def test_ignores_identifiers_order(self):
trial_identifiers = collections.OrderedDict([
('nct', 'NCT000000'),
('drks', 'DRKS0000000'),
])
record_identifiers = collections.OrderedDict([
('drks', 'DRKS0000000'),
('nct', 'NCT000000'),
])
assert trial_identifiers.items() != record_identifiers.items(), \
'Identifiers items must be different unless sorted'
query_result = [
{
'id': uuid.uuid1(),
'trial_identifiers': trial_identifiers,
'records_identifiers': record_identifiers,
},
]
db_mock = mock.MagicMock()
db_mock['trials'] = mock.Mock()
db_mock.query.return_value = query_result
conf = {}
conn = {'database': db_mock}
processor.process(conf, conn)
db_mock['trials'].update.assert_not_called()
def test_ignores_identifiers_order(self):
trial_identifiers = collections.OrderedDict([
('nct', 'NCT000000'),
('drks', 'DRKS0000000'),
])
record_identifiers = collections.OrderedDict([
('drks', 'DRKS0000000'),
('nct', 'NCT000000'),
])
assert trial_identifiers.items() != record_identifiers.items(), \
'Identifiers items must be different unless sorted'
query_result = [
{
'id': uuid.uuid1(),
'trial_identifiers': trial_identifiers,
'records_identifiers': record_identifiers,
},
]
db_mock = mock.MagicMock()
db_mock['trials'] = mock.Mock()
db_mock.query.return_value = query_result
conf = {}
conn = {'database': db_mock}
processor.process(conf, conn)
db_mock['trials'].update.assert_not_called()
def test_doesnt_update_identifiers_if_theyre_a_subset_of_the_trials_identifiers(self):
query_result = [
{
'id': uuid.uuid1(),
'trial_identifiers': {'nct': 'NCT00000', 'ictrp': 'ICTRP0000000'},
'records_identifiers': {'ictrp': 'ICTRP0000000'},
},
]
db_mock = mock.MagicMock()
db_mock['trials'] = mock.Mock()
db_mock.query.return_value = query_result
conf = {}
conn = {'database': db_mock}
processor.process(conf, conn)
db_mock['trials'].update.assert_not_called()
def test_doesnt_update_identifiers_if_theyre_a_subset_of_the_trials_identifiers(self):
query_result = [
{
'id': uuid.uuid1(),
'trial_identifiers': {'nct': 'NCT00000', 'ictrp': 'ICTRP0000000'},
'records_identifiers': {'ictrp': 'ICTRP0000000'},
},
]
db_mock = mock.MagicMock()
db_mock['trials'] = mock.Mock()
db_mock.query.return_value = query_result
conf = {}
conn = {'database': db_mock}
processor.process(conf, conn)
db_mock['trials'].update.assert_not_called()
def test_it_uses_records_identifiers_when_there_are_multiple_ids_from_same_source(self,
conn, trial, record):
trial_attrs = {
'id': trial,
'identifiers': {'nct': 'NCT87654321'},
}
conn['database']['trials'].update(trial_attrs, ['id'])
record_attrs = {
'id': record,
'trial_id': trial ,
'identifiers': {'nct': 'NCT12345678'},
}
conn['database']['records'].update(record_attrs, ['id'])
processor.process({}, conn)
updated_trial = conn['database']['trials'].find_one(id=trial)
assert updated_trial['identifiers'] == record_attrs['identifiers']
def test_updates_trial_with_records_identifiers(self, conn, trial, record):
trial_attrs = {
'id': trial,
'identifiers': {},
}
conn['database']['trials'].update(trial_attrs, ['id'])
trial_last_updated = datetime.datetime.utcnow()
record_attrs = {
'id': record,
'trial_id': trial,
'identifiers': {'nct': 'NCT11111', 'ictrp': 'ICTRP000000'},
}
conn['database']['records'].update(record_attrs, ['id'])
processor.process({}, conn)
updated_trial = conn['database']['trials'].find_one(id=trial)
assert updated_trial['identifiers'] == record_attrs['identifiers']
assert updated_trial['updated_at'].replace(tzinfo=None) > trial_last_updated
def test_it_uses_records_identifiers_when_there_are_multiple_ids_from_same_source(self):
query_result = [
{
'id': uuid.uuid1(),
'trial_identifiers': {'nct': 'NCT00000'},
'records_identifiers': {'nct': 'NCT11111'},
},
]
db_mock = mock.MagicMock()
db_mock['trials'] = mock.Mock()
db_mock.query.return_value = query_result
conf = {}
conn = {'database': db_mock}
processor.process(conf, conn)
expected_identifiers = query_result[0]['records_identifiers']
updated_trial, _ = db_mock['trials'].update.call_args[0]
assert updated_trial.get('identifiers') == expected_identifiers
def test_merges_identifiers(self):
query_result = [
{
'id': uuid.uuid1(),
'trial_identifiers': {'nct': 'NCT000000'},
'records_identifiers': {'ictrp': 'ICTRP000000'},
},
]
db_mock = mock.MagicMock()
db_mock['trials'] = mock.Mock()
db_mock.query.return_value = query_result
conf = {}
conn = {'database': db_mock}
processor.process(conf, conn)
expected_identifiers = {'nct': 'NCT000000', 'ictrp': 'ICTRP000000'}
updated_trial, _ = db_mock['trials'].update.call_args[0]
assert updated_trial.get('identifiers') == expected_identifiers
def test_merges_identifiers(self, conn, trial, record):
trial_attrs = {
'id': trial,
'identifiers': {'nct': 'NCT87654321'},
}
conn['database']['trials'].update(trial_attrs, ['id'])
trial_last_updated = datetime.datetime.utcnow()
record_attrs = {
'id': record,
'trial_id': trial ,
'identifiers': {'isrctn': 'ISRCTN71203361'},
}
conn['database']['records'].update(record_attrs, ['id'])
expected_identifiers = deepcopy(record_attrs['identifiers'])
expected_identifiers.update(trial_attrs['identifiers'])
processor.process({}, conn)
updated_trial = conn['database']['trials'].find_one(id=trial)
assert updated_trial['identifiers'] == expected_identifiers
assert updated_trial['updated_at'].replace(tzinfo=None) > trial_last_updated
def test_updates_trial_with_records_identifiers(self, datetime_mock):
query_result = [
{
'id': uuid.uuid1(),
'trial_identifiers': {},
'records_identifiers': {'nct': 'NCT11111', 'ictrp': 'ICTRP000000'},
},
]
db_mock = mock.MagicMock()
db_mock['trials'] = mock.Mock()
db_mock.query.return_value = query_result
datetime_mock.utcnow.return_value = 'the_date'
conf = {}
conn = {'database': db_mock}
processor.process(conf, conn)
expected_trial = {
'id': query_result[0]['id'].hex,
'identifiers': query_result[0]['records_identifiers'],
'updated_at': datetime.datetime.utcnow(),
}
db_mock['trials'].update.assert_called_with(expected_trial, ['id'])