rework on plots title, legend and name + generate html page with plots

.gitignore

@@ -1,3 +1,4 @@
-output
+static/plots
 data
+build
 .svn

README.md

@@ -24,4 +24,6 @@ python owid.py <country_trigram> <var_1> <var_2> <var..n>
 python dress.py
 ```
 
-**NOTE** : `-r` option is used to fetch update data
+**NOTE** : 
+* `-r` option is used to fetch update data
+* `dress.py` includes **--to-html** to generate html page with plots

drees.py

@@ -10,6 +10,7 @@ from typing import Any, Dict, List, Optional, OrderedDict, Tuple
 
 import numpy as np
 import requests
+from jinja2 import Environment, FileSystemLoader, select_autoescape
 from matplotlib import dates as md
 from matplotlib import pyplot as plt
 
@@ -20,7 +21,11 @@ DATE_FORMAT = "%Y-%m-%d"
 
 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"
+STATIC_REPOSITORY = "static"
+OUTPUT_REPOSITORY = os.path.join(STATIC_REPOSITORY, "plots")
+BUILD_REPOSITORY = "build"
+
+MAIN_URL = "https://covid.thegux.fr/"
 
 # cycler could be better, but for ages plots it's ok
 AGE_COLORS = {
@@ -41,9 +46,9 @@ class DreesEnum(bytes, Enum):
 
 
 class Field(DreesEnum):
-    HC = (0, "hc")
+    HC = (0, "Hospitalisations")
-    SC = (1, "sc")
+    SC = (1, "Soins critiques")
-    DC = (2, "dc")
+    DC = (2, "Décés")
 
 
 class VacStatus(DreesEnum):
@@ -109,7 +114,7 @@ def get_enum_age(value):
 
 def get_enum_field(value):
     for field in Field:
-        if field.label == value:
+        if field.name.lower() == value:
             return field.value
 
 
@@ -141,9 +146,8 @@ def group_by_age_date(data: Dict[str, Any]) -> Dict[dt, Any]:
         if vac_status not in dic_data_grouped[date][age]:
             dic_data_grouped[date][age][vac_status] = OrderedDict()
         for field in Field:
-            dic_data_grouped[date][age][vac_status][field.label] = row_fields[
+            field_name = field.name.lower()
-                field.label
+            dic_data_grouped[date][age][vac_status][field_name] = row_fields[field_name]
-            ]
     logging.info("data restructured")
     return dic_data_grouped
 
@@ -284,7 +288,7 @@ def analyse(np_data: np.ndarray, np_date: np.ndarray) -> None:
             mean_vac_percent = np.round(
                 np.nanmean(np_percent_vac[:, age_group.value, field.value]) * 100, 2
             )
-            print(f"{field.label} - {age_group.label} - vac : {mean_vac_percent}%")
+            print(f"{field.name} - {age_group.label} - vac : {mean_vac_percent}%")
 
     logging.info("--- age by field and vac status mean percent ---")
     for field in Field:
@@ -297,22 +301,20 @@ def analyse(np_data: np.ndarray, np_date: np.ndarray) -> None:
             percent_age_mean = np.round(
                 np.nanmean(np_percent_age[:, age_group.value]), 2
             )
-            print(
+            print(f"age: {age_group.label} - field: {field.name} = {percent_age_mean}%")
-                f"age: {age_group.label} - field: {field.label} = {percent_age_mean}%"
-            )
 
             percent_age_vac_mean = np.round(
                 np.nanmean(np_percent_age_vac[:, age_group.value]), 2
             )
             print(
-                f"age: {age_group.label} - status: vac - field: {field.label} = {percent_age_vac_mean}%"
+                f"age: {age_group.label} - status: vac - field: {field.name} = {percent_age_vac_mean}%"
             )
 
             percent_age_unvac_mean = np.round(
                 np.nanmean(np_percent_age_unvac[:, age_group.value]), 2
             )
             print(
-                f"age: {age_group.label} - status: unvac - field: {field.label} = {percent_age_unvac_mean}%"
