File size: 12,751 Bytes
44459bb |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 |
import os
from unittest import mock
import pytest
from folding_studio.cli import app
from folding_studio.utils.data_model import (
PredictRequestCustomFiles,
PredictRequestParams,
)
from folding_studio.utils.headers import get_auth_headers
from folding_studio_data_models import (
BatchMessageStatus,
BatchPublication,
FeatureMode,
FoldingModel,
Message,
MessageStatus,
OpenFoldParameters,
Publication,
)
from typer.testing import CliRunner
runner = CliRunner()
@pytest.fixture(autouse=True)
def mock_get_auth_headers(request):
if "apikeytest" in request.keywords:
os.environ["FOLDING_API_KEY"] = "MY_KEY"
return_value = get_auth_headers()
else:
return_value = {"Authorization": "Bearer identity_token"}
with mock.patch(
"folding_studio.api_call.predict.simple_predict.get_auth_headers",
return_value=return_value,
) as m:
yield m
@pytest.fixture(autouse=True)
def mock_batch_prediction_from_file():
batch_pub = BatchPublication(
publications=[
Publication(
folding_model=FoldingModel.OPENFOLD,
message=Message(
pipeline_name="alphafold_inference_pipeline",
user_id="default-user",
project_code="default-project",
parameters=OpenFoldParameters(),
experiment_id="dummy-experiment",
model_preset="monomer",
fasta_file_name=f"monomer_{idx}.fasta",
ignore_cache=False,
),
status=MessageStatus.PUBLISHED,
)
for idx in range(3)
],
batch_id="batch_id",
cached_publications=[],
status=BatchMessageStatus.PUBLISHED,
cached=False,
)
with mock.patch(
"folding_studio.commands.predict.openfold_predict.batch_prediction_from_file",
return_value=batch_pub.model_dump(mode="json"),
) as m:
yield m
@pytest.fixture()
def mock_batch_prediction():
batch_pub = BatchPublication(
publications=[
Publication(
folding_model=FoldingModel.OPENFOLD,
message=Message(
pipeline_name="alphafold_inference_pipeline",
user_id="default-user",
project_code="default-project",
parameters=OpenFoldParameters(),
experiment_id="dummy-experiment",
model_preset="monomer",
fasta_file_name=f"monomer_{idx}.fasta",
ignore_cache=False,
),
status=MessageStatus.PUBLISHED,
)
for idx in range(3)
],
batch_id="batch_id",
cached_publications=[],
status=BatchMessageStatus.PUBLISHED,
cached=False,
)
with mock.patch(
"folding_studio.commands.predict.openfold_predict.batch_prediction",
return_value=batch_pub.model_dump(mode="json"),
) as m:
yield m
@pytest.fixture()
def mock_simple_prediction():
pub = Publication(
folding_model=FoldingModel.OPENFOLD,
message=Message(
pipeline_name="alphafold_inference_pipeline",
user_id="default-user",
project_code="default-project",
parameters=OpenFoldParameters(),
experiment_id="dummy-experiment",
model_preset="monomer",
fasta_file_name="monomer.fasta",
ignore_cache=False,
),
status=MessageStatus.PUBLISHED,
)
with mock.patch(
"folding_studio.commands.predict.openfold_predict.simple_prediction",
return_value=pub.model_dump(mode="json"),
) as m:
yield m
@pytest.fixture()
def default_params():
yield PredictRequestParams(
ignore_cache=False,
template_mode=FeatureMode.SEARCH,
custom_template_ids=[],
msa_mode=FeatureMode.SEARCH,
max_msa_clusters=-1,
max_extra_msa=-1,
gap_trick=False,
num_recycle=3,
random_seed=0,
model_subset=[],
project_code="FOLDING_DEV",
)
def test_predict_with_unsupported_file_fails(tmp_files):
result = runner.invoke(
app, ["predict", "openfold", str(tmp_files["invalid_source"])]
)
assert result.exit_code == 2
assert "Invalid value for 'SOURCE'" in result.stdout
def test_predict_with_directory_containing_unsupported_file_fails(tmp_files):
result = runner.invoke(app, ["predict", "openfold", str(tmp_files["invalid_dir"])])
assert result.exit_code == 2
assert "Invalid value for 'SOURCE'" in result.stdout
def test_predict_with_empty_directory_fails(tmp_files):
result = runner.invoke(app, ["predict", "openfold", str(tmp_files["empty_dir"])])
assert result.exit_code == 2
assert "Invalid value for 'SOURCE'" in result.stdout
def test_predict_with_unsupported_custom_template_file_fails(tmp_files):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files["monomer_fasta"]),
"--custom-template",
tmp_files["invalid_template"],
],
)
assert result.exit_code == 2
assert "Invalid value for '--custom-template'" in result.stdout
def test_predict_with_unsupported_custom_msa_file_fails(tmp_files):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files["monomer_fasta"]),
"--custom-msa",
tmp_files["invalid_msa"],
],
)
assert result.exit_code == 2
assert "Invalid value for '--custom-msa'" in result.stdout
@pytest.mark.parametrize(
"mock_simple_prediction",
(
MessageStatus.PUBLISHED,
MessageStatus.NOT_PUBLISHED_DONE,
MessageStatus.NOT_PUBLISHED_PENDING,
),
indirect=True,
)
def test_predict_with_fasta_file_pass(
mock_simple_prediction: mock.Mock,
tmp_files,
default_params,
):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files["monomer_fasta"]),
"--metadata-file",
