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utils.py
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utils.py
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"""Common utils for extraction modules."""
import json
from cfg import cfg
import firebase_admin
from firebase_admin import credentials
from firebase_admin import db
import pandas as pd
import requests
import ssl
import warnings
ssl._create_default_https_context = ssl._create_unverified_context
warnings.filterwarnings("ignore")
def publish_gist(json_files, description, gist_id):
"""Publish multiple files to Github gist."""
# print headers,parameters,payload
headers = {'Authorization': f'token {cfg.github.api_token}'}
params = {'scope': 'gist'}
payload = {"description": description,
"public": True,
"files": json_files
}
# make a request
print(payload)
res = requests.patch(cfg.github.api_url + gist_id,
headers=headers,
params=params,
data=json.dumps(payload))
print(res)
def initialize_firebase_db(creds_path, db_url):
"""Initialize Firebase Realtime database."""
cred = credentials.Certificate(creds_path)
firebase_admin.initialize_app(cred, {'databaseURL': db_url})
def publish_firebase(category, filename, content):
"""Publish json file into Firebase Realtime db."""
ref = db.reference()
data_ref = ref.child(f"{category}/{filename}")
data_ref.set(content)
def read_scs_csv(url):
"""Read CSV file with Cantabria's historical data from SCS."""
# cases = pd.read_csv(cfg.input.path + cfg.input.hospitals)
cases = pd.read_csv(url, na_filter=False, skipfooter=0,
sep=';',
engine='python',
dtype={'CASOS RESIDENCIAS': object,
'AISLAMIENTO DOM.': object,
'TOTAL TEST': object,
'TEST PCR': object})
cases = cases.loc[:, ~cases.columns.str.contains('^Unnamed')]
cases.columns = cases.columns.str.title()
cases.columns = cases.columns.str.replace('Fecha\*', 'Fecha')
cases.columns = cases.columns.str.replace('Casos Nuevos\*', 'Casos Nuevos')
cases.columns = cases.columns.str.replace(
'Casos Nuevos Pcr\*', 'Casos Nuevos')
cases.columns = cases.columns.str.replace('Uci', 'UCI')
cases.columns = cases.columns.str.replace('Hospitalizados UCI', 'UCI')
cases.columns = cases.columns.str.replace('Pcr', 'PCR')
cases.columns = cases.columns.str.replace('Hosp. ', '')
cases.columns = cases.columns.str.replace('Prof. ', '')
cases.columns = cases.columns.str.replace('Humv', 'Valdecilla')
cases.columns = cases.columns.str.replace('Dom.', 'Domiciliario')
cases.columns = cases.columns.str.replace('Total Casos', 'Casos')
cases.columns = cases.columns.str.replace(
'C. Resid. Activos', 'Residencias Activos')
cases.columns = cases.columns.str.replace(
'P. Sanit. Activos', 'Sanitarios Activos')
cases.columns = cases.columns.str.replace(
'Incidencia Ac 14', 'Incidencia 14 dias')
# cases.columns = cases.columns.str.replace('Total Hospitalizados', 'Hospitalizados activos')
cases['Fecha'] = cases['Fecha'].str.replace('\*\*', '')
# cases.drop(cases.tail(3).index, inplace=True)
return cases
def read_scs_municipal(url):
"""Read CSV file with Cantabria's municipal data from SCS."""
# cases = pd.read_csv(cfg.input.path + cfg.input.hospitals)
raw_data = pd.read_csv(url, na_filter=False, sep=';', skipfooter=1,
engine='python',
dtype={'Codigo': object})
raw_data.columns = raw_data.columns.str.title()
raw_data.columns = raw_data.columns.str.replace('Código', 'Codigo')
raw_data.columns = raw_data.columns.str.replace('Municipio', 'Texto')
raw_data.columns = raw_data.columns.str.replace('Casos',
'NumeroCasos')
raw_data.columns = raw_data.columns.str.replace('Activos',
'NumeroCasosActivos')
raw_data.columns = raw_data.columns.str.replace('Curados',
'NumeroCurados')
raw_data.columns = raw_data.columns.str.replace('Fallecidos',
'NumeroFallecidos')
return raw_data
def read_scs_age(url):
"""Read CSV file with Cantabria's municipal data from SCS."""