+                f"age: {age_group.label} - status: unvac - field: {field.name} = {percent_age_unvac_mean}%"
             )
 
 
@@ -324,7 +326,8 @@ def plot_bar_age_percent_vac_status_by_field(
 ) -> None:
     fig, ax = get_plot_fig(figsize=(22, 8), locator=md.WeekdayLocator())
     bottom = np_data_vac_status[:, 0]
-    title = "vac" if is_vac else "no vac"
+    suffix = "vac" if is_vac else "unvac"
+    title = "Vaccinés" if is_vac else "Non vaccinés"
     for age_group in AgeGroup:
         percents_age = np_data_vac_status[:, age_group.value]
         if age_group.value > 0:
@@ -351,7 +354,7 @@ def plot_bar_age_percent_vac_status_by_field(
     )
     save_and_close_fig(
         fig,
-        os.path.join(OUTPUT_REPOSITORY, f"age_percent_{title}_{field.label}"),
+        os.path.join(OUTPUT_REPOSITORY, f"age_percent_{suffix}_{field.name.lower()}"),
         has_legend=False,
     )
 
@@ -385,13 +388,13 @@ def plot_cumulative_field(
         np_cumulate_unvac: np.ndarray = np.cumsum(
             np_data_unvac[:, age_group.value, field.value], axis=0
         )
-        plt.plot(np_date, np_cumulate_vac, label=f"{age_group.label} vac")
+        plt.plot(np_date, np_cumulate_vac, label=f"{age_group.label} Vaccinés")
-        plt.plot(np_date, np_cumulate_unvac, label=f"{age_group.label} no vac")
+        plt.plot(np_date, np_cumulate_unvac, label=f"{age_group.label} Non vaccinés")
 
-    plt.title(f"nombre de {field.label} cumulé par age")
+    plt.title(f"{field.label} cumulés par âge")
     plt.xlabel("date")
     save_and_close_fig(
-        fig, os.path.join(OUTPUT_REPOSITORY, f"cumulative_{field.label}")
+        fig, os.path.join(OUTPUT_REPOSITORY, f"cumulative_{field.name.lower()}")
     )
 
 
@@ -411,11 +414,13 @@ def plot_fields_by_age_vac(
         )
         plt.xlabel("date")
         plt.ylabel("nombre")
-        plt.title(f"{age_group.label}ans - {vac_status.label}")
+        plt.title(f"{age_group.label} - {vac_status.label}")
 
     save_and_close_fig(
         fig,
-        os.path.join(OUTPUT_REPOSITORY, f"all_{age_group.label}_{vac_status.label}"),
+        os.path.join(
+            OUTPUT_REPOSITORY, f"all_{age_group.name.lower()}_{vac_status.name.lower()}"
+        ),
     )
 
 
@@ -440,8 +445,10 @@ def plot_bar_data_by_age_field(
         unvac_percent = np.round(
             np_percent_unvac[idx_date, age_group.value, field.value] * 100, 2
         )
-        bar_vac = ax.bar(idx_date, vac_percent, color="b", label="vac")
+        bar_vac = ax.bar(idx_date, vac_percent, color="b", label="Vaccinés")
-        ax.bar(idx_date, unvac_percent, bottom=vac_percent, color="r", label="no vac")
+        ax.bar(
+            idx_date, unvac_percent, bottom=vac_percent, color="r", label="Non vaccinés"
+        )
         ax.bar_label(
             bar_vac, label_type="edge", color="black", fontsize="7", fmt="%.0f"
         )
@@ -458,11 +465,14 @@ def plot_bar_data_by_age_field(
             for idx, d in enumerate(np_date.astype(dt))
         ],
     )
-    plt.legend(["vac", "no vac"], loc="upper right", frameon=True)
+    plt.legend(["Vaccinés", "Non vaccinés"], loc="upper right", frameon=True)
 
     save_and_close_fig(
         fig,
-        os.path.join(OUTPUT_REPOSITORY, f"vac_percent_{age_group.label}_{field.label}"),
+        os.path.join(
+            OUTPUT_REPOSITORY,
+            f"vac_percent_{age_group.name.lower()}_{field.name.lower()}",
+        ),
         has_legend=False,
     )
 
@@ -489,6 +499,27 @@ def get_age_field_args() -> List[Tuple[AgeGroup, Field]]:
     return pool_args
 
 
+def generate_html_page() -> None:
+    logging.info("generating html page with plots...")
