From fccd8bbd43d06dcd7503880cc52da4076e8e123a Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <cramakri@ethz.ch>
Date: Sat, 4 Apr 2020 00:17:37 +0200
Subject: [PATCH] refactor: initialize converters with the atlas
---
notebooks/process/standardize_datasets.ipynb | 146 +++++++-----------
.../covid_19_dashboard/converters/__init__.py | 50 ++++--
.../converters/covidtracking.py | 2 +-
.../covid_19_dashboard/converters/italy.py | 2 +-
.../covid_19_dashboard/converters/spain.py | 2 +-
.../converters/switzerland.py | 2 +-
6 files changed, 98 insertions(+), 106 deletions(-)
diff --git a/notebooks/process/standardize_datasets.ipynb b/notebooks/process/standardize_datasets.ipynb
index 8a294aab2..9f5e326aa 100644
--- a/notebooks/process/standardize_datasets.ipynb
+++ b/notebooks/process/standardize_datasets.ipynb
@@ -1,31 +1,8 @@
{
- "nbformat": 4,
- "nbformat_minor": 2,
- "metadata": {
- "language_info": {
- "name": "python",
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "version": "3.7.7-final"
- },
- "orig_nbformat": 2,
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "npconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": 3,
- "kernelspec": {
- "name": "python37764bitvenvvenv814492364d964019a25eb1cf3dc3e99c",
- "display_name": "Python 3.7.7 64-bit ('.venv': venv)"
- }
- },
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -46,7 +23,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -64,15 +41,18 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "name": "stdout",
- "text": "using: <class 'covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.italy.ItalyCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.spain.SpainCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.switzerland.OpenZHCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.italy.ItalyCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.covidtracking.CovidtrackingCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.italy.ItalyCaseConverter'>\nusing: <class 'covid_19_dashboard.converters.spain.SpainCaseConverter'>\n"
- }
- ],
+ "outputs": [],
+ "source": [
+ "converter = CaseConverter(\"../../data/atlas/\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
"source": [
"df_list = []\n",
"for path in [\n",
@@ -81,14 +61,14 @@
" '../../data/covidtracking/', \n",
" '../../data/covid-19-spain'\n",
"]:\n",
- " df_list.append(CaseConverter.read_convert(path))\n",
+ " df_list.append(converter.read_convert(path))\n",
"df_all = pd.concat(df_list).reset_index(drop=True)\n",
"df_all['date'] = pd.to_datetime(df_all.date)"
]
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -97,19 +77,9 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "output_type": "execute_result",
- "data": {
- "text/plain": " date country region_iso region_label tested positive deceased \\\n0 2020-02-27 ESP ES-AN AndalucÃa None 1 NaN \n1 2020-02-28 ESP ES-AN AndalucÃa None 6 NaN \n2 2020-02-29 ESP ES-AN AndalucÃa None 8 NaN \n3 2020-03-01 ESP ES-AN AndalucÃa None 12 NaN \n4 2020-03-02 ESP ES-AN AndalucÃa None 12 NaN \n.. ... ... ... ... ... ... ... \n622 2020-03-26 ESP ES-RI La Rioja None 995 43.0 \n623 2020-03-27 ESP ES-RI La Rioja None 1236 55.0 \n624 2020-03-28 ESP ES-RI La Rioja None 1436 65.0 \n625 2020-03-29 ESP ES-RI La Rioja None 1629 68.0 \n626 2020-03-30 ESP ES-RI La Rioja None 1733 71.0 \n\n population positive_100k deceased_100k \n0 8409738 0.011891 NaN \n1 8409738 0.071346 NaN \n2 8409738 0.095128 NaN \n3 8409738 0.142692 NaN \n4 8409738 0.142692 NaN \n.. ... ... ... \n622 315675 315.197592 13.621604 \n623 315675 391.541934 17.422982 \n624 315675 454.898234 20.590797 \n625 315675 516.037063 21.541142 \n626 315675 548.982339 22.491486 \n\n[627 rows x 10 columns]",
