def test_missing_extras():
"""https://github.com/sacdallago/bio_embeddings/issues/105"""
# Make sure those are in sync
assert set(name_to_embedder) == set(DEFAULT_MAX_AMINO_ACIDS)
with mock.patch("bio_embeddings.embed.pipeline.name_to_embedder", {}):
with pytest.raises(
InvalidParameterError,
match="The extra for the protocol seqvec is missing. "
"See https://docs.bioembeddings.com/#installation on how to install all extras",
):
run(
protocol="seqvec",
prefix=MagicMock(),
stage_name=MagicMock(),
remapped_sequences_file=MagicMock(),
mapping_file=MagicMock(),
)
def test_seqvec():
with mock.patch("bio_embeddings.embed.seqvec_embedder.ElmoEmbedder",
MockElmoEmbedder), TemporaryDirectory() as tmp_dir:
Path(tmp_dir).joinpath("seqvec_stage").mkdir()
out = run(
protocol="seqvec",
stage_name="seqvec_stage",
weights_file="mocked.txt",
options_file="mocked.txt",
seqvec_version=1,
prefix=tmp_dir,
remapped_sequences_file="test-data/remapped_sequences_file.fasta",
mapping_file="test-data/mapping_file.csv",
)
# TODO: Check output
print(out)