def test_run_prefix__success(mocker):
"""Test run prefix success."""
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
mocked_get_sample_sheet = mocker.patch.object(
APIClient,
"get_sample_sheet",
return_value=SampleSheet(**MOCKED_UPLOADS),
)
mocked_add_samples_to_project = mocker.patch.object(
APIClient,
"add_samples_to_project",
return_value=UploadSamples(**{}),
)
res = runner.invoke(
run_prefix,
[
str(uuid4()),
"gncv://batch",
"--email",
"*****@*****.**",
"--password",
"123",
],
)
assert res.exit_code == 0
mocked_login.assert_called_once()
mocked_get_sample_sheet.assert_called_once()
mocked_add_samples_to_project.assert_called_once()
assert "Number of samples assigned to the project" in res.output
assert "Assigning metadata to the uploaded samples." not in res.output
def test_run_prefix__filter_success(mocker):
"""Test run prefix when filter returns some paths."""
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
mocked_uploads_copy = copy.deepcopy(MOCKED_UPLOADS)
del mocked_uploads_copy["results"][1]
mocked_get_sample_sheet = mocker.patch.object(
APIClient,
"get_sample_sheet",
return_value=SampleSheet(**mocked_uploads_copy),
)
mocked_add_samples_to_project = mocker.patch.object(
APIClient,
"add_samples_to_project",
)
res = runner.invoke(
run_prefix,
[
str(uuid4()),
"gncv://batch",
"--status",
"unassigned",
"--email",
"*****@*****.**",
"--password",
"123",
],
)
assert res.exit_code == 0
mocked_login.assert_called_once()
mocked_get_sample_sheet.assert_called_once()
mocked_add_samples_to_project.assert_called_once()
assert "Number of samples assigned to the project" in res.output
assert "Assigning metadata to the uploaded samples." not in res.output
def test_run_prefix__filter_empty(mocker):
"""Test run prefix when all paths are filtered out."""
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
mocked_get_sample_sheet = mocker.patch.object(
APIClient,
"get_sample_sheet",
return_value=SampleSheet(**MOCKED_EMPTY_UPLOADS),
)
mocked_add_samples_to_project = mocker.patch.object(
APIClient,
"add_samples_to_project",
return_value=UploadSamples(**{}),
)
res = runner.invoke(
run_prefix,
[
str(uuid4()),
"gncv://batch",
"--status",
"assigned",
"--email",
"*****@*****.**",
"--password",
"123",
],
)
assert res.exit_code == 1
mocked_login.assert_called_once()
mocked_get_sample_sheet.assert_called_once()
mocked_add_samples_to_project.assert_not_called()
assert "No matching paths found" in res.output
def test_run_prefix__assigning_samples_failed(mocker):
"""Test run prefix when assigning samples fails."""
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
mocked_get_sample_sheet = mocker.patch.object(
APIClient,
"get_sample_sheet",
return_value=SampleSheet(**MOCKED_UPLOADS),
)
mocked_add_samples_to_project = mocker.patch.object(
APIClient,
"add_samples_to_project",
side_effect=APIClientError(message="", status_code=404),
)
res = runner.invoke(
run_prefix,
[
str(uuid4()),
"gncv://batch",
"--email",
"*****@*****.**",
"--password",
"123",
],
)
assert res.exit_code == 1
mocked_login.assert_called_once()
mocked_get_sample_sheet.assert_called_once()
mocked_add_samples_to_project.assert_called_once()
assert "You do not have the sufficient permission" not in res.output
assert "There was an error assigning" in res.output
def test_upload_and_run_immediately_something_went_wrong(
credentials, mocker, project_id, recording, vcr
):
"""Upload and assign right away did't work."""
runner = CliRunner()
with runner.isolated_filesystem():
os.mkdir("cli_test_data")
with open("cli_test_data/test.fastq.gz", "w") as fastq_file:
fastq_file.write("AAABBB")
mocked_get_credentials = mocker.patch(
"gencove.command.upload.main.get_s3_client_refreshable",
side_effect=get_s3_client_refreshable,
)
mocked_upload_file = mocker.patch(
"gencove.command.upload.main.upload_file", side_effect=upload_file
)
if not recording:
# Mock get_upload credentials only if using the cassettes, since
# we mock the return value.
upload_details_response = get_vcr_response(
"/api/v2/uploads-post-data/", vcr
)
mocked_get_upload_details = mocker.patch.object(
APIClient,
"get_upload_details",
return_value=UploadsPostData(**upload_details_response),
)
mocked_get_sample_sheet = mocker.patch.object(
APIClient,
"get_sample_sheet",
return_value=SampleSheet(
**{"meta": {"next": None}, "results": []}
),
)
mocked_assign_sample = mocker.patch.object(
APIClient, "add_samples_to_project"
)
res = runner.invoke(
upload,
[
"cli_test_data",
*credentials,
"--run-project-id",
project_id,
],
)
assert res.exit_code == 0
mocked_get_credentials.assert_called_once()
if not recording:
mocked_get_upload_details.assert_called_once()
mocked_upload_file.assert_called_once()
mocked_get_sample_sheet.assert_called()
mocked_assign_sample.assert_not_called()
def test_list_empty(mocker, credentials):
"""Test user has no uploads."""
