diff --git a/notebooks/examples/italy-covid-19.ipynb b/notebooks/examples/italy-covid-19.ipynb index 9b38f6dde0569104a69572b9b99f4bb8248e13b4..03cbf73d4e6a6d90b01fb33782079ff531f26d42 100644 --- a/notebooks/examples/italy-covid-19.ipynb +++ b/notebooks/examples/italy-covid-19.ipynb @@ -25,8 +25,6 @@ "metadata": {}, "outputs": [], "source": [ - "import ipywidgets as widgets\n", - "\n", "import pandas as pd\n", "import altair as alt\n", "\n", @@ -814,4 +812,4 @@ }, "nbformat": 4, "nbformat_minor": 4 -} +} \ No newline at end of file diff --git a/notebooks/process/standardize_datasets.ipynb b/notebooks/process/standardize_datasets.ipynb index af00ae37762bf09edf17e8cfc85aff1e05eb5130..1e406b6f2d290fd3854724471d11ad4c6e6045e8 100644 --- a/notebooks/process/standardize_datasets.ipynb +++ b/notebooks/process/standardize_datasets.ipynb @@ -47,20 +47,20 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 6, "metadata": {}, "outputs": [ { "output_type": "stream", "name": "stdout", - "text": "Using <covid_19_dashboard.converters.switzerland.OpenZHCaseConverter object at 0x11cccf5d0> for ../../data/openzh-covid-19\nUsing <covid_19_dashboard.converters.italy.ItalyCaseConverter object at 0x11cccf550> for ../../data/covid-19-italy\nUsing <covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter object at 0x11cccf410> for ../../data/covidtracking/\nUsing <covid_19_dashboard.converters.spain.SpainCaseConverter object at 0x11cccf590> for ../../data/covid-19-spain\nUsing <covid_19_dashboard.converters.jhu.JhuCsseGlobalCaseConverter object at 0x11cccf4d0> for ../../data/covid-19_jhu-csse/\n" + "text": "Using <covid_19_dashboard.converters.switzerland.OpenZHCaseConverter object at 0x11fcb6390> for ../../data/openzh-covid-19\nUsing <covid_19_dashboard.converters.italy.ItalyRegionalCaseConverter object at 0x11fcb6310> for ../../data/covid-19-italy/dpc-covid19-ita-regioni.csv\nUsing <covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter object at 0x11fcb6250> for ../../data/covidtracking/\nUsing <covid_19_dashboard.converters.spain.SpainCaseConverter object at 0x11fcb6450> for ../../data/covid-19-spain\nUsing <covid_19_dashboard.converters.jhu.JhuCsseGlobalCaseConverter object at 0x11fcb6410> for ../../data/covid-19_jhu-csse/\n" } ], "source": [ "df_list = []\n", "for path in [\n", " '../../data/openzh-covid-19', \n", - " '../../data/covid-19-italy', \n", + " '../../data/covid-19-italy/dpc-covid19-ita-regioni.csv', \n", " '../../data/covidtracking/', \n", " '../../data/covid-19-spain',\n", " \"../../data/covid-19_jhu-csse/\"\n", @@ -72,7 +72,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 7, "metadata": {}, "outputs": [ { @@ -82,7 +82,7 @@ "text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>date</th>\n <th>country</th>\n <th>country_label</th>\n <th>region_iso</th>\n <th>region_label</th>\n <th>admin2</th>\n <th>admin2_label</th>\n <th>tested</th>\n <th>positive</th>\n <th>deceased</th>\n <th>positive_100k</th>\n <th>deceased_100k</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>2020-02-28</td>\n <td>CHE</td>\n <td>Switzerland</td>\n <td>CH-AG</td>\n <td>Aargau</td>\n <td></td>\n <td></td>\n <td>NaN</td>\n <td>1.0</td>\n <td>NaN</td>\n <td>0.147448</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>1</th>\n <td>2020-03-02</td>\n <td>CHE</td>\n <td>Switzerland</td>\n <td>CH-AG</td>\n <td>Aargau</td>\n <td></td>\n <td></td>\n <td>NaN</td>\n <td>2.0</td>\n <td>NaN</td>\n <td>0.294895</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>2</th>\n <td>2020-03-03</td>\n <td>CHE</td>\n <td>Switzerland</td>\n <td>CH-AG</td>\n <td>Aargau</td>\n <td></td>\n <td></td>\n <td>NaN</td>\n <td>6.0</td>\n <td>NaN</td>\n <td>0.884686</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>3</th>\n <td>2020-03-04</td>\n <td>CHE</td>\n <td>Switzerland</td>\n <td>CH-AG</td>\n <td>Aargau</td>\n <td></td>\n <td></td>\n <td>NaN</td>\n <td>7.0</td>\n <td>NaN</td>\n <td>1.032133</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>4</th>\n <td>2020-03-05</td>\n <td>CHE</td>\n <td>Switzerland</td>\n <td>CH-AG</td>\n <td>Aargau</td>\n <td></td>\n <td></td>\n <td>NaN</td>\n <td>9.0</td>\n <td>NaN</td>\n <td>1.327028</td>\n <td>NaN</td>\n </tr>\n </tbody>\n</table>\n</div>" }, "metadata": {}, - "execution_count": 5 + "execution_count": 7 } ], "source": [ @@ -91,27 +91,7 @@ }, { "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "output_type": "execute_result", - "data": { - "text/plain": " date country country_label region_iso