- "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>region_iso</th>\n <th>region_label</th>\n <th>tested</th>\n <th>positive</th>\n <th>deceased</th>\n <th>population</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>2020-02-27</td>\n <td>ESP</td>\n <td>ES-AN</td>\n <td>AndalucÃa</td>\n <td>None</td>\n <td>1</td>\n <td>NaN</td>\n <td>8409738</td>\n <td>0.011891</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>1</th>\n <td>2020-02-28</td>\n <td>ESP</td>\n <td>ES-AN</td>\n <td>AndalucÃa</td>\n <td>None</td>\n <td>6</td>\n <td>NaN</td>\n <td>8409738</td>\n <td>0.071346</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>2</th>\n <td>2020-02-29</td>\n <td>ESP</td>\n <td>ES-AN</td>\n <td>AndalucÃa</td>\n <td>None</td>\n <td>8</td>\n <td>NaN</td>\n <td>8409738</td>\n <td>0.095128</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>3</th>\n <td>2020-03-01</td>\n <td>ESP</td>\n <td>ES-AN</td>\n <td>AndalucÃa</td>\n <td>None</td>\n <td>12</td>\n <td>NaN</td>\n <td>8409738</td>\n <td>0.142692</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>4</th>\n <td>2020-03-02</td>\n <td>ESP</td>\n <td>ES-AN</td>\n <td>AndalucÃa</td>\n <td>None</td>\n <td>12</td>\n <td>NaN</td>\n <td>8409738</td>\n <td>0.142692</td>\n <td>NaN</td>\n </tr>\n <tr>\n <th>...</th>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n </tr>\n <tr>\n <th>622</th>\n <td>2020-03-26</td>\n <td>ESP</td>\n <td>ES-RI</td>\n <td>La Rioja</td>\n <td>None</td>\n <td>995</td>\n <td>43.0</td>\n <td>315675</td>\n <td>315.197592</td>\n <td>13.621604</td>\n </tr>\n <tr>\n <th>623</th>\n <td>2020-03-27</td>\n <td>ESP</td>\n <td>ES-RI</td>\n <td>La Rioja</td>\n <td>None</td>\n <td>1236</td>\n <td>55.0</td>\n <td>315675</td>\n <td>391.541934</td>\n <td>17.422982</td>\n </tr>\n <tr>\n <th>624</th>\n <td>2020-03-28</td>\n <td>ESP</td>\n <td>ES-RI</td>\n <td>La Rioja</td>\n <td>None</td>\n <td>1436</td>\n <td>65.0</td>\n <td>315675</td>\n <td>454.898234</td>\n <td>20.590797</td>\n </tr>\n <tr>\n <th>625</th>\n <td>2020-03-29</td>\n <td>ESP</td>\n <td>ES-RI</td>\n <td>La Rioja</td>\n <td>None</td>\n <td>1629</td>\n <td>68.0</td>\n <td>315675</td>\n <td>516.037063</td>\n <td>21.541142</td>\n </tr>\n <tr>\n <th>626</th>\n <td>2020-03-30</td>\n <td>ESP</td>\n <td>ES-RI</td>\n <td>La Rioja</td>\n <td>None</td>\n <td>1733</td>\n <td>71.0</td>\n <td>315675</td>\n <td>548.982339</td>\n <td>22.491486</td>\n </tr>\n </tbody>\n</table>\n<p>627 rows × 10 columns</p>\n</div>"
- },
- "metadata": {},
- "execution_count": 5
- }
- ],
+ "outputs": [],
"source": [
"\n",
"SpainCaseConverter.convert(df_esp)"
@@ -117,7 +87,7 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -126,19 +96,9 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "output_type": "execute_result",
- "data": {
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{\"date\": \"2020-03-19T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-TI\", \"region_label\": \"Ticino\", \"tested\": null, \"positive\": 638.0, \"deceased\": 15.0, \"population\": 353343, \"positive_100k\": 180.56109785675676, \"deceased_100k\": 4.245166877509955}, {\"date\": \"2020-03-20T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-TI\", \"region_label\": \"Ticino\", \"tested\": null, \"positive\": 834.0, \"deceased\": 22.0, \"population\": 353343, \"positive_100k\": 236.0312783895535, \"deceased_100k\": 6.226244753681267}, {\"date\": \"2020-03-21T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-TI\", \"region_label\": \"Ticino\", \"tested\": null, \"positive\": 918.0, \"deceased\": 28.0, \"population\": 353343, \"positive_100k\": 259.8042129036092, \"deceased_100k\": 7.9243115046852495}, {\"date\": \"2020-03-22T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-TI\", \"region_label\": \"Ticino\", \"tested\": null, \"positive\": 939.0, \"deceased\": 37.0, \"population\": 353343, \"positive_100k\": 265.74744653212315, \"deceased_100k\": 10.471411631191222}, {\"date\": \"2020-03-23T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-TI\", \"region_label\": \"Ticino\", \"tested\": null, \"positive\": 1165.0, \"deceased\": 48.0, \"population\": 353343, \"positive_100k\": 329.70796081993984, \"deceased_100k\": 13.584534008031856}, {\"date\": \"2020-03-24T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-TI\", \"region_label\": \"Ticino\", \"tested\": null, \"positive\": 1211.0, \"deceased\": 53.0, \"population\": 353343, \"positive_100k\": 342.726472577637, \"deceased_100k\": 14.999589633868506}, {\"date\": \"2020-03-25T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-TI\", \"region_label\": \"Ticino\", \"tested\": null, \"positive\": 1354.0, \"deceased\": 60.0, \"population\": 353343, \"positive_100k\": 383.19706347656523, \"deceased_100k\": 16.98066751003982}, {\"date\": \"2020-03-26T00:00:00\", \"country\": \"CHE\", 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\"vega-lite\"});\n</script>",
- "text/plain": "alt.Chart(...)"
