def test_list_project_samples(mocker, credentials, project_id, recording, vcr): # pylint: disable=unused-argument
"""Test project samples being outputed to the shell."""
runner = CliRunner()
if not recording:
# Mock get_project_samples only if using the cassettes,
# since we mock the return value.
mocked_samples = get_vcr_response("/api/v2/project-samples/", vcr,
operator.contains)
mocked_get_project_samples = mocker.patch.object(
APIClient,
"get_project_samples",
return_value=ProjectSamples(**mocked_samples),
)
res = runner.invoke(
list_project_samples,
[project_id, *credentials],
)
assert res.exit_code == 0
if not recording:
mocked_get_project_samples.assert_called_once()
output_line = io.BytesIO()
sys.stdout = output_line
for mocked_sample in mocked_samples["results"]:
mocked_sample = SampleDetails(**mocked_sample)
echo_data("\t".join([
str(mocked_sample.last_status.created.isoformat()),
str(mocked_sample.id),
mocked_sample.client_id,
mocked_sample.last_status.status,
mocked_sample.archive_last_status.status,
]))
assert output_line.getvalue() == res.output.encode()
def test_download_stdout_no_flag(
credentials, mocker, project_id_download, recording, vcr
):
"""Test command exits if no flag provided and stdout defined."""
runner = CliRunner()
if not recording:
# Mock only if using the cassettes, since we mock the return value.
get_project_samples_response = get_vcr_response(
"/api/v2/project-samples/", vcr, operator.contains
)
mocked_project_samples = mocker.patch.object(
APIClient,
"get_project_samples",
return_value=ProjectSamples(**get_project_samples_response),
)
res = runner.invoke(
download,
[
"-",
"--project-id",
project_id_download,
*credentials,
],
)
assert res.exit_code == 1
output_line = io.BytesIO()
sys.stdout = output_line
echo("ERROR: Cannot have - as a destination without download-urls.")
assert output_line.getvalue() in res.output.encode()
if not recording:
mocked_project_samples.assert_called_once()
def test_list_empty(mocker, credentials, project_id):
"""Test project has no samples."""
runner = CliRunner()
mocked_get_project_samples = mocker.patch.object(
APIClient,
"get_project_samples",
return_value=ProjectSamples(results=[], meta=dict(next=None)),
)
res = runner.invoke(
list_project_samples,
[project_id, *credentials],
)
assert res.exit_code == 0
mocked_get_project_samples.assert_called_once()
assert res.output == ""
def test_download_urls_to_file(
credentials, mocker, project_id_download, recording, vcr
):
"""Test saving downloaded urls output to a json file."""
runner = CliRunner()
if not recording:
# Mock only if using the cassettes, since we mock the return value.
get_project_samples_response = get_vcr_response(
"/api/v2/project-samples/", vcr, operator.contains
)
mocked_project_samples = mocker.patch.object(
APIClient,
"get_project_samples",
return_value=ProjectSamples(**get_project_samples_response),
)
get_sample_details_response = get_vcr_response(
"/api/v2/samples/", vcr, operator.contains
)
sample = SampleDetails(**get_sample_details_response)
mocked_sample_details = mocker.patch.object(
APIClient,
"get_sample_details",
return_value=sample,
)
mocked_output_list = mocker.patch(
"gencove.command.download.main.Download.output_list"
)
with runner.isolated_filesystem():
res = runner.invoke(
download,
[
"output.json",
"--project-id",
project_id_download,
*credentials,
"--download-urls",
],
)
assert res.exit_code == 0
mocked_output_list.assert_called_once()
if not recording:
mocked_project_samples.assert_called_once()
mocked_sample_details.assert_called_once()
def test_project_id_provided_filter_not_archived(credentials, mocker):
"""Check happy flow."""
runner = CliRunner()
with runner.isolated_filesystem():
mocked_project_samples = mocker.patch.object(
APIClient,
"get_project_samples",
return_value=ProjectSamples(
**{"results": [], "meta": {"next": None}}
),
)
mocked_sample_details = mocker.patch.object(
APIClient, "get_sample_details"
)
mocked_qc_metrics = mocker.patch.object(
APIClient, "get_sample_qc_metrics"
)
mocked_get_metadata = mocker.patch.object(APIClient, "get_metadata")
mocked_download_file = mocker.patch(
"gencove.command.download.main.download_file"
)
res = runner.invoke(
download,
[
"cli_test_data",
"--project-id",
"123",
*credentials,
],
)
assert res.exit_code == 1
mocked_project_samples.assert_called_once()
mocked_qc_metrics.assert_not_called()
mocked_get_metadata.assert_not_called()
mocked_download_file.assert_not_called()
mocked_sample_details.assert_not_called()
def test_project_id_provided_skip_existing_qc_and_metadata(
credentials, mocker, project_id_download, recording, vcr
):
"""Check happy flow."""
