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Vaccinatation data #6

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4254233
Add vaccination data
ballinc Oct 1, 2021
a0f008e
Add missed swagger params
ballinc Oct 1, 2021
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31 changes: 17 additions & 14 deletions app.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,12 +31,13 @@
]
SOURCES = [
"https://github.com/CSSEGISandData/COVID-19",
"https://github.com/govex/COVID-19",
"https://www.worldometers.info/coronavirus/"
]
route_homepage = {
"documentation": f"{BASE_PATH}/doc",
"routes": ROUTES,
"<data_type>": "confirmed | recovered | deaths",
"<data_type>": "confirmed | recovered | deaths | vaccinated",
"Api version": API_VERSION,
"discord": "https://discord.gg/wTxbQYb",
"sources": SOURCES,
Expand All @@ -52,6 +53,8 @@

app = Flask(__name__)
app.url_map.strict_slashes = False
# Flask orders the dates wrong for some reason ?!?!
app.config['JSON_SORT_KEYS'] = False
limiter = Limiter(
app,
get_remote_address,
Expand Down Expand Up @@ -431,96 +434,96 @@ def get(self, data_type: int):
@api.route(f"/api/{API_VERSION}/history/<data_type>/<country>/")
class HistoryDataTypeCountry(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`", "country": "Full name or ISO-3166-1"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`", "country": "Full name or ISO-3166-1"})
def get(self, data_type: str, country: str):
return history_country(data_type, country)


@api.route(f"/api/{API_VERSION}/history/<data_type>/<country>/<region>")
class HistoryDataTypeRegion(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`", "country": "Full name or ISO-3166-1", "region": "Region name"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`", "country": "Full name or ISO-3166-1", "region": "Region name"})
def get(self, data_type: str, country: str, region: str):
return history_region(data_type, country, region)


@api.route(f"/api/{API_VERSION}/history/<data_type>/<country>/regions")
class HistoryDataTypeRegions(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`", "country": "Full name or ISO-3166-1"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`", "country": "Full name or ISO-3166-1"})
def get(self, data_type: str, country: str):
return history_region_all(data_type, country)


@api.route(f"/api/{API_VERSION}/history/<data_type>/total")
class HistoryDataTypeTotal(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`"})
def get(self, data_type: str):
return history_region_world(data_type)


@api.route(f"/api/{API_VERSION}/proportion/<data_type>/")
class ProportionDataType(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`"})
def get(self, data_type: str):
return proportion(data_type)

@api.route(f"/api/{API_VERSION}/proportion/<data_type>/total")
class ProportionDataTypeTotal(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`"},
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`"},
description="Returns the percentage of the world's population to be affected by COVID-19")
def get(self, data_type: str):
return proportion_region_world(data_type)

@api.route(f"/api/{API_VERSION}/proportion/<data_type>/<country>/")
class ProportionDataTypeCountry(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`", "country": "Full name or ISO-3166-1"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`", "country": "Full name or ISO-3166-1"})
def get(self, data_type: str, country: str):
return proportion_country(data_type, country)

@api.route(f"/api/{API_VERSION}/daily/<data_type>/")
class DailyDataType(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`"})
def get(self, data_type: str):
return daily(data_type)

@api.route(f"/api/{API_VERSION}/daily/<data_type>/total")
class DailyDataTypeTotal(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`"})
def get(self, data_type: str):
return daily_region_world(data_type)

@api.route(f"/api/{API_VERSION}/daily/<data_type>/<country>/")
class DailyDataTypeCountry(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`", "country": "Full name or ISO-3166-1"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`", "country": "Full name or ISO-3166-1"})
def get(self, data_type: str, country: str):
return daily_country(data_type, country)

@api.route(f"/api/{API_VERSION}/proportion-daily/<data_type>/")
class ProportionDailyDataType(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`"})
def get(self, data_type: str):
return proportion_daily(data_type)

@api.route(f"/api/{API_VERSION}/proportion-daily/<data_type>/total")
class ProportionDailyDataTypeTotal(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`"})
def get(self, data_type: str):
return proportion_daily_region_world(data_type)

@api.route(f"/api/{API_VERSION}/proportion-daily/<data_type>/<country>")
class ProportionDailyDataTypeCountry(Resource):
@api.doc(responses=responses,
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths`", "country": "Full name or ISO-3166-1"})
params={"data_type": "Input accepted : `confirmed` | `recovered` | `deaths` | `vaccinated`", "country": "Full name or ISO-3166-1"})
def get(self, data_type: str, country: str):
return proportion_daily_country(data_type, country)

