def test_project_retrieve(capsys, requests_mock):
p_obj = factories.ProjectFactory()
args = {
"sodar_url": SODAR_SERVER_URL,
"sodar_api_token": SODAR_API_TOKEN,
"project_uuid": p_obj.sodar_uuid,
}
tpl = "%(sodar_url)sproject/api/retrieve/%(project_uuid)s"
requests_mock.register_uri(
"GET",
tpl % args,
headers={"Authorization": "Token %s" % args["sodar_api_token"]},
json=cattr.unstructure(p_obj),
)
main([
"--sodar-server-url",
SODAR_SERVER_URL,
"--sodar-api-token",
SODAR_API_TOKEN,
"project",
"retrieve",
p_obj.sodar_uuid,
])
captured = capsys.readouterr()
assert json.dumps(cattr.unstructure(p_obj)) + "\n" == captured.out
def test_samplesheet_import(capsys, requests_mock):
p_base = Path(__file__).parent / "data" / "isatab"
i_obj = factories.InvestigationFactory()
args = {
"sodar_url": SODAR_SERVER_URL,
"sodar_api_token": SODAR_API_TOKEN,
"project_uuid": i_obj.project,
}
tpl = "%(sodar_url)ssamplesheets/api/import/%(project_uuid)s"
requests_mock.register_uri(
"POST",
tpl % args,
headers={"Authorization": "Token %s" % args["sodar_api_token"]},
json=cattr.unstructure(i_obj),
)
main([
"--sodar-server-url",
SODAR_SERVER_URL,
"--sodar-api-token",
SODAR_API_TOKEN,
"samplesheet",
"import",
i_obj.project,
str(p_base / "i_Investigation.txt"),
str(p_base / "s_test.txt"),
str(p_base / "a_test_exome_sequencing_nucleotide_sequencing.txt"),
])
captured = capsys.readouterr()
assert json.dumps(cattr.unstructure(i_obj)) + "\n" == captured.out
def test_project_create(capsys, requests_mock):
p_obj = factories.ProjectFactory()
args = {"sodar_url": SODAR_SERVER_URL, "sodar_api_token": SODAR_API_TOKEN}
args["project"] = p_obj
tpl = "%(sodar_url)sproject/api/create"
requests_mock.register_uri(
"POST",
tpl % args,
headers={"Authorization": "Token %s" % args["sodar_api_token"]},
json=cattr.unstructure(p_obj),
)
main([
"--sodar-server-url",
SODAR_SERVER_URL,
"--sodar-api-token",
SODAR_API_TOKEN,
"project",
"create",
"--parent-uuid",
"YYY",
"--title",
"The title",
"--owner-uuid",
"OOO",
])
captured = capsys.readouterr()
assert cattr.unstructure(p_obj) == json.loads(captured.out)
def test_call_landingzone_retrieve(capsys, requests_mock):
lz_obj = factories.LandingZoneFactory()
args = {
"sodar_url": SODAR_SERVER_URL,
"sodar_api_token": SODAR_API_TOKEN,
"landingzone_uuid": lz_obj.sodar_uuid,
}
tpl = "%(sodar_url)slandingzones/api/retrieve/%(landingzone_uuid)s"
requests_mock.register_uri(
"GET",
tpl % args,
headers={"Authorization": "Token %s" % args["sodar_api_token"]},
json=cattr.unstructure(lz_obj),
)
main([
"--sodar-server-url",
SODAR_SERVER_URL,
"--sodar-api-token",
SODAR_API_TOKEN,
"landingzone",
"retrieve",
lz_obj.sodar_uuid,
])
captured = capsys.readouterr()
assert json.dumps(cattr.unstructure(lz_obj)) + "\n" == captured.out
def test_samplesheet_export(capsys, requests_mock, tmpdir):
p_base = Path(__file__).parent / "data" / "isatab"
result = {
"investigation": {
"path": "i_Investigation.txt",
"tsv": (p_base / "i_Investigation.txt").open("rt").read(),
},
"studies": {
"s_test.txt": {
"tsv": (p_base / "s_test.txt").open("rt").read()
}
},
"assays": {
"a_test_exome_sequencing_nucleotide_sequencing.txt": {
"tsv":
(p_base / "a_test_exome_sequencing_nucleotide_sequencing.txt"
).open("rt").read()
}
},
}
i_obj = factories.InvestigationFactory()
args = {
"sodar_url": SODAR_SERVER_URL,
"sodar_api_token": SODAR_API_TOKEN,
"project_uuid": i_obj.project,
}
tpl = "%(sodar_url)ssamplesheets/api/export/json/%(project_uuid)s"
