def test_load_bioinfo_sample(vogue_config, caplog):
"""Test load bioinfo sample upload in vogue api"""
# GIVEN a vogue api and a vogue config
vogue_api = VogueAPI(vogue_config)
dummy_stdout = "dummy_stdout"
dummy_stderr = "dummy_stderr"
dummy_returncode_success = 0
test_load_bioinfo_sample_inputs = {"analysis_case_name": "dummy_case"}
load_bioinfo_sample_call = [
"load",
"bioinfo",
"sample",
"--analysis-case",
test_load_bioinfo_sample_inputs["analysis_case_name"],
]
load_bioinfo_sample_call_command = " ".join(load_bioinfo_sample_call)
caplog.set_level(logging.INFO)
# WHEN instantiating a vogue api and input data
with mock.patch.object(subprocess, "run") as mocked:
mocked.return_value.stdout = dummy_stdout.encode("utf-8")
mocked.return_value.stderr = dummy_stderr.encode("utf-8")
mocked.return_value.returncode = dummy_returncode_success
vogue_api.load_bioinfo_sample(
load_bioinfo_inputs=test_load_bioinfo_sample_inputs)
# THEN assert that command is in log output
assert load_bioinfo_sample_call_command in caplog.text
def fixture_vogue_api(process):
"""
vogue API fixture
"""
_vogue_api = VogueAPI(CONFIG)
_vogue_api.process = process
return _vogue_api
def test_load_bioinfo_raw(vogue_config, caplog):
"""Test load bioinfo raw upload in vogue api"""
# GIVEN a vogue api and a vogue config
vogue_api = VogueAPI(vogue_config)
dummy_stdout = "dummy_stdout"
dummy_stderr = "dummy_stderr"
dummy_returncode_success = 0
test_load_bioinfo_raw_inputs = {
"samples": "dummy_sample",
"analysis_result_file": "dummy_file_name",
"analysis_type": "dummy_analysis_type",
"analysis_case_name": "dummy_analysis_case_name",
"analysis_workflow_version": "dummy_version_3.1415",
"case_analysis_type": "dummy_multiqc",
"analysis_workflow_name": "dummy_best_workflow",
}
load_bioinfo_raw_call = [
"load",
"bioinfo",
"raw",
"--sample-list",
test_load_bioinfo_raw_inputs["samples"],
"--analysis-result",
test_load_bioinfo_raw_inputs["analysis_result_file"],
"--analysis-type",
test_load_bioinfo_raw_inputs["analysis_type"],
"--analysis-case",
test_load_bioinfo_raw_inputs["analysis_case_name"],
"--workflow-version",
test_load_bioinfo_raw_inputs["analysis_workflow_version"],
"--case-analysis-type",
test_load_bioinfo_raw_inputs["case_analysis_type"],
"--analysis-workflow",
test_load_bioinfo_raw_inputs["analysis_workflow_name"],
]
load_bioinfo_raw_call_command = " ".join(load_bioinfo_raw_call)
caplog.set_level(logging.INFO)
# WHEN instantiating a vogue api and input data
with mock.patch.object(subprocess, "run") as mocked:
mocked.return_value.stdout = dummy_stdout.encode("utf-8")
mocked.return_value.stderr = dummy_stderr.encode("utf-8")
mocked.return_value.returncode = dummy_returncode_success
vogue_api.load_bioinfo_raw(
load_bioinfo_inputs=test_load_bioinfo_raw_inputs)
# THEN assert that command is in log output
assert load_bioinfo_raw_call_command in caplog.text
def vogue_api():
"""
vogue API fixture
"""
_vogue_api = VogueAPI(VOGUECONFIG)
return _vogue_api
def vogue_api(self) -> VogueAPI:
api = self.__dict__.get("vogue_api_")
if api is None:
LOG.debug("Instantiating vogue api")
api = VogueAPI(config=self.dict())
self.vogue_api_ = api
return api
def test_instatiate(vogue_config):
"""Test to instantiate a vogue api"""
# GIVEN a vogue api with a config
# WHEN instantiating a vogue api
vogue_api = VogueAPI(vogue_config)
# THEN assert that the adapter was properly instantiated
assert vogue_api.vogue_binary == vogue_config["vogue"]["binary_path"]