view_model.algorithms = tuple(choices.values())
range_values = sim_operation.range_values
metadata = {
DataTypeMetaData.KEY_BURST: time_series_index.fk_parent_burst
}
metadata, user_group = self._prepare_metadata(
metadata, metric_algo.algorithm_category, None, {})
meta_str = json.dumps(metadata)
parent_burst = dao.get_generic_entity(
BurstConfiguration, time_series_index.fk_parent_burst, 'id')[0]
metric_operation_group_id = parent_burst.fk_metric_operation_group
metric_operation = Operation(sim_operation.fk_launched_by,
sim_operation.fk_launched_in,
metric_algo.id,
json.dumps({'gid': view_model.gid.hex}),
meta_str,
op_group_id=metric_operation_group_id,
range_values=range_values)
metric_operation.visible = False
stored_metric_operation = dao.store_entity(metric_operation)
metrics_datatype_group = dao.get_generic_entity(
DataTypeGroup, metric_operation_group_id, 'fk_operation_group')[0]
if metrics_datatype_group.fk_from_operation is None:
metrics_datatype_group.fk_from_operation = metric_operation.id
OperationService._store_view_model(stored_metric_operation,
sim_operation.project, view_model)
return stored_metric_operation
def test_get_available_bursts_happy(self):
"""
Test that all the correct burst are returned for the given project.
"""
project = Project("second_test_proj", self.test_user.id, "description")
second_project = dao.store_entity(project)
test_project_bursts = [TestFactory.store_burst(self.test_project.id).id for _ in range(4)]
second_project_bursts = [TestFactory.store_burst(second_project.id).id for _ in range(3)]
returned_test_project_bursts = [burst.id for burst in
self.burst_service.get_available_bursts(self.test_project.id)]
returned_second_project_bursts = [burst.id for burst in
self.burst_service.get_available_bursts(second_project.id)]
assert len(test_project_bursts) == len(returned_test_project_bursts), \
"Incorrect bursts retrieved for project %s." % self.test_project
assert len(second_project_bursts) == len(returned_second_project_bursts), \
"Incorrect bursts retrieved for project %s." % second_project
assert set(second_project_bursts) == set(returned_second_project_bursts), \
"Incorrect bursts retrieved for project %s." % second_project
assert set(test_project_bursts) == set(returned_test_project_bursts), \
"Incorrect bursts retrieved for project %s." % self.test_project