def save_indicators(results):
date = results["Date"]
country = results["Country"]
tests = results["Tests"]
confirmed_cases = results["ConfirmedCases"]
deaths = results["Deaths"]
if not math.isnan(tests):
with open(
"data/daily/indicators/covid-19-{}-{}-tests.csv".format(
date, format_country(country)
),
"w",
) as f:
f.write("{},{},{},{}\n".format(date, country, "Tests", tests))
if not math.isnan(confirmed_cases):
with open(
"data/daily/indicators/covid-19-{}-{}-confirmed-cases.csv".format(
date, format_country(country)
),
"w",
) as f:
f.write(
"{},{},{},{}\n".format(date, country, "ConfirmedCases", confirmed_cases)
)
if not math.isnan(deaths):
with open(
"data/daily/indicators/covid-19-{}-{}-deaths.csv".format(
date, format_country(country)
),
"w",
) as f:
f.write("{},{},{},{}\n".format(date, country, "Deaths", deaths))
def save_daily_areas(date, country, rows):
csv_file = "data/daily/covid-19-cases-{}-{}.csv".format(
date, format_country(country)
)
with open(csv_file, "w") as csvfile:
writer = csv.writer(csvfile)
writer.writerows(rows)
def write_indicator_file(date, country, indicator, value):
with open(
"data/daily/indicators/covid-19-{}-{}-{}.csv".format(
date, format_country(country), camel_to_hyphens(indicator)),
"w",
) as f:
f.write("{},{},{},{}\n".format(date, country, indicator, value))
def crawl_json(date, country, check_only):
if country == "UK":
local_data_file = "data/raw/phe/coronavirus-covid-19-number-of-cases-in-{}-{}.json".format(
format_country(country), date)
if not os.path.exists(local_data_file):
data_url = get_json_url(date)
if data_url is None:
if check_only:
return DatasetUpdate.UPDATE_NOT_AVAILABLE
sys.stderr.write("No data available for {}\n".format(date))
sys.exit(1)
if check_only:
return DatasetUpdate.UPDATE_AVAILABLE
r = requests.get(data_url)
with open(local_data_file, "w") as f:
f.write(r.text)
if check_only:
return DatasetUpdate.ALREADY_UPDATED
with open(local_data_file) as f:
json_data = json.load(f)
totalUKCases = json_data["overview"]["K02000001"]["totalCases"][
"value"]
totalUKDeaths = json_data["overview"]["K02000001"]["deaths"][
"value"]
englandCases = json_data["countries"]["E92000001"]["totalCases"][
"value"]
englandDeaths = json_data["countries"]["E92000001"]["deaths"][
"value"]
with sqlite3.connect('data/covid-19-uk.db') as conn:
c = conn.cursor()
c.execute(
f"INSERT OR REPLACE INTO indicators VALUES ('{date}', 'UK', 'ConfirmedCases', {totalUKCases})"
)
c.execute(
f"INSERT OR REPLACE INTO indicators VALUES ('{date}', 'UK', 'Deaths', {totalUKDeaths})"
)
c.execute(
f"INSERT OR REPLACE INTO indicators VALUES ('{date}', 'England', 'ConfirmedCases', {englandCases})"
)
c.execute(
f"INSERT OR REPLACE INTO indicators VALUES ('{date}', 'England', 'Deaths', {englandDeaths})"
)
# get area data for England
daily_areas = parse_daily_areas_json(date, "England", json_data)
if daily_areas is not None:
#save_daily_areas(date, "England", daily_areas)
save_daily_areas_to_sqlite(date, "England", daily_areas)
def crawl_json(date, country, check_only):
if country == "UK":
# See https://github.com/PublicHealthEngland/coronavirus-dashboard
blobs_url = "https://publicdashacc.blob.core.windows.net/publicdata?restype=container&comp=list"
local_data_file = "data/raw/phe/coronavirus-covid-19-number-of-cases-in-{}-{}.json".format(
format_country(country), date
)
if not os.path.exists(local_data_file):
r = requests.get(blobs_url)
blobs_xml = r.text
blobs_dict = xmltodict.parse(blobs_xml)
blob_names = sorted([o["Name"] for o in blobs_dict["EnumerationResults"]["Blobs"]["Blob"] if o["Name"]])
