def populate_icd_table_UE1():
# with open('/var/www/html/items-rest/raw_data/icd10-code-lists/UE1.csv', 'r') as code_file:
with open('./raw_data/icd10-code-lists/UE1.csv', 'r') as code_file:
code_reader = csv.reader(code_file)
for row in code_reader:
code_list = "UE1"
new_icd_object = IcdModel(code_list, *row)
entry = IcdModel.find_by_list_and_code(new_icd_object.code_list,
new_icd_object.code)
if entry:
continue
new_icd_object.save_to_db()
def get(self, search_term):
if len(search_term) < 3:
return {'message': "Please search for a term at least 3 characters long."}, 400
entries = IcdModel.search(search_term)
if entries:
return {'results': [entry.json() for entry in entries]}, 200
return {'message': "No results match the search term '{}'.".format(search_term)}, 404
def post(self, code_list, code):
if IcdModel.find_by_list_and_code(code_list, code):
return {'message': "A '{}' code already exists in list '{}'.".format(code, code_list)}, 400
data = Icd.parser.parse_args()
entry = IcdModel(code_list, code, data['description'])
try:
entry.save_to_db()
except:
return {'message': "Something we wrong inserting the code."}, 500
return entry.json(), 201
def put(self, code_list, code):
entry = IcdModel.find_by_list_and_code(code_list, code)
data = Icd.parser.parse_args()
if entry:
entry.description = data['description']
else:
entry = IcdModel(code_list, code, data['description'])
try:
entry.save_to_db()
except:
return {'message': "Something we wrong inserting the code."}, 500
return entry.json(), 201
def get(self):
entries = [entry.json() for entry in IcdModel.find_all()]
return {'all_codes': entries}
def get(self, search_term):
entries = IcdModel.search(search_term)
if entries:
return {'results': [entry.json() for entry in entries]}, 200
return {'message': "No results match the search term '{}'.".format(search_term)}, 404
def get(self, code):
code = code.upper()
entries = IcdModel.find_by_code(code)
if entries:
return {'results': [entry.json() for entry in entries]}, 200
return {'message': "No results match the code '{}'.".format(code)}, 404
def delete(self, code_list, code):
entry = IcdModel.find_by_list_and_code(code_list, code)
if entry:
entry.delete_from_db()
return {'message': "Deleted code '{}' from list '{}'.".format(code, code_list)}, 200
return {'message': "Code '{}' not found in list '{}'.".format(code, code_list)}, 404
def get(self, code_list, code):
entry = IcdModel.find_by_list_and_code(code_list, code)
if entry:
return entry.json(), 200
return {'message': "'{}' code not found in the '{}' list.".format(code, code_list)}, 404
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 get(self):
def strip_whitespace(string):
return ('').join(string.split(' '))
country_code_input = request.args.get('country', type=str)
year_input = request.args.get('year', type=str)
sex_code_input = request.args.get('sex', type=str)
cause_code_input = request.args.get('cause', type=str)
admin_code_input = request.args.get('admin', type=str)
subdiv_code_input = request.args.get('subdiv', type=str)
if not country_code_input or not year_input or not sex_code_input or not cause_code_input:
return {
'message':
"Please add at least a year, country, sex and cause variable"
}, 400
country_code_list = strip_whitespace(country_code_input).split(',')
year_list = strip_whitespace(year_input).split(',')
sex_code_list = strip_whitespace(sex_code_input).split(',')
cause_code_list = strip_whitespace(cause_code_input).split(',')
cause_code_list = list(map(lambda x: x.upper(), cause_code_list))
cause_code_list_extended = {}
for icd_code in filter(valid_cause, cause_code_list):
complete_icd_codes = [
code.json() for code in IcdModel.find_by_code(icd_code)
]
for icd_code in complete_icd_codes:
matching_codes = [
matching_icd_code.json() for matching_icd_code in
IcdModel.search_specific(icd_code['description'])
]
