def test_create_classification_with_bad_value(_demo_client):
classification = IndividualVariantClassification()
classification.variant_id = 2105
classification.individual_id = 8258
classification.classification = "iknownothingofthis"
classification.notes = "".join(
["bla" for _ in range(random.randint(10, 100))])
classification.pubmed_id = str(random.randint(10, 1000000))
response = _demo_client.post("/variant-classification",
json=classification.as_dict(),
content_type="application/json")
assert response.status_code == 500
def test_create_classification_with_non_existing_individual(_demo_client):
classification = IndividualVariantClassification()
classification.variant_id = 2105
classification.individual_id = 123456789
classification.classification = "pathogenic"
classification.notes = "".join(
["bla" for _ in range(random.randint(10, 100))])
classification.pubmed_id = str(random.randint(10, 1000000))
response = _demo_client.post("/variant-classification",
json=classification.as_dict(),
content_type="application/json")
assert response.status_code == 401
def test_create_classification_with_admin_user(_admin_client):
classification = IndividualVariantClassification()
classification.variant_id = 8090
classification.individual_id = 8258
classification.classification = "pathogenic"
classification.notes = "".join(
["bla" for _ in range(random.randint(10, 100))])
classification.pubmed_id = str(random.randint(10, 1000000))
_assert_variant_classification(_admin_client, classification, "Admin")
def test_get_classifications_by_individual(_admin_client):
# sets 3 variant classifications for a given individual
phenopolis_id = "PH00008258"
individual_id = int(phenopolis_id.replace("PH", ""))
classification1 = IndividualVariantClassification()
classification1.variant_id = 8090
classification1.individual_id = individual_id
classification1.classification = "pathogenic"
_assert_variant_classification(_admin_client, classification1, "Admin")
classification2 = IndividualVariantClassification()
classification2.variant_id = 13309
classification2.individual_id = individual_id
classification2.classification = "pathogenic"
_assert_variant_classification(_admin_client, classification2, "Admin")
classification3 = IndividualVariantClassification()
classification3.variant_id = 22678
classification3.individual_id = individual_id
classification3.classification = "pathogenic"
_assert_variant_classification(_admin_client, classification3, "Admin")
# creates this one just to check it does not come in the output
classification4 = IndividualVariantClassification()
classification4.variant_id = 3491
classification4.individual_id = 8256
classification4.classification = "pathogenic"
_assert_variant_classification(_admin_client, classification4, "Admin")
response = _admin_client.get(
f"/variant-classifications-by-individual/{phenopolis_id}")
assert response.status_code == 200
classifications = response.json
assert len(classifications) >= 3
observed_variant_ids = [c.get("variant_id") for c in classifications]
assert 8090 in observed_variant_ids
assert 13309 in observed_variant_ids
assert 22678 in observed_variant_ids
assert 3491 not in observed_variant_ids
observed_individual_ids = set(
[c.get("individual_id") for c in classifications])
assert individual_id in observed_individual_ids
assert len(observed_individual_ids) == 1