def test_samp_clean_fail(mongodb_settings):
base = SampleStore(mongodb_settings)
for key, doc, uuid_val in sample.CLEAN:
resp = base.add_update_document(doc)
assert resp['uuid'] is not None
with pytest.raises(ValueError,
match="Must specify at least one field to clean"):
update_result = base.clean_fields("experiment.lab.foo", [])
with pytest.raises(ValueError,
match="Experiment id is not namespaced 'invalid_exp'"):
update_result = base.clean_fields("invalid_exp",
["control_type", "standard_type"])
with pytest.raises(ValueError,
match="Field to clean is not declared 'invalid_field'"):
update_result = base.clean_fields("experiment.lab.foo",
["invalid_field"])
with pytest.raises(ValueError,
match="Field to clean is a token field 'uuid'"):
update_result = base.clean_fields("experiment.lab.foo", ["uuid"])
with pytest.raises(ValueError,
match="Field to clean is a uuid field 'sample_id'"):
update_result = base.clean_fields("experiment.lab.foo", ["sample_id"])
with pytest.raises(ValueError,
match="Field to clean is a read only field '_salt'"):
update_result = base.clean_fields("experiment.lab.foo", ["_salt"])
with pytest.raises(ValueError,
match="Field to clean is required 'measurements'"):
update_result = base.clean_fields("experiment.lab.foo",
["measurements"])
def test_samp_clean(mongodb_settings):
base = SampleStore(mongodb_settings)
for key, doc, uuid_val in sample.CLEAN:
resp = base.add_update_document(doc)
assert resp['uuid'] is not None
assert "control_type" in base.query(
{"sample_id": "sample1.lab.experiment.lab.4"})[0]
assert "standard_type" in base.query(
{"sample_id": "sample1.lab.experiment.lab.4"})[0]
assert "control_type" not in base.query(
{"sample_id": "sample2.lab.experiment.lab.4"})[0]
assert "standard_type" not in base.query(
{"sample_id": "sample2.lab.experiment.lab.4"})[0]
assert "control_type" not in base.query(
{"sample_id": "sample1.lab.experiment.lab.5"})[0]
assert "standard_type" not in base.query(
{"sample_id": "sample1.lab.experiment.lab.5"})[0]
assert "control_type" not in base.query(
{"sample_id": "sample2.lab.experiment.lab.5"})[0]
assert "standard_type" not in base.query(
{"sample_id": "sample2.lab.experiment.lab.5"})[0]
update_result = base.clean_fields("experiment.lab.4",
["control_type", "standard_type"])
assert (update_result.matched_count == 2)
assert (update_result.modified_count == 1)
# should be removed from sample1.lab.experiment.lab.4
assert "control_type" not in base.query(
{"sample_id": "sample1.lab.experiment.lab.4"})[0]
assert "standard_type" not in base.query(
{"sample_id": "sample1.lab.experiment.lab.4"})[0]
# no effect on experiment without fields
update_result = base.clean_fields("experiment.lab.5",
["control_type", "standard_type"])
assert (update_result.matched_count == 2)
assert (update_result.modified_count == 0)
# no effect on previously cleaned experiment
update_result = base.clean_fields("experiment.lab.4",
["control_type", "standard_type"])
assert (update_result.matched_count == 2)
assert (update_result.modified_count == 0)
# no effect on non-matching experiment
update_result = base.clean_fields("experiment.lab.foo1",
["control_type", "standard_type"])
assert (update_result.matched_count == 0)
assert (update_result.modified_count == 0)
def test_samp_add(mongodb_settings):
base = SampleStore(mongodb_settings)
for key, doc, uuid_val in sample.CREATES:
resp = base.add_update_document(doc)
assert resp['uuid'] is not None
def test_samp_issue_uuid(mongodb_settings):
base = SampleStore(mongodb_settings)
identifier_string = 'emerald.sample.unrepresentative-sample'
identifier_string_uuid = base.get_typeduuid(identifier_string,
binary=False)
assert identifier_string_uuid == '10382668-9f1c-591d-b9f3-fca72a191225'
def test_samp_uuid_tytpe(mongodb_settings):
base = SampleStore(mongodb_settings)
assert base.get_uuid_type() == 'sample'
def test_samp_name(mongodb_settings):
base = SampleStore(mongodb_settings)
assert base.name == 'samples'
def test_samp_schema(mongodb_settings):
base = SampleStore(mongodb_settings)
assert isinstance(base.schema, dict)
def test_samp_db_list_collection_names(mongodb_settings):
base = SampleStore(mongodb_settings)
assert base.db.list_collection_names() is not None
def test_samp_delete(mongodb_settings):
base = SampleStore(mongodb_settings)
for key, doc, uuid_val in sample.DELETES:
resp = base.delete_document(uuid_val)
assert resp.raw_result == {'n': 1, 'ok': 1.0}
def test_samp_db_heritable_schema(mongodb_settings):
base = SampleStore(mongodb_settings)
assert 'contents' in base.get_indexes()
assert 'title' not in base.get_indexes()
def test_samp_update(mongodb_settings):
base = SampleStore(mongodb_settings)
for key, doc, uuid_val in sample.UPDATES:
resp = base.add_update_document(doc, uuid=uuid_val)
assert resp['uuid'] == uuid_val
def test_samp_db_init(mongodb_settings):
base = SampleStore(mongodb_settings)