# pylint: disable=too-many-locals
runner = CliRunner()
with runner.isolated_filesystem():
if not recording:
# Mock only if using the cassettes, since we mock the return value.
get_project_samples_response = get_vcr_response(
"/api/v2/project-samples/", vcr, operator.contains
)
mocked_project_samples = mocker.patch.object(
APIClient,
"get_project_samples",
return_value=ProjectSamples(**get_project_samples_response),
)
get_sample_details_response = get_vcr_response(
"/api/v2/samples/", vcr, operator.contains
)
mocked_sample_details = mocker.patch.object(
APIClient,
"get_sample_details",
return_value=SampleDetails(**get_sample_details_response),
)
get_sample_qc_metrics_response = get_vcr_response(
"/api/v2/sample-quality-controls/", vcr, operator.contains
)
mocked_qc_metrics = mocker.patch.object(
APIClient,
"get_sample_qc_metrics",
return_value=SampleQC(**get_sample_qc_metrics_response),
)
get_metadata_response = get_vcr_response(
"/api/v2/sample-metadata/", vcr, operator.contains
)
mocked_get_metadata = mocker.patch.object(
APIClient,
"get_metadata",
return_value=SampleMetadata(**get_metadata_response),
)
mocked_download_file = mocker.patch(
"gencove.command.download.main.download_file",
side_effect=download_file,
)
res = runner.invoke(
download,
[
"cli_test_data",
"--project-id",
project_id_download,
*credentials,
"--no-skip-existing",
],
)
assert res.exit_code == 0
if not recording:
mocked_project_samples.assert_called_once()
mocked_sample_details.assert_called_once()
mocked_qc_metrics.assert_called_once()
mocked_get_metadata.assert_called_once()
mocked_download_file.assert_called_once()
# call it the second time
mocked_qc_metrics = mocker.patch.object(
APIClient, "get_sample_qc_metrics"
)
mocked_get_metadata = mocker.patch.object(APIClient, "get_metadata")
res = runner.invoke(
download,
[
"cli_test_data",
"--project-id",
project_id_download,
*credentials,
"--skip-existing",
],
)
assert res.exit_code == 0
mocked_qc_metrics.assert_not_called()
mocked_get_metadata.assert_not_called()
def test_download_stdout_with_flag(
credentials, mocker, project_id_download, recording, vcr
):
"""Test command outputs json to stdout."""
# pylint: disable=too-many-locals
runner = CliRunner()
if not recording:
# Mock only if using the cassettes, since we mock the return value.
get_project_samples_response = get_vcr_response(
"/api/v2/project-samples/", vcr, operator.contains
)
mocked_project_samples = mocker.patch.object(
APIClient,
"get_project_samples",
return_value=ProjectSamples(**get_project_samples_response),
)
get_sample_details_response = get_vcr_response(
"/api/v2/samples/", vcr, operator.contains
)
sample = SampleDetails(**get_sample_details_response)
mocked_sample_details = mocker.patch.object(
APIClient,
"get_sample_details",
return_value=sample,
)
res = runner.invoke(
download,
[
"-",
"--project-id",
project_id_download,
*credentials,
"--download-urls",
],
)
assert res.exit_code == 0
if not recording:
mocked_project_samples.assert_called_once()
mocked_sample_details.assert_called_once()
output_line = io.BytesIO()
sys.stdout = output_line
for _ in get_project_samples_response["results"]:
archive_last_status_created = (
sample.archive_last_status.created.isoformat()
)
download_url = "https://example.com/r1.fastq.gz"
mocked_result = json.dumps(
[
{
"gencove_id": MOCK_UUID,
"client_id": "mock_client_id",
"last_status": {
"id": MOCK_UUID,
"status": sample.last_status.status,
"created": sample.last_status.created.isoformat(),
},
"archive_last_status": {
"id": MOCK_UUID,
"status": sample.archive_last_status.status,
"created": archive_last_status_created,
"transition_cutoff": None,
},
"files": {
"fastq-r1": {
"id": MOCK_UUID,
"download_url": download_url,
}
},
}
],
indent=4,
)
echo(mocked_result)
assert output_line.getvalue() in res.output.encode()