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_upload_and_run_immediately_slow_response_retry(
credentials, mocker, project_id, recording, vcr
):
"""Upload and assign right away and retry on slow response."""
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",
side_effect=APIClientTimeout(
"Could not connect to the api server"
),
)
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()
if not recording:
mocked_get_upload_details.assert_called_once()
assert mocked_get_sample_sheet.call_count == 5
assert "there was an error automatically running them" in res.output
def test_upload_without_progressbar(credentials, mocker, recording, vcr):
"""Upload do not show the progress bar."""
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"
)
if not recording:
# Mock get_upload_details 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),
)
res = runner.invoke(
upload,
[
"cli_test_data",
*credentials,
"--no-progress",
],
)
assert res.exit_code == 0
mocked_get_credentials.assert_called_once()
mocked_upload_file.assert_called_once()
assert mocked_upload_file.call_args[1]["no_progress"]
if not recording:
mocked_get_upload_details.assert_called_once()
def test_upload(credentials, vcr, recording, mocker):
"""Sanity check that upload is ok."""
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.
response = get_vcr_response("/api/v2/uploads-post-data/", vcr)
mocked_get_upload_details = mocker.patch.object(
APIClient,
"get_upload_details",
return_value=UploadsPostData(**response),
)
mocked_upload_file = mocker.patch(
"gencove.command.upload.main.upload_file", side_effect=upload_file
)
res = runner.invoke(
upload,
["cli_test_data", *credentials],
)
assert not res.exception
assert res.exit_code == 0
assert (
"Uploading cli_test_data/test.fastq.gz to gncv://" in res.output
)
assert "All files were successfully uploaded." in res.output
mocked_get_credentials.assert_called_once()
if not recording:
mocked_get_upload_details.assert_called_once()
mocked_upload_file.assert_called_once()
assert not mocked_upload_file.call_args[1]["no_progress"]
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
)