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Merged
paulineribeyre merged 4 commits into from
Jan 26, 2022
Merged

PXP-9266 Split SSL and isolation level tests #364

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09da47e
Split SSL and isolation level tests
paulineribeyre Jan 19, 2022
012d5f7
trigger tests
paulineribeyre Jan 20, 2022
6e14e06
Merge branch 'master' of github.com:uc-cdis/sheepdog into feat/ssl-is…
paulineribeyre Jan 26, 2022
84aeb7d
reduce code duplication
paulineribeyre Jan 26, 2022
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2 changes: 1 addition & 1 deletion .secrets.baseline
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
"files": null,
"lines": null
},
"generated_at": "2021-12-21T20:46:37Z",
"generated_at": "2022-01-26T15:40:06Z",
"plugins_used": [
{
"name": "AWSKeyDetector"
Expand Down
18 changes: 12 additions & 6 deletions tests/integration/datadict/conftest.py
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Expand Up @@ -151,16 +151,22 @@ def teardown():
return _app


@pytest.fixture(params=[False, True, None])
@pytest.fixture()
def use_ssl(request):
# return False, True, None
return request.param
try:
# one of [False, True, None]
return request.param
except:
return None


@pytest.fixture(params=("READ_COMMITTED", "REPEATABLE_READ", "SERIALIZABLE", None))
@pytest.fixture()
def isolation_level(request):
# return 'READ_COMMITTED', 'REPEATABLE_READ', 'SERIALIZABLE', None
return request.param
try:
# one of ["READ_COMMITTED", "REPEATABLE_READ", "SERIALIZABLE", None]
return request.param
except:
return None


@pytest.fixture
Expand Down
42 changes: 21 additions & 21 deletions tests/integration/datadict/submission/test_endpoints.py
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Original file line number Diff line number Diff line change
Expand Up @@ -340,7 +340,7 @@ def put_example_entities_together(client, headers):
return client.put(path, headers=headers, data=json.dumps(data))


def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter):
def do_test_post_example_entities_together(client, submitter):
with open(os.path.join(DATA_DIR, "case.json"), "r") as f:
case_sid = json.loads(f.read())["submitter_id"]
print(case_sid)
Expand All @@ -356,6 +356,10 @@ def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter
assert condition_to_check, resp.data


def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter):
do_test_post_example_entities_together(client, submitter)


def test_dictionary_list_entries(client, pg_driver, cgci_blgsp, submitter):
resp = client.get("/v0/submission/CGCI/BLGSP/_dictionary")
print(resp.data)
Expand Down Expand Up @@ -505,7 +509,7 @@ def test_disallow_cross_project_references(client, pg_driver, cgci_blgsp, submit
assert resp.status_code == 400, resp.data


def test_delete_entity(client, pg_driver, cgci_blgsp, submitter):
def do_test_delete_entity(client, submitter):
resp = client.put(
BLGSP_PATH,
headers=submitter,
Expand All @@ -524,6 +528,10 @@ def test_delete_entity(client, pg_driver, cgci_blgsp, submitter):
assert resp.status_code == 200, resp.data


def test_delete_entity(client, pg_driver, cgci_blgsp, submitter):
do_test_delete_entity(client, submitter)


def test_catch_internal_errors(monkeypatch, client, pg_driver, cgci_blgsp, submitter):
"""
Monkey patch an essential function to just raise an error and assert that
Expand Down Expand Up @@ -698,7 +706,7 @@ def test_valid_file_index(
assert index_client.get(sur_entity["id"]), "No indexd document created"


def test_submit_valid_tsv(client, pg_driver, cgci_blgsp, submitter):
def do_test_submit_valid_tsv(client, submitter):
"""
Test that we can submit a valid TSV file
"""
Expand All @@ -710,9 +718,7 @@ def test_submit_valid_tsv(client, pg_driver, cgci_blgsp, submitter):
}

