def test_get_samples_using_description(test_client):
"""
Test 'get_samples' method using a description
"""
context = test_client
sample_1, sample_2, _, patient_1 = load_test_samples()
sample_3, sample_4, _, patient_2 = load_test_samples()
with context:
_, code = operations.add_patients(patient_1)
assert code == 201
_, code = operations.add_patients(patient_2)
assert code == 201
_, code = operations.add_samples(sample_1)
assert code == 201
_, code = operations.add_samples(sample_2)
assert code == 201
_, code = operations.add_samples(sample_3)
assert code == 201
_, code = operations.add_samples(sample_4)
assert code == 201
response, code = operations.get_samples(patient_1["patient_id"], description=sample_1["description"])
assert code == 200
assert response["patient_id"] == sample_1["patient_id"]
def test_get_samples(test_client):
"""
Test 'get_samples' method
"""
context = test_client
sample_1, sample_2, _, patient_1 = load_test_samples()
sample_3, sample_4, _, patient_2 = load_test_samples()
with context:
_, code = operations.add_patients(patient_1)
assert code == 201
_, code = operations.add_patients(patient_2)
assert code == 201
_, code = operations.add_samples(sample_1)
assert code == 201
_, code = operations.add_samples(sample_2)
assert code == 201
_, code = operations.add_samples(sample_3)
assert code == 201
_, code = operations.add_samples(sample_4)
assert code == 201
response, code = operations.get_samples(patient_1["patient_id"])
samples = [s["sample_id"] for s in response["samples"]]
descriptions = [s["description"] for s in response["samples"]]
assert code == 200
assert len(samples) == 2
assert sample_1["sample_id"] in samples
assert sample_1["description"] in descriptions
assert sample_2["sample_id"] in samples
assert sample_2["description"] in descriptions
def test_get_patient(test_client):
"""
Test 'get_patient' method
"""
context = test_client
patient_1, patient_2, _ = load_test_patients()
with context:
operations.add_patients(patient_1)
operations.add_patients(patient_2)
result, code = operations.get_patients()
assert len(result) == 2
assert code == 200
assert patient_1["patient_id"] in result
def test_add_same_patient(test_client):
"""
Test adding same patient twice
"""
context = test_client
patient_1, _, _ = load_test_patients()
with context:
response, code = operations.add_patients(patient_1)
assert code == 201
assert response["code"] == 201
response, code = operations.add_patients(patient_1)
assert code == 400
assert response["code"] == 400
def test_get_samples_with_tags(test_client):
"""
Test 'get_samples' using tags
"""
context = test_client
sample_1, sample_2, patient_1 = load_test_samples_with_tags()
patient_id = patient_1["patient_id"]
tags = sample_1["tags"]
with context:
_, code = operations.add_patients(patient_1)
assert code == 201
_, code = operations.add_samples(sample_1)
assert code == 201
_, code = operations.add_samples(sample_2)
assert code == 201
response, code = operations.get_samples(patient_id, tags)
assert code == 200
assert response["patient_id"] == patient_id
assert len(response["samples"]) == 2
response, code = operations.get_samples(patient_id, ["Adult"])
assert code == 200
assert response["patient_id"] == patient_id
assert len(response["samples"]) == 1
response, code = operations.get_samples(
patient_id, ["Non existent tag"]
)
assert code == 200
assert not response
def test_add_patients(test_client):
"""
Test add_patients method
"""
context = test_client
patient_1, patient_2, patient_3 = load_test_patients()
with context:
response, code = operations.add_patients(patient_1)
assert code == 201
assert response["code"] == 201
response, code = operations.add_patients(patient_2)
assert code == 201
assert response["code"] == 201
# Invalid 'patient_id'
response, code = operations.add_patients(patient_3)
assert code == 500
assert response["code"] == 500
def test_add_samples(test_client):
"""
Test 'add_samples' method
"""
context = test_client
sample_1, sample_2, _, patient_1 = load_test_samples()
with context:
_, code = operations.add_patients(patient_1)
assert code == 201
response, code = operations.add_samples(sample_1)
assert code == 201
assert response["code"] == 201
def test_get_samples_invalid_patient_id(test_client):
"""
Test 'get_samples' when patient_id values are invalid
"""
context = test_client
sample_1, sample_2, _, patient_1 = load_test_samples()
_, _, _, patient_2 = load_test_samples()
with context:
_, code = operations.add_patients(patient_1)
assert code == 201
_, code = operations.add_samples(sample_1)
assert code == 201
_, code = operations.add_samples(sample_2)
assert code == 201
