def test_loqusdb_api_cases(loqus_api_app, monkeypatch):
"""Test fetching info on number of cases from loqusdb API"""
nr_snvs = 15
nr_svs = 12
# GIVEN a mocked loqus API
def mockapi(*args):
return {
"content": {
"nr_cases_snvs": nr_snvs,
"nr_cases_svs": nr_svs
},
"status_code": 200,
}
monkeypatch.setattr(loqus_extension, "api_get", mockapi)
with loqus_api_app.app_context():
# WHEN fetching the nr_cases with SNV variants
n_cases = loqusdb.case_count("snv", "default")
# THEN the API should parse the returned info correctly
assert n_cases == nr_snvs
# WHEN fetching the nr_cases with SV variants
n_cases = loqusdb.case_count("sv", "default")
# THEN the API should parse the returned info correctly
assert n_cases == nr_svs
def test_loqus_api_cases_no_instance(loqus_api_app):
"""Test fetching info on number of cases from loqusdb API when the instance is not available"""
with loqus_api_app.app_context():
# WHEN fetching the nr_cases with SNV variants from an instance not available
n_cases = loqusdb.case_count("snv", "default")
# THEN the API shoud return 0 cases
assert n_cases == 0
def test_loqusdb_api_cases_not_found(loqus_api_app, monkeypatch):
"""Test fetching info on number of cases from loqusdb API when the API is not funct"""
def mockapi(*args):
return {"message": {"details": "not found"}}
monkeypatch.setattr(loqus_extension, "api_get", mockapi)
with loqus_api_app.app_context():
# WHEN fetching the nr_cases with SNV variants
n_cases = loqusdb.case_count("snv", "default")
# THEN the if no cases are found, it should return 0 cases
assert n_cases == 0
def test_loqusdb_exe_case_count_CalledProcessError(loqus_exe_app, monkeypatch):
"""Test the case count function in loqus extension that raises an exception"""
# GIVEN replacing subprocess.check_output to raise CalledProcessError
def mockcommand(*args):
raise subprocess.CalledProcessError(123, "case_count")
monkeypatch.setattr(loqus_extension, "execute_command", mockcommand)
with loqus_exe_app.app_context():
# THEN assert exception is caught and the value 0 is returned
assert 0 == loqusdb.case_count(variant_category="snv")
def test_loqusdb_exe_cases_ValueError(loqus_exe_app, monkeypatch):
"""Test the case count function in loqus extension"""
# GIVEN a return value from loqusdb which is not an int
def mockcommand(*args):
return "nonsense"
monkeypatch.setattr(loqus_extension, "execute_command", mockcommand)
with loqus_exe_app.app_context():
# THEN assert a value error is raised, but passed, and 0 is returned
assert loqusdb.case_count(variant_category="snv") == 0
def test_loqusdb_exe_cases(loqus_exe_app, monkeypatch):
"""Test the case count function in loqus executable extension"""
nr_cases = 15
# GIVEN a return value from loqusdb using a mocker
def mockcommand(*args):
return_value = b"%d" % nr_cases
return return_value
monkeypatch.setattr(loqus_extension, "execute_command", mockcommand)
with loqus_exe_app.app_context():
# WHEN fetching the number of cases
res = loqusdb.case_count(variant_category="snv")
# THEN assert the output is parsed correct
assert res == nr_cases