raw_data = pd.read_csv(url, na_filter=False,
skipfooter=0,
sep=';',
dtype={'Fecha': object,
'Rango_edad': object,
'Sexo': object,
'Casos_confirmados': int,
'Hospitalizados': int,
'Ingresos_uci': int,
'Fallecidos': int})
return raw_data
def read_scs_historic_age():
raw_data = pd.read_csv('./data/input/covid19_edad_sexo.csv',
sep=';')
return raw_data
def read_scs_historic_municipal():
raw_data = pd.read_csv('./data/input/covid19_municipalizado.csv',
na_values=None,
sep=';',
dtype={'Codigo': object})
raw_data.columns = raw_data.columns.str.title()
raw_data.columns = raw_data.columns.str.replace('Código', 'Codigo')
raw_data.columns = raw_data.columns.str.replace('Municipio', 'Texto')
raw_data.columns = raw_data.columns.str.replace('Casos',
'NumeroCasos')
raw_data.columns = raw_data.columns.str.replace('Activos',
'NumeroCasosActivos')
raw_data.columns = raw_data.columns.str.replace('Curados',
'NumeroCurados')
raw_data.columns = raw_data.columns.str.replace('Fallecidos',
'NumeroFallecidos')
raw_data['Fecha'] = pd.to_datetime(
raw_data['Fecha'], format='%d/%m/%Y', errors='coerce')
raw_data['Fecha'] = raw_data['Fecha'].dt.strftime("%d-%m-%Y")
return raw_data
def read_vaccine_csv():
"""Read CSV file with Cantabria's historical data from SCS."""
vaccine = pd.read_csv(cfg.input.path + cfg.input.vaccine,
sep=';')
vaccine = vaccine.fillna(0)
return vaccine
def read_vaccine_general():
"""Read CSV file with Cantabria's historical data from SCS."""
vaccine = pd.read_excel(cfg.input.path + cfg.input.vaccine,
sheet_name='general',
na_filter=False,)
return vaccine
def read_vaccine_week():
"""Read CSV file with Cantabria's historical data from SCS."""
vaccine = pd.read_excel(cfg.input.path + cfg.input.vaccine,
sheet_name='semanas',
na_filter=False,)
return vaccine
def read_vaccine_age():
"""Read CSV file with Cantabria's historical data from SCS."""
vaccine = pd.read_excel(cfg.input.path + cfg.input.vaccine,
sheet_name='edades',
na_filter=False,)
return vaccine
def read_vaccine_types():
"""Read CSV file with Cantabria's historical data from SCS."""
vaccine = pd.read_excel(cfg.input.path + cfg.input.vaccine,
sheet_name='tipos',
na_filter=False,)
return vaccine
def read_rho_csv(url):
"""Read CSV file with Cantabria's historical data from SCS."""
rho = pd.read_csv(url,
na_filter=False,
sep=';')
rho.columns = rho.columns.str.replace('Date', 'Fecha')
rho.columns = rho.columns.str.replace('Mean\(R\)', 'Media (R)')
rho.columns = rho.columns.str.replace(
'Quantile\.0\.025\(R\)', 'Cuantil 0,025 (R)')
rho.columns = rho.columns.str.replace(
'Quantile\.0\.975\(R\)', 'Cuantil 0,975 (R)')
rho = rho.apply(lambda x: x.str.replace(',', '.'))
return rho
def read_restimation(url):
"""Read CSV file with Cantabria's historical data from SCS."""
estimation = pd.read_csv(url,
na_filter=False,
sep=',')
estimation.columns = estimation.columns.str.replace('FECHA', 'Fecha')
estimation.columns = estimation.columns.str.replace(
'CASOS.NUEVOS.PCR.', 'Positivos')
estimation.columns = estimation.columns.str.replace(
'POSITIVOS_LS', 'Positivos LS')
estimation.columns = estimation.columns.str.replace(
'POSITIVOS_LI', 'Positivos LI')
# rho.columns = rho.columns.str.replace('Quantile\.0\.975\(R\)', 'Cuantil 0,975 (R)')
# arima = arima.apply(lambda x: x.str.replace(',','.'))
return estimation