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Develop markers for api tests according to credentials required FDS-1026 #1289

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merged 4 commits into from
Sep 15, 2023
Merged

Develop markers for api tests according to credentials required FDS-1026 #1289

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0cc187a
add credential marks to api tests
GiaJordan Sep 8, 2023
10e0a95
document test marks
GiaJordan Sep 8, 2023
559d12b
clean and mark missed test
GiaJordan Sep 8, 2023
c1f8780
change marker name
GiaJordan Sep 14, 2023
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10 changes: 9 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -148,5 +148,13 @@ markers = [
"""\
rule_benchmark: marks tests covering \
validation rule benchmarking
"""
""",
"""\
synapse_credentials_needed: marks api tests that \
require synapse credentials to run
""",
"""\
empty_token: marks api tests that \
send empty credentials in the request
"""
]
20 changes: 20 additions & 0 deletions tests/test_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,7 @@ def syn_token(config:Configuration):

@pytest.mark.schematic_api
class TestSynapseStorage:
@pytest.mark.synapse_credentials_needed
@pytest.mark.parametrize("return_type", ["json", "csv"])
def test_get_storage_assets_tables(self, client, syn_token, return_type):
params = {
Expand All @@ -120,6 +121,8 @@ def test_get_storage_assets_tables(self, client, syn_token, return_type):
os.remove(response_dt)
else:
pass

@pytest.mark.synapse_credentials_needed
@pytest.mark.parametrize("full_path", [True, False])
@pytest.mark.parametrize("file_names", [None, "Sample_A.txt"])
def test_get_dataset_files(self,full_path, file_names, syn_token, client):
Expand Down Expand Up @@ -150,6 +153,7 @@ def test_get_dataset_files(self,full_path, file_names, syn_token, client):
else:
assert ["syn25705259","Boolean Test"] and ["syn23667202","DataTypeX_table"] in response_dt

@pytest.mark.synapse_credentials_needed
def test_get_storage_project_dataset(self, syn_token, client):
params = {
"access_token": syn_token,
Expand All @@ -162,6 +166,7 @@ def test_get_storage_project_dataset(self, syn_token, client):
response_dt = json.loads(response.data)
assert ["syn26251193","Issue522"] in response_dt

@pytest.mark.synapse_credentials_needed
def test_get_storage_project_manifests(self, syn_token, client):

params = {
Expand All @@ -174,6 +179,7 @@ def test_get_storage_project_manifests(self, syn_token, client):

assert response.status_code == 200

@pytest.mark.synapse_credentials_needed
def test_get_storage_projects(self, syn_token, client):

params = {
Expand All @@ -185,6 +191,7 @@ def test_get_storage_projects(self, syn_token, client):

assert response.status_code == 200

@pytest.mark.synapse_credentials_needed
@pytest.mark.parametrize("entity_id", ["syn34640850", "syn23643253", "syn24992754"])
def test_get_entity_type(self, syn_token, client, entity_id):
params = {
Expand All @@ -203,6 +210,7 @@ def test_get_entity_type(self, syn_token, client, entity_id):
elif entity_id == "syn24992754":
assert response_dt == "project"

@pytest.mark.synapse_credentials_needed
@pytest.mark.parametrize("entity_id", ["syn30988314", "syn27221721"])
def test_if_in_assetview(self, syn_token, client, entity_id):
params = {
Expand Down Expand Up @@ -399,6 +407,7 @@ def ifPandasDataframe(self, response_dt):
assert isinstance(df, pd.DataFrame)


@pytest.mark.empty_token
#@pytest.mark.parametrize("output_format", [None, "excel", "google_sheet", "dataframe (only if getting existing manifests)"])
@pytest.mark.parametrize("output_format", ["excel"])
@pytest.mark.parametrize("data_type", ["Biospecimen", "Patient", "all manifests", ["Biospecimen", "Patient"]])
Expand Down Expand Up @@ -455,6 +464,7 @@ def test_generate_existing_manifest(self, client, data_model_jsonld, data_type,
self.ifGoogleSheetExists(response_dt)