Expand Down
79 changes: 60 additions & 19 deletions src/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
CSV_CONFIRMED = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
CSV_DEATHS = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"
CSV_RECOVERED = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv"
CSV_VACCINATED = "https://raw.githubusercontent.com/govex/COVID-19/master/data_tables/vaccine_data/global_data/time_series_covid19_vaccine_doses_admin_global.csv"

CSV_CONFIRMED_US = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv"
CSV_DEATHS_US = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_US.csv"
Expand All @@ -27,6 +28,7 @@
CSV_CONFIRMED_FPATH = "csv_confirmed.csv"
CSV_DEATHS_FPATH = "csv_deaths.csv"
CSV_RECOVERD_FPATH = "csv_recovered.csv"
CSV_VACCINATED_FPATH = "csv_vaccinated.csv"

CSV_POPULATIONS = "data/populations.csv"
populations = {}
Expand Down Expand Up @@ -70,14 +72,17 @@ def update():
dl_csv(CSV_CONFIRMED, CSV_CONFIRMED_FPATH)
dl_csv(CSV_DEATHS, CSV_DEATHS_FPATH)
dl_csv(CSV_RECOVERED, CSV_RECOVERD_FPATH)
dl_csv(CSV_VACCINATED, CSV_VACCINATED_FPATH)
dl_csv(CSV_CONFIRMED_US, CSV_CONFIRMED_FPATH_US)
dl_csv(CSV_DEATHS_US, CSV_DEATHS_FPATH_US)
csv_to_json(CSV_CONFIRMED_FPATH)
csv_to_json(CSV_DEATHS_FPATH)
csv_to_json(CSV_RECOVERD_FPATH)
csv_to_json(CSV_VACCINATED_FPATH, is_govex=True)
region_csv_to_json(CSV_CONFIRMED_FPATH)
region_csv_to_json(CSV_DEATHS_FPATH)
region_csv_to_json(CSV_RECOVERD_FPATH)
region_csv_to_json(CSV_VACCINATED_FPATH, is_govex=True)
region_csv_to_json(CSV_CONFIRMED_FPATH_US, is_us=True)
region_csv_to_json(CSV_DEATHS_FPATH_US, is_us=True)
store_data()
Expand All @@ -87,26 +92,42 @@ def dl_csv(csv_type, fpath):
with open(fpath, "w+") as f:
f.write(r.text)

def csv_to_json(csv_fpath):
def csv_to_json(csv_fpath, is_govex=False):
csv_json = {}

if is_govex:
province_key = "Province_State"
country_key = "Country_Region"
key_start = 12
date_format = "%Y-%m-%d"
else:
province_key = "Province/State"
country_key = "Country/Region"
key_start = 4
date_format = "%m/%d/%y"

with open("iso-3166.json", "r") as isof:
iso_data = json.load(isof)
with open(csv_fpath, "r") as csv_file:
data = csv.DictReader(csv_file)
for row in data:
if row["Country/Region"] not in csv_json:
if row["Country/Region"] in SPECIAL_CASES:
country = SPECIAL_CASES[row["Country/Region"]]["name"]
if row[country_key] not in csv_json:
if row[country_key] in SPECIAL_CASES:
country = SPECIAL_CASES[row[country_key]]["name"]
else:
country = row["Country/Region"]
country = row[country_key]
csv_json[country] = {"history": {}}
for key in list(row.keys())[4:]:
new_k = datetime.datetime.strptime(key, "%m/%d/%y").strftime("%m/%d/%y")
csv_json[country]["history"][new_k] = int(row[key])
else:
for key in list(row.keys())[4:]:
new_k = datetime.datetime.strptime(key, "%m/%d/%y").strftime("%m/%d/%y")
csv_json[country]["history"][new_k] += int(row[key])
for key in list(row.keys())[key_start:]:
new_k = datetime.datetime.strptime(key, date_format).strftime("%m/%d/%y")
csv_json[country]["history"][new_k] = int(row[key]) if (row[key] != '') else 0
elif is_govex != True:
for key in list(row.keys())[key_start:]:
new_k = datetime.datetime.strptime(key, date_format).strftime("%m/%d/%y")
csv_json[country]["history"][new_k] += int(row[key]) if (row[key] != '') else 0

