From 680faf0d8b02891770ee88a10303089dce132409 Mon Sep 17 00:00:00 2001
From: lrdossan <luis.aleixo@cern.ch>
Date: Tue, 11 Jun 2024 15:18:27 +0200
Subject: [PATCH 1/6] read raw values from xlsx files

---
 caimira/apps/calculator/static/js/co2_form.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/caimira/apps/calculator/static/js/co2_form.js b/caimira/apps/calculator/static/js/co2_form.js
index e846bbcf..6b69c7f2 100644
--- a/caimira/apps/calculator/static/js/co2_form.js
+++ b/caimira/apps/calculator/static/js/co2_form.js
@@ -74,7 +74,7 @@ function uploadFile(endpoint) {
       }
     }
 
-    const data = XLSX.utils.sheet_to_json(worksheet, { header: 1, raw: false });
+    const data = XLSX.utils.sheet_to_json(worksheet, { header: 1, raw: true });
     // Check if there is any data below the header row
     if (data.length <= 1) {
       $("#upload-error")

From c9b296bd0daadf0a04378b84a0ba8c76af05aef3 Mon Sep 17 00:00:00 2001
From: lrdossan <luis.aleixo@cern.ch>
Date: Tue, 11 Jun 2024 15:21:45 +0200
Subject: [PATCH 2/6] added fix to predictive CO2 concentration plot

---
 caimira/apps/calculator/static/js/report.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/caimira/apps/calculator/static/js/report.js b/caimira/apps/calculator/static/js/report.js
index 7c804dd9..d33d7eee 100644
--- a/caimira/apps/calculator/static/js/report.js
+++ b/caimira/apps/calculator/static/js/report.js
@@ -541,7 +541,7 @@ function draw_generic_concentration_plot(
         h_lines,
     ) {
 
-    list_of_scenarios = (plot_svg_id === 'CO2_concentration_graph') ? CO2_concentrations : alternative_scenarios
+    list_of_scenarios = (plot_svg_id === 'CO2_concentration_graph') ? {'CO₂ concentration': {'concentrations': CO2_concentrations}} : alternative_scenarios
     // H:M format
     var time_format = d3.timeFormat('%H:%M');
     // D3 array of ten categorical colors represented as RGB hexadecimal strings.
@@ -698,7 +698,7 @@ function draw_generic_concentration_plot(
     }
 
     function update_concentration_plot(concentration_data) {
-        list_of_scenarios = (plot_svg_id === 'CO2_concentration_graph') ? CO2_concentrations : alternative_scenarios
+        list_of_scenarios = (plot_svg_id === 'CO2_concentration_graph') ? {'CO₂ concentration': {'concentrations': CO2_concentrations}} : alternative_scenarios
         var highest_concentration = 0.
 
         for (scenario in list_of_scenarios) {

From 1215f1d7b7797224b5aba362792cee8bc789a102 Mon Sep 17 00:00:00 2001
From: lrdossan <luis.aleixo@cern.ch>
Date: Tue, 11 Jun 2024 17:35:19 +0200
Subject: [PATCH 3/6] temporarily disabled ARVE sensors data

---
 caimira/apps/calculator/static/js/form.js     | 11 ++---
 .../templates/cern/calculator.form.html.j2    | 42 ++++++++++---------
 2 files changed, 28 insertions(+), 25 deletions(-)

diff --git a/caimira/apps/calculator/static/js/form.js b/caimira/apps/calculator/static/js/form.js
index 71023c2a..406a454d 100644
--- a/caimira/apps/calculator/static/js/form.js
+++ b/caimira/apps/calculator/static/js/form.js
@@ -1014,13 +1014,14 @@ $(document).ready(function () {
   //Check all radio buttons previously selected
   $("input[type=radio]:checked").each(function() {require_fields(this)});
 
+  // TEMPORARILY DISABLED
   // On CERN theme, when the arve_sensors_option changes we want to make its respective
   // children show/hide.
-  if ($("input[type=radio][name=arve_sensors_option]").length > 0) {
-    $("input[type=radio][name=arve_sensors_option]").change(on_use_sensors_data_change);
-    // Call the function now to handle forward/back button presses in the browser.
-    on_use_sensors_data_change(url);
-  }
+  // if ($("input[type=radio][name=arve_sensors_option]").length > 0) {
+  //   $("input[type=radio][name=arve_sensors_option]").change(on_use_sensors_data_change);
+  //   // Call the function now to handle forward/back button presses in the browser.
+  //   on_use_sensors_data_change(url);
+  // }
 
   // When the ventilation_type changes we want to make its respective
   // children show/hide.
diff --git a/caimira/apps/templates/cern/calculator.form.html.j2 b/caimira/apps/templates/cern/calculator.form.html.j2
index 4e5ae90a..2bab2783 100644
--- a/caimira/apps/templates/cern/calculator.form.html.j2
+++ b/caimira/apps/templates/cern/calculator.form.html.j2
@@ -5,28 +5,30 @@
       <span class="tooltip_text">?</span>
   </div>
 