str(tmp_files["metadata_file"]),
"--project-code",
"FOLDING_DEV",
],
)
assert result.exit_code == 0, result.output
custom_files = PredictRequestCustomFiles(templates=[], msas=[])
mock_simple_prediction.assert_called_once_with(
file=tmp_files["monomer_fasta"],
folding_model=FoldingModel.OPENFOLD,
params=default_params,
custom_files=custom_files,
project_code="FOLDING_DEV",
)
@pytest.mark.parametrize(
"mock_simple_prediction",
(
MessageStatus.PUBLISHED,
MessageStatus.NOT_PUBLISHED_DONE,
MessageStatus.NOT_PUBLISHED_PENDING,
),
indirect=True,
)
def test_predict_with_fasta_file_pass_with_project_code_from_env_var(
mock_simple_prediction: mock.Mock, tmp_files, default_params
):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files["monomer_fasta"]),
"--metadata-file",
str(tmp_files["metadata_file"]),
# Here we deliberately leave out the
# "--project-code" option to check that
# env variable is correctly used
],
)
assert result.exit_code == 0, result.output
custom_files = PredictRequestCustomFiles(templates=[], msas=[])
mock_simple_prediction.assert_called_once_with(
file=tmp_files["monomer_fasta"],
params=default_params,
custom_files=custom_files,
folding_model=FoldingModel.OPENFOLD,
project_code="FOLDING_DEV",
)
def test_predict_unset_project_code_fails(tmp_files, remove_project_code_from_env_var):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files["monomer_fasta"]),
],
)
assert result.exit_code == 2, result.output
@pytest.mark.parametrize(
"mock_simple_prediction",
(
MessageStatus.PUBLISHED,
MessageStatus.NOT_PUBLISHED_DONE,
MessageStatus.NOT_PUBLISHED_PENDING,
),
indirect=True,
)
def test_predict_with_fasta_file_with_templates_masks_pass(
mock_simple_prediction: mock.Mock, tmp_files, default_params, valid_templates_masks
):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files["monomer_fasta"]),
"--templates-masks-file",
str(valid_templates_masks),
"--custom-template",
str(tmp_files["valid_template_3"]),
"--custom-template",
str(tmp_files["valid_template_4"]),
"--metadata-file",
str(tmp_files["metadata_file"]),
"--project-code",
"FOLDING_DEV",
],
)
assert result.exit_code == 0, result.output
custom_files = PredictRequestCustomFiles(
templates=[tmp_files["valid_template_3"], tmp_files["valid_template_4"]],
msas=[],
templates_masks_files=[valid_templates_masks],
)
mock_simple_prediction.assert_called_once_with(
file=tmp_files["monomer_fasta"],
folding_model=FoldingModel.OPENFOLD,
params=default_params,
custom_files=custom_files,
project_code="FOLDING_DEV",
)
def test_predict_with_fasta_file_with_templates_masks_fail(
tmp_files, valid_templates_masks
):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files["monomer_fasta"]),
"--templates-masks-file",
str(valid_templates_masks),
"--custom-template",
str(tmp_files["valid_template_3"]),
"--custom-template",
str(tmp_files["valid_template_2"]),
"--metadata-file",
str(tmp_files["metadata_file"]),
"--project-code",
"FOLDING_DEV",
],
)
assert result.exit_code == 1, result.output
assert "Check your input command." in str(result.exception)
def test_predict_with_fasta_file_with_multi_seed_pass(
mock_batch_prediction: mock.Mock,
tmp_files,
default_params,
):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files["monomer_fasta"]),
"--num-seed",
5,
"--metadata-file",
str(tmp_files["metadata_file"]),
"--project-code",
"FOLDING_DEV",
],
)
assert result.exit_code == 0, result.output
custom_files = PredictRequestCustomFiles(templates=[], msas=[])
mock_batch_prediction.assert_called_once_with(
files=[tmp_files["monomer_fasta"]],
folding_model=FoldingModel.OPENFOLD,
params=default_params,
custom_files=custom_files,
num_seed=5,
project_code="FOLDING_DEV",
)
def test_predict_with_directory_pass(
mock_batch_prediction: mock.Mock,
tmp_files,
default_params,
):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files["valid_dir"]),
"--metadata-file",
str(tmp_files["metadata_file"]),
"--project-code",
"FOLDING_DEV",
],
)
assert result.exit_code == 0, result.output
custom_files = PredictRequestCustomFiles(templates=[], msas=[])
mock_batch_prediction.assert_called_once_with(
files=mock.ANY,
params=default_params,
folding_model=FoldingModel.OPENFOLD,
custom_files=custom_files,
num_seed=None,
project_code="FOLDING_DEV",
)
_, kwargs = mock_batch_prediction.call_args
assert sorted(kwargs["files"]) == sorted(
list(tmp_files["valid_dir"].iterdir()),
)
@pytest.mark.parametrize("file", ["valid_batch_file_json", "valid_batch_file_csv"])
def test_predict_with_json_batch_file_pass(
file, mock_batch_prediction_from_file: mock.Mock, tmp_files
):
result = runner.invoke(
app,
[
"predict",
"openfold",
str(tmp_files[file]),
"--metadata-file",
str(tmp_files["metadata_file"]),
"--project-code",
"FOLDING_DEV",
],
)
assert result.exit_code == 0, result.output
mock_batch_prediction_from_file.assert_called_once_with(
file=tmp_files[file],
project_code="FOLDING_DEV",
)
|