def populate_mortality_table():
# this takes way too long. Don't use.
# with open('/var/www/html/items-rest/raw_data/Mort-ICD10.csv', 'r') as mort_file:
with open('./raw_data/Mort-ICD10.csv', 'r') as mort_file:
mort_reader = csv.reader(mort_file)
for row in mort_reader:
new_mortality_entry = MortalityDataModel(*row)
new_mortality_entry.save_to_db()
def get(self):
query = {}
country_code = request.args.get('country', type=str)
if country_code:
if not valid_country_code(country_code):
return {
'message':
'{} is not a valid country_code'.format(country_code)
}, 400
query['country_code'] = country_code
year = request.args.get('year', type=str)
if year:
if not valid_year(year):
return {'message': 'Please enter a valid year'}, 400
query['year'] = year
sex = request.args.get('sex', type=str)
if sex:
if not valid_sex(sex):
return {'message': 'Please enter a valid sex code'}, 400
query['sex'] = sex
admin = request.args.get('admin', type=str)
if admin:
if not valid_admin(admin):
return {'message': 'Please enter a valid admin code'}, 400
query['admin_code'] = admin
subdiv = request.args.get('subdiv', type=str)
if subdiv:
if not valid_subdiv(subdiv):
return {'message': 'Please enter a valid subdiv code'}, 400
query['subdiv_code'] = subdiv
cause = request.args.get('cause', type=str)
if cause:
cause_upper = cause.upper()
if not valid_cause(cause_upper):
return {'message': 'Please enter a valid cause code'}, 400
cause_code_list_extended = {}
icd_codes = [
code.json() for code in IcdModel.find_by_code(cause_upper)
]
for icd_code in icd_codes:
matching_codes = [
matching_icd_code.json() for matching_icd_code in
IcdModel.search_specific(icd_code['description'])
]
unspecified_codes = []
generic_codes = []
pattern = "unspecified"
match = re.search(pattern, icd_code['description'])
if not match:
unspecified_code = icd_code['description'] + \
" (unspecified)"
unspecified_codes = [
matching_icd_code.json() for matching_icd_code in
IcdModel.search_specific(unspecified_code)
]
else:
position = match.span()
start = position[0] - 2
end = position[1] + 1
generic_code = icd_code['description'][0:start] + \
icd_code['description'][end:]
generic_codes = [
matching_icd_code.json() for matching_icd_code in
IcdModel.search_specific(generic_code)
]
for matching_code in matching_codes:
cause_code_list_extended[
matching_code['list']] = matching_code['code']
if generic_codes:
for matching_code in generic_codes:
cause_code_list_extended[
matching_code['list']] = matching_code['code']
if unspecified_codes:
for matching_code in unspecified_codes:
cause_code_list_extended[
matching_code['list']] = matching_code['code']
if "103" not in cause_code_list_extended:
try:
cause_code_list_extended['103'] = cause_code_list_extended[
'104'][:-1]
except:
pass
code_list_entry = CodeListRefModel.find_by_year_and_country(
year, country_code)
try:
cause = cause_code_list_extended[code_list_entry.code_list]
except:
return {
'message':
"Can't find matching cause code for the specified country."
}, 400
query['cause'] = cause
results = [
entry.json()
for entry in MortalityDataModel.search_mortalities(query)
]
if code_list_entry.code_list == "104" and len(cause_code_list_extended[
code_list_entry.code_list]) == 3 and len(results) == 0:
cause = cause + "9"
query['cause'] = cause
results = [
entry.json()
for entry in MortalityDataModel.search_mortalities(query)
]
if code_list_entry.code_list == "10M" and len(cause_code_list_extended[
code_list_entry.code_list]) == 3 and len(results) == 0:
cause = cause + "9"
query['cause'] = cause
result = [
entry.json()
for entry in MortalityDataModel.search_mortalities(query)
]
if code_list_entry.code_list == "10M" and len(cause_code_list_extended[
code_list_entry.code_list]) == 4 and len(results) == 0:
cause = cause[:-1]
query['cause'] = cause
result = [
entry.json()
for entry in MortalityDataModel.search_mortalities(query)
]
if not results:
return {'message': "No mortality entries match your query."}, 404
if results:
if len(results) > 1:
return {
'message':
"More than one population entry was found matching your query."
}, 400
for entry in results:
pop_query = {}
pop_query['country_code'] = entry['country']['code']
pop_query['year'] = entry['year']
pop_query['sex'] = entry['sex']['code']
admin = entry['admin']
if admin != "None":
pop_query['admin'] = admin['code']
subdiv = entry['subdiv']
if subdiv != "None":
pop_query['subdiv'] = subdiv['code']
pop_data = PopulationModel.search_single_population(pop_query)
if pop_data:
pop_data = pop_data.json()
else:
country = CountryModel.find_by_code(country_code).json()
return {
'message':
"No population data available for '{}' in year {} for sex '{}'."
