add tests for who endpoints

tests/test_data/test_who_calculation_valid.json

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+{"birth_data":{"birth_date":"2020-04-12","gestation_weeks":40,"gestation_days":0,"estimated_date_delivery":"2020-04-12","estimated_date_delivery_string":"Sun 12 April, 2020","sex":"female"},"measurement_dates":{"observation_date":"2028-06-12","chronological_decimal_age":8.167008898015059,"corrected_decimal_age":8.167008898015059,"chronological_calendar_age":"8 years and 2 months","corrected_calendar_age":"8 years and 2 months","corrected_gestational_age":{"corrected_gestation_weeks":null,"corrected_gestation_days":null},"comments":{"clinician_corrected_decimal_age_comment":"Born at term. No correction for gestation has been made.","lay_corrected_decimal_age_comment":"Your child was born at term. No correction for gestation has been made.","clinician_chronological_decimal_age_comment":"Born at term. No correction for gestation has been made.","lay_chronological_decimal_age_comment":"Your child was born at term. No correction for gestation has been made."},"corrected_decimal_age_error":null,"chronological_decimal_age_error":null},"child_observation_value":{"measurement_method":"height","observation_value":115.0,"observation_value_error":null},"measurement_calculated_values":{"corrected_sds":-2.139034562567385,"corrected_centile":1.6216,"corrected_centile_band":"This height measurement is on or near the 2nd centile.","chronological_sds":-2.139034562567385,"chronological_centile":1.6216,"chronological_centile_band":"This height measurement is on or near the 2nd centile.","corrected_measurement_error":null,"chronological_measurement_error":null,"corrected_percentage_median_bmi":null,"chronological_percentage_median_bmi":null},"plottable_data":{"centile_data":{"chronological_decimal_age_data":{"x":8.167008898015059,"y":115.0,"b":10.0,"centile":1.6216,"sds":-2.139034562567385,"bone_age_label":"This bone age is advanced","events_text":["Growth hormone start","Growth Hormone Deficiency diagnosis"],"bone_age_type":"greulich-pyle","bone_age_sds":2.0,"bone_age_centile":98.0,"observation_error":null,"age_type":"chronological_age","calendar_age":"8 years and 2 months","lay_comment":"Your child was born at term. No correction for gestation has been made.","clinician_comment":"Born at term. No correction for gestation has been made.","age_error":null,"centile_band":"This height measurement is on or near the 2nd centile.","observation_value_error":null},"corrected_decimal_age_data":{"x":8.167008898015059,"y":115.0,"b":10.0,"centile":1.6216,"sds":-2.139034562567385,"bone_age_label":"This bone age is advanced","events_text":["Growth hormone start","Growth Hormone Deficiency diagnosis"],"bone_age_type":"greulich-pyle","bone_age_sds":2.0,"bone_age_centile":98.0,"observation_error":null,"age_type":"corrected_age","calendar_age":"8 years and 2 months","corrected_gestational_age":"","lay_comment":"Your child was born at term. No correction for gestation has been made.","clinician_comment":"Born at term. No correction for gestation has been made.","age_error":null,"centile_band":"This height measurement is on or near the 2nd centile.","observation_value_error":null}},"sds_data":{"chronological_decimal_age_data":{"x":8.167008898015059,"y":-2.139034562567385,"b":10.0,"centile":1.6216,"sds":null,"bone_age_label":"This bone age is advanced","events_text":["Growth hormone start","Growth Hormone Deficiency diagnosis"],"bone_age_type":"greulich-pyle","bone_age_sds":2.0,"bone_age_centile":98.0,"observation_error":null,"age_type":"chronological_age","calendar_age":"8 years and 2 months","lay_comment":"Your child was born at term. No correction for gestation has been made.","clinician_comment":"Born at