#print(csv_json[country]["history"])
#csv_json[country]["history"] = dict(sorted(csv_json[country]["history"].items(), key=lambda p: p[1]))
#print(csv_json[country]["history"])

for k in csv_json.keys():
for iso in iso_data:
Expand All @@ -124,16 +145,30 @@ def csv_to_json(csv_fpath):
with open(csv_fpath.replace(".csv", ".json"), "w+") as f:
f.write(str(json.dumps(csv_json)))

def region_csv_to_json(csv_fpath, is_us=False):
def region_csv_to_json(csv_fpath, is_us=False, is_govex=False):
csv_json = {}
if is_us:
province_key = "Province_State"
country_key = "Country_Region"
key_start = 12
date_format = "%m/%d/%y"
else:
province_key = "Province/State"
country_key = "Country/Region"
key_start = 4
date_format = "%m/%d/%y"

if is_govex:
province_key = "Province_State"
country_key = "Country_Region"
key_start = 12
date_format = "%Y-%m-%d"
elif is_us == False:
province_key = "Province/State"
country_key = "Country/Region"
key_start = 4
date_format = "%m/%d/%y"

with open("iso-3166.json", "r") as isof:
iso_data = json.load(isof)
with open(csv_fpath, "r") as csv_file:
Expand All @@ -150,24 +185,24 @@ def region_csv_to_json(csv_fpath, is_us=False):
csv_json[country] = {"regions": {}}
province = row[province_key]
for key in list(row.keys())[key_start:]:
new_k = datetime.datetime.strptime(key, "%m/%d/%y").strftime("%m/%d/%y")
new_k = datetime.datetime.strptime(key, date_format).strftime("%m/%d/%y")
if province not in csv_json[country]["regions"]:
csv_json[country]["regions"][province] = {
"history": {}
}
csv_json[country]["regions"][province]["history"][new_k] = int(float(row[key]))
else:
csv_json[country]["regions"][province]["history"][new_k] = int(float(row[key])) if (row[key] != '') else 0
elif is_govex != True:
province = row[province_key]
for key in list(row.keys())[key_start:]:
new_k = datetime.datetime.strptime(key, "%m/%d/%y").strftime("%m/%d/%y")
new_k = datetime.datetime.strptime(key, date_format).strftime("%m/%d/%y")
if province not in csv_json[country]["regions"]:
csv_json[country]["regions"][province] = {
"history": {}
}
if is_us and csv_json[country]["regions"][province]["history"].get(new_k):
csv_json[country]["regions"][province]["history"][new_k] += int(float(row[key]))
csv_json[country]["regions"][province]["history"][new_k] += int(float(row[key])) if (row[key] != '') else 0
else:
csv_json[country]["regions"][province]["history"][new_k] = int(float(row[key]))
csv_json[country]["regions"][province]["history"][new_k] = int(float(row[key])) if (row[key] != '') else 0


for k in csv_json.keys():
Expand Down Expand Up @@ -208,11 +243,16 @@ def replace_null_value(dataset: list):
data_c = read_json(CSV_CONFIRMED_FPATH.replace(".csv", ".json"))
data_r = read_json(CSV_RECOVERD_FPATH.replace(".csv", ".json"))
data_d = read_json(CSV_DEATHS_FPATH.replace(".csv", ".json"))
data_v = read_json(CSV_VACCINATED_FPATH.replace(".csv", ".json"))
for kv_replace in dataset:
tmp = kv_replace
confirmed = find_val_replace_null(tmp["country"], data_c, tmp["totalCases"])
recovered = find_val_replace_null(tmp["country"], data_r, tmp["totalRecovered"])
deaths = find_val_replace_null(tmp["country"], data_d, tmp["totalDeaths"])
# TODO: find / calculate data for whole world vaccinations
if tmp["country"] in data_v:
tmp["totalVaccinated"] = list(data_v[tmp["country"]]["history"].values())[-1]

if tmp["totalCases"] is None:
tmp["totalCases"] = confirmed
if tmp["activeCases"] is None:
Expand All @@ -223,6 +263,7 @@ def replace_null_value(dataset: list):
tmp["totalDeaths"] = deaths
if tmp["totalRecovered"] is None:
tmp["totalRecovered"] = recovered

new_dataset.append(tmp)
return new_dataset

Expand Down