_, code = operations.add_patients(patient_2)
assert code == 201
response, code = operations.get_samples(patient_2["patient_id"])
assert code == 200
assert not response
def test_add_samples_no_description(test_client):
"""
Test adding sample with missing description
"""
context = test_client
sample_1, _, _, patient_1 = load_test_samples()
del sample_1["description"]
with context:
_, code = operations.add_patients(patient_1)
assert code == 201
response, code = operations.add_samples(sample_1)
assert code == 400
assert response["code"] == 400
def test_add_samples_with_tags(test_client):
"""
Test adding samples with tags
"""
context = test_client
sample_1, sample_2, patient_1 = load_test_samples_with_tags()
with context:
_, code = operations.add_patients(patient_1)
assert code == 201
_, code = operations.add_samples(sample_1)
assert code == 201
_, code = operations.add_samples(sample_2)
assert code == 201
def test_add_sample_twice(test_client):
"""
Test adding the same sample twice
"""
context = test_client
sample_1, _, _, patient_1 = load_test_samples()
with context:
_, code = operations.add_patients(patient_1)
assert code == 201
response, code = operations.add_samples(sample_1)
assert code == 201
assert response["code"] == 201
response, code = operations.add_samples(sample_1)
assert code == 400
assert response["code"] == 400
def test_add_segments(test_client):
"""
Test 'add_segments' method
"""
context = test_client
patient, sample, segment, _, _ = load_test_segment()
with context:
response, code = operations.add_patients(patient)
assert code == 201
assert response["code"] == 201
response, code = operations.add_samples(sample)
assert code == 201
assert response["code"] == 201
response, code = operations.add_segments(segment)
assert code == 201
assert response["code"] == 201
def test_add_segment_no_patient(test_client):
"""
Test "add_segment" method when patient is not provided
"""
context = test_client
patient, sample, segment, _, _ = load_test_segment()
segment["patient_id"] = ""
with context:
response, code = operations.add_patients(patient)
assert code == 201
assert response["code"] == 201
response, code = operations.add_samples(sample)
assert code == 201
assert response["code"] == 201
response, code = operations.add_segments(segment)
assert code == 400
assert response["code"] == 400
def test_get_segment(test_client):
"""
Test 'get_segments' method
"""
context = test_client
patient_1, sample_1, segment_1, segment_2, segment_3 = load_test_segment()
patient_2, sample_2, segment_4, segment_5, segment_6 = load_test_segment()
patient_id = segment_1["patient_id"]
sample_id = segment_1["sample_id"]
chromosome_number = segment_1["segments"][0]["chromosome_number"]
start_position = segment_1["segments"][0]["start_position"]
end_position = segment_1["segments"][0]["end_position"]
copy_number = segment_1["segments"][0]["copy_number"]
copy_number_ploidy_corrected = segment_1["segments"][0][
"copy_number_ploidy_corrected"
]
with context:
response, code = operations.add_patients(patient_1)
assert code == 201
assert response["code"] == 201
response, code = operations.add_patients(patient_2)
assert code == 201
assert response["code"] == 201
response, code = operations.add_samples(sample_1)
assert code == 201
assert response["code"] == 201
response, code = operations.add_samples(sample_2)
assert code == 201
assert response["code"] == 201
response, code = operations.add_segments(segment_1)
assert code == 201
assert response["code"] == 201
response, code = operations.add_segments(segment_2)
assert code == 201
assert response["code"] == 201
response, code = operations.add_segments(segment_3)
assert code == 201
assert response["code"] == 201
response, code = operations.add_segments(segment_4)
assert code == 201
assert response["code"] == 201
response, code = operations.add_segments(segment_5)
assert code == 201
assert response["code"] == 201
response, code = operations.add_segments(segment_6)
assert code == 201
assert response["code"] == 201
response, code = operations.get_segments(
patient_id,
sample_id,
chromosome_number,
start_position,
end_position,
)
assert len(response) == 1
assert code == 200
assert response[0]["chromosome_number"] == chromosome_number
assert response[0]["start_position"] == start_position
assert response[0]["end_position"] == end_position
assert response[0]["copy_number"] == copy_number
assert (
response[0]["copy_number_ploidy_corrected"]
== copy_number_ploidy_corrected
)
response, code = operations.get_segments(
patient_id,
sample_id,
chromosome_number,
start_position=12522,
end_position=34326,
)
assert code == 200
assert len(response) == 2
