def test_get_merged_vcf__bad_project_id(mocker):
"""Test get merged file failure when non-uuid string is used as
project id.
"""
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
mocked_get_project = mocker.patch.object(
APIClient,
"get_project",
return_value=Project(id=str(uuid4())),
)
res = runner.invoke(
get_merged_vcf,
[
"1111111",
"--email",
"*****@*****.**",
"--password",
"123",
],
)
assert res.exit_code == 1
mocked_login.assert_called_once()
mocked_get_project.assert_not_called()
assert "Project ID is not valid" in res.output
def test_list_projects__with_unexpected_keys(mocker, credentials):
"""Test projects being outputed to the shell where webhook_url, roles and
some randomly generated values are part of the response.
"""
runner = CliRunner()
mocked_get_projects = mocker.patch.object(
APIClient,
"list_projects",
return_value=Projects(**MOCKED_PROJECTS_WITH_UNEXPECTED_KEYS),
)
mocked_get_pipeline_capabilities = mocker.patch.object(
APIClient,
"get_pipeline_capabilities",
return_value=PipelineCapabilities(**MOCKED_PIPELINE_CAPABILITY),
)
res = runner.invoke(list_projects, credentials)
assert res.exit_code == 0
mocked_get_projects.assert_called_once()
mocked_get_pipeline_capabilities.assert_called_once()
project = Project(**MOCKED_PROJECTS_WITH_UNEXPECTED_KEYS["results"][0])
pipeline = PipelineCapabilities(**MOCKED_PIPELINE_CAPABILITY)
output_line = io.BytesIO()
sys.stdout = output_line
echo("\t".join([
str(project.created),
str(project.id),
project.name.replace("\t", " "),
pipeline.name,
]))
assert output_line.getvalue() == res.output.encode()
def augment_projects_with_pipeline_capabilities(self, projects):
"""Fetch pipeline capabilities and append it to the project.
Args:
projects (list[Project]): list of projects
Returns:
list[Project]: same list of projects with pipeline capabilities
uuid replaced with PipelineCapability
"""
for project in projects:
pipeline_capabilities = self.get_pipeline_capabilities(
project.pipeline_capabilities)
project_dict = dict(project)
project_dict["pipeline_capabilities"] = pipeline_capabilities
yield Project(**project_dict)
def test_get_merged_vcf__empty(mocker):
"""Test project doesn't have a merged VCF file."""
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",
return_value=Project(
id=project_id,
name="Project Cadmus",
description="",
created="2020-06-11T02:14:00.541889Z",
organization=str(uuid4()),
sample_count=3,
pipeline_capabilites=str(uuid4()),
files=[],
),
)
res = runner.invoke(
get_merged_vcf,
[
project_id,
"--email",
"*****@*****.**",
"--password",
"123",
],
)
assert res.exit_code == 1
mocked_login.assert_called_once()
mocked_get_project.assert_called_once()
assert (
"No files to process for project {}".format(project_id) in res.output
)
def test_list_projects(mocker, credentials, recording, vcr):
"""Test projects being outputed to the shell."""
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),
)
get_pipeline_capabilities_response = get_vcr_response(
"/api/v2/pipeline-capabilities/", vcr, operator.contains)
mocked_get_pipeline_capabilities = mocker.patch.object(
APIClient,
"get_pipeline_capabilities",
return_value=PipelineCapabilities(
**get_pipeline_capabilities_response),
)
res = runner.invoke(list_projects, credentials)
assert res.exit_code == 0
if not recording:
mocked_get_projects.assert_called_once()
projects = list_projects_response["results"]
assert mocked_get_pipeline_capabilities.call_count == len(projects)
output_line = io.BytesIO()
sys.stdout = output_line
for project in projects:
project = Project(**project)
echo("\t".join([
str(project.created),
str(project.id),
project.name.replace("\t", " "),
get_pipeline_capabilities_response["name"],
]))
assert output_line.getvalue() == res.output.encode()
def test_get_merged_vcf__success__project_with_legacy_webhhok_url(mocker):
"""Test project download merged VCF success."""
project_id = str(uuid4())
file_id = str(uuid4())
runner = CliRunner()
mocked_login = mocker.patch.object(APIClient, "login", return_value=None)
mocked_get_project = mocker.patch.object(
APIClient,
"get_project",
return_value=Project(
id=project_id,
name="Project Cadmus",
description="",
created="2020-06-11T02:14:00.541889Z",
organization=str(uuid4()),
webhook_url="",
sample_count=3,
pipeline_capabilites=str(uuid4()),
files=[
{
"id": "755ec682-e4a5-414a-a5be-07e0af11cf75",
"s3_path": (
"app-data/output/apps/merge_vcfs/"
"{file_id}/{file_id}.vcf.bgz".format(file_id=file_id)
),
"size": None,
"download_url": (
"https://bucket.s3.amazonaws.com/output/apps/"
"merge_vcfs/{file_id}/{file_id}.vcf.bgz".format(
file_id=file_id
)
),
"file_type": "impute-vcf-merged",
}
],
),
)
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 == 0
mocked_login.assert_called_once()
mocked_get_project.assert_called_once()
mocked_download_file.assert_called_once_with(
"{}.vcf.bgz".format(file_id),
"https://bucket.s3.amazonaws.com/output/apps/"
"merge_vcfs/{file_id}/{file_id}.vcf.bgz".format(file_id=file_id),
no_progress=False,
)