requests_mock.register_uri(
"GET",
tpl % args,
headers={"Authorization": "Token %s" % args["sodar_api_token"]},
json=result,
)
main([
"--sodar-server-url",
SODAR_SERVER_URL,
"--sodar-api-token",
SODAR_API_TOKEN,
"samplesheet",
"export",
"--print-output",
"--write-output",
str(tmpdir),
i_obj.project,
])
captured = capsys.readouterr()
assert json.dumps(result) + "\n" == captured.out
assert list(sorted(x.basename for x in tmpdir.listdir())) == [
"a_test_exome_sequencing_nucleotide_sequencing.txt",
"i_Investigation.txt",
"s_test.txt",
]
def test_call_landingzone_submit_validate(capsys, requests_mock):
lz_obj = factories.LandingZoneFactory()
# Move landing zone
m_args = {
"sodar_url": SODAR_SERVER_URL,
"sodar_api_token": SODAR_API_TOKEN,
"landingzone_uuid": lz_obj.sodar_uuid,
}
m_tpl = "%(sodar_url)slandingzones/api/submit/validate/%(landingzone_uuid)s"
m_result = factories.LandingZoneFactory(
sodar_uuid=m_args["landingzone_uuid"])
requests_mock.register_uri(
"POST",
m_tpl % m_args,
headers={"Authorization": "Token %s" % m_args["sodar_api_token"]},
json=cattr.unstructure(m_result),
)
# Retrieve landing zone.
r_args = m_args.copy()
r_tpl = "%(sodar_url)slandingzones/api/retrieve/%(landingzone_uuid)s"
r_result = m_result
requests_mock.register_uri(
"GET",
r_tpl % r_args,
headers={"Authorization": "Token %s" % r_args["sodar_api_token"]},
json=cattr.unstructure(r_result),
)
main([
"--sodar-server-url",
SODAR_SERVER_URL,
"--sodar-api-token",
SODAR_API_TOKEN,
"landingzone",
"validate",
lz_obj.sodar_uuid,
])
captured = capsys.readouterr()
assert json.dumps(cattr.unstructure(r_result)) + "\n" == captured.out
def test_project_list(capsys, requests_mock):
args = {"sodar_url": SODAR_SERVER_URL, "sodar_api_token": SODAR_API_TOKEN}
tpl = "%(sodar_url)sproject/api/list"
p_obj = factories.ProjectFactory()
requests_mock.register_uri(
"GET",
tpl % args,
headers={"Authorization": "Token %s" % args["sodar_api_token"]},
json=cattr.unstructure([p_obj]),
)
main([
"--sodar-server-url",
SODAR_SERVER_URL,
"--sodar-api-token",
SODAR_API_TOKEN,
"project",
"list",
])
captured = capsys.readouterr()
assert json.dumps(cattr.unstructure([p_obj])) + "\n" == captured.out
def test_call_landingzone_create(capsys, requests_mock):
# Query project information.
project = factories.ProjectFactory()
i_args = {
"sodar_url": SODAR_SERVER_URL,
"sodar_api_token": SODAR_API_TOKEN,
"project_uuid": project.sodar_uuid,
}
i_tpl = "%(sodar_url)ssamplesheets/api/investigation/retrieve/%(project_uuid)s"
investigation = factories.InvestigationFactory()
requests_mock.register_uri(
"GET",
i_tpl % i_args,
headers={"Authorization": "Token %s" % i_args["sodar_api_token"]},
json=cattr.unstructure(investigation),
)
# Creation of landing zone.
l_tpl = "%(sodar_url)slandingzones/api/create/%(project_uuid)s"
lz_obj = factories.LandingZoneFactory(project=i_args["project_uuid"])
requests_mock.register_uri(
"POST",
l_tpl % i_args,
headers={"Authorization": "Token %s" % i_args["sodar_api_token"]},
json=cattr.unstructure(lz_obj),
)
main([
"--sodar-server-url",
SODAR_SERVER_URL,
"--sodar-api-token",
SODAR_API_TOKEN,
"landingzone",
"create",
project.sodar_uuid,
])
captured = capsys.readouterr()
assert json.dumps(cattr.unstructure(lz_obj)) + "\n" == captured.out
def test_no_args():
with pytest.raises(SystemExit) as pytest_wrapped_e:
main([])
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 1