.format(country['description'], year, sex)
}, 404
del entry['infant_age_breakdown']
del entry['age_format']
del entry['infant_age_format']
things_to_skip = [
"country", "admin", "subdiv", "year", "code_list", "cause",
"sex", "infant_age_breakdown"
]
for key, value in entry.items():
if key in things_to_skip:
continue
# format age_breakdown data per 100,000
if key == "age_breakdown":
ages_to_delete = []
for age_range, value in entry[key].items():
pop = pop_data[key].get(age_range)
entry[key][age_range] = pop
if pop:
if pop == "0":
continue
entry[key][age_range] = str(
round_up(
float(value) / float(pop) * 100000, 3))
if pop == None:
ages_to_delete.append(age_range)
for index in ages_to_delete:
del entry[key][index]
else:
entry[key] = str(
round_up(
float(value) / float(pop_data[key]) * 100000,
3))
return {'adjusted_entries': results}, 200
def delete(self, country_code, year, sex, cause):
data = MortalityDataChange.parser.parse_args()
if not valid_country_code(country_code):
return {
'message':
'{} is not a valid country_code'.format(country_code)
}, 400
if not valid_year(year):
return {'message': 'Please enter a valid year'}, 400
if not valid_sex(sex):
return {'message': 'Please enter a valid sex code'}, 400
cause_upper = cause.upper()
if not valid_cause(cause_upper):
return {'message': 'Please enter a valid cause code'}, 400
# post_format tells us if we have an admin or subdiv code
post_format = [0, 0]
admin_code = data['admin_code']
if admin_code:
if not valid_admin(admin_code):
return {'message': 'Please enter a valid admin code'}, 400
post_format[0] = 1
# delete null value from data object
subdiv_code = data['subdiv_code']
if subdiv_code:
if not valid_subdiv(subdiv_code):
return {'message': 'Please enter a valid subdiv code'}, 400
post_format[1] = 1
# if have admin and subdiv
if post_format[0] and post_format[1]:
entry = MortalityDataModel.find_by_casysc(country_code, admin_code,
subdiv_code, year, sex,
cause)
# if have admin
if post_format[0] and not post_format[1]:
entry = MortalityDataModel.find_by_caysc(country_code, admin_code,
year, sex, cause)
# if have subdiv
if post_format[1] and not post_format[0]:
entry = MortalityDataModel.find_by_csysc(country_code, subdiv_code,
year, sex, cause)
# if have neither admin or data
if not post_format[0] and not post_format[1]:
entry = MortalityDataModel.find_by_cysc(country_code, year, sex,
cause)
if entry:
if len(entry) > 1:
return {
'message':
"More than one mortality entry was found with the given parameters. Please supply either an admin or subdiv code as required.",
'entries': [mortality.json() for mortality in entry]
}, 400
entry[0].delete_from_db()
return {'message': 'Entry deleted.'}
return {'message': 'Item not found.'}, 404
def put(self, country_code, year, sex, cause):
data = MortalityDataChange.parser.parse_args()
# validation
if not valid_country_code(country_code):
return {
'message':
'{} is not a valid country_code'.format(country_code)
}, 400
if not valid_year(year):
return {'message': 'Please enter a valid year'}, 400
if not valid_sex(sex):
return {'message': 'Please enter a valid sex code'}, 400
cause_upper = cause.upper()
if not valid_cause(cause_upper):
return {'message': 'Please enter a valid cause code'}, 400
# post_format tells us if we have an admin or subdiv code
post_format = [0, 0]
admin_code = data['admin_code']
if admin_code:
if not valid_admin(admin_code):
return {'message': 'Please enter a valid admin code'}, 400
post_format[0] = 1
del data['admin_code']
subdiv_code = data['subdiv_code']
if subdiv_code:
if not valid_subdiv(subdiv_code):
return {'message': 'Please enter a valid subdiv code'}, 400
post_format[1] = 1
del data['subdiv_code']
# if have admin and subdiv
if post_format[0] and post_format[1]:
entry = MortalityDataModel.find_by_casysc(country_code, admin_code,
subdiv_code, year, sex,
cause)
# if have admin
if post_format[0] and not post_format[1]:
entry = MortalityDataModel.find_by_caysc(country_code, admin_code,
year, sex, cause)
# if have subdiv
if post_format[1] and not post_format[0]:
entry = MortalityDataModel.find_by_csysc(country_code, subdiv_code,
