def _extract_tables(html_content) -> DataFrame:
selector = "table.ms-rteTable-4"
# Tables keep changing order, so iterate through all until one looks good
table_count = count_html_tables(html_content, selector=selector)
for table_index in range(table_count):
yield read_html(
html_content,
header=True,
selector=selector,
parser=_html_cell_parser,
table_index=table_index,
)
def parse(self, sources: List[str], aux: Dict[str, DataFrame], **parse_opts) -> DataFrame:
if parse_opts.get("debug"):
print("File name:", sources[0])
# Get the file contents from source
html_content = open(sources[0]).read()
# We need to set locale in order to parse dates properly
locale.setlocale(locale.LC_TIME, parse_opts.get("locale", "en_US") + ".UTF-8")
# Tables keep changing order, so iterate through all until one looks good
table_count = count_html_tables(html_content, selector="table.wikitable")
data: DataFrame = None
for table_index in range(table_count):
data = read_html(
html_content,
header=True,
selector="table.wikitable",
parser=wiki_html_cell_parser,
table_index=table_index,
skiprows=parse_opts.get("skiprows", 0),
)
if parse_opts.get("debug"):
print("\n[%d] Data:" % (table_index + 1))
print(data.columns)
print(data.head(50))
# Some of the tables are in Spanish
data = data.rename(columns={"Fecha": "Date"})
# Set first date column as index, drop other date columns
columns_lowercase = [(col or "").lower() for col in data.columns]
date_index = columns_lowercase.index("date") if "date" in columns_lowercase else 0
del_index = [i for i, col in enumerate(columns_lowercase) if col == "date"][1:]
data = data.iloc[:, [i for i, _ in enumerate(data.columns) if i not in del_index]]
data = data.set_index(data.columns[date_index])
# data = data.iloc[:, :-parse_opts.get('skipcols', 0)]
if parse_opts.get("droprows") is not None:
try:
data = data.drop(parse_opts["droprows"].split(","))
except:
pass
# Pivot the table to fit our preferred format
data = pivot_table(data, pivot_name="subregion")
data = data[~data["subregion"].isna()]
if parse_opts.get("debug"):
print("\n[%d] Pivoted:" % (table_index + 1))
print(data.head(50))
# Make sure all dates include year
date_format = parse_opts["date_format"]
if "%Y" not in date_format:
date_format = date_format + "-%Y"
data["date"] = data["date"].astype(str) + "-%d" % datetime.datetime.now().year
# Parse into datetime object, drop if not possible
data["date"] = data["date"].apply(lambda date: safe_datetime_parse(date, date_format))
data = data[~data["date"].isna()]
# If the dataframe is not empty, then we found a good one
if len(data) > 10 and len(data["subregion"].unique()) > 3:
break
# Make sure we have *some* data
assert data is not None and len(data) > 0
# Convert all dates to ISO format
data["date"] = data["date"].apply(lambda date: date.date().isoformat())
# Get the confirmed and deaths data from the table
data["confirmed"] = data["value"].apply(lambda x: safe_int_cast(self._parenthesis(x)[0]))
data["deceased"] = data["value"].apply(lambda x: safe_int_cast(self._parenthesis(x)[1]))
# Add up all the rows with same Date and subregion
data = data.sort_values(["date", "subregion"])
data = (
data.drop(columns=["value"])
.groupby(["subregion", "date"])
.agg(self._aggregate_region_values)
)
data = data.reset_index().sort_values(["date", "subregion"])
# Add the appropriate columns to the data
value_columns = ["confirmed", "deceased"]
for col in value_columns:
data["new_" + col] = None
data["total_" + col] = None
# Iterate over the individual subregions to process the values per group
for region in data["subregion"].unique():
mask = data["subregion"] == region
for column in value_columns:
# We can forward-fill values if data is cumsum
if parse_opts.get("cumsum"):
data.loc[mask, column] = data.loc[mask, column].ffill()
# Fill NA with zero to allow for column-wide operations
zero_filled = data.loc[mask, column].fillna(0)
# Only perform operation if the column is not all NaN
if sum(zero_filled) > 0:
# Compute diff of the values region by region if required
if parse_opts.get("cumsum"):
data.loc[mask, "new_" + column] = zero_filled.diff()
data.loc[mask, "total_" + column] = zero_filled
# If values are already new daily counts, then empty most likely means zero
else:
data.loc[mask, "new_" + column] = zero_filled
data.loc[mask, "total_" + column] = zero_filled.cumsum()
# Get rid of rows which have all null values
data = data.dropna(how="all", subset=value_columns)
# Add the country code to all records
data["country_code"] = parse_opts["country"]
# Labels can be any arbitrary column name
data = data.rename(columns={"subregion": "match_string"})
# Drop columns if requested
if "drop_column" in parse_opts:
data = data.drop(columns=[parse_opts["drop_column"]])
# Filter out the appropriate levels
aggregation_level = parse_opts.get("aggregation_level", 1)
if aggregation_level == 1:
null_column = "subregion2_code"
elif aggregation_level == 2:
null_column = "subregion1_code"
data[null_column] = None
# Remove known values that are just noise
data["_match_string"] = data["match_string"].apply(lambda x: x.lower())
data = data[
~data["_match_string"].isin(
[
"cml",
"new",
"total",
"tests",
"deaths",
"abroad",
"airport",
"current",
"newcases",
"acumulado",
"repatriated",
"totaltested",
"confirmed cases",
"unassigned\ncases",
"airport screening",
]
)
]
data = data[~data["_match_string"].apply(lambda x: "princess" in x or "total" in x)]
# Output the results
if parse_opts.get("debug"):
print("\nOutput:")
print(data.head(50))
return data