@pytest.mark.empty_token
@pytest.mark.parametrize("output_format", ["excel", "google_sheet", "dataframe (only if getting existing manifests)", None])
@pytest.mark.parametrize("data_type", ["all manifests", ["Biospecimen", "Patient"], "Patient"])
def test_generate_new_manifest(self, caplog, client, data_model_jsonld, data_type, output_format):
Expand Down Expand Up @@ -621,6 +631,7 @@ def test_validate_manifest(self, data_model_jsonld, client, json_str, restrict_r
assert "errors" in response_dt.keys()
assert "warnings" in response_dt.keys()

@pytest.mark.synapse_credentials_needed
def test_get_datatype_manifest(self, client, syn_token):
params = {
"access_token": syn_token,
Expand All @@ -642,6 +653,7 @@ def test_get_datatype_manifest(self, client, syn_token):
"Year of Birth": "Int64",
"entityId": "string"}

@pytest.mark.synapse_credentials_needed
# small manifest: syn51078535; big manifest: syn51156998
@pytest.mark.parametrize("manifest_id, expected_component, expected_file_name", [("syn51078535", "BulkRNA-seqAssay", "synapse_storage_manifest.csv"), ("syn51156998", "Biospecimen", "synapse_storage_manifest_biospecimen.csv")])
@pytest.mark.parametrize("new_manifest_name",[None,"Example.csv"])
Expand Down Expand Up @@ -694,6 +706,8 @@ def test_manifest_download(self, config: Configuration, client, syn_token, manif
os.remove(manifest_file_path)
except:
pass

@pytest.mark.synapse_credentials_needed
# test downloading a manifest with access restriction and see if the correct error message got raised
def test_download_access_restricted_manifest(self, client, syn_token):
params = {
Expand All @@ -707,6 +721,7 @@ def test_download_access_restricted_manifest(self, client, syn_token):
raise TypeError('the type error got raised')
assert exc_info.value.args[0] == "the type error got raised"

@pytest.mark.synapse_credentials_needed
@pytest.mark.parametrize("as_json", [None, True, False])
@pytest.mark.parametrize("new_manifest_name", [None, "Test"])
def test_dataset_manifest_download(self, client, as_json, syn_token, new_manifest_name):
Expand Down Expand Up @@ -735,6 +750,7 @@ def test_dataset_manifest_download(self, client, as_json, syn_token, new_manifes
assert isinstance(response_path, str)
assert response_path.endswith(".csv")

@pytest.mark.synapse_credentials_needed
@pytest.mark.submission
def test_submit_manifest_table_and_file_replace(self, client, syn_token, data_model_jsonld, test_manifest_submit):
"""Testing submit manifest in a csv format as a table and a file. Only replace the table
Expand All @@ -755,6 +771,7 @@ def test_submit_manifest_table_and_file_replace(self, client, syn_token, data_mo
response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")})
assert response_csv.status_code == 200

@pytest.mark.synapse_credentials_needed
@pytest.mark.submission
def test_submit_manifest_file_only_replace(self, client, syn_token, data_model_jsonld, test_manifest_submit):
"""Testing submit manifest in a csv format as a file
Expand All @@ -773,6 +790,7 @@ def test_submit_manifest_file_only_replace(self, client, syn_token, data_model_j
response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")})
assert response_csv.status_code == 200

@pytest.mark.synapse_credentials_needed
@pytest.mark.submission
def test_submit_manifest_json_str_replace(self, client, syn_token, data_model_jsonld):
"""Submit json str as a file
Expand All @@ -794,6 +812,7 @@ def test_submit_manifest_json_str_replace(self, client, syn_token, data_model_js
response = client.post('http://localhost:3001/v1/model/submit', query_string = params, data={"file_name":''})
assert response.status_code == 200

@pytest.mark.synapse_credentials_needed
@pytest.mark.submission
def test_submit_manifest_w_file_and_entities(self, client, syn_token, data_model_jsonld, test_manifest_submit):
params = {
Expand All @@ -812,6 +831,7 @@ def test_submit_manifest_w_file_and_entities(self, client, syn_token, data_model
response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")})
assert response_csv.status_code == 200

@pytest.mark.synapse_credentials_needed
@pytest.mark.submission
def test_submit_manifest_table_and_file_upsert(self, client, syn_token, data_model_jsonld, test_upsert_manifest_csv, ):
params = {
Expand Down