def test_is_digit(self):
mapper = XML2JSONMapper()
ok_(mapper.isdigit('1'))
ok_(mapper.isdigit('0'))
ok_(mapper.isdigit('1.5'))
ok_(mapper.isdigit('-10'))
ok_(mapper.isdigit('-20.5'))
ok_(mapper.isdigit('+1245.33434'))
ok_(mapper.isdigit('-1245.33434'))
ok_(mapper.isdigit('0.00'))
ok_(not mapper.isdigit('I'))
ok_(not mapper.isdigit('I0'))
ok_(not mapper.isdigit('.'))
def test_empty_date_handling(self):
mapper = XML2JSONMapper()
map_input = MagicMock()
map_input.filename = os.path.join(dirname(os.path.abspath(__file__)), "test_blank_orig_date.xml")
map_dict = {}
def add(id, json):
map_dict[id] = json
map_output = MagicMock()
map_output.add = add
mapper.map_shard(map_input, map_output)
uid = "USA-USFDACVM-2016-US-017128"
ae = map_dict[uid]
eq_(None, ae.get("original_receive_date"))
def test_non_numeric_denominator(self):
mapper = XML2JSONMapper()
map_input = MagicMock()
map_input.filename = os.path.join(dirname(os.path.abspath(__file__)), "test-non-numeric-denominator.xml")
map_dict = {}
def add(id, json):
map_dict[id] = json
map_output = MagicMock()
map_output.add = add
mapper.map_shard(map_input, map_output)
uid = "USA-USFDACVM-2016-US-017128"
ae = map_dict[uid]
eq_(uid, ae["unique_aer_id_number"])
eq_(uid, ae["@id"])
eq_("0", ae["drug"][0]["dose"]["denominator"])
eq_("Unknown", ae["drug"][0]["dose"]["denominator_unit"])
def test_xml_to_json(self):
mapper = XML2JSONMapper()
map_input = MagicMock()
map_input.filename = os.path.join(dirname(os.path.abspath(__file__)),
"test.xml")
map_dict = {}
def add(id, json):
map_dict[id] = json
map_output = MagicMock()
map_output.add = add
mapper.map_shard(map_input, map_output)
uid = "USA-USFDACVM-2016-US-017128"
ae = map_dict[uid]
eq_(uid, ae["unique_aer_id_number"])
eq_(uid, ae["@id"])
eq_("N141203", ae["report_id"])
eq_("20160502", ae["original_receive_date"])
eq_("Food and Drug Administration Center for Veterinary Medicine",
ae["receiver"]["organization"])
eq_("7500 Standish Place (HFV-210) Room N403",
ae["receiver"]["street_address"])
eq_("Rockville", ae["receiver"]["city"])
eq_("MD", ae["receiver"]["state"])
eq_("20855", ae["receiver"]["postal_code"])
eq_("USA", ae["receiver"]["country"])
eq_("Other", ae["primary_reporter"])
eq_("Animal Owner", ae["secondary_reporter"])
eq_("Safety Issue", ae["type_of_information"])
eq_("true", ae["serious_ae"])
eq_("2", ae["number_of_animals_treated"])
eq_("3", ae["number_of_animals_affected"])
eq_("Dog", ae["animal"]["species"])
eq_("Male", ae["animal"]["gender"])
eq_("Neutered", ae["animal"]["reproductive_status"])
eq_("NOT APPLICABLE",
ae["animal"]["female_animal_physiological_status"])
eq_("7.00", ae["animal"]["age"]["min"])
eq_("17.5", ae["animal"]["age"]["max"])
eq_("Year", ae["animal"]["age"]["unit"])
eq_("Measured", ae["animal"]["age"]["qualifier"])
eq_("6.123", ae["animal"]["weight"]["min"])
eq_("16.123", ae["animal"]["weight"]["max"])
eq_("Kilogram", ae["animal"]["weight"]["unit"])
eq_("Measured", ae["animal"]["weight"]["qualifier"])
eq_("false", ae["animal"]["breed"]["is_crossbred"])
eq_("Terrier - Yorkshire", ae["animal"]["breed"]["breed_component"])
eq_("Ongoing", ae["outcome"][0]["medical_status"])
