def loaded_sdf(
elastic_repository: ElasticRepository,
resource_loader: Callable[[str], str],
) -> IndigoRecord:
resource = resource_loader("resources/rand_queries_small.sdf")
sdf = iterate_file(Path(resource))
elastic_repository.index_records(sdf, chunk_size=10)
time.sleep(5)
return next(
iterate_file(Path(resource_loader("resources/rand_queries_small.sdf")))
)
def loaded_sdf(
elastic_repository_molecule: ElasticRepository,
resource_loader,
) -> IndigoRecordMolecule:
resource = resource_loader("molecules/rand_queries_small.sdf")
sdf = iterate_file(Path(resource))
elastic_repository_molecule.index_records(sdf, chunk_size=10)
time.sleep(5)
return next(
iterate_file(Path(resource_loader("molecules/rand_queries_small.sdf")))
)
def test_create_index(
elastic_repository_molecule: ElasticRepository,
resource_loader,
):
sdf = iterate_file(
Path(resource_loader("molecules/rand_queries_small.sdf")))
elastic_repository_molecule.index_records(sdf, chunk_size=10)
def test_create_index(
elastic_repository: ElasticRepository,
resource_loader: Callable[[str], str],
):
sdf = iterate_file(
Path(resource_loader("resources/rand_queries_small.sdf")))
elastic_repository.index_records(sdf, chunk_size=10)
def test_iterate_sdf(resource_loader: Callable[[str], str]):
results = []
for step in range(0, 2):
if 0 == step:
sdf = helpers.iterate_sdf(
resource_loader("resources/rand_queries_small.sdf"))
else:
sdf = helpers.iterate_file(
Path(resource_loader("resources/rand_queries_small.sdf")))
i = 0
for i, _ in enumerate(sdf, start=1):
pass
results.append(i)
assert results[0] == results[1]
def test_iterate_cml(resource_loader: Callable[[str], str]):
results = []
for step in range(0, 2):
if 0 == step:
cml = helpers.iterate_cml(
resource_loader("resources/tetrahedral-all.cml"))
else:
cml = helpers.iterate_file(
Path(resource_loader("resources/tetrahedral-all.cml")))
i = 0
for i, _ in enumerate(cml, start=1):
pass
results.append(i)
assert results[0] == results[1]
def test_iterate_smiles(resource_loader: Callable[[str], str]):
results = []
for step in range(0, 2):
if 0 == step:
smiles = helpers.iterate_smiles(
resource_loader("resources/pubchem_slice_50.smi"))
else:
smiles = helpers.iterate_file(
Path(resource_loader("resources/pubchem_slice_50.smi")))
i = 0
for i, _ in enumerate(smiles, start=1):
pass
results.append(i)
assert results[0] == results[1]
def test_range_search(
elastic_repository_molecule: ElasticRepository,
indigo_fixture: Indigo,
resource_loader,
):
for i, item in enumerate(
iterate_file(
Path(resource_loader("molecules/rand_queries_small.sdf")))):
item.ind_number = i
elastic_repository_molecule.index_record(item)
result = elastic_repository_molecule.filter(ind_number=RangeQuery(1, 10))
i = 0
for _ in result:
i += 1
assert i == 10