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pharmpy's Issues

Init ATCEngine does not set RxCUIEngine root_url

When ATCEngine is initialized with root_url, the object does not pass root_url to the RxCUIEngine. Therefore, the incorrect url is queried instead and an error is raised.

Problematic line:

self.rce = RxCUIEngine(cache_only=cache_only)

Test script

    from pharmpy.atc import ATCEngine
    import unittest
    
    class ATCEngineTestCase(unittest.TestCase):
    
        def test_atc(self):
            ae = ATCEngine(root_url="http://host.docker.internal:4000/REST")
            print(vars(ae))
            out = ae.get_atc("50090347201")
            self.assertEqual(out[0]["id"], "A10BH")
            out = ae.get_atc(["50090347201"])
            self.assertEqual(out[0][0]["id"], "A10BH")
    
    if __name__=="__main__":
        unittest.main()

Partial output

    {'root_url': 'http://host.docker.internal:4000/REST', 'cache_fn': 'data/cache_atc.json', 'cache': {}, 'rce': <pharmpy.rxcui.RxCUIEngine object at 0x7f72b34ff358>, 'session': <requests.sessions.Session object at 0x7f72b34ff748>, 'cache_only': False}
    E
    ======================================================================
    ERROR: test_atc (__main__.ATCEngineTestCase)
    ----------------------------------------------------------------------
    
    Traceback (most recent call last):
      File "mederrata_stage1/scripts/dataformatting/shortscripts/atc_crosswalk_test.py", line 9, in test_atc
        out = ae.get_atc("50090347201")
      File "/usr/local/lib/python3.6/dist-packages/pharmpy/atc.py", line 77, in get_atc
        rxcui_lst = self.rce.get_rxcui(ndc_lst)
      File "/usr/local/lib/python3.6/dist-packages/pharmpy/rxcui.py", line 46, in get_rxcui
        r = self.session.get(url)
      File "/usr/local/lib/python3.6/dist-packages/requests/sessions.py", line 543, in get
        return self.request('GET', url, **kwargs)
      File "/usr/local/lib/python3.6/dist-packages/requests/sessions.py", line 530, in request
        resp = self.send(prep, **send_kwargs)
      File "/usr/local/lib/python3.6/dist-packages/requests/sessions.py", line 643, in send
        r = adapter.send(request, **kwargs)
      File "/usr/local/lib/python3.6/dist-packages/requests/adapters.py", line 516, in send
        raise ConnectionError(e, request=request)
    requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=4000): Max retries exceeded with url: /REST/ndcstatus.json?ndc=50090347201 (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f72b34ff080>: Failed to establish a new connection: [Errno 111] Connection refused',))

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