-  <div class="split">
-    <div>Use data from ARVE sensors:</div>
-    <div>
-    <input class="ml-2" type="radio" id="arve_sensor_no" name="arve_sensors_option" value=0 checked="checked">
-      <label for="arve_sensor_no">No</label>
-    <input class="ml-2" type="radio" id="arve_sensor_yes" name="arve_sensors_option" value=1 data-enables="#DIVsensors_data">
-      <label for="arve_sensor_yes">Yes</label>
-    </div>
-  </div>
-  <p id="offline_sensors" class="red_text mb-2" style="display: none">All sensors are offline.</p>
-  <p id="arve_api_error_message" class="red_text mb-2" style="display:none; max-width: 85%;">Unauthorized - Something went wrong during the ARVE API authentication process.</p> 
-  <div id="DIVsensors_data" class="mb-1" style="display:none">
-    <div class="form-group row mb-0">
-      <div class="col-sm-4"><label class="col-form-label">Sensor:</label></div>
-      <div class="col-sm-6">
-        <select id="sensors" name="sensor_in_use" class="form-control">
-        </select>
+  <div class="d-none">
+    <div class="split">
+      <div>Use data from ARVE sensors:</div>
+      <div>
+      <input class="ml-2" type="radio" id="arve_sensor_no" name="arve_sensors_option" value=0 checked="checked">
+        <label for="arve_sensor_no">No</label>
+      <input class="ml-2" type="radio" id="arve_sensor_yes" name="arve_sensors_option" value=1 data-enables="#DIVsensors_data">
+        <label for="arve_sensor_yes">Yes</label>
       </div>
     </div>
-    <div>
-      <div><label>Temperature: </label><span class="ml-3 font-weight-bold" id="sensor_temperature"></span></div> 
-      <div><label>Relative Humidity: </label><span class="ml-3 font-weight-bold" id="sensor_humidity"></span></div>
+    <p id="offline_sensors" class="red_text mb-2" style="display: none">All sensors are offline.</p>
+    <p id="arve_api_error_message" class="red_text mb-2" style="display:none; max-width: 85%;">Unauthorized - Something went wrong during the ARVE API authentication process.</p> 
+    <div id="DIVsensors_data" class="mb-1" style="display:none">
+      <div class="form-group row mb-0">
+        <div class="col-sm-4"><label class="col-form-label">Sensor:</label></div>
+        <div class="col-sm-6">
+          <select id="sensors" name="sensor_in_use" class="form-control">
+          </select>
+        </div>
+      </div>
+      <div>
+        <div><label>Temperature: </label><span class="ml-3 font-weight-bold" id="sensor_temperature"></span></div> 
+        <div><label>Relative Humidity: </label><span class="ml-3 font-weight-bold" id="sensor_humidity"></span></div>
+      </div>
     </div>
   </div>
 {% endblock room_data %}
\ No newline at end of file

From 0bec4041aef3bba854e48aacee1e213d57d5c289 Mon Sep 17 00:00:00 2001
From: lrdossan <luis.aleixo@cern.ch>
Date: Tue, 11 Jun 2024 17:36:05 +0200
Subject: [PATCH 4/6] handled cases data to be updated only when probabilistic
 exposure (incidence rate) is checked

---
 caimira/apps/calculator/__init__.py       | 60 +++++++++++++----------
 caimira/apps/calculator/static/js/form.js | 20 ++++----
 2 files changed, 44 insertions(+), 36 deletions(-)

diff --git a/caimira/apps/calculator/__init__.py b/caimira/apps/calculator/__init__.py
index 98df93a5..e5f2e976 100644
--- a/caimira/apps/calculator/__init__.py
+++ b/caimira/apps/calculator/__init__.py
@@ -378,40 +378,48 @@ class ArveData(BaseRequestHandler):
 
 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'
+        http_client = tornado.httpclient.AsyncHTTPClient()
         try:
-            response = await http_client.fetch(HTTPRequest(
-                url=URL,
-                method='GET',
-            ),
-            raise_error=True)
+            country_name = await self.get_country_name(country, http_client)
+            if not country_name:
+                return self.finish('Country not found')
+
+            cases_data = await self.get_cases_data(country_name, http_client)
+            if not cases_data:
+                return self.finish('Data not available')
+
+            return self.finish(str(round(cases_data)))
         except Exception as e:
             print("Something went wrong: %s" % e)
+            return self.finish('Internal Server Error', status_code=500)
 