region_label admin2 \\\n0 2020-02-28 CHE Switzerland CH-AG Aargau \n1 2020-03-02 CHE Switzerland CH-AG Aargau \n2 2020-03-03 CHE Switzerland CH-AG Aargau \n3 2020-03-04 CHE Switzerland CH-AG Aargau \n4 2020-03-05 CHE Switzerland CH-AG Aargau \n... ... ... ... ... ... ... \n14281 2020-03-30 UZB UZB Uzbekistan \n14282 2020-03-30 VNM VNM Vietnam \n14283 2020-03-30 PSE PSE West Bank and Gaza \n14284 2020-03-30 ZMB ZMB Zambia \n14285 2020-03-30 ZWE ZWE Zimbabwe \n\n admin2_label tested positive deceased positive_100k deceased_100k \n0 NaN 1.0 NaN 0.147448 NaN \n1 NaN 2.0 NaN 0.294895 NaN \n2 NaN 6.0 NaN 0.884686 NaN \n3 NaN 7.0 NaN 1.032133 NaN \n4 NaN 9.0 NaN 1.327028 NaN \n... ... ... ... ... ... ... \n14281 149.0 2.0 0.452126 0.006069 \n14282 203.0 0.0 0.212476 0.000000 \n14283 116.0 1.0 2.538800 0.021886 \n14284 35.0 0.0 0.201708 0.000000 \n14285 7.0 1.0 0.048480 0.006926 \n\n[14286 rows x 12 columns]", - 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\"2020-04-06T00:00:00\", \"country\": \"USA\", \"country_label\": \"United States of America\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": 91375, \"positive\": 7984.0, \"deceased\": 338.0, \"positive_100k\": 111.3474082370584, \"deceased_100k\": 4.713855709434587, \"sinceDay0\": 33}, {\"index\": 413, \"date\": \"2020-03-27T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 1578.0, \"deceased\": 11.0, \"positive_100k\": 103.74971728530778, \"deceased_100k\": 0.723223631266404, \"sinceDay0\": 0}, {\"index\": 414, \"date\": \"2020-03-28T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 1720.0, \"deceased\": 15.0, \"positive_100k\": 113.08587688892862, \"deceased_100k\": 0.9862140426360054, \"sinceDay0\": 1}, {\"index\": 415, \"date\": \"2020-03-29T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 1758.0, \"deceased\": 15.0, \"positive_100k\": 115.58428579693985, \"deceased_100k\": 0.9862140426360054, \"sinceDay0\": 2}, {\"index\": 416, \"date\": \"2020-03-30T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 1874.0, \"deceased\": 21.0, \"positive_100k\": 123.2110077266583, \"deceased_100k\": 1.3806996596904075, \"sinceDay0\": 3}, {\"index\": 417, \"date\": \"2020-03-31T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 1960.0, \"deceased\": 25.0, \"positive_100k\": 128.8653015711047, \"deceased_100k\": 1.643690071060009, \"sinceDay0\": 4}, {\"index\": 418, \"date\": \"2020-04-01T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 2148.0, \"deceased\": 29.0, \"positive_100k\": 141.225850905476, \"deceased_100k\": 1.9066804824296106, \"sinceDay0\": 5}, {\"index\": 419, \"date\": \"2020-04-02T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 2323.0, \"deceased\": 36.0, \"positive_100k\": 152.73168140289604, \"deceased_100k\": 2.366913702326413, \"sinceDay0\": 6}, {\"index\": 420, \"date\": \"2020-04-03T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 2452.0, \"deceased\": 38.0, \"positive_100k\": 161.2131221695657, \"deceased_100k\": 2.4984089080112137, \"sinceDay0\": 7}, {\"index\": 421, \"date\": \"2020-04-04T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 2492.0, \"deceased\": 41.0, \"positive_100k\": 163.8430262832617, \"deceased_100k\": 2.695651716538415, \"sinceDay0\": 8}, {\"index\": 422, \"date\": \"2020-04-05T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 2522.0, \"deceased\": 45.0, \"positive_100k\": 165.81545436853372, \"deceased_100k\": 2.9586421279080164, \"sinceDay0\": 9}, {\"index\": 423, \"date\": \"2020-04-06T00:00:00\", \"country\": \"CHE\", \"country_label\": \"Switzerland\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"admin2\": \"\", \"admin2_label\": \"\", \"tested\": null, \"positive\": 2590.0, \"deceased\": 48.0, \"positive_100k\": 170.28629136181695, \"deceased_100k\": 3.1558849364352177, \"sinceDay0\": 10}]}}, {\"mode\": \"vega-lite\"});\n</script>", "text/plain": "alt.HConcatChart(...)" }, "metadata": {}, - "execution_count": 10 + "execution_count": 11 } ], "source": [ @@ -212,6 +192,13 @@ "days_log_100k = plotting.make_region_since_chart(base, 'deceased_100k', 'sinceDay0', 'region_label', 'Days since 10th death', 'Deaths/100k', 'Deaths/100k', 'Region')\n", "alt.hconcat(days_log, days_log_100k)" ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/__init__.