- },
- "metadata": {},
- "execution_count": 9
- }
- ],
+ "outputs": [],
"source": [
"base = alt.Chart(df_all[df_all.region_label.isin(regions)])\n",
"base.mark_line().encode(alt.X('date'), alt.Y('positive', scale=alt.Scale(type='linear')), color='region_label')"
@@ -146,19 +106,9 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "output_type": "execute_result",
- "data": {
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- "text/plain": "alt.HConcatChart(...)"
- },
- "metadata": {},
- "execution_count": 10
- }
- ],
+ "outputs": [],
"source": [
"since_df_positive = helper.make_since_df(df_all[df_all.region_label.isin(regions)], region_column='region_label', start_case=100)\n",
"base = alt.Chart(since_df_positive).properties(height=300,width=300)\n",
@@ -169,19 +119,9 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "output_type": "execute_result",
- "data": {
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\"2020-03-11T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 2442.0, \"positive\": 2442.0, \"deceased\": 24.0, \"population\": 7170351, \"positive_100k\": 34.05691018473154, \"deceased_100k\": 0.3347116480071896, \"sinceDay0\": 0}, {\"index\": 2396, \"date\": \"2020-03-12T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 3374.0, \"positive\": 3374.0, \"deceased\": 29.0, \"population\": 7170351, \"positive_100k\": 47.054879182344074, \"deceased_100k\": 0.40444324134202075, \"sinceDay0\": 1}, {\"index\": 2395, \"date\": \"2020-03-13T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 4807.0, \"positive\": 4807.0, \"deceased\": 31.0, \"population\": 7170351, \"positive_100k\": 67.03995383210669, \"deceased_100k\": 0.4323358786759532, \"sinceDay0\": 2}, {\"index\": 2394, \"date\": \"2020-03-14T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 6569.0, \"positive\": 6569.0, \"deceased\": 37.0, \"population\": 7170351, \"positive_100k\": 91.61336732330119, \"deceased_100k\": 0.5160137906777507, \"sinceDay0\": 3}, {\"index\": 2393, \"date\": \"2020-03-15T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 7764.0, \"positive\": 7764.0, \"deceased\": 40.0, \"population\": 7170351, \"positive_100k\": 108.27921813032584, \"deceased_100k\": 0.5578527466786494, \"sinceDay0\": 4}, {\"index\": 2392, \"date\": \"2020-03-16T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 10220.0, \"positive\": 10220.0, \"deceased\": 42.0, \"population\": 7170351, \"positive_100k\": 142.53137677639492, \"deceased_100k\": 0.5857453840125818, \"sinceDay0\": 5}, {\"index\": 2391, \"date\": \"2020-03-17T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 12486.0, \"positive\": 12486.0, \"deceased\": 48.0, \"population\": 7170351, \"positive_100k\": 174.1337348757404, \"deceased_100k\": 0.6694232960143792, \"sinceDay0\": 6}, {\"index\": 2390, \"date\": \"2020-03-18T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 14129.0, \"positive\": 14129.0, \"deceased\": 52.0, \"population\": 7170351, \"positive_100k\": 197.0475364455659, \"deceased_100k\": 0.7252085706822441, \"sinceDay0\": 7}, {\"index\": 2389, \"date\": \"2020-03-19T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 17105.0, \"positive\": 17105.0, \"deceased\": 66.0, \"population\": 7170351, \"positive_100k\": 238.55178079845743, \"deceased_100k\": 0.9204570320197714, \"sinceDay0\": 8}, {\"index\": 2388, \"date\": \"2020-03-20T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 20712.0, \"positive\": 20712.0, \"deceased\": 74.0, \"population\": 7170351, \"positive_100k\": 288.8561522302046, \"deceased_100k\": 1.0320275813555013, \"sinceDay0\": 9}, {\"index\": 2387, \"date\": \"2020-03-21T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 23243.0, \"positive\": 23243.0, \"deceased\": 83.0, \"population\": 7170351, \"positive_100k\": 