year, sex, cause)
# if have neither admin or data
if not post_format[0] and not post_format[1]:
entry = MortalityDataModel.find_by_cysc(country_code, year, sex,
cause)
code_list = data['code_list']
if entry:
entry.code_list = code_list
entry.age_format = data['age_format']
entry.infant_age_format = data['infant_age_format']
entry.deaths1 = data['deaths1']
entry.deaths2 = data['deaths2']
entry.deaths3 = data['deaths3']
entry.deaths4 = data['deaths4']
entry.deaths5 = data['deaths5']
entry.deaths6 = data['deaths6']
entry.deaths7 = data['deaths7']
entry.deaths8 = data['deaths8']
entry.deaths9 = data['deaths9']
entry.deaths10 = data['deaths10']
entry.deaths11 = data['deaths11']
entry.deaths12 = data['deaths12']
entry.deaths13 = data['deaths13']
entry.deaths14 = data['deaths14']
entry.deaths15 = data['deaths15']
entry.deaths16 = data['deaths16']
entry.deaths17 = data['deaths17']
entry.deaths18 = data['deaths18']
entry.deaths19 = data['deaths19']
entry.deaths20 = data['deaths20']
entry.deaths21 = data['deaths21']
entry.deaths22 = data['deaths22']
entry.deaths23 = data['deaths23']
entry.deaths24 = data['deaths24']
entry.deaths25 = data['deaths25']
entry.deaths26 = data['deaths26']
entry.infant_deaths1 = data['infant_deaths1']
entry.infant_deaths2 = data['infant_deaths2']
entry.infant_deaths3 = data['infant_deaths3']
entry.infant_deaths4 = data['infant_deaths4']
else:
del data['code_list']
entry = MortalityDataModel(country_code, admin_code, subdiv_code,
year, code_list, cause, sex, **data)
new_code_list_ref = CodeListRefModel(year, country_code, code_list)
try:
code_list_ref = CodeListRefModel.find_by_year_and_country(
year, country_code)
if code_list_ref.code_list != code_list:
code_list_ref.code_list = code_list
code_list_ref.save_to_db()
else:
new_code_list_ref.save_to_db()
entry.save_to_db()
except:
return {"message": "An error occurred inserting the data."}, 500
return entry.json(), 201
def post(self, country_code, year, sex, cause):
data = MortalityDataChange.parser.parse_args()
if not valid_country_code(country_code):
return {
'message':
'{} is not a valid country_code'.format(country_code)
}, 400
if not valid_year(year):
return {'message': 'Please enter a valid year'}, 400
if not valid_sex(sex):
return {'message': 'Please enter a valid sex code'}, 400
cause_upper = cause.upper()
if not valid_cause(cause_upper):
return {'message': 'Please enter a valid cause code'}, 400
# post_format tells us if we have an admin or subdiv code while allowing us to change their values
post_format = [0, 0]
admin_code = data['admin_code']
if admin_code:
if not valid_admin(admin_code):
return {'message': 'Please enter a valid admin code'}, 400
post_format[0] = 1
# delete null value from data object
del data['admin_code']
subdiv_code = data['subdiv_code']
if subdiv_code:
if not valid_subdiv(subdiv_code):
return {'message': 'Please enter a valid subdiv code'}, 400
post_format[1] = 1
del data['subdiv_code']
# if have admin and subdiv
if post_format[0] and post_format[1]:
if MortalityDataModel.find_by_casysc(country_code, admin_code,
subdiv_code, year, sex,
cause):
return {
'message':
"An entry already exists for your given year, country, admin, subdiv sex and cause."
}, 400
# if have admin
if post_format[0] and not post_format[1]:
if MortalityDataModel.find_by_caysc(country_code, admin_code, year,
sex, cause):
return {
'message':
"An entry already exists for your given year, country, sex and admin."
}, 400
subdiv_code = ""
# delete the null values from the data object
del data['subdiv_code']
# if have subdiv
if post_format[1] and not post_format[0]:
if MortalityDataModel.find_by_csysc(country_code, subdiv_code,
year, sex, cause):
return {
'message':
"An entry already exists for your given year, country, subdiv, sex and cause."
}, 400
admin_code = ""
del data['admin_code']
# if have neither admin or data
if not post_format[0] and not post_format[1]:
if MortalityDataModel.find_by_cysc(country_code, year, sex, cause):
return {
'message':
"An entry already exists for your given year, country, sex and cause."