-        country_name = json.loads(response.body)['name']['common']
-
-        # Get global incident rates
-        URL = 'https://covid19.who.int/WHO-COVID-19-global-data.csv'
+    async def get_country_name(self, country_code, http_client):
+        url = f'https://restcountries.com/v3.1/alpha/{country_code}?fields=name'
         try:
-            response = await http_client.fetch(HTTPRequest(
-                url=URL,
-                method='GET',
-            ),
-            raise_error=True)
+            response = await http_client.fetch(url)
+            if response.code != 200:
+                return None
+            data = json.loads(response.body)
+            return data['name']['common'] if 'name' in data else None
         except Exception as e:
             print("Something went wrong: %s" % e)
+            return None
 
-        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())))
+    async def get_cases_data(self, country_name, http_client):
+        url = 'https://covid19.who.int/WHO-COVID-19-global-data.csv'
+        try:
+            response = await http_client.fetch(url)
+            if response.code != 200:
+                return None
+            data = response.body.decode('utf-8')
+            df = pd.read_csv(StringIO(data))
+            cases = df[df['Country'] == country_name]
+            if cases.empty:
+                return None
+            return cases['New_cases'].mean()
+        except Exception as e:
+            print("Something went wrong: %s" % e)
+            return None
 
 
 class GenericExtraPage(BaseRequestHandler):
diff --git a/caimira/apps/calculator/static/js/form.js b/caimira/apps/calculator/static/js/form.js
index 406a454d..98e7834e 100644
--- a/caimira/apps/calculator/static/js/form.js
+++ b/caimira/apps/calculator/static/js/form.js
@@ -293,6 +293,10 @@ function on_exposure_change() {
     if (this.checked) {
       getChildElement($(this)).show();
       require_fields(this);
+      if (this.id == "p_probabilistic_exposure") {
+        // Update geographic_cases
+        geographic_cases($('[name="location_name"]')[0].value.split(', ')[1]);
+      };
     }
     else {
       getChildElement($(this)).hide();
@@ -423,8 +427,10 @@ function geographic_cases(location_country_name) {
     url: `${$('#url_prefix').data().calculator_prefix}/cases/${location_country_name}`,
     type: 'GET',
     success: function (result) {
-      $('#geographic_cases').val(result);
-      result != '' ? $('#source_geographic_cases').show() : $('#source_geographic_cases').hide();
+      if (result != 'Country not found') {
+        $('#geographic_cases').val(result);
+        result != 'Country not found' ? $('#source_geographic_cases').show() : $('#source_geographic_cases').hide();
+      }
     },
     error: function(_, _, errorThrown) {
       console.log(errorThrown);
@@ -983,8 +989,8 @@ $(document).ready(function () {
   // Handle geographic location input
   if (Array.from(url.searchParams).length > 0) {
     if (!url.searchParams.has('location_name')) {
-      $('[name="location_name"]').val('Geneva')
-      $('[name="location_select"]').val('Geneva')
+      $('[name="location_name"]').val('Geneva, CHE')
+      $('[name="location_select"]').val('Geneva, CHE')
     }
     if (!url.searchParams.has('location_latitude')) {
       $('[name="location_latitude"]').val('46.20833')
@@ -993,10 +999,6 @@ $(document).ready(function () {
       $('[name="location_longitude"]').val('6.14275')
     }
   }
-
-  // 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());
   
@@ -1200,8 +1202,6 @@ $(document).ready(function () {
             $('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']);
           }
         });
 

From 1368e33864f076661f11fbf26e9f59e9932b2af7 Mon Sep 17 00:00:00 2001
From: lrdossan <luis.aleixo@cern.ch>
Date: Wed, 31 Jul 2024 16:47:36 +0200
Subject: [PATCH 5/6] complete removal of cases class and related logic

---
 caimira/apps/calculator/__init__.py           | 47 -------------------
 caimira/apps/calculator/static/js/form.js     | 22 ---------
 .../templates/base/calculator.form.html.j2    |  3 --
 3 files changed, 72 deletions(-)

diff --git a/caimira/apps/calculator/__init__.py b/caimira/apps/calculator/__init__.py
index e5f2e976..5a746648 100644
--- a/caimira/apps/calculator/__init__.py
+++ b/caimira/apps/calculator/__init__.py
@@ -376,52 +376,6 @@ class ArveData(BaseRequestHandler):
         return self.finish(response.body)
 
