def fixture_genotype_api(genotype_config: dict) -> GenotypeAPI:
"""
genotype API fixture
"""
_genotype_api = GenotypeAPI(genotype_config)
_genotype_api.set_dry_run(True)
return _genotype_api
def test_export_sample_no_output(genotype_api: GenotypeAPI, caplog):
"""Test to get genotype via the api"""
# GIVEN a genotype api
# GIVEN a process that does not return any output
# WHEN export_sample is calling the GenotypeAPI witch is returning a empty string
# THEN assert CaseNotFoundError
with pytest.raises(CaseNotFoundError):
genotype_api.export_sample(days="")
def test_update_analysis_sex(genotype_api: GenotypeAPI, caplog):
"""Test to update the sample sex function"""
caplog.set_level(logging.DEBUG)
# GIVEN a sample id and a sex
sample = "sample"
sex = "female"
# WHEN running the update sample sex command
genotype_api.update_analysis_sex(sample, sex)
# THEN assert that the correct message was logged
assert f"Set predicted sex for sample {sample} to {sex} for the sequence analysis"
def test_genotype_api_upload(genotype_api: GenotypeAPI, caplog):
"""Test to run the upload functionality in the genotype API"""
caplog.set_level(logging.DEBUG)
# GIVEN a genotype api and a samples sex dictionary and a bcf_path
sample_id = "a_sample_id"
samples_sex = {sample_id: {"pedigree": "Female", "analysis": "Female"}}
bcf_path = "path_to_file.bcf"
# WHEN running the update command
genotype_api.upload(bcf_path, samples_sex)
# THEN assert that the correct information was communicated
assert f"loading VCF genotypes for sample(s): {sample_id}" in caplog.text
def test_export_sample(genotype_api: GenotypeAPI,
genotype_export_sample_output: str, caplog):
"""Test that get_trending calls the genotype API with correct command."""
caplog.set_level(logging.DEBUG)
# GIVEN a genotype api and argument days
days = 20
# GIVEN that the process returns some output
genotype_api.process.stdout = genotype_export_sample_output
# WHEN running get_trending
genotype_api.export_sample(days=days)
# THEN assert subprocess is running the GenotypeAPI with correct command
call = ["config/path", "export-sample", "-d", str(days)]
assert " ".join(call) in caplog.text
def genotypeapi():
"""
genotype API fixture
"""
_genotype_api = GenotypeAPI(CONFIG)
return _genotype_api
def genotype_api(self) -> GenotypeAPI:
api = self.__dict__.get("genotype_api_")
if api is None:
LOG.debug("Instantiating genotype api")
api = GenotypeAPI(config=self.dict())
self.genotype_api_ = api
return api
def test_instantiate(genotype_config: dict):
"""Test to instantiate a genotype api"""
# GIVEN a genotype api with a config
# WHEN instantiating a genotype api
genotype_api = GenotypeAPI(genotype_config)
# THEN assert that the adapter was properly instantiated
assert genotype_api.process.config == genotype_config["genotype"][
"config_path"]
assert genotype_api.process.binary == genotype_config["genotype"][
"binary_path"]