}, 400
del data['admin_code']
admin_code = ""
del data['subdiv_code']
subdiv_code = ""
# code list needs to be a named variable as it comes before cause and sex in the table structure
code_list = data['code_list']
del data['code_list']
entry = MortalityDataModel(country_code, admin_code, subdiv_code, year,
code_list, cause, sex, **data)
new_code_list_ref = CodeListRefModel(year, country_code, code_list)
try:
code_list_ref = CodeListRefModel.find_by_year_and_country(
year, country_code)
if code_list_ref.code_list != code_list:
code_list_ref.code_list = code_list
code_list_ref.save_to_db()
else:
new_code_list_ref.save_to_db()
entry.save_to_db()
except:
return {"message": "An error occurred inserting the data."}, 500
return entry.json(), 201
def get(self):
query = {}
country_code = request.args.get('country', type=str)
if country_code:
if not valid_country_code(country_code):
return {
'message':
'{} is not a valid country_code'.format(country_code)
}, 400
query['country_code'] = country_code
year = request.args.get('year', type=str)
if year:
if not valid_year(year):
return {'message': 'Please enter a valid year'}, 400
query['year'] = year
sex = request.args.get('sex', type=str)
if sex:
if not valid_sex(sex):
return {'message': 'Please enter a valid sex code'}, 400
query['sex'] = sex
admin = request.args.get('admin', type=str)
if admin:
if not valid_admin(admin):
return {'message': 'Please enter a valid admin code'}, 400
query['admin_code'] = admin
subdiv = request.args.get('subdiv', type=str)
if subdiv:
if not valid_subdiv(subdiv):
return {'message': 'Please enter a valid subdiv code'}, 400
query['subdiv_code'] = subdiv
cause = request.args.get('cause', type=str)
if cause:
cause_upper = cause.upper()
if not valid_cause(cause_upper):
return {'message': 'Please enter a valid cause code'}, 400
cause_code_list_extended = {}
icd_codes = [
code.json() for code in IcdModel.find_by_code(cause_upper)
]
for icd_code in icd_codes:
matching_codes = [
matching_icd_code.json() for matching_icd_code in
IcdModel.search_specific(icd_code['description'])
]
unspecified_codes = []
generic_codes = []
pattern = "unspecified"
match = re.search(pattern, icd_code['description'])
if not match:
unspecified_code = icd_code['description'] + \
" (unspecified)"
unspecified_codes = [
matching_icd_code.json() for matching_icd_code in
IcdModel.search_specific(unspecified_code)
]
else:
position = match.span()
start = position[0] - 2
end = position[1] + 1
generic_code = icd_code['description'][0:start] + \
icd_code['description'][end:]
generic_codes = [
matching_icd_code.json() for matching_icd_code in
IcdModel.search_specific(generic_code)
]
for matching_code in matching_codes:
cause_code_list_extended[
matching_code['list']] = matching_code['code']
if generic_codes:
for matching_code in generic_codes:
cause_code_list_extended[
matching_code['list']] = matching_code['code']
if unspecified_codes:
for matching_code in unspecified_codes:
cause_code_list_extended[
matching_code['list']] = matching_code['code']
if "103" not in cause_code_list_extended:
try:
cause_code_list_extended[
'103'] = cause_code_list_extended['104'][:-1]
except:
pass
code_list_entry = CodeListRefModel.find_by_year_and_country(
year, country_code)
try:
cause = cause_code_list_extended[code_list_entry.code_list]
except:
return {
'message':
"Can't find matching cause code for the specified country."
}, 400
query['cause'] = cause
result = [
entry.json()
for entry in MortalityDataModel.search_mortalities(query)
]
if code_list_entry.code_list == "104" and len(
cause_code_list_extended[
code_list_entry.code_list]) == 3 and len(result) == 0:
cause = cause + "9"
query['cause'] = cause
result = [
entry.json()
for entry in MortalityDataModel.search_mortalities(query)
]
if code_list_entry.code_list == "10M" and len(
cause_code_list_extended[
code_list_entry.code_list]) == 3 and len(result) == 0:
cause = cause + "9"
query['cause'] = cause
result = [
entry.json()
for entry in MortalityDataModel.search_mortalities(query)
]
if code_list_entry.code_list == "10M" and len(
cause_code_list_extended[
code_list_entry.code_list]) == 4 and len(result) == 0:
cause = cause[:-1]
query['cause'] = cause
result = [
entry.json()
for entry in MortalityDataModel.search_mortalities(query)
]
if result:
if len(result) > 1:
return {
'message':
"More than one mortality entry was found matching your query, please be more specific."
}, 400
return {'entry': result[0]}, 200
return {'message': "No mortalities match your query."}, 404