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vujson.py
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vujson.py
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#!/usr/bin/env python3
# See: https://github.com/pr3d4t0r/COVIDvu/blob/master/LICENSE
# vim: set fileencoding=utf-8:
import json
import os
import sys
import pandas as pd
import re
import utils
# *** initializations ***
pd.options.mode.chained_assignment = None
# *** constants ***
JH_CSSE_DATA_HOME = 'COVID-19'
JH_CSSE_PATH = os.path.join(os.path.join(os.getcwd(), JH_CSSE_DATA_HOME), 'csse_covid_19_data/csse_covid_19_time_series')
JH_CSSE_FILE_CONFIRMED = os.path.join(JH_CSSE_PATH, 'time_series_19-covid-Confirmed.csv')
JH_CSSE_FILE_DEATHS = os.path.join(JH_CSSE_PATH, 'time_series_19-covid-Deaths.csv')
JH_CSSE_FILE_RECOVERED = os.path.join(JH_CSSE_PATH, 'time_series_19-covid-Recovered.csv')
US_REGIONS = {
'Northeast': sorted([ 'CT', 'ME', 'MA', 'NH', 'RI', 'VT', 'NJ', 'NY', 'PA', ]),
'Midwest': sorted([ 'IL', 'IN', 'MI', 'OH', 'WI', 'IA', 'KS', 'MN', 'MO', 'NE', 'ND', 'SD', ]),
'South': sorted([ 'DE', 'GA', 'FL', 'MD', 'NC', 'SC', 'VA', 'DC', 'WV', 'AL', 'KY', 'MS', 'TN', 'AR', 'LA', 'OK', 'TX', ]),
'West': sorted([ 'AZ', 'CO', 'ID', 'MT', 'NV', 'NM', 'UT', 'WY', 'AK', 'CA', 'HI', 'OR', 'WA', ] ),
}
# *** functions ***
def allCases(fileName = JH_CSSE_FILE_CONFIRMED, includeGeoLocation = False):
cases = pd.read_csv(fileName).groupby(['Country/Region']).sum().T
if not includeGeoLocation:
cases = cases.iloc[2:]
cases.index = pd.to_datetime(cases.index)
cases = utils.computeGlobal(cases)
cases = utils.computeCasesOutside( cases,
[ 'Mainland China', '!Global' ],
'!Outside Mainland China' )
return cases
def _resampleByStateUS(casesUS):
states = []
stateCodes = pd.read_csv('stateCodesUS.csv')
for province in casesUS.columns:
match = re.search(r', ([A-Z][A-Z])', province)
if match:
postalCode = match.groups()[0]
code = stateCodes[stateCodes['postalCode'] == postalCode]
assert code.shape[0] == 1
states.append(code['state'].iloc[0])
elif 'Diamond Princess' in province:
states.append('Diamond Princess')
else:
states.append('Unassigned')
casesUS.columns = states
casesUS = casesUS.groupby(casesUS.columns, axis=1).sum()
casesUS['!Total US'] = casesUS.sum(axis=1)
casesUS = casesUS.reindex(sorted(casesUS.columns), axis=1)
return casesUS
def _resampleByRegionUS(casesUS):
regions = []
for province in casesUS.columns:
match = re.search(r', ([A-Z][A-Z])', province)
if match:
postalCode = match.groups()[0]
regionFound = False
for region in US_REGIONS:
if postalCode in US_REGIONS[region]:
regions.append(region)
regionFound = True
break
if not regionFound:
raise ValueError(f'{postalCode} not found in US_REGIONS')
elif 'Diamond Princess' in province:
regions.append('Diamond Princess')
else:
regions.append('Unassigned')
casesUS.columns = regions
casesUS = casesUS.groupby(casesUS.columns, axis=1).sum()
casesUS['!Total US'] = casesUS.sum(axis=1)
casesUS = casesUS.reindex(sorted(casesUS.columns), axis=1)
return casesUS
def allUSCases(fileName = JH_CSSE_FILE_CONFIRMED):
cases = pd.read_csv(JH_CSSE_FILE_CONFIRMED)
casesUS = cases[cases['Country/Region']=='US'].drop('Country/Region', axis=1).set_index('Province/State').T
casesUS = casesUS.iloc[2:]
casesUS.index = pd.to_datetime(casesUS.index)
casesUS.index = casesUS.index.map(lambda s: s.date())
casesByStateUS = _resampleByStateUS(casesUS.copy())
casesByRegionUS = _resampleByRegionUS(casesUS.copy())
return casesByStateUS, casesByRegionUS
def _dumpJSON(cases, target):
with open(target, 'w') as outputJSON:
json.dump(cases, outputJSON)
def dumpGlobalCasesAsJSONFor(cases, target = None, indent = 2):
"""
cases: dataframe output from the allCases() function; confirmed,
deaths, recovered
target: string or file stream; if None, return a JSON string
"""
dataSource = cases.transpose()
keys = dataSource.keys()
result = dataSource[keys].iloc[:].to_json(orient = 'table',
indent = indent)
# TODO: https://github.com/pr3d4t0r/COVIDvu/issues/33
result = json.loads(result)['data']
if target:
_dumpJSON(result, target)
return result
def dumpUSCasesAsJSONFor(cases, target = None, scope = 'US', indent = 2):
keys = cases.keys()
cases.index = cases.index.map(lambda s: s.strftime('%m/%d/%Y'))
result = cases[keys].to_dict()
target = target.replace('.json', '-%s.json' % scope)
if target:
_dumpJSON(result, target)
return result
def _main(target):
if 'confirmed' == target:
sourceFileName = JH_CSSE_FILE_CONFIRMED
elif 'deaths' == target:
sourceFileName = JH_CSSE_FILE_DEATHS
elif 'recovered' == target:
sourceFileName = JH_CSSE_FILE_RECOVERED
else:
raise NotImplementedError
casesUS, \
casesUSRegions = allUSCases(sourceFileName)
outputFileName = target+'.json'
dumpGlobalCasesAsJSONFor(allCases(sourceFileName, includeGeoLocation = True), outputFileName)
dumpUSCasesAsJSONFor(casesUS, outputFileName)
dumpUSCasesAsJSONFor(casesUSRegions, outputFileName, 'US-Regions')
# *** main ***
if '__main__' == __name__:
# TODO: Parse command line for real? Decide.
#
# Usage: vujson.py casetype
# where castype is one or more of:
#
# - confirmed
# - deaths
# - recovered
for argument in sys.argv[1:]:
_main(argument)