def test_migrate_report_qa_2(self):
engine = self._get_temp_db(5)
t_db = TransactionDB(engine)
last_message = {
'data': {
'report_qa_score_outcomes': {
'mdbrain_nd': 'good',
'mdbrain_ms': 'acceptable'
}
}
}
tr_1 = Transaction()
tr_1.last_message = json.dumps(last_message)
t_id = t_db.create_transaction(tr_1)
tr_1 = t_db.get_transaction(t_id)
# by default TransactionsDB doesn't set this field
self.assertEqual(None, tr_1.qa_score)
# execute migrate python script
model = get_transaction_model(engine)
migrations.migrate_qa_scores(t_db.session, model)
t_db.session.commit()
tr_2 = t_db.get_transaction(t_id)
self.assertTrue('mdbrain_ms:acceptable' in tr_2.qa_score)
self.assertTrue('mdbrain_nd:good' in tr_2.qa_score)
t_db.close()
def test_migrate_institution(self):
engine = self._get_temp_db(2)
t_db = TransactionDB(engine)
last_message = {
'data': {
'dicom_info': {
't1': {
'header': {
'InstitutionName': 'MockInstitution'
}
}
}
}
}
tr_1 = Transaction()
tr_1.last_message = json.dumps(last_message)
t_id = t_db.create_transaction(tr_1)
# remove institution field
session = t_db.session
tr_2 = t_db.get_transaction(t_id)
tr_2.institution = ''
session.commit()
self.assertEqual('', t_db.get_transaction(t_id).institution)
# execute migrate python script
model = get_transaction_model(engine)
migrations.migrate_institution(session, model)
session.commit()
tr_2 = t_db.get_transaction(t_id)
self.assertEqual('MockInstitution', tr_2.institution)
t_db.close()
def test_migrate_study_date(self):
engine = self._get_temp_db(4)
t_db = TransactionDB(engine)
last_message = {
'data': {
'dicom_info': {
't1': {
'header': {
'StudyDate': '20190101'
}
}
}
}
}
tr_1 = Transaction()
tr_1.last_message = json.dumps(last_message)
t_id = t_db.create_transaction(tr_1)
tr_1 = t_db.get_transaction(t_id)
# by default TransactionsDB doesn't set this field
self.assertEqual(None, tr_1.study_date)
# execute migrate python script
model = get_transaction_model(engine)
migrations.migrate_study_date(t_db.session, model)
t_db.session.commit()
tr_2 = t_db.get_transaction(t_id)
self.assertEqual('20190101', tr_2.study_date)
t_db.close()
def test_migrate_analysis_type_2(self):
engine = self._get_temp_db(5)
t_db = TransactionDB(engine)
last_message = {
'data': {
'report_pdf_paths': {
'mdbrain_nd': 'path1',
'mdbrain_ms': 'path2'
}
}
}
tr_1 = Transaction()
tr_1.last_message = json.dumps(last_message)
t_id = t_db.create_transaction(tr_1)
tr_1 = t_db.get_transaction(t_id)
# by default TransactionsDB doesn't set this field
self.assertEqual(None, tr_1.analysis_type)
# execute migrate python script
model = get_transaction_model(engine)
migrations.migrate_analysis_types(t_db.session, model)
t_db.session.commit()
tr_2 = t_db.get_transaction(t_id)
self.assertTrue('mdbrain_ms' in tr_2.analysis_type)
self.assertTrue('mdbrain_nd' in tr_2.analysis_type)
t_db.close()
def test_multi_session(self):
engine = temp_db.get_temp_db()
# no db created yet
t = Transaction()
t.name = 'Pere'
t_db_1 = TransactionDB(engine, False)
_ = TransactionDB(engine)
t_db_1.create_transaction(t)
t_1 = t_db_1.get_transaction(1)
self.assertEqual('Pere', t_1.name)
def child_process_fn(folder, name):
transaction_db = _get_temp_db(folder)
for _ in range(TEST_RANGE):
transaction_db.create_transaction(Transaction(name=name))
try:
transaction_db.get_transaction(1)
except TransactionDBException:
pass
def test_read_transaction_from_dict_is_complete(self):
# get all variables of transaction except non generic types
# Test that these variables are read from the deserialization
# function
non_generic_vars = [
'start_date', 'end_date', 'birth_date', 'task_state',
'data_uploaded', 'creation_date'
]
CALLABLES = types.FunctionType, types.MethodType
var = [
key for key, value in Transaction.__dict__.items()
if not isinstance(value, CALLABLES)
]
var = [
key for key in var if key[0] != '_' and key not in non_generic_vars
]
t = Transaction()
counter = 0
for key in var:
counter += 1
setattr(t, key, counter)
t2 = Transaction()
t2.read_dict(t.to_dict())
counter = 0
for key in var:
counter += 1
self.assertEqual(counter, getattr(t2, key))
def test_migrate_version(self):
engine = self._get_temp_db(5)
t_db = TransactionDB(engine)
last_message = {'data': {'version': '2.2.1'}}
tr_1 = Transaction()
tr_1.last_message = json.dumps(last_message)
t_id = t_db.create_transaction(tr_1)
tr_1 = t_db.get_transaction(t_id)
# by default TransactionsDB doesn't set this field
self.assertEqual(None, tr_1.version)
# execute migrate python script
model = get_transaction_model(engine)
migrations.migrate_version(t_db.session, model)
t_db.session.commit()
tr_2 = t_db.get_transaction(t_id)
self.assertEqual('2.2.1', tr_2.version)
t_db.close()
def test_read_dict_dates(self):