 
-class CasesData(BaseRequestHandler):
-    async def get(self, country):
-        http_client = tornado.httpclient.AsyncHTTPClient()
-        try:
-            country_name = await self.get_country_name(country, http_client)
-            if not country_name:
-                return self.finish('Country not found')
-
-            cases_data = await self.get_cases_data(country_name, http_client)
-            if not cases_data:
-                return self.finish('Data not available')
-
-            return self.finish(str(round(cases_data)))
-        except Exception as e:
-            print("Something went wrong: %s" % e)
-            return self.finish('Internal Server Error', status_code=500)
-
-    async def get_country_name(self, country_code, http_client):
-        url = f'https://restcountries.com/v3.1/alpha/{country_code}?fields=name'
-        try:
-            response = await http_client.fetch(url)
-            if response.code != 200:
-                return None
-            data = json.loads(response.body)
-            return data['name']['common'] if 'name' in data else None
-        except Exception as e:
-            print("Something went wrong: %s" % e)
-            return None
-
-    async def get_cases_data(self, country_name, http_client):
-        url = 'https://covid19.who.int/WHO-COVID-19-global-data.csv'
-        try:
-            response = await http_client.fetch(url)
-            if response.code != 200:
-                return None
-            data = response.body.decode('utf-8')
-            df = pd.read_csv(StringIO(data))
-            cases = df[df['Country'] == country_name]
-            if cases.empty:
-                return None
-            return cases['New_cases'].mean()
-        except Exception as e:
-            print("Something went wrong: %s" % e)
-            return None
-
-
 class GenericExtraPage(BaseRequestHandler):
 
     def initialize(self, active_page: str, filename: str):
@@ -517,7 +471,6 @@ def make_app(
         (get_root_calculator_url(r'/report-json'), ConcentrationModelJsonResponse),
         (get_root_calculator_url(r'/baseline-model/result'), StaticModel),
         (get_root_calculator_url(r'/api/arve/v1/(.*)/(.*)'), ArveData),
-        (get_root_calculator_url(r'/cases/(.*)'), CasesData),
         # Generic Pages
         (get_root_url(r'/about'), GenericExtraPage, {
             'active_page': 'about',
diff --git a/caimira/apps/calculator/static/js/form.js b/caimira/apps/calculator/static/js/form.js
index 98e7834e..e63bbb45 100644
--- a/caimira/apps/calculator/static/js/form.js
+++ b/caimira/apps/calculator/static/js/form.js
@@ -293,10 +293,6 @@ function on_exposure_change() {
     if (this.checked) {
       getChildElement($(this)).show();
       require_fields(this);
-      if (this.id == "p_probabilistic_exposure") {
-        // Update geographic_cases
-        geographic_cases($('[name="location_name"]')[0].value.split(', ')[1]);
-      };
     }
     else {
       getChildElement($(this)).hide();
@@ -422,22 +418,6 @@ 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) {
-      if (result != 'Country not found') {
-        $('#geographic_cases').val(result);
-        result != 'Country not found' ? $('#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
@@ -999,8 +979,6 @@ $(document).ready(function () {
       $('[name="location_longitude"]').val('6.14275')
     }
   }
-  // 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
diff --git a/caimira/apps/templates/base/calculator.form.html.j2 b/caimira/apps/templates/base/calculator.form.html.j2
index aa6271bf..1d444a5d 100644
--- a/caimira/apps/templates/base/calculator.form.html.j2
+++ b/caimira/apps/templates/base/calculator.form.html.j2
@@ -477,9 +477,6 @@
         <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">

From 627a090171fa14465314b608ab2ce3b50392bcfb Mon Sep 17 00:00:00 2001
From: lrdossan <luis.aleixo@cern.ch>
Date: Thu, 1 Aug 2024 09:54:02 +0200
Subject: [PATCH 6/6] adjusted predictive CO2 graph on its minimum y axis
 domain

---
 caimira/apps/calculator/static/js/report.js | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/caimira/apps/calculator/static/js/report.js b/caimira/apps/calculator/static/js/report.js
index d33d7eee..786794d0 100644
--- a/caimira/apps/calculator/static/js/report.js
+++ b/caimira/apps/calculator/static/js/report.js
@@ -541,7 +541,15 @@ function draw_generic_concentration_plot(
         h_lines,
     ) {
 
-    list_of_scenarios = (plot_svg_id === 'CO2_concentration_graph') ? {'CO₂ concentration': {'concentrations': CO2_concentrations}} : alternative_scenarios
+    if (plot_svg_id === 'CO2_concentration_graph') {
+        list_of_scenarios = {'CO₂ concentration': {'concentrations': CO2_concentrations}};
+        min_y_axis_domain = 400;
+    }
+    else {
+        list_of_scenarios = alternative_scenarios;
+        min_y_axis_domain = 0;
+    }
+
     // H:M format
     var time_format = d3.timeFormat('%H:%M');
     // D3 array of ten categorical colors represented as RGB hexadecimal strings.
@@ -706,7 +714,7 @@ function draw_generic_concentration_plot(
             highest_concentration = Math.max(highest_concentration, Math.max(...scenario_concentrations));
         }
 
-        yRange.domain([0., highest_concentration*1.1]);
+        yRange.domain([min_y_axis_domain, highest_concentration*1.1]);
         yAxisEl.transition().duration(1000).call(yAxis);
 
         for (const [scenario_name, data] of Object.entries(data_for_scenarios)) {