def test_get_batch__not_empty__slow_response_retry(credentials, mocker):
"""Test project batches slow response retry."""
runner = CliRunner()
with runner.isolated_filesystem():
batch_id = str(uuid4())
mocked_get_batch = mocker.patch.object(
APIClient,
"get_batch",
side_effect=APIClientTimeout(
"Could not connect to the api server"),
)
mocked_download_file = mocker.patch(
"gencove.command.projects.get_batch.main.download.utils."
"download_file")
res = runner.invoke(
get_batch,
[
batch_id,
*credentials,
"--output-filename",
"test.zip",
],
)
assert res.exit_code == 1
assert mocked_get_batch.call_count == 2
mocked_download_file.assert_not_called()
def test_get_metadata__slow_response_retry(mocker):
"""Test sample get metadata slow response retry."""
sample_id = str(uuid4())
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
metadata = {"somekey": "somevalue"}
mocked_get_metadata = mocker.patch.object(
APIClient,
"get_metadata",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
res = runner.invoke(
get_metadata,
[
sample_id,
"--email",
"*****@*****.**",
"--password",
"123",
"--output-filename",
"-",
],
)
assert res.exit_code == 1
mocked_login.assert_called_once()
assert mocked_get_metadata.call_count == 2
output_line = io.BytesIO()
sys.stdout = output_line
echo(json.dumps(metadata, indent=4))
assert output_line.getvalue() not in res.output.encode()
def test_status_merged_vcf__slow_response_retry(mocker):
"""Test status merged VCF slow response retry."""
project_id = str(uuid4())
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
mocked_retrieve_merged_vcf = mocker.patch.object(
APIClient,
"retrieve_merged_vcf",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
res = runner.invoke(
status_merged_vcf,
[
project_id,
"--email",
"*****@*****.**",
"--password",
"123",
],
)
assert res.exit_code == 1
mocked_login.assert_called_once()
assert mocked_retrieve_merged_vcf.call_count == 5
def test_get_merged_vcf__slow_response_retry(mocker):
"""Test project download merged VCF slow response retry."""
project_id = str(uuid4())
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
mocked_get_project = mocker.patch.object(
APIClient,
"get_project",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
with runner.isolated_filesystem():
mocked_download_file = mocker.patch(
"gencove.command.projects.get_merged_vcf.main.download.utils."
"download_file"
)
res = runner.invoke(
get_merged_vcf,
[
project_id,
"--email",
"*****@*****.**",
"--password",
"123",
],
)
assert res.exit_code == 1
mocked_login.assert_called_once()
assert mocked_get_project.call_count == 5
mocked_download_file.assert_not_called()
def test_list_projects_slow_response_dump_log(mocker, credentials,
dump_filename):
"""Test projects slow response dumps a log filet."""
del os.environ["GENCOVE_SAVE_DUMP_LOG"]
runner = CliRunner()
mocker.patch.object(
APIClient,
"list_projects",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
python_version = sys.version_info
logs = [
f"Python version: {python_version.major}.{python_version.minor}.{python_version.micro}", # noqa: E501 # pylint: disable=line-too-long
f"CLI version: {version()}",
f"OS details: {platform()}",
f"boto3 version: {boto3.__version__}",
"Retrieving projects",
"Get projects page",
"Could not connect to the api server",
]
with runner.isolated_filesystem():
res = runner.invoke(list_projects, credentials)
assert res.exit_code == 1
assert (
f"Please attach the debug log file located in {dump_filename} to a bug report." # noqa: E501 # pylint: disable=line-too-long
in res.output)
with open(dump_filename, encoding="utf8") as log_file:
log_content = log_file.read()
for log in logs:
assert log in log_content
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_list_uploads_slow_response_retry(mocker, credentials):
"""Test list uploads slow response retry."""
runner = CliRunner()
mocked_get_sample_sheet = mocker.patch.object(
APIClient,
"get_sample_sheet",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
res = runner.invoke(list_uploads, credentials)
assert res.exit_code == 1
assert mocked_get_sample_sheet.call_count == 5
assert (
res.output == "ERROR: Could not connect to the api server\nAborted!\n")
def test_basespace_list__slow_response_retry_list(mocker):
"""Test BaseSpace projects slow response retry on the list."""
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
mocked_list_basespace_projects = mocker.patch.object(
APIClient,
"list_basespace_projects",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
res = runner.invoke(basespace_list,
["--email", "*****@*****.**", "--password", "123"])
assert res.exit_code == 1
mocked_login.assert_called_once()
assert mocked_list_basespace_projects.call_count == 2
def test_list_projects_slow_response_retry_list(mocker, credentials):
"""Test projects slow response retry on the list."""
runner = CliRunner()
mocked_get_projects = mocker.patch.object(
APIClient,
"list_projects",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
mocked_get_pipeline_capabilities = mocker.patch.object(
APIClient, "get_pipeline_capabilities")
res = runner.invoke(list_projects, credentials)
assert res.exit_code == 1
assert mocked_get_projects.call_count == 2
mocked_get_pipeline_capabilities.assert_not_called()
def test_list_project_samples_slow_response_retry(mocker, credentials):
"""Test project samples slow response retry."""
runner = CliRunner()
mocked_get_project_samples = mocker.patch.object(
APIClient,
"get_project_samples",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
res = runner.invoke(
list_project_samples,
[str(uuid4()), *credentials],
)
assert res.exit_code == 1
assert mocked_get_project_samples.call_count == 2
def test_list_project_batch_types__not_empty_slow_response_retry(
mocker, credentials):
"""Test project batch types being outputed to the shell."""
runner = CliRunner()
mocked_get_project_batch_types = mocker.patch.object(
APIClient,
"get_project_batch_types",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
res = runner.invoke(
list_project_batch_types,
[str(uuid4()), *credentials],
)
assert res.exit_code == 1
assert mocked_get_project_batch_types.call_count == 2
def test_autoimport_list_uploads_slow_response_retry(mocker, credentials):
"""Test list jobs slow response retry."""
runner = CliRunner()
mocked_list_s3_autoimport_jobs = mocker.patch.object(
APIClient,
"list_s3_autoimport_jobs",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
res = runner.invoke(autoimport_list, credentials)
assert res.exit_code == 1
assert mocked_list_s3_autoimport_jobs.call_count == 2
assert ("\n".join([
"ERROR: There was an error listing S3 autoimport jobs.",
"ERROR: Could not connect to the api server",
"Aborted!\n",
]) == res.output)
def test_list_projects_slow_response_retry_pipeline(mocker, credentials,
recording, vcr):
"""Test projects slow repsonse retry on the pipeline capabilities."""
runner = CliRunner()
if not recording:
# Mock list_projects only if using the cassettes, since we mock the
# return value.
list_projects_response = get_vcr_response("/api/v2/projects/", vcr)
mocked_get_projects = mocker.patch.object(
APIClient,
"list_projects",
return_value=Projects(**list_projects_response),
)
mocked_get_pipeline_capabilities = mocker.patch.object(
APIClient,
"get_pipeline_capabilities",
side_effect=APIClientTimeout("Could not connect to the api server"),
)
res = runner.invoke(list_projects, credentials)
assert res.exit_code == 1
if not recording:
mocked_get_projects.assert_called_once()
assert mocked_get_pipeline_capabilities.call_count == 3