+    os.makedirs(BUILD_REPOSITORY, exist_ok=True)
+    env = Environment(
+        loader=FileSystemLoader("templates"), autoescape=select_autoescape()
+    )
+    template = env.get_template("index.template.html")
+    data = template.render(
+        **{
+            "fields": Field,
+            "ages": AgeGroup,
+            "status": VacStatus,
+            "static": os.path.join(MAIN_URL, STATIC_REPOSITORY),
+            "src": DATA_URL,
+        }
+    )
+    with open(os.path.join(BUILD_REPOSITORY, "index.html"), "w") as f:
+        f.write(data)
+    logging.info("html page build")
+
+
 if __name__ == "__main__":
     """
     This script aims to plot DRESS data
@@ -517,13 +548,18 @@ if __name__ == "__main__":
         "--no-plot",
         action="store_true",
         default=False,
-        help="redownload data for updates",
+        help="no plot data",
+    )
+    parser.add_argument(
+        "-th",
+        "--to-html",
+        action="store_true",
+        default=False,
+        help="create an html with the plots",
     )
 
     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
     )
@@ -533,6 +569,7 @@ if __name__ == "__main__":
     analyse(np_data, np_date)
 
     if not args.no_plot:
+        os.makedirs(OUTPUT_REPOSITORY, exist_ok=True)
         plot_fields_args = get_age_vac_args()
         f_fields = partial(plot_fields_by_age_vac, np_data, np_date)
         plot_vac_percent_age_args = get_age_field_args()
@@ -544,3 +581,6 @@ if __name__ == "__main__":
         for field in Field:
             plot_cumulative_field(np_data, np_date, field)
             plot_bar_age_percent_by_field(np_data, np_date, field)
+
+    if args.to_html:
+        generate_html_page()

static/css/index.css

@@ -0,0 +1,31 @@
+.main-container {
+    display: flex;
+    flex-direction: column;
+    flex-wrap: nowrap;
+    justify-content: center;
+    text-align: center;
+}
+
+.plot-container {
+    display: flex;
+    flex-direction: row;
+    justify-content: center;
+    align-items: center;
+    flex-wrap: wrap;
+}
+
+.plot-item {
+    flex: 0 1 33%
+}
+
+.img-bars {
+    width: 1500px;
+    height: 500px;
+    border: solid
+}
+ 
+img {
+    width: 100%;
+    height: 100%;
+    object-fit: contain;
+}

templates/index.template.html

@@ -0,0 +1,45 @@
+<!DOCTYPE html>
+<html>
+    <head>
+        <title>Covid data extraction from DRESS dataset</title>
+        <meta charset="UTF-8">
+        <meta name="keywords" content="thegux, covid">
+        <link rel="stylesheet" href="{{ static }}/css/index.css">
+        <meta name="description" content="A simple page to share some useful data about covid 19">
+    </head>
+    <body>
+        <div class="main-container">
+            <h1>Thegux covid-19</h1>
+            <div>source : <a href="{{ src }}">Data DRESS</a></div>
+            <h3>Hospitalisations/Soins critiques/Décés par status vaccinal groupés par tranches d'âges</h3>
+            {% for field in fields %}
+                <img src="{{ static }}/plots/age_percent_vac_{{ field.name.lower() }}.png"/>
+                <img src="{{ static }}/plots/age_percent_unvac_{{ field.name.lower() }}.png"/>
+            {% endfor %}
+            <h3>Hospitalisations/Soins critiques/Décés par tranches d'âges groupés par status vaccinal</h3>
+            {% for age in ages %}
+                {% for field in fields %}
+                    <img src="{{ static }}/plots/vac_percent_{{ age.name.lower() }}_{{ field.name.lower() }}.png"/>
+                {% endfor %}
+            {% endfor %}
+            <h3>Hospitalisations/Soins critiques/Décés par tranches d'âges et status vaccinal</h3>
+            <div class="plot-container">
+                {% for age in ages %}
+                    {% for vac_status in status %}
+                        <div class="plot-item">
+                            <img src="{{ static }}/plots/all_{{ age.name.lower() }}_{{ vac_status.name.lower() }}.png"/>
+                        </div>
+                    {% endfor %}
+                {% endfor %}
+            </div>
+            <h3>Hospitalisations/Soins critiques/Décés cumulés par tranches d'âges et status vaccinal</h3>
+            <div class="plot-container">
+                {% for field in fields %}
+                    <div class="plot-item">
+                        <img src="{{ static }}/plots/cumulative_{{ field.name.lower() }}.png"/>
+                    </div>
+                {% endfor %}
+            </div>
+        </div>
+    </body>
+</html>