term. No correction for gestation has been made.","age_error":null,"centile_band":"This height measurement is on or near the 2nd centile.","observation_value_error":null},"corrected_decimal_age_data":{"x":8.167008898015059,"y":-2.139034562567385,"b":10.0,"centile":1.6216,"sds":null,"bone_age_label":"This bone age is advanced","events_text":["Growth hormone start","Growth Hormone Deficiency diagnosis"],"bone_age_type":"greulich-pyle","bone_age_sds":2.0,"bone_age_centile":98.0,"observation_error":null,"age_type":"corrected_age","calendar_age":"8 years and 2 months","corrected_gestational_age":"","lay_comment":"Your child was born at term. No correction for gestation has been made.","clinician_comment":"Born at term. No correction for gestation has been made.","age_error":null,"centile_band":"This height measurement is on or near the 2nd centile.","observation_value_error":null}}},"bone_age":{"bone_age":10.0,"bone_age_type":"greulich-pyle","bone_age_sds":2.0,"bone_age_centile":98.0,"bone_age_text":"This bone age is advanced"},"events_data":{"events_text":["Growth hormone start","Growth Hormone Deficiency diagnosis"]}}

tests/test_who.py

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+"""
+Tests for the UK-WHO endpoints
+"""
+
+# standard imports
+import json
+import hashlib
+
+# third party imports
+from fastapi.testclient import TestClient
+import pytest
+
+# local / rcpch imports
+from main import app
+
+client = TestClient(app)
+
+
+def test_who_calculation_with_valid_request():
+
+    body = {
+        "birth_date": "2020-04-12",
+        "observation_date": "2028-06-12",
+        "observation_value": 115,
+        "sex": "female",
+        "gestation_weeks": 40,
+        "gestation_days": 0,
+        "measurement_method": "height",
+        "bone_age": 10,
+        "bone_age_centile": 98,
+        "bone_age_sds": 2.0,
+        "bone_age_text": "This bone age is advanced",
+        "bone_age_type": "greulich-pyle",
+        "events_text": ["Growth hormone start", "Growth Hormone Deficiency diagnosis"],
+    }
+
+    response = client.post("/who/calculation", json=body)
+
+    assert response.status_code == 200
+
+    # load the known-correct response from file
+    with open(r"tests/test_data/test_who_calculation_valid.json", "r") as file:
+        calculation_file = file.read()
+    # load the two JSON responses as Python Dicts so enable comparison (slow but more reliable)
+    assert response.json() == json.loads(calculation_file)
+
+
+def test_who_calculation_with_invalid_request():
+
+    # this is a garbage request which should trigger appropriate validation responses
+    body = {
+        "birth_date": "invalid_birth_date",
+        "observation_date": "invalid_observation_date",
+        "observation_value": "invalid_observation_value",
+        "sex": "invalid_sex",
+        "gestation_weeks": "invalid_gestation_weeks",
+        "gestation_days": "invalid_gestation_days",
+        "measurement_method": "invalid_measurement_method",
+    }
+
+    response = client.post("/who/calculation", json=body)
+
+    assert response.status_code == 422
+
+    # restructure the response to make it easier to assert tests specifically
+    validation_errors = {error["loc"][1]: error for error in response.json()["detail"]}
+    assert (
+        validation_errors["birth_date"]["msg"]
+        == "Value error, time data 'invalid_birth_date' does not match format '%Y-%m-%d'"
+    )
+    assert (
+        validation_errors["gestation_days"]["msg"]
+        == "Input should be a valid integer, unable to parse string as an integer"
+    )
+    assert (
+        validation_errors["gestation_weeks"]["msg"]
+        == "Input should be a valid integer, unable to parse string as an integer"
+    )
+    assert (