# test that date and datetimes are parsed correctly
engine = temp_db.get_temp_db()
t_db = TransactionDB(engine)
datetime_vars = ['start_date', 'end_date', 'data_uploaded']
date_vars = ['birth_date']
t = Transaction()
for key in datetime_vars:
setattr(t, key, datetime(2020, 2, 1, 18, 30, 4))
for key in date_vars:
setattr(t, key, datetime(2020, 2, 1))
t_r = Transaction().read_dict(t.to_dict())
t_id = t_db.create_transaction(t_r)
t_r_from_db = t_db.get_transaction(t_id)
self.assertEqual(datetime(2020, 2, 1, 18, 30, 4),
t_r_from_db.start_date)
self.assertEqual(datetime(2020, 2, 1, 18, 30, 4), t_r_from_db.end_date)
self.assertEqual(date(2020, 2, 1), t_r_from_db.birth_date)
def test_study_metadata_to_dict(self):
md = StudiesMetadata()
md.origin = 'dicom_grazer'
md.c_move_time = datetime.utcnow()
md.study_id = 's1'
self.assertEqual(
{
'origin': 'dicom_grazer',
'c_move_time': Transaction._datetime_to_str(md.c_move_time),
'study_id': 's1'
}, md.to_dict())
def _get_test_transaction(self):
t = Transaction()
# we only need to fill metadata before creating a new transaction
t.name = 'Pere'
t.patient_id = '1'
t.study_id = 'S1'
t.birth_date = datetime(1982, 10, 29)
return t
def test_migrate_sequences(self):
engine = self._get_temp_db(3)
t_db = TransactionDB(engine)
last_message = {
'data': {
'dicom_info': {
't1': {
'header': {
'SeriesDescription': 'T1_sequence'
}
},
't2': {
'header': {
'SeriesDescription': 'T2_sequence'
}
}
}
}
}
tr_1 = Transaction()
tr_1.last_message = json.dumps(last_message)
t_id = t_db.create_transaction(tr_1)
# remove sequences field
session = t_db.session
tr_2 = t_db.get_transaction(t_id)
tr_2.institution = ''
session.commit()
self.assertEqual('', t_db.get_transaction(t_id).institution)
# execute migrate python script
model = get_transaction_model(engine)
migrations.migrate_sequences(session, model)
session.commit()
tr_2 = t_db.get_transaction(t_id)
self.assertEqual('T1_sequence;T2_sequence', tr_2.sequences)
t_db.close()
def test_read_transaction_from_dict(self):
d = {
'transaction_id': 1,
'name': 'John Doe',
'birth_date': '01/02/2020'
}
t = Transaction().read_dict(d)
engine = temp_db.get_temp_db()
t_db = TransactionDB(engine)
t_id = t_db.create_transaction(t)
t_from_db = t_db.get_transaction(t_id)
self.assertEqual(d['transaction_id'], t_from_db.transaction_id)
self.assertEqual(d['name'], t_from_db.name)
self.assertEqual(date(2020, 2, 1), t_from_db.birth_date)
def test_migrations(self):
temp_folder = tempfile.mkdtemp(
suffix='_test_migrations_transaction_db_')
temp_db_path = os.path.join(temp_folder, 't_v1.db')
shutil.copy('tests/fixtures/t_v1.db', temp_db_path)
engine = create_engine('sqlite:///' + temp_db_path)
# should execute all migrations code
t_db = TransactionDB(engine, create_db=True, db_file_path=temp_db_path)
self.assertTrue(os.path.exists(temp_db_path + '.v_1.bkp'))
# add a new transaction with the current model
t = Transaction()
t_db.create_transaction(t)
shutil.rmtree(temp_folder)
def test_read_dict_task_state(self):
# test that task state is parsed correctly
t = Transaction()
t.task_state = TaskState.completed
t_r = Transaction().read_dict(t.to_dict())
self.assertEqual(TaskState.completed, t_r.task_state)
def create_transaction(
self, t: Transaction,
user_id=None, product_id=None, analysis_type=None,
qa_score=None,
processing_state='waiting',
task_state='queued') -> int:
"""will set the provided transaction object as queued,
add it to the DB and return the transaction id.
If the transaction has a last_message JSON with chosen T1/T2,
it will index the sequence names as well.
Parameters
----------
user_id: int
product_id: int
"""
try:
if task_state == 'failed':
t.task_state = TaskState.failed
else:
t.task_state = TaskState.queued
t.processing_state = processing_state
if not t.creation_date:
t.creation_date = datetime.datetime.utcnow()
if product_id:
t.product_id = product_id
if analysis_type:
t.analysis_type = analysis_type
if qa_score:
t.qa_score = qa_score
self.session.add(t)
# when we commit, we get the transaction ID
self.session.commit()
if user_id:
user = self.session.query(User).get(user_id)
if not user:
raise TransactionDBException(("The provided user doesn't "
"exist"))
ut = UserTransaction()
ut.user_id = user_id
ut.transaction_id = t.transaction_id
self.session.add(ut)
self.session.commit()
# set the transaction id in the task object
if t.last_message:
try:
lm = json.loads(t.last_message)
lm['t_id'] = t.transaction_id
t.last_message = json.dumps(lm)
except Exception:
pass
# index.set_index_institution(t)
index.set_index_sequences(t)
self.session.commit()
return t.transaction_id
except Exception:
self.session.rollback()
try:
if(t.transaction_id):
self.session.delete(t)
except:
pass
raise