def test_init_setup_prefix(mongodb_settings, agave, samples_uri):
ag_sys, ag_path, ag_file = agavehelpers.from_agave_uri(samples_uri)
db = sampleset_module.SampleSetProcessor(mongodb_settings,
agave=agave,
samples_uri=samples_uri,
path_prefix=ag_path).setup()
assert db is not None
def test_process_from_file_w_uri(mongodb_settings, agave, filename,
samples_uri):
db = sampleset_module.SampleSetProcessor(mongodb_settings,
agave=agave,
samples_file=filename,
samples_uri=samples_uri).setup()
dbp = db.process(strategy='replace')
assert dbp is True
def sampleset_processor(mongodb_settings):
return sampleset.SampleSetProcessor(mongodb_settings)
def test_iter_process_merge(mongodb_settings, filename):
jsonpath = os.path.join(DATA_DIR, filename)
db = sampleset_module.SampleSetProcessor(mongodb_settings,
samples_file=jsonpath).setup()
dbp = db.process(strategy='merge')
assert dbp is True
def test_init_setup(mongodb_settings, agave, samples_uri):
db = sampleset_module.SampleSetProcessor(mongodb_settings,
agave=agave,
samples_uri=samples_uri).setup()
assert db is not None
def test_init_setup_no_agave(mongodb_settings, samples_uri):
with pytest.raises(Exception):
db = sampleset_module.SampleSetProcessor(
mongodb_settings, agave=None, samples_uri=samples_uri).setup()
assert db is not None