324.1542847762962, \"deceased_100k\": 1.1575444493581972, \"sinceDay0\": 10}, {\"index\": 2386, \"date\": \"2020-03-22T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 27121.0, \"positive\": 27121.0, \"deceased\": 94.0, \"population\": 7170351, \"positive_100k\": 378.2381085667912, \"deceased_100k\": 1.310953954694826, \"sinceDay0\": 11}, {\"index\": 2385, \"date\": \"2020-03-23T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 30875.0, \"positive\": 30875.0, \"deceased\": 95.0, \"population\": 7170351, \"positive_100k\": 430.5925888425825, \"deceased_100k\": 1.3249002733617923, \"sinceDay0\": 12}, {\"index\": 2384, \"date\": \"2020-03-24T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 33933.0, \"positive\": 33933.0, \"deceased\": 110.0, \"population\": 7170351, \"positive_100k\": 473.2404313261652, \"deceased_100k\": 1.5340950533662856, \"sinceDay0\": 13}, {\"index\": 2383, \"date\": \"2020-03-25T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 34181.0, \"positive\": 34181.0, \"deceased\": 123.0, \"population\": 7170351, \"positive_100k\": 476.69911835557286, \"deceased_100k\": 1.7153971960368468, \"sinceDay0\": 14}, {\"index\": 2382, \"date\": \"2020-03-26T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 34292.0, \"positive\": 34292.0, \"deceased\": 132.0, \"population\": 7170351, \"positive_100k\": 478.2471597276061, \"deceased_100k\": 1.8409140640395427, \"sinceDay0\": 15}, {\"index\": 2381, \"date\": \"2020-03-27T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 46380.0, \"positive\": 46380.0, \"deceased\": 147.0, \"population\": 7170351, \"positive_100k\": 646.830259773894, \"deceased_100k\": 2.0501088440440363, \"sinceDay0\": 16}, {\"index\": 2380, \"date\": \"2020-03-28T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 52738.0, \"positive\": 52738.0, \"deceased\": 175.0, \"population\": 7170351, \"positive_100k\": 735.5009538584652, \"deceased_100k\": 2.4406057667190906, \"sinceDay0\": 17}, {\"index\": 2379, \"date\": \"2020-03-29T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 59206.0, \"positive\": 59206.0, \"deceased\": 189.0, \"population\": 7170351, \"positive_100k\": 825.7057429964028, \"deceased_100k\": 2.635854228056618, \"sinceDay0\": 18}, {\"index\": 2378, \"date\": \"2020-03-30T00:00:00\", \"country\": \"USA\", \"region_iso\": \"US-WA\", \"region_label\": \"Washington\", \"tested\": 65462.0, \"positive\": 65462.0, \"deceased\": 195.0, \"population\": 7170351, \"positive_100k\": 912.9539125769436, \"deceased_100k\": 2.7195321400584156, \"sinceDay0\": 19}, {\"index\": 309, \"date\": \"2020-03-27T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"tested\": null, \"positive\": 1578.0, \"deceased\": 11.0, \"population\": 1520968, \"positive_100k\": 103.74971728530778, \"deceased_100k\": 0.723223631266404, \"sinceDay0\": 0}, {\"index\": 310, \"date\": \"2020-03-28T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"tested\": null, \"positive\": 1720.0, \"deceased\": 15.0, \"population\": 1520968, \"positive_100k\": 113.08587688892862, \"deceased_100k\": 0.9862140426360054, \"sinceDay0\": 1}, {\"index\": 311, \"date\": \"2020-03-29T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"tested\": null, \"positive\": 1758.0, \"deceased\": 15.0, \"population\": 1520968, \"positive_100k\": 115.58428579693985, \"deceased_100k\": 0.9862140426360054, \"sinceDay0\": 2}, {\"index\": 312, \"date\": \"2020-03-30T00:00:00\", \"country\": \"CHE\", \"region_iso\": \"CH-ZH\", \"region_label\": \"Z\\u00fcrich\", \"tested\": null, \"positive\": 1874.0, \"deceased\": 21.0, \"population\": 1520968, \"positive_100k\": 123.2110077266583, \"deceased_100k\": 1.3806996596904075, \"sinceDay0\": 3}]}}, {\"mode\": \"vega-lite\"});\n</script>",
- "text/plain": "alt.HConcatChart(...)"