+        validation_errors["measurement_method"]["msg"]
+        == "Input should be 'height', 'weight', 'ofc' or 'bmi'"
+    )
+    assert (
+        validation_errors["observation_date"]["msg"]
+        == "Input should be a valid date or datetime, invalid character in year"
+    )
+    assert (
+        validation_errors["observation_value"]["msg"]
+        == "Input should be a valid number, unable to parse string as a number"
+    )
+    assert validation_errors["sex"]["msg"] == "Input should be 'male' or 'female'"
+
+@pytest.mark.parametrize("input", [
+    { "measurement_method": "height", "observation_value": 200, "birth_date": "2015-10-26", "observation_date": "2020-09-01", "sex": "female" }, # height too tall
+    { "measurement_method": "height", "observation_value": 5, "birth_date": "2015-10-26", "observation_date": "2020-09-01", "sex": "female" }, # height too short
+    { "measurement_method": "weight", "observation_value": 200, "birth_date": "2015-10-26", "observation_date": "2020-09-01", "sex": "female" }, # weight too high
+    { "measurement_method": "weight", "observation_value": 1, "birth_date": "2015-10-26", "observation_date": "2020-09-01", "sex": "female" }, # weight too low
+    { "measurement_method": "ofc", "observation_value": 500, "birth_date": "2015-10-26", "observation_date": "2020-09-01", "sex": "female" }, # head circumference too high
+    { "measurement_method": "ofc", "observation_value": 1, "birth_date": "2015-10-26", "observation_date": "2020-09-01", "sex": "female" }, # head circumference too low
+    { "measurement_method": "ofc", "observation_value": 500, "birth_date": "2015-10-26", "observation_date": "2034-09-01", "sex": "male" }, # 19y boy head circumference beyond age range
+    { "measurement_method": "ofc", "observation_value": 1, "birth_date": "2015-10-26", "observation_date": "2033-09-01", "sex": "female" }, # 18y girl head circumference beyond age range
+    { "measurement_method": "height", "observation_value": 175, "birth_date": "2015-10-26", "observation_date": "2036-09-01", "sex": "female" }, # height too old (>20y)
+    { "measurement_method": "height", "observation_value": 45, "birth_date": "2015-10-26", "observation_date": "2015-10-26", "sex": "female", "gestation_weeks": 23, "gestation_days": 0 }, # height too young (<25 weeks)
+    { "measurement_method": "weight", "observation_value": 200, "birth_date": "2015-10-26", "observation_date": "2036-09-01", "sex": "female" }, # weight too old (>20y)
+    { "measurement_method": "weight", "observation_value": 1, "birth_date": "2015-10-26", "observation_date": "2015-10-26", "sex": "female", "gestation_weeks": 22, "gestation_days": 0 }, # weight too young (<23 weeks)
+])
+def test_who_chart_with_valid_request_for_outside_range_values(input):
+
+    body = input
+    response = client.post("/who/calculation", json=body)
+
+    assert response.status_code == 422
+
+
+@pytest.mark.parametrize("input", [
+    { "measurement_method": "height", "sex": "male" },
+    { "measurement_method": "weight", "sex": "male" },
+    { "measurement_method": "ofc", "sex": "male" },
+    { "measurement_method": "bmi", "sex": "male" },
+    { "measurement_method": "height", "sex": "female" },
+    { "measurement_method": "weight", "sex": "female" },
+    { "measurement_method": "ofc", "sex": "female" },
+    { "measurement_method": "bmi", "sex": "female" }
+])
+def test_who_chart_data_with_valid_request(input):
+    body = input | {
+        "centile_format": "cole-nine-centiles",
+        "is_sds": False,
+    }
+
+    response = client.post("/who/chart-coordinates", json=body)
+
+    assert response.status_code == 200
+
+    # TODO: Check the actual values returned. We do already validate it against the schema though.