# try to make it possible to compare countries that use different code lists
# check if contains "unspecified". if not, add it and search again. else remove "(unspecified)"
# TODO: in case that unspecified doesn't match. sum up all instances of code + extra digit.
# e.g. A02 input by user. if code list is 104, sum all A020, A021, ...A029. return sum
# TODO: if user input is 4 digit cause code, remove last digit and search for 103 code list with that
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
# add "" to admin and subdiv lists to ensure some results if no specific code given
admin_code_list = []
if admin_code_input:
admin_code_list = strip_whitespace(admin_code_input).split(',')
admin_code_list.append("")
subdiv_code_list = []
if subdiv_code_input:
subdiv_code_list = strip_whitespace(subdiv_code_input).split(',')
subdiv_code_list.append("")
# results of each mortality adj search
results = []
# loop over all permutations of list items and validate codes.
for country_code in filter(valid_country_code, country_code_list):
for year in filter(valid_year, year_list):
for sex in filter(valid_sex, sex_code_list):
for cause in filter(valid_cause, cause_code_list):
for admin in filter(valid_admin, admin_code_list):
for subdiv in filter(valid_subdiv,
subdiv_code_list):
# generate query
code_list_entry = CodeListRefModel.find_by_year_and_country(
year, country_code)
try:
cause = cause_code_list_extended[
code_list_entry.code_list]
except:
continue
query = {}
query['country_code'] = country_code
query['sex'] = sex
query['year'] = year
query['cause'] = cause
query['admin_code'] = admin
query['subdiv_code'] = subdiv
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:
continue
# adjust for population and add to results list
for entry in result:
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()
del entry['infant_age_breakdown']
del entry['age_format']
del entry['infant_age_format']
del entry['age_breakdown']
entry[
'all_ages'] = "No population data."
continue
# remove infant mortality data as no related population data given
del entry['infant_age_breakdown']
# delete age format numbers as now irrelevant
del entry['age_format']
del entry['infant_age_format']
# divide mortality data by corresponding population number and multiply by 100,000
# population is population of that specific age/sex. not total country population
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))
# append to results list if anything found
if result:
results.append(result[0])
if len(results) == 0:
return {'message': "No mortality entries match your query."}, 404
return {'results': results}, 200
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
def get(self):
country_code_input = request.args.get('country', type=str)
year_input = request.args.get('year', type=str)
sex_code_input = request.args.get('sex', type=str)
cause_code_input = request.args.get('cause', type=str)
admin_code_input = request.args.get('admin', type=str)
subdiv_code_input = request.args.get('subdiv', type=str)
if not country_code_input or not year_input or not sex_code_input or not cause_code_input:
return {
'message':
"Please add at least a year, country, sex and cause variable"
}, 400
country_code_list = strip_whitespace(country_code_input).split(',')
year_list = strip_whitespace(year_input).split(',')
sex_code_list = strip_whitespace(sex_code_input).split(',')
cause_code_list = strip_whitespace(cause_code_input).split(',')
cause_code_list = list(map(lambda x: x.upper(), cause_code_list))
cause_code_list_extended = {}
for icd_code in filter(valid_cause, cause_code_list):
complete_icd_codes = [
code.json() for code in IcdModel.find_by_code(icd_code)
]
for icd_code in complete_icd_codes:
matching_codes = [
matching_icd_code.json() for matching_icd_code in
IcdModel.search_specific(icd_code['description'])
]
# try to make it possible to compare countries that use different code lists
# check if contains "unspecified". if not, add it and search again. else remove "(unspecified)"
# TODO: in case that unspecified doesn't match. sum up all instances of code + extra digit.
# e.g. A02 input by user. if code list is 104, sum all A020, A021, ...A029. return sum
# TODO: if user input is 4 digit cause code, remove last digit and search for 103 code list with that
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
# add "" to admin and subdiv lists to ensure some results if no specific code given
admin_code_list = []
if admin_code_input:
admin_code_list = strip_whitespace(admin_code_input).split(',')
admin_code_list.append("")
subdiv_code_list = []
if subdiv_code_input:
subdiv_code_list = strip_whitespace(subdiv_code_input).split(',')
subdiv_code_list.append("")
# TODO: replace nested for loops with product function? - itertools.product or from itertools import product
# def product(*args, **kwds):
# # product('ABCD', 'xy') --> Ax Ay Bx By Cx Cy Dx Dy
# # product(range(2), repeat=3) --> 000 001 010 011 100 101 110 111
# pools = map(tuple, args) * kwds.get('repeat', 1)
# result = [[]]
# for pool in pools:
# result = [x+[y] for x in result for y in pool]
# for prod in result:
# yield tuple(prod)
results = []
for country_code in filter(valid_country_code, country_code_list):
for year in filter(valid_year, year_list):
for sex in filter(valid_sex, sex_code_list):
for cause in filter(valid_cause, cause_code_list):
for admin in filter(valid_admin, admin_code_list):
for subdiv in filter(valid_subdiv,
subdiv_code_list):
code_list_entry = CodeListRefModel.find_by_year_and_country(
year, country_code)
try:
cause = cause_code_list_extended[
code_list_entry.code_list]
except:
continue
query = {}
query['country_code'] = country_code
query['sex'] = sex
query['year'] = year
query['cause'] = cause
query['admin_code'] = admin
query['subdiv_code'] = subdiv
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:
results.append(result[0])
continue
if len(results) == 0:
return {
'message': 'No mortality data matches your search parameters'
}, 404
return {'results': results}, 200
def valid_cause(cause):
cause = cause.upper()
if IcdModel.find_by_code(cause):
return True
return False