eq_("1", ae["outcome"][0]["number_of_animals_affected"])
eq_("Good", ae["health_assessment_prior_to_exposure"]["condition"])
eq_("Veterinarian",
ae["health_assessment_prior_to_exposure"]["assessed_by"])
eq_("20150601", ae["onset_date"])
eq_("14", ae["duration"]["value"])
eq_("Month", ae["duration"]["unit"])
eq_("11", ae["reaction"][0]["veddra_version"])
eq_("2227", ae["reaction"][0]["veddra_term_code"])
eq_("Dental disease", ae["reaction"][0]["veddra_term_name"])
eq_("1", ae["reaction"][0]["number_of_animals_affected"])
eq_("Actual", ae["reaction"][0]["accuracy"])
eq_("11", ae["reaction"][1]["veddra_version"])
eq_("1026", ae["reaction"][1]["veddra_term_code"])
eq_("Localised pain NOS (see other 'SOCs' for specific pain)",
ae["reaction"][1]["veddra_term_name"])
eq_("1", ae["reaction"][1]["number_of_animals_affected"])
eq_("Actual", ae["reaction"][1]["accuracy"])
eq_("2", ae["reaction"][13]["veddra_version"])
eq_("99115", ae["reaction"][13]["veddra_term_code"])
eq_("INEFFECTIVE, HEARTWORM LARVAE",
ae["reaction"][13]["veddra_term_name"])
eq_("1", ae["reaction"][13]["number_of_animals_affected"])
eq_("Actual", ae["reaction"][13]["accuracy"])
eq_("10 days", ae["time_between_exposure_and_onset"])
eq_("true", ae["treated_for_ae"])
eq_(8, len(ae["drug"]))
eq_("20150601", ae["drug"][0]["first_exposure_date"])
eq_("20151201", ae["drug"][0]["last_exposure_date"])
eq_("1", ae["drug"][0]["frequency_of_administration"]["value"])
eq_("Day", ae["drug"][0]["frequency_of_administration"]["unit"])
eq_("Animal Owner", ae["drug"][0]["administered_by"])
eq_("Oral", ae["drug"][0]["route"])
eq_("0.50", ae["drug"][0]["dose"]["numerator"])
eq_("tablet", ae["drug"][0]["dose"]["numerator_unit"])
eq_("1", ae["drug"][0]["dose"]["denominator"])
eq_("Unknown", ae["drug"][0]["dose"]["denominator_unit"])
eq_("false", ae["drug"][0]["used_according_to_label"])
eq_([u'Route Off-Label', u'Underdosed'],
ae["drug"][0]["off_label_use"])
eq_("false", ae["drug"][0]["previous_exposure_to_drug"])
eq_("false", ae["drug"][0]["previous_ae_to_drug"])
eq_("false", ae["drug"][0]["ae_abated_after_stopping_drug"])
eq_("true", ae["drug"][0]["ae_reappeared_after_resuming_drug"])
eq_("20160101", ae["drug"][0]["manufacturing_date"])
eq_("71423", ae["drug"][0]["lot_number"])
eq_("20180228", ae["drug"][0]["lot_expiration"])
eq_("1111-2222", ae["drug"][0]["product_ndc"])
eq_("Deramaxx Chewable Tablets", ae["drug"][0]["brand_name"])
eq_("Tablet", ae["drug"][0]["dosage_form"])
eq_("Elanco US Inc", ae["drug"][0]["manufacturer"]["name"])
eq_("USA-USFDACVM-N141203",
ae["drug"][0]["manufacturer"]["registration_number"])
eq_("1", ae["drug"][0]["number_of_defective_items"])
eq_("11", ae["drug"][0]["number_of_items_returned"])
eq_("QM01AH94", ae["drug"][0]["atc_vet_code"])
eq_("Deracoxib", ae["drug"][0]["active_ingredients"][0]["name"])
eq_("25", ae["drug"][0]["active_ingredients"][0]["dose"]["numerator"])
eq_("Milligram",
ae["drug"][0]["active_ingredients"][0]["dose"]["numerator_unit"])
eq_("1", ae["drug"][0]["active_ingredients"][0]["dose"]["denominator"])
eq_("dose",
ae["drug"][0]["active_ingredients"][0]["dose"]["denominator_unit"])