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/__init__.py index d90252255cb448e558c96d8f3885deb648408597..28576987ad94395092573b9cc81e0522c1ba7f15 100644 --- a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/__init__.py +++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/__init__.py @@ -43,6 +43,7 @@ class CaseConverterImpl: conversion_dict = {} column_list = [] + neg_column_list = [] common_columns = [ "date", "country", @@ -60,7 +61,7 @@ class CaseConverterImpl: def __init__(self, atlas_folder): """Initialze the converter with the path to the atlas""" - self.atlas_folder = atlas_folder + self.atlas_folder = Path(atlas_folder) def can_convert(self, path): """Returns true if the class can convert the Dataframe.""" @@ -68,7 +69,9 @@ class CaseConverterImpl: df = self.read_data(path) except (FileNotFoundError, ValueError): return False - return all([col in df.columns for col in self.__class__.column_list]) + return all([col in df.columns for col in self.__class__.column_list]) and all( + [col not in df.columns for col in self.__class__.neg_column_list] + ) def read_data(self, path): """Read in the data from a directory path.""" diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/italy.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/italy.py index 48a85458851c2df831d1eddbeba7c9e10f8d29dc..66b5673f52cc945f491e92bd7c22f952bd31acf3 100644 --- a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/italy.py +++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/italy.py @@ -5,12 +5,13 @@ Converters for covid-19 data from Italy. from pathlib import Path import pandas as pd +import zipfile from . import CaseConverterImpl as CaseConverter from .. import helper -class ItalyCaseConverter(CaseConverter): +class ItalyRegionalCaseConverter(CaseConverter): """ Converter for data from Italian Civil Protection and made available at https://github.com/pcm-dpc/COVID-19 @@ -29,10 +30,10 @@ class ItalyCaseConverter(CaseConverter): def convert(self, df): # rename the existing columns - df_conv = df.rename(columns=ItalyCaseConverter.conversion_dict) + df_conv = df.rename(columns=ItalyRegionalCaseConverter.conversion_dict) # get metadata for regions of italy - metadata = pd.read_csv(self.atlas_folder / 'wikidata' / 'ita-population.csv') + metadata = pd.read_csv(self.atlas_folder / "wikidata" / "ita-population.csv") metadata["istatid"] = metadata.istatid.astype(int) df_conv = _correct_trentino(df_conv) merged = pd.merge(df_conv, metadata, on="istatid").drop_duplicates() @@ -41,7 +42,47 @@ class ItalyCaseConverter(CaseConverter): def read_data(self, path): """Read in the data for Italy.""" - df = pd.read_csv(Path(path) / "dpc-covid19-ita-regioni.csv") + if Path(path).is_dir(): + raise ValueError("Must specify a specific file.") + df = pd.read_csv(Path(path)) + return df + + +class ItalyNationalCaseConverter(CaseConverter): + """ + Converter for data from Italian Civil Protection + and made available at https://github.com/pcm-dpc/COVID-19 + """ + + conversion_dict = { + "data": "date", + "totale_casi": "positive", + "tamponi": "tested", + "deceduti": "deceased", + "stato": "country", + } + + column_list = ["data", "stato", "totale_casi"] + neg_column_list = ["codice_regione"] + + def convert(self, df): + # get population data from worldbank + zf = zipfile.ZipFile(Path("../../data/atlas") / "worldbank" / "SP.POP.TOTL.zip") + pop_df = pd.read_csv( + zf.open("API_SP.POP.TOTL_DS2_en_csv_v2_821007.csv"), skiprows=4 + ) + df["population"] = float(pop_df[pop_df["Country Code"] == "ITA"]["2018"]) + + # rename the existing columns + df_conv = df.rename(columns=ItalyRegionalCaseConverter.conversion_dict) + + return self._set_common_columns(df_conv) + + def read_data(self, path): + """Read in the data for Italy.""" + if Path(path).is_dir(): + raise ValueError("Must specify a specific file.") + df = pd.read_csv(Path(path)) return df @@ -62,4 +103,5 @@ def _correct_trentino(df): return df -ItalyCaseConverter._register() +ItalyRegionalCaseConverter._register() +ItalyNationalCaseConverter._register() \ No newline at end of file diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/switzerland.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/switzerland.py index b8f19e776ee292f54ceff7ed8d40f0e862b0c491..14c4267396567a4002dd4ccf80650f9f84880cd4 100644 --- a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/switzerland.py +++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/switzerland.py @@ -51,7 +51,7 @@ class OpenZHCaseConverter(CaseConverter): merged["country"] = "CHE" # standardize the canton names - merged["regionLabel"] = merged.apply( + merged["region_label"] = merged.apply( lambda row: _standardize_canton_name(row["region_label"]), axis=1 )