NHS SNOMED term browser api

medicines.py

import requests as rq
from furl import furl
import time
import sys, threading
import pickle

sys.setrecursionlimit(10 ** 7)  # max depth of recursion
threading.stack_size(2 ** 27)


BASE_URL = "https://termbrowser.nhs.uk/sct-browser-api/snomed/uk-edition/v20211124/concepts/"
ANTIBACTERIAL_AGENT = 346325008


def get_children(id):
    time.sleep(0.05)
    f = furl(BASE_URL)
    f.path.segments.append(id)
    f.path.segments.append("children")
    f.args["form"] = "inferred"
    r = rq.get(f.url)
    return r.json()


def get_active_ingredients(id):
    time.sleep(0.05)
    f = furl(BASE_URL)
    f.path.segments.append(id)
    r = rq.get(f.url)
    data = r.json()
    return [
        (r["target"]["conceptId"], r["target"]["defaultTerm"])
        for r in data["relationships"]
        if r["type"]["defaultTerm"]
        == "Has specific active ingredient (attribute)"
    ]


def walk(c):
    children = get_children(c["conceptId"])
    if len(children) == 0:
        yield (c["conceptId"], get_active_ingredients(c["conceptId"]))
    else:
        for c in children:
            yield from walk(c)
    # if c["definitionStatus"] == "Primitive":
    #     yield (c["conceptId"], get_active_ingredients(c["conceptId"]))
    # else:
    #     children = get_children(c["conceptId"])
    #     for c in children:
    #         yield from walk(c)


data = get_children(ANTIBACTERIAL_AGENT)

results = {}

for c in data:
    results[(c["conceptId"], c["defaultTerm"])] = [a for a in walk(c)]

with open("results.pickle", "wb") as f:
    pickle.dump(results, f)


with open("categories.csv", "w") as f:
    for c in list(results.keys()):
        f.write(f'"{c[0]}","{c[1]}"\n')

with open("ingredients.csv", "w") as f:
    f.write("category_id,product_id,ingredient_id,ingredient\n")
    for k, v in results.items():
        category = k[0]
        for p in v:
            product = p[0]
            for ingredient in p[1]:
                f.write(
                    f'"{category}","{product}","{ingredient[0]}","{ingredient[1]}"\n'
                )