# convert to TSV (save to file)
file_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "data/experiment_tmp.tsv"
)
file_path = os.path.join(DATA_DIR, "experiment_tmp.tsv")
with open(file_path, "w") as f:
dw = csv.DictWriter(f, sorted(data.keys()), delimiter="\t")
dw.writeheader()
Expand All @@ -731,6 +737,10 @@ def test_submit_valid_tsv(client, pg_driver, cgci_blgsp, submitter):
assert resp.status_code == 200, resp.data


def test_submit_valid_tsv(client, pg_driver, cgci_blgsp, submitter):
do_test_submit_valid_tsv(client, submitter)


def test_submit_valid_csv(client, pg_driver, cgci_blgsp, submitter):
"""
Test that we can submit a valid CSV file
Expand Down Expand Up @@ -792,9 +802,7 @@ def test_can_submit_with_asterisk_tsv(client, pg_driver, cgci_blgsp, submitter):
"*projects.id": "daa208a7-f57a-562c-a04a-7a7c77542c98",
}
# convert to TSV (save to file)
file_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "data/experiment_tmp.tsv"
)
file_path = os.path.join(DATA_DIR, "experiment_tmp.tsv")
with open(file_path, "w") as f:
dw = csv.DictWriter(f, sorted(data.keys()), delimiter="\t")
dw.writeheader()
Expand Down Expand Up @@ -1038,9 +1046,7 @@ def test_duplicate_submission(app, pg_driver, cgci_blgsp, submitter):
}

# convert to TSV (save to file)
file_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "data/experiment_tmp.tsv"
)
file_path = os.path.join(DATA_DIR, "experiment_tmp.tsv")
with open(file_path, "w") as f:
dw = csv.DictWriter(f, sorted(data.keys()), delimiter="\t")
dw.writeheader()
Expand Down Expand Up @@ -1149,9 +1155,7 @@ def test_zero_decimal_float(client, pg_driver, cgci_blgsp, submitter):
}

# convert to TSV (save to file)
file_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "data/experiment_tmp.tsv"
)
file_path = os.path.join(DATA_DIR, "experiment_tmp.tsv")
with open(file_path, "w") as f:
dw = csv.DictWriter(f, sorted(data.keys()), delimiter="\t")
dw.writeheader()
Expand Down Expand Up @@ -1302,9 +1306,7 @@ def test_update_to_null_valid_tsv(client, pg_driver, cgci_blgsp, submitter):
}

# convert to TSV (save to file)
file_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "data/experiment_tmp.tsv"
)
file_path = os.path.join(DATA_DIR, "experiment_tmp.tsv")
with open(file_path, "w") as f:
dw = csv.DictWriter(f, sorted(data.keys()), delimiter="\t")
dw.writeheader()
Expand Down Expand Up @@ -1368,9 +1370,7 @@ def test_update_to_null_invalid_tsv(client, pg_driver, cgci_blgsp, submitter):
}

# convert to TSV (save to file)
file_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "data/experiment_tmp.tsv"
)
file_path = os.path.join(DATA_DIR, "experiment_tmp.tsv")
with open(file_path, "w") as f:
dw = csv.DictWriter(f, sorted(data.keys()), delimiter="\t")
dw.writeheader()
Expand Down
43 changes: 43 additions & 0 deletions tests/integration/datadict/test_ssl_and_isolation_level.py
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@@ -0,0 +1,43 @@
"""
Copy of a few functional tests in order to test that SSL and isolation level
settings work.
"""

import pytest

from tests.integration.datadict.submission.test_endpoints import (
do_test_post_example_entities_together,
do_test_delete_entity,
do_test_submit_valid_tsv,
do_test_export,
)


USE_SSL = [False, True, None]
ISOLATION_LEVELS = ["READ_COMMITTED", "REPEATABLE_READ", "SERIALIZABLE", None]


@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
@pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter):
do_test_post_example_entities_together(client, submitter)


@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
@pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
def test_delete_entity(client, pg_driver, cgci_blgsp, submitter):
do_test_delete_entity(client, submitter)


@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
@pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
def test_submit_valid_tsv(client, pg_driver, cgci_blgsp, submitter):
do_test_submit_valid_tsv(client, submitter)


@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
@pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
def test_export_all_node_types(
client, pg_driver, cgci_blgsp, submitter, require_index_exists_off
):
do_test_export(client, pg_driver, submitter, "experimental_metadata", "tsv")
18 changes: 12 additions & 6 deletions tests/integration/datadictwithobjid/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -149,16 +149,22 @@ def teardown():
return _app


@pytest.fixture(params=[None, False, True])
@pytest.fixture()
def use_ssl(request):
# return None, False, True
return request.param
try:
# one of [False, True, None]
return request.param
except:
return None


