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from pathlib import Path
import pytest
from folding_studio.cli import app
from folding_studio.query import ChaiQuery
from typer.testing import CliRunner
runner = CliRunner()
RESTRAINTS_CSV_CONTENT = """
chainA,res_idxA,chainB,res_idxB,connection_type,confidence,min_distance_angstrom,max_distance_angstrom,comment,restraint_id
A,C387,B,Y101,contact,1.0,0.0,5.5,protein-heavy,restraint_1
C,I32,A,S483,contact,1.0,0.0,5.5,protein-light,restraint_2
"""
@pytest.fixture(scope="module")
def tmp_files(tmp_directory: Path, tmp_files: dict):
"""Generate temporary files."""
# A valid restraints CSV file
valid_restraints = tmp_directory / "example_restraints.csv"
valid_restraints.write_text(RESTRAINTS_CSV_CONTENT)
tmp_files["valid_restraints"] = valid_restraints
yield tmp_files
def test_chai_fold_with_invalid_source(tmp_files):
"""
Running the command with an unsupported file type should return an error.
"""
result = runner.invoke(
app,
[
"predict",
"chai",
str(tmp_files["invalid_source"]),
"--project-code",
"TEST_PROJECT",
],
)
assert result.exit_code != 0
def test_chai_fold_with_valid_fasta_file(
mock_send_request, mock_download_results, tmp_files
):
"""
Running the command with a valid FASTA file (without restraints) should
process successfully and generate the correct payload.
"""
result = runner.invoke(
app,
[
"predict",
"chai",
str(tmp_files["monomer_fasta"]),
"--project-code",
"TEST_PROJECT",
"--output",
tmp_files["output_dir"],
],
)
assert result.exit_code == 0, result.output
expected_query = ChaiQuery.from_file(
path=str(tmp_files["monomer_fasta"]),
use_msa_server=True,
use_templates_server=False,
num_trunk_recycles=3,
seed=0,
num_diffn_timesteps=200,
restraints=None,
recycle_msa_subsample=0,
num_trunk_samples=1,
)
mock_send_request.assert_called_once()
actual_query = mock_send_request.call_args[0][0]
payload = actual_query.payload
expected = expected_query.payload
assert payload == expected
mock_download_results.assert_called_once()
def test_chai_fold_with_valid_fasta_and_restraints(
mock_send_request, mock_download_results, tmp_files
):
"""
Running the command with a valid FASTA file and a valid restraints CSV file
should include the restraints content in the payload.
"""
result = runner.invoke(
app,
[
"predict",
"chai",
str(tmp_files["monomer_fasta"]),
"--project-code",
"TEST_PROJECT",
"--restraints",
str(tmp_files["valid_restraints"]),
"--output",
tmp_files["output_dir"],
],
)
assert result.exit_code == 0, result.output
restraints_content = tmp_files["valid_restraints"].read_text().strip()
expected_query = ChaiQuery.from_file(
path=str(tmp_files["monomer_fasta"]),
use_msa_server=True,
use_templates_server=False,
num_trunk_recycles=3,
seed=0,
num_diffn_timesteps=200,
restraints=str(tmp_files["valid_restraints"]),
recycle_msa_subsample=0,
num_trunk_samples=1,
)
mock_send_request.assert_called_once()
actual_query = mock_send_request.call_args[0][0]
payload = actual_query.payload
expected = expected_query.payload
assert payload == expected
assert payload["restraints"] == restraints_content
mock_download_results.assert_called_once()
def test_chai_fold_with_valid_fasta_directory(
mock_send_request, mock_download_results, tmp_files
):
"""
Running the command with a directory containing valid FASTA files should
process successfully and submit a single request for the directory.
"""
result = runner.invoke(
app,
[
"predict",
"chai",
str(tmp_files["valid_dir"]),
"--project-code",
"TEST_PROJECT",
"--output",
tmp_files["output_dir"],
],
)
assert result.exit_code == 0, result.output
expected_query = ChaiQuery.from_directory(
path=str(tmp_files["valid_dir"]),
use_msa_server=True,
use_templates_server=False,
num_trunk_recycles=3,
seed=0,
num_diffn_timesteps=200,
restraints=None,
recycle_msa_subsample=0,
num_trunk_samples=1,
)
expected_fasta_files = expected_query.payload["fasta_files"]
actual_fasta_files = [
call_args[0][0].payload["fasta_files"]
for call_args in mock_send_request.call_args_list
]
# Check that the expected FASTA files match one of the actual request payloads
assert expected_fasta_files in actual_fasta_files, (
f"FASTA file {expected_fasta_files} was expected but not found in actual requests."
)
mock_download_results.assert_called()
def test_chai_fold_with_empty_directory(tmp_files):
"""
Running the command with an empty directory should return an error,
since no FASTA files are available.
"""
result = runner.invoke(
app,
[
"predict",
"chai",
str(tmp_files["empty_dir"]),
"--project-code",
"TEST_PROJECT",
"--output",
tmp_files["output_dir"],
],
)
assert result.exit_code != 0, result.output
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