- },
- "metadata": {},
- "execution_count": 11
- }
- ],
+ "outputs": [],
"source": [
"since_df_deceased = helper.make_since_df(df_all[df_all.region_label.isin(regions)], column='deceased', region_column='region_label', start_case=10)\n",
"base = alt.Chart(since_df_deceased).properties(height=300,width=300)\n",
@@ -189,13 +129,33 @@
"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": []
}
- ]
-}
\ No newline at end of file
+ ],
+ "metadata": {
+ "file_extension": ".py",
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.7.7"
+ },
+ "mimetype": "text/x-python",
+ "name": "python",
+ "npconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": 3
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
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 7bad5783c..7a8e3e037 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
@@ -30,6 +30,47 @@ class CaseConverter():
"deceased_100k",
]
+ def __init__(self, atlas_folder):
+ """Initialze the converter with the path to the atlas"""
+ self.atlas_folder = atlas_folder
+ self.converters = []
+ self.init_converters()
+
+ def init_converters(self):
+ self.converters = [cls(self.atlas_folder) for cls in CaseConverter._converter_registry]
+
+ def read_convert(self, path):
+ """Converts the Dataframe into the common format."""
+ for converter in self.converters:
+ if converter.can_convert(path):
+ print(f'Using {converter} for {path}')
+ return converter.convert(converter.read_data(path))
+ raise NotImplementedError(f"{path} could not be read and converted.")
+
+
+
+class CaseConverterImpl:
+ """Base converter class."""
+
+ conversion_dict = {}
+ column_list = []
+ common_columns = [
+ "date",
+ "country",
+ "region_iso",
+ "region_label",
+ "tested",
+ "positive",
+ "deceased",
+ "population",
+ "positive_100k",
+ "deceased_100k",
+ ]
+
+ def __init__(self, atlas_folder):
+ """Initialze the converter with the path to the atlas"""
+ self.atlas_folder = atlas_folder
+
@classmethod
def can_convert(cls, path):
"""Returns true if the class can convert the Dataframe."""
@@ -39,15 +80,6 @@ class CaseConverter():
return False
return all([col in df.columns for col in cls.column_list])
- @classmethod
- def read_convert(cls, path):
- """Converts the Dataframe into the common format."""
- for converter in cls._converter_registry:
- if converter.can_convert(path):
- print(f'Using {converter} for {path}')
- return converter.convert(converter.read_data(path))
- raise NotImplementedError(f"{path} could not be read and converted.")
-
@classmethod
def read_data(cls, path):
"""Read in the data from a directory path."""
diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/covidtracking.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/covidtracking.py
index 13b6aec15..c2e6c0699 100644
--- a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/covidtracking.py
+++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/covidtracking.py
@@ -7,7 +7,7 @@ from pathlib import Path
import pandas as pd
-from . import CaseConverter
+from . import CaseConverterImpl as CaseConverter
from .. import helper
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 11873554a..ea683e92e 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
@@ -6,7 +6,7 @@ from pathlib import Path
import pandas as pd
-from . import CaseConverter
+from . import CaseConverterImpl as CaseConverter
from .. import helper
diff --git a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/spain.py b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/spain.py
index df0f2c391..f33b6c256 100644
--- a/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/spain.py
+++ b/src/covid-19/covid_19_dashboard/covid_19_dashboard/converters/spain.py
@@ -6,7 +6,7 @@ from pathlib import Path
import pandas as pd
-from . import CaseConverter
+from . import CaseConverterImpl as CaseConverter
from .. import helper
# regional populations extracted from wikidata and wikipedia
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 035e0d7f2..924d984fd 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
@@ -6,7 +6,7 @@ from pathlib import Path
import pandas as pd
-from . import CaseConverter
+from . import CaseConverterImpl as CaseConverter
from .. import helper
--
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