rename main script + init drees data plotter + update README.md

README.md

@@ -1,6 +1,11 @@
 # README
 
-A simple covid plotter. Data are provided by : https://github.com/owid/covid-19-data/tree/master/public/data
+A simple covid plotter. 
+
+Data are provided by : 
+* https://github.com/owid/covid-19-data/tree/master/public/data
+* https://data.drees.solidarites-sante.gouv.fr/api/records/1.0/search/?dataset=covid-19-resultats-par-age-issus-des-appariements-entre-si-vic-si-dep-et-vac-si&q=&rows=-1&facet=date&facet=vac_statut&facet=age"
+
 
 ## Installation
 
@@ -11,8 +16,12 @@ pip install -r requirements.txt
 ## Launch
 
 ```bash
-python main.py <country_trigram> <var_1> <var_2> <var..n>
+# owid dataset
-# Ex : python main.py FRA new_cases_smoothed new_deaths_smoothed people_fully_vaccinated hosp_patients
+python owid.py <country_trigram> <var_1> <var_2> <var..n>
+# Ex : python owid.py FRA new_cases_smoothed new_deaths_smoothed people_fully_vaccinated hosp_patients
+
+# drees dataset
+python dress.py
 ```
 
 **NOTE** : `-r` option is used to fetch update data

drees.py

@@ -0,0 +1,160 @@
+import argparse
+import json
+import logging
+import os
+from enum import Enum
+from typing import Any, Dict, List, Optional, OrderedDict
+
+import requests
+from matplotlib import dates as md
+from matplotlib import pyplot as plt
+
+FORMAT = "%(asctime)s - %(levelname)s - %(message)s"
+logging.basicConfig(format=FORMAT, level=logging.INFO)
+
+DATA_URL = "https://data.drees.solidarites-sante.gouv.fr/api/records/1.0/search/?dataset=covid-19-resultats-par-age-issus-des-appariements-entre-si-vic-si-dep-et-vac-si&q=&rows=-1&facet=date&facet=vac_statut&facet=age"
+DATA_REPOSITORY = "data"
+OUTPUT_REPOSITORY = "output"
+
+
+class Field(str, Enum):
+    HC = "hc"
+    SC = "sc"
+    DC = "dc"
+    EFF = "effectif"
+
+
+class VacStatus(str, Enum):
+    NC = "Non-vaccinés"
+    PDR = "Primo dose récente"
+    PDE = "Primo dose efficace"
+    CM3MSR = "Complet de moins de 3 mois - sans rappel"
+    CM3MAR = "Complet de moins de 3 mois - avec rappel"
+    CM36MSR = "Complet entre 3 mois et 6 mois - sans rappel"
+    CM36MAR = "Complet entre 3 mois et 6 mois - avec rappel"
+
+
+class AgeGroup(str, Enum):
+    VERY_YOUNG = "[0,19]"
+    YONG = "[20,39]"
+    MID_OLD = "[40,59]"
+    OLD = "[60,79]"
+    VERY_OLD = "[80;+]"
+
+
+def get_data(
+    file_path: Optional[str] = None,
+    extension: Optional[str] = "json",
+    refresh=False,
+) -> Dict[str, Any]:
+    """
+    Collect covid data by age from DREES
+    """
+    os.makedirs(DATA_REPOSITORY, exist_ok=True)
+    data_url = DATA_URL.format(extension=extension)
+    if data_url.endswith("/"):
+        data_url = data_url[:-1]
+    file_path = (
+        os.path.join(DATA_REPOSITORY, data_url.split("/")[-1])
+        if file_path is None
+        else file_path
+    )
+    if not os.path.isfile(file_path) or refresh:
+        r = requests.get(data_url)
+        if not r.content:
+            raise ValueError("no data provided froim the url : {}".format(data_url))
+        with open(file_path, "wb") as f:
+            f.write(r.content)
+            return json.loads(r.content)
+    return json.load(open(file_path, "rb"))
+
+
+def group_by_age_date(data: Dict[str, Any], fields: List[str]) -> Dict[str, Any]:
+    """
+    Group the original dictionnary into a more readable one
+    'date': {
+        'age' : {
+            'vac_status' : {
+                'hc',
+                'sc',
+                'dc',
+                ...
+            }
+        }
+    }
+    """
+    dic_data_grouped: Dict[str, Any] = OrderedDict()
+    for row in data["records"]:
+        row_fields = row["fields"]
+        date = row_fields["date"]
+        age = row_fields["age"]
+        vac_status = row_fields["vac_statut"]
+        if date not in dic_data_grouped:
+            dic_data_grouped[date] = OrderedDict()
+        if age not in dic_data_grouped[date]:
+            dic_data_grouped[date][age] = OrderedDict()
+        if vac_status not in dic_data_grouped[date][age]:
+            dic_data_grouped[date][age][vac_status] = OrderedDict()
+        for field in fields:
+            dic_data_grouped[date][age][vac_status][field] = row_fields[field]
+    return dic_data_grouped
+
+
+def plot(dic_data_grouped: Dict[str, Any], age: str, vac_status: str) -> None:
+    """
+    Plot data by vaccine status and age
+    """
+    x: List[str] = list()
+    hc: List[float] = list()
+    sc: List[float] = list()
+    dc: List[float] = list()
+    fig, ax = plt.subplots()
+    for date, dic_age_grouped in dic_data_grouped.items():
+        print(Field.HC.value)
+        hc.append(dic_age_grouped[age][vac_status][Field.HC.value])
+        sc.append(dic_age_grouped[age][vac_status][Field.SC.value])
+        dc.append(dic_age_grouped[age][vac_status][Field.DC.value])
+        x.append(date)
+    plt.plot(x, hc, label="hospitalisation")
+    plt.plot(x, sc, label="soin_critique")
+    plt.plot(x, dc, label="deces")
+    plt.xlabel("date")
+    plt.ylabel("nombre")
+    plt.title(f"{age}ans - {vac_status}")
+    ax.grid(True)
+    ax.xaxis.set_major_locator(md.MonthLocator())
+    fig.autofmt_xdate()
+    plt.legend()
+    plt.savefig(os.path.join(OUTPUT_REPOSITORY, f"{age}_{vac_status}.pdf"))
+
+
+if __name__ == "__main__":
+    """
+    This script aims to plot DRESS data with vaccine status and ages grouped
+    Main indicators are :
+        - hospitalisations
+        - criticals
+        - deaths
+    """
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "-r",
+        "--refresh",
+        action="store_true",
+        default=False,
+        help="redownload data for updates",
+    )
+
+    args = parser.parse_args()
+
+    os.makedirs(OUTPUT_REPOSITORY, exist_ok=True)
+
+    dic_data: Dict[str, Any] = get_data(
+        file_path=os.path.join(DATA_REPOSITORY, "dress.json"), refresh=args.refresh
+    )
+    dic_data_grouped: Dict[str, Any] = group_by_age_date(
+        dic_data, [x.value for x in Field]
+    )
+    plot(dic_data_grouped, AgeGroup.YONG, VacStatus.NC.value)
+    plot(dic_data_grouped, AgeGroup.YONG, VacStatus.CM3MSR.value)