@pytest.fixture(params=("READ_COMMITTED", "REPEATABLE_READ", "SERIALIZABLE", None))
@pytest.fixture()
def isolation_level(request):
# return 'READ_COMMITTED', 'REPEATABLE_READ', 'SERIALIZABLE', None
return request.param
try:
# one of ["READ_COMMITTED", "REPEATABLE_READ", "SERIALIZABLE", None]
return request.param
except:
return None


@pytest.fixture
Expand Down
26 changes: 9 additions & 17 deletions tests/integration/datadictwithobjid/submission/test_endpoints.py
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Expand Up @@ -14,8 +14,12 @@
from moto import mock_s3
from datamodelutils import models as md
from sheepdog.transactions.upload import UploadTransaction

from tests.integration.datadict.submission.utils import data_fnames
from tests.integration.datadictwithobjid.submission.utils import extended_data_fnames
from tests.integration.datadict.submission.test_endpoints import (
do_test_export,
)

BLGSP_PATH = "/v0/submission/CGCI/BLGSP/"
BRCA_PATH = "/v0/submission/TCGA/BRCA/"
Expand Down Expand Up @@ -355,7 +359,7 @@ def put_example_entities_together(client, headers):
return client.put(path, headers=headers, data=json.dumps(data))


def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter):
def do_test_post_example_entities_together(client, submitter):
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@paulineribeyre paulineribeyre Jan 26, 2022

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not importing it from datadict because the datadictwithobjid test data might be different

with open(os.path.join(DATA_DIR, "case.json"), "r") as f:
case_sid = json.loads(f.read())["submitter_id"]
assert case_sid
Expand All @@ -371,6 +375,10 @@ def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter
assert condition_to_check, resp.data


def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter):
do_test_post_example_entities_together(client, submitter)


def test_dictionary_list_entries(client, pg_driver, cgci_blgsp, submitter):
resp = client.get("/v0/submission/CGCI/BLGSP/_dictionary")
print(resp.data)
Expand Down Expand Up @@ -708,22 +716,6 @@ def test_export_entity_by_id(client, pg_driver, cgci_blgsp, submitter):
assert data[0]["id"] == case_id


def do_test_export(client, pg_driver, submitter, node_type, format_type):
post_example_entities_together(client, submitter, extended_data_fnames)
experimental_metadata_count = add_and_get_new_experimental_metadata_count(pg_driver)
r = get_export_data(client, submitter, node_type, format_type, False)
assert r.status_code == 200, r.data
assert r.headers["Content-Disposition"].endswith(format_type)
if format_type == "tsv":
str_data = str(r.data, "utf-8")
assert len(str_data.strip().split("\n")) == experimental_metadata_count + 1
return str_data
else:
js_data = json.loads(r.data)
assert len(js_data["data"]) == experimental_metadata_count
return js_data


def get_export_data(client, submitter, node_type, format_type, without_id):
path = "/v0/submission/CGCI/BLGSP/export/?node_label={}&format={}".format(
node_type, format_type
Expand Down
45 changes: 45 additions & 0 deletions tests/integration/datadictwithobjid/test_ssl_and_isolation_level.py
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@@ -0,0 +1,45 @@
"""
Copy of a few functional tests in order to test that SSL and isolation level
settings work.
"""

import pytest

from tests.integration.datadictwithobjid.submission.test_endpoints import (
do_test_post_example_entities_together,
)
from tests.integration.datadict.submission.test_endpoints import (
do_test_delete_entity,
do_test_submit_valid_tsv,
do_test_export,
)


USE_SSL = [False, True, None]
ISOLATION_LEVELS = ["READ_COMMITTED", "REPEATABLE_READ", "SERIALIZABLE", None]


@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
@pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
def test_post_example_entities_together(client, pg_driver, cgci_blgsp, submitter):
do_test_post_example_entities_together(client, submitter)


@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
@pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
def test_delete_entity(client, pg_driver, cgci_blgsp, submitter):
do_test_delete_entity(client, submitter)


@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
@pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
def test_submit_valid_tsv(client, pg_driver, cgci_blgsp, submitter):
do_test_submit_valid_tsv(client, submitter)


@pytest.mark.parametrize("use_ssl", USE_SSL, indirect=True)
@pytest.mark.parametrize("isolation_level", ISOLATION_LEVELS, indirect=True)
def test_export_all_node_types(
client, pg_driver, cgci_blgsp, submitter, require_index_exists_off
):
do_test_export(client, pg_driver, submitter, "experimental_metadata", "tsv")