def test_empty_database(real_adapter):
## GIVEN an empty database
adapter = real_adapter
## WHEN asking for data
data = get_dashboard_info(adapter)
## THEN assert that the data is empty
assert data.get("total_cases") == 0
def test_empty_database(real_adapter):
## GIVEN an empty database
adapter = real_adapter
## WHEN asking for data
data = get_dashboard_info(adapter)
## THEN assert that the data is empty
assert data.get('total_cases') == 0
def test_one_case(real_adapter, case_obj):
## GIVEN an database with one case
adapter = real_adapter
adapter._add_case(case_obj)
## WHEN asking for data
data = get_dashboard_info(adapter)
## THEN assert there is one case in the data
for group in data["cases"]:
if group["status"] == "all":
assert group["count"] == 1
elif group["status"] == case_obj["status"]:
assert group["count"] == 1
def test_one_case(real_adapter, case_obj):
## GIVEN an database with one case
adapter = real_adapter
adapter._add_case(case_obj)
## WHEN asking for data
data = get_dashboard_info(adapter)
## THEN assert there is one case in the data
for group in data['cases']:
if group['status'] == 'all':
assert group['count'] == 1
elif group['status'] == case_obj['status']:
assert group['count'] == 1
def test_one_causative(real_adapter, case_obj):
## GIVEN an database with two cases where one has a causative
adapter = real_adapter
adapter._add_case(case_obj)
case_obj["causatives"] = ["a variant"]
case_obj["_id"] = "test1"
adapter._add_case(case_obj)
## WHEN asking for data
institute_id = case_obj["owner"]
data = get_dashboard_info(adapter, institute_id=institute_id)
## THEN assert there is one case in the causative information
for info in data["overview"]:
if info["title"] == "Causative variants":
assert info["count"] == 1
else:
assert info["count"] == 0
def test_one_causative(real_adapter, case_obj):
## GIVEN an database with two cases where one has a causative
adapter = real_adapter
adapter._add_case(case_obj)
case_obj['causatives'] = ['a variant']
case_obj['_id'] = 'test1'
adapter._add_case(case_obj)
## WHEN asking for data
institute_id = case_obj['owner']
data = get_dashboard_info(adapter, institute_id=institute_id)
## THEN assert there is one case in the causative information
for info in data['overview']:
if info['title'] == 'Causative variants':
assert info['count'] == 1
else:
assert info['count'] == 0
def test_one_causative(real_adapter, case_obj):
## GIVEN an database with two cases where one has a causative
adapter = real_adapter
adapter._add_case(case_obj)
case_obj['causatives'] = ['a variant']
case_obj['_id'] = 'test1'
adapter._add_case(case_obj)
## WHEN asking for data
institute_id = case_obj['owner']
data = get_dashboard_info(adapter, institute_id=institute_id)
## THEN assert there is one case in the causative information
for info in data['overview']:
if info['title'] == 'Causative variants':
assert info['count'] == 1
else:
assert info['count'] == 0
def test_with_slice_query(real_adapter, case_obj):
## GIVEN an database with one case
adapter = real_adapter
adapter._add_case(case_obj)
## WHEN asking for data
case_display_id = case_obj["display_name"]
institute_id = case_obj["owner"]
slice_query = f"case:{case_display_id}"
data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query)
## THEN assert there is one case in the data
for group in data["cases"]:
if group["status"] == "all":
assert group["count"] == 1
elif group["status"] == case_obj["status"]:
assert group["count"] == 1
def test_with_slice_query(real_adapter, case_obj):
## GIVEN an database with one case
adapter = real_adapter
adapter._add_case(case_obj)
## WHEN asking for data
case_display_id = case_obj['display_name']
institute_id = case_obj['owner']
slice_query = case_display_id
data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query)
## THEN assert there is one case in the data
for group in data['cases']:
if group['status'] == 'all':
assert group['count'] == 1
elif group['status'] == case_obj['status']:
assert group['count'] == 1
def test_with_slice_query(real_adapter, case_obj):
## GIVEN an database with one case
adapter = real_adapter
adapter._add_case(case_obj)
## WHEN asking for data
case_display_id = case_obj['display_name']
institute_id = case_obj['owner']
slice_query = case_display_id
data = get_dashboard_info(adapter,
institute_id=institute_id,
slice_query=slice_query)
## THEN assert there is one case in the data
for group in data['cases']:
if group['status'] == 'all':
assert group['count'] == 1
elif group['status'] == case_obj['status']:
assert group['count'] == 1
def test_with_phenotype_group_query(real_adapter, case_obj):
## GIVEN an database with one case
adapter = real_adapter
adapter._add_case(case_obj)
phenotype = {"phenotype_id": "HP:0000001", "feature": "Bioterm"}
## WITH a phenotype set for one case
case_obj["phenotype_groups"] = [phenotype]
case_obj["_id"] = "test1"
adapter._add_case(case_obj)
## WHEN querying for cases with that phenotype id
institute_id = case_obj["owner"]
slice_query = "pheno_group:HP:0000001"
data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query)
## THEN assert there is one case in the data
for group in data["cases"]:
if group["status"] == "all":
assert group["count"] == 1
elif group["status"] == case_obj["status"]:
assert group["count"] == 1
def test_with_phenotype_group_query(real_adapter, case_obj):
## GIVEN an database with one case
adapter = real_adapter
adapter._add_case(case_obj)
phenotype = {'phenotype_id': 'HP:0000001' , 'feature':'Bioterm'}
## WITH a phenotype set for one case
case_obj['phenotype_groups'] = [ phenotype ]
case_obj['_id'] = 'test1'
adapter._add_case(case_obj)
## WHEN querying for cases with that phenotype id
institute_id = case_obj['owner']
slice_query = 'PG:0000001'
data = get_dashboard_info(adapter, institute_id=institute_id, slice_query=slice_query)
## THEN assert there is one case in the data
for group in data['cases']:
if group['status'] == 'all':
assert group['count'] == 1
elif group['status'] == case_obj['status']:
assert group['count'] == 1
def test_with_phenotype_group_query(real_adapter, case_obj):
## GIVEN an database with one case
adapter = real_adapter
adapter._add_case(case_obj)
phenotype = {'phenotype_id': 'HP:0000001', 'feature': 'Bioterm'}
## WITH a phenotype set for one case
case_obj['phenotype_groups'] = [phenotype]
case_obj['_id'] = 'test1'
adapter._add_case(case_obj)
## WHEN querying for cases with that phenotype id
institute_id = case_obj['owner']
slice_query = 'PG:0000001'
data = get_dashboard_info(adapter,
institute_id=institute_id,
slice_query=slice_query)
## THEN assert there is one case in the data
for group in data['cases']:
if group['status'] == 'all':
assert group['count'] == 1
elif group['status'] == case_obj['status']:
assert group['count'] == 1
