Merge branch 'feature/global_incident_rates' into 'master'

Global incident rates

Closes #279

See merge request cara/caimira!405

caimira/apps/calculator/__init__.py

@@ -8,6 +8,8 @@ import base64
 import functools
 import html
 import json
+import pandas as pd
+from io import StringIO
 import os
 from pathlib import Path
 import traceback
@@ -298,6 +300,44 @@ class ArveData(BaseRequestHandler):
         self.set_header("Content-Type", 'application/json')
         return self.finish(response.body)
 
+    
+class CasesData(BaseRequestHandler):
+    async def get(self, country):
+        http_client = AsyncHTTPClient()
+        # First we need the country to fetch the data
+        URL = f'https://restcountries.com/v3.1/alpha/{country}?fields=name'
+        try:
+            response = await http_client.fetch(HTTPRequest(
+                url=URL,
+                method='GET',
+            ),
+            raise_error=True)
+        except Exception as e:
+            print("Something went wrong: %s" % e)
+
+        country_name = json.loads(response.body)['name']['common']
+        
+        # Get global incident rates
+        URL = 'https://covid19.who.int/WHO-COVID-19-global-data.csv'
+        try:
+            response = await http_client.fetch(HTTPRequest(
+                url=URL,
+                method='GET',
+            ),
+            raise_error=True)
+        except Exception as e:
+            print("Something went wrong: %s" % e)
+
+        df = pd.read_csv(StringIO(response.body.decode('utf-8')), index_col=False)
+        cases = df.loc[df['Country'] == country_name]
+        # 7-day rolling average
+        current_date = str(datetime.datetime.now()).split(' ')[0]
+        eight_days_ago = str(datetime.datetime.now() - datetime.timedelta(days=7)).split(' ')[0]
+        cases = cases.set_index(['Date_reported'])
+        # If any of the 'New_cases' is 0, it means the data is not updated.
+        if (cases.loc[eight_days_ago:current_date]['New_cases'] == 0).any(): return self.finish('')
+        return self.finish(str(round(cases.loc[eight_days_ago:current_date]['New_cases'].mean())))
+
 
 def make_app(
         debug: bool = False,
@@ -317,6 +357,7 @@ def make_app(
         (calculator_prefix + r'/baseline-model/result', StaticModel),
         (calculator_prefix + r'/user-guide', ReadmeHandler),
         (calculator_prefix + r'/api/arve/v1/(.*)/(.*)', ArveData),
+        (calculator_prefix + r'/cases/(.*)', CasesData),
         (calculator_prefix + r'/static/(.*)', StaticFileHandler, {'path': calculator_static_dir}),
     ]
 

caimira/apps/calculator/static/js/form.js

@@ -418,6 +418,20 @@ function show_sensors_data(url) {
   }
 };
 
+function geographic_cases(location_country_name) {
+  $.ajax({
+    url: `${$('#url_prefix').data().calculator_prefix}/cases/${location_country_name}`,
+    type: 'GET',
+    success: function (result) {
+      $('#geographic_cases').val(result);
+      result != '' ? $('#source_geographic_cases').show() : $('#source_geographic_cases').hide();
+    },
+    error: function(_, _, errorThrown) {
+      console.log(errorThrown);
+    }
+  });
+}
+
 $("#sensors").change(function (el) {
   sensor_id = DATA_FROM_SENSORS.findIndex(function(sensor) {
     return sensor.RoomId == el.target.value
@@ -930,6 +944,12 @@ $(document).ready(function () {
     }
   }
 
+  // Update geographic_cases
+  geographic_cases('CHE');
+
+  // Handle WHO source message if geographic_cases pre-defined value is modified by user
+  $('#geographic_cases').change(() => $('#source_geographic_cases').hide());
+  
   // When the document is ready, deal with the fact that we may be here
   // as a result of a forward/back browser action. If that is the case, update
   // the visibility of some of our inputs.
@@ -1120,9 +1140,12 @@ $(document).ready(function () {
           success: function (locations) {
             // If there isn't precisely one result something is very wrong.
             geocoded_loc = locations.candidates[0];
+            
             $('input[name="location_name"]').val(selectedSuggestion.text);
             $('input[name="location_latitude"]').val(geocoded_loc.location.y.toPrecision(7));
             $('input[name="location_longitude"]').val(geocoded_loc.location.x.toPrecision(7));
+            // Update geographic_cases
+            geographic_cases(geocoded_loc.attributes['country']);
           }
         });
 

caimira/apps/templates/base/calculator.form.html.j2

@@ -386,8 +386,13 @@
         <div class="col-sm-6 pl-0 align-self-center"><input type="number" step="any" id="geographic_population" class="non_zero form-control" name="geographic_population" placeholder="Inhabitants (#)" min="0"></div>
       </div>
       <div class="form-group row">
-        <div class="col-sm-4"><label class="col-form-label">New confirmed cases (weekly):</label></div>
-        <div class="col-sm-6 pl-0 align-self-center"><input type="number" step="any" id="geographic_cases" class="non_zero form-control" name="geographic_cases" placeholder="Cases (#7-day rolling avg)" min="0"></div>
+        <div class="col-sm-4"><label class="col-form-label pt-0">New confirmed cases (weekly):</label></div>
+        <div class="col-sm-6 pl-0 align-self-center">
+          <input type="number" step="any" id="geographic_cases" class="non_zero form-control" name="geographic_cases" placeholder="Cases (#7-day rolling avg)" min="0">
+          <small id="source_geographic_cases" class="form-text text-muted" style="display: none">
+            Source: World Health Organization.
+          </small>
+        </div>
       </div>
       <div class="form-group row">
       <div class="col-sm-4"><label class="col-form-label">Confidence level:</label></div>

setup.py

@@ -28,6 +28,7 @@ REQUIREMENTS: dict = {
         'memoization',
         'mistune',
         'numpy',
+        'pandas',
         'psutil',
         'python-dateutil',
         'retry',