dt = dateparser.parse(date, date_formats=['%Y-%m-%d'], locales=["en-GB"])
blob_names_for_date = [name for name in blob_names if name.startswith("data_{}".format(dt.strftime('%Y%m%d')))]
if len(blob_names_for_date) == 0:
if check_only:
return DatasetUpdate.UPDATE_NOT_AVAILABLE
sys.stderr.write("No data available for {}\n".format(date))
sys.exit(1)
if check_only:
return DatasetUpdate.UPDATE_AVAILABLE
# Use most recent date
data_url = "https://c19pub.azureedge.net/{}".format(blob_names_for_date[-1])
r = requests.get(data_url)
with open(local_data_file, "w") as f:
f.write(r.text)
if check_only:
return DatasetUpdate.ALREADY_UPDATED
with open(local_data_file) as f:
json_data = json.load(f)
totalUKCases = json_data["overview"]["K02000001"]["totalCases"]["value"]
totalUKDeaths = json_data["overview"]["K02000001"]["deaths"]["value"]
englandCases = json_data["countries"]["E92000001"]["totalCases"]["value"]
englandDeaths = json_data["countries"]["E92000001"]["deaths"]["value"]
with sqlite3.connect('data/covid-19-uk.db') as conn:
c = conn.cursor()
c.execute(f"INSERT OR REPLACE INTO indicators VALUES ('{date}', 'UK', 'ConfirmedCases', {totalUKCases})")
c.execute(f"INSERT OR REPLACE INTO indicators VALUES ('{date}', 'UK', 'Deaths', {totalUKDeaths})")
c.execute(f"INSERT OR REPLACE INTO indicators VALUES ('{date}', 'England', 'ConfirmedCases', {englandCases})")
c.execute(f"INSERT OR REPLACE INTO indicators VALUES ('{date}', 'England', 'Deaths', {englandDeaths})")
# get area data for England
daily_areas = parse_daily_areas_json(date, "England", json_data)
if daily_areas is not None:
#save_daily_areas(date, "England", daily_areas)
save_daily_areas_to_sqlite(date, "England", daily_areas)
def crawl_html(date, country, check_only):
html_url = get_html_url(date, country)
local_html_file = "data/raw/coronavirus-covid-19-number-of-cases-in-{}-{}.html".format(
format_country(country), date)
save_html_file = False
try:
with open(local_html_file) as f:
html = f.read()
if check_only:
return DatasetUpdate.ALREADY_UPDATED
except FileNotFoundError:
r = requests.get(html_url)
html = r.text
save_html_file = True
results = parse_totals(country, html)
if results is None:
if check_only:
return DatasetUpdate.UPDATE_AVAILABLE
sys.stderr.write(
"Can't find numbers. Perhaps the page format has changed?\n")
sys.exit(1)
elif results["Date"] != date:
if check_only:
return DatasetUpdate.UPDATE_NOT_AVAILABLE
sys.stderr.write("Page is dated {}, but want {}\n".format(
results["Date"], date))
sys.exit(1)
if check_only:
return DatasetUpdate.UPDATE_AVAILABLE
daily_areas = parse_daily_areas(date, country, html)
print_totals(results)
#save_indicators(results)
save_indicators_to_sqlite(results)
if daily_areas is not None:
#save_daily_areas(date, country, daily_areas)
save_daily_areas_to_sqlite(date, country, daily_areas)
if save_html_file:
with open(local_html_file, "w") as f:
f.write(html)
def convert(indicators_csv_file):
indicators = pd.read_csv(indicators_csv_file)
for country in ["England", "Northern Ireland", "Scotland", "UK", "Wales"]:
wide = indicators[indicators["Country"] == country]
wide = wide.pivot(index="Date", columns="Indicator", values="Value")
wide = wide.reindex(columns=["Tests", "ConfirmedCases", "Deaths"])
# don't use to_csv since pandas can't write NA ints
with open(
"data/covid-19-totals-{}.csv".format(format_country(country)),
"w") as f:
f.write("Date,Tests,ConfirmedCases,Deaths\n")
for (i, d) in wide.to_dict("index").items():
f.write("{},{},{},{}\n".format(
i,
format_int(d["Tests"]),
format_int(d["ConfirmedCases"]),
format_int(d["Deaths"]),
))