+
+
+def test_who_chart_data_with_invalid_request():
+    body = {"measurement_method": "invalid_measurement_method", "sex": "invalid_sex"}
+
+    response = client.post("/who/chart-coordinates", json=body)
+
+    assert response.status_code == 422
+
+
+def test_who_fictional_child_data_with_valid_request():
+
+    body = {
+        "measurement_method": "height",
+        "sex": "female",
+        "start_chronological_age": 0,
+        "end_age": 1,
+        "gestation_weeks": 40,
+        "gestation_days": 0,
+        "measurement_interval_type": "days",
+        "measurement_interval_number": 30,
+        "start_sds": 0,
+        "drift": False,
+        "drift_range": -0.05,
+        "noise": False,
+        "noise_range": 0.005,
+    }
+
+    response = client.post("/who/fictional-child-data", json=body)
+
+    assert response.status_code == 200
+
+    # load the known-correct response from file
+    with open(
+        r"tests/test_data/test_who_fictional_child_data_valid.json", "r"
+    ) as file:
+        fictional_child_data_file = file.read()
+    # load the two JSON responses as Python Dicts so enable comparison (slow but more reliable)
+    assert response.json() == json.loads(fictional_child_data_file)
+
+
+def test_who_fictional_child_data_with_invalid_request():
+
+    body = {
+        "measurement_method": "invalid_measurement_method",
+        "sex": "invalid_sex",
+        "start_chronological_age": "invalid_start_chronological_age",
+        "end_age": "invalid_end_age",
+        "gestation_weeks": "invalid_gestation_weeks",
+        "gestation_days": "invalid_gestation_days",
+        "measurement_interval_type": "invalid_measurement_interval_type",
+        "measurement_interval_number": "invalid_measurement_interval_number",
+        "start_sds": "invalid_start_sds",
+        "drift": "invalid_drift",
+        "drift_range": "invalid_drift_range",
+        "noise": "invalid_noise",
+        "noise_range": "invalid_noise_range",
+    }
+
+    response = client.post("/who/fictional-child-data", json=body)
+
+    assert response.status_code == 422
+
+    # COMMENTED OUT FOR BRANCH 'dockerise' PENDING DECISION ON #166 (API Test Suite) (pacharanero, 2024-02-07 )
+    # restructure the response to make it easier to assert tests specifically
+    validation_errors = {error["loc"][1]: error for error in response.json()["detail"]}
+    assert (
+        validation_errors["measurement_method"]["msg"]
+        == "Input should be 'height', 'weight', 'ofc' or 'bmi'"
+    )
+    assert validation_errors["sex"]["msg"] == "Input should be 'male' or 'female'"
+    assert (
+        validation_errors["start_chronological_age"]["msg"]
+        == "Input should be a valid number, unable to parse string as a number"
+    )
+    assert (
+        validation_errors["end_age"]["msg"]
+        == "Input should be a valid number, unable to parse string as a number"
+    )
+    assert (
+        validation_errors["gestation_weeks"]["msg"]
+        == "Input should be a valid integer, unable to parse string as an integer"
+    )
+    assert (
+        validation_errors["gestation_days"]["msg"]
+        == "Input should be a valid integer, unable to parse string as an integer"
+    )
+    assert (
+        validation_errors["measurement_interval_type"]["msg"]
+        == "Input should be 'd', 'day', 'days', 'w', 'week', 'weeks', 'm', 'month', 'months', 'y', 'year' or 'years'"
+    )
+    assert (
+        validation_errors["measurement_interval_number"]["msg"]
+        == "Input should be a valid integer, unable to parse string as an integer"
+    )
+    assert (
+        validation_errors["start_sds"]["msg"]
+        == "Input should be a valid number, unable to parse string as a number"
+    )
+    assert (
+        validation_errors["drift"]["msg"]
+        == "Input should be a valid boolean, unable to interpret input"
+    )
+    assert (
+        validation_errors["drift_range"]["msg"]
+        == "Input should be a valid number, unable to parse string as a number"
+    )
+    assert (
+        validation_errors["noise"]["msg"]
+        == "Input should be a valid boolean, unable to interpret input"
+    )
+    assert (
+        validation_errors["noise_range"]["msg"]
+        == "Input should be a valid number, unable to parse string as a number"
+    )