runner = CliRunner()
mocked_get_projects = mocker.patch.object(
APIClient,
"get_sample_sheet",
return_value=SampleSheet(results=[], meta=dict(next=None)),
)
res = runner.invoke(list_uploads, credentials)
assert res.exit_code == 0
mocked_get_projects.assert_called_once()
assert "" in res.output
def test_list_uploads(mocker, credentials, recording, vcr):
"""Test list uploads being outputed to the shell."""
runner = CliRunner()
if not recording:
sample_sheet_response = get_vcr_response("/api/v2/sample-sheet/", vcr)
mocked_get_sample_sheet = mocker.patch.object(
APIClient,
"get_sample_sheet",
return_value=SampleSheet(**sample_sheet_response),
)
res = runner.invoke(list_uploads, credentials)
assert res.exit_code == 0
if not recording:
mocked_get_sample_sheet.assert_called()
uploads = sample_sheet_response["results"]
uploads = "\n".join([
"\t".join([
upload["client_id"],
upload["fastq"]["r1"]["upload"],
upload["fastq"]["r1"]["destination_path"],
]) for upload in uploads
])
assert f"{uploads}\n" == res.output
def test_upload_and_run_immediately_without_progressbar(
credentials, mocker, project_id, recording, vcr
):
"""Upload and assign right away."""
# pylint: disable=too-many-locals
runner = CliRunner()
with runner.isolated_filesystem():
os.mkdir("cli_test_data")
with open("cli_test_data/test.fastq.gz", "w") as fastq_file:
fastq_file.write("AAABBB")
mocked_get_credentials = mocker.patch(
"gencove.command.upload.main.get_s3_client_refreshable",
side_effect=get_s3_client_refreshable,
)
mocked_upload_file = mocker.patch(
"gencove.command.upload.main.upload_file", side_effect=upload_file
)
mocked_regular_progress_bar = mocker.patch(
"gencove.command.upload.main.get_regular_progress_bar",
side_effect=get_regular_progress_bar,
)
if not recording:
# Mock get_upload credentials only if using the cassettes, since
# we mock the return value.
upload_details_response = get_vcr_response(
"/api/v2/uploads-post-data/", vcr
)
mocked_get_upload_details = mocker.patch.object(
APIClient,
"get_upload_details",
return_value=UploadsPostData(**upload_details_response),
)
sample_sheet_response = get_vcr_response(
"/api/v2/sample-sheet/", vcr
)
mocked_get_sample_sheet = mocker.patch.object(
APIClient,
"get_sample_sheet",
return_value=SampleSheet(**sample_sheet_response),
)
project_sample_response = get_vcr_response(
"/api/v2/project-samples/", vcr, operator.contains
)
mocked_assign_sample = mocker.patch.object(
APIClient,
"add_samples_to_project",
return_value=UploadSamples(**project_sample_response),
)
res = runner.invoke(
upload,
[
"cli_test_data",
*credentials,
"--run-project-id",
project_id,
"--no-progress",
],
)
assert res.exit_code == 0
mocked_get_credentials.assert_called_once()
mocked_upload_file.assert_called_once()
mocked_regular_progress_bar.assert_not_called()
if not recording:
mocked_get_upload_details.assert_called_once()
mocked_get_sample_sheet.assert_called()
mocked_assign_sample.assert_called_once()
def test_upload_and_run_immediately_with_stdout(
credentials, mocker, project_id, recording, vcr
):
"""Upload and assign right away, then print out the results."""
# pylint: disable=too-many-locals
runner = CliRunner()
with runner.isolated_filesystem():
os.mkdir("cli_test_data")
with open("cli_test_data/test.fastq.gz", "w") as fastq_file:
fastq_file.write("AAABBB")
mocked_get_credentials = mocker.patch(
"gencove.command.upload.main.get_s3_client_refreshable",
side_effect=get_s3_client_refreshable,
)
if not recording:
# Mock get_upload credentials only if using the cassettes, since
# we mock the return value.
upload_details_response = get_vcr_response(
"/api/v2/uploads-post-data/", vcr
)
mocked_get_upload_details = mocker.patch.object(
APIClient,
"get_upload_details",
return_value=UploadsPostData(**upload_details_response),
)
sample_sheet_response = get_vcr_response(
"/api/v2/sample-sheet/", vcr
)
mocked_get_sample_sheet = mocker.patch.object(
APIClient,
"get_sample_sheet",
return_value=SampleSheet(**sample_sheet_response),
)
project_sample_response = get_vcr_response(
"/api/v2/project-samples/", vcr, operator.contains
)
mocked_assign_sample = mocker.patch.object(
APIClient,
"add_samples_to_project",
return_value=UploadSamples(**project_sample_response),
)
# These mocks needs to be here and without side effect otherwise
# a weird behavior on the stdout will happend and the test fails.
mocked_upload_file = mocker.patch(
"gencove.command.upload.main.upload_file"
)
mocker.patch(
"gencove.command.upload.main.get_regular_progress_bar",
)
res = runner.invoke(
upload,
[
"cli_test_data",
*credentials,
"--run-project-id",
project_id,
"--output",
"-",
],
)
assert res.exit_code == 0
mocked_get_credentials.assert_called_once()
if not recording:
mocked_upload_file.assert_called_once()
mocked_get_upload_details.assert_called_once()
mocked_get_sample_sheet.assert_called()
mocked_assign_sample.assert_called_once()
# r2 fastq key is not present on the file
assert (
project_sample_response["uploads"][0]["fastq"]["r2"] is None
)
del project_sample_response["uploads"][0]["fastq"]["r2"]
assert (
json.dumps(project_sample_response["uploads"], indent=4)
in res.output
)