Merge branch 'master' into 'RESTwireframe'

# Conflicts:
#   cara/apps/calculator/static/form.html

cara/apps/calculator/__init__.py

@@ -3,15 +3,11 @@ from pathlib import Path
 
 from tornado.web import Application, RequestHandler, StaticFileHandler
 
-import cara.models
+from . import model_generator
+from .report_generator import build_report
 
 
-def build_model(request: dict) -> cara.models.Model:
-    return None
-
-
-def build_response(model: cara.models.Model):
-    return {'items': 'foobar'}
+DEBUG = True
 
 
 class ConcentrationModel(RequestHandler):
@@ -19,19 +15,41 @@ class ConcentrationModel(RequestHandler):
         requested_model_config = {
             name: self.get_argument(name) for name in self.request.arguments
         }
+        if DEBUG:
+            from pprint import pprint
+            pprint(requested_model_config)
+
         try:
-            model = build_model(requested_model_config)
+            form = model_generator.FormData.from_dict(requested_model_config)
+            model = form.build_model(
+                # TODO: This argument to be removed.
+                tmp_raw_form_data=requested_model_config,
+            )
         except (KeyboardInterrupt, SystemExit):
             raise
         except Exception as err:
+            if DEBUG:
+                import traceback
+                traceback.print_last()
             response_json = {'code': 400, 'error': f'Your request was invalid {err}'}
             self.set_status(400)
             self.finish(json.dumps(response_json))
             return
 
-        response_json = build_response(model)
-        response_json['room_name'] = requested_model_config.get('room_name', 'unknown')
-        self.write(response_json)
+        report = build_report(model, form)
+        self.finish(report)
+
+
+class StaticModel(RequestHandler):
+    def get(self):
+        requested_model_config = model_generator.baseline_raw_form_data()
+        form = model_generator.FormData.from_dict(model_generator.baseline_raw_form_data())
+        model = form.build_model(
+            # TODO: This argument to be removed.
+            tmp_raw_form_data=requested_model_config,
+        )
+        report = build_report(model, form)
+        self.finish(report)
 
 
 def make_app(debug=False, prefix='/calculator'):
@@ -41,7 +59,10 @@ def make_app(debug=False, prefix='/calculator'):
             prefix + r'()', StaticFileHandler, {'path': static_dir / 'form.html'}
         ),
         (
-            prefix + r'/api/calculator', ConcentrationModel
+            prefix + r'/report', ConcentrationModel
+        ),
+        (
+            prefix + r'/baseline-model/result', StaticModel
         ),
         (
             prefix + r'/static/(.*)',

cara/apps/calculator/model_generator.py

@@ -0,0 +1,190 @@
+from cara.models import Model
+from dataclasses import dataclass
+import typing
+
+from cara import models
+
+
+@dataclass
+class FormData:
+    ceiling_height: float
+
+    @classmethod
+    def from_dict(cls, form_data: typing.Dict) -> "FormData":
+        # TODO: This fixup is a problem with the form.html.
+        form_data['ceiling_height'] = 1
+
+        return cls(
+            ceiling_height=float(form_data['ceiling_height']),
+        )
+
+    # TODO: Remove the tmp_raw_form_data usage.
+    def build_model(self, tmp_raw_form_data) -> Model:
+        return model_from_form(self, tmp_raw_form_data)
+
+    def ventilation(self) -> models.Ventilation:
+        # TODO
+        pass
+
+    def present_interval(self) -> models.Interval:
+        # TODO
+        pass
+
+
+def model_from_form(form: FormData, tmp_raw_form_data) -> models.Model:
+    d = tmp_raw_form_data
+
+    # TODO: This fixup is a problem with the form.html.
+    d['coffee_breaks'] = 1
+    d['activity_type'] = 'Training'
+    d['lunch_start'] = '12:00'
+    d['lunch_finish'] = '13:00'
+
+    # Initializes room with volume either given directly or as product of area and height
+    if d['volume_type'] == 'room_volume':
+        volume = int(d['room_volume'])
+    else:
+        volume = int(float(d['floor_area']) * form.ceiling_height)
+    room = models.Room(volume=volume)
+
+    # Initializes a ventilation instance as a window if 'natural' is selected, or as a HEPA-filter otherwise
+    if d['ventilation_type'] == 'natural':
+        if d['windows_open'] == 'always':
+            period, duration = 120, 120
+        else:
+            period, duration = 15, 120
+        # I multiply the opening width by the number of windows to simulate the correct window area
+        ventilation = models.WindowOpening(active=models.PeriodicInterval(period=period, duration=duration),
+                                           inside_temp=293, outside_temp=283, cd_b=0.6,
+                                           window_height=float(d['window_height']),
+                                           opening_length=float(d['opening_distance']) * int(d['windows_number']))
+    else:
+        q_air_mech = float(d['air_changes']) if d['air_type'] == 'air_changes' else float(d['air_supply'])
+        ventilation = models.HEPAFilter(active=models.PeriodicInterval(period=120, duration=120),
+                                        q_air_mech=q_air_mech)
+
+    # Initializes the virus as SARS_Cov_2
+    virus = models.Virus.types['SARS_CoV_2']
+
+    # Defines all of the parameters required to construct a list of intervals where the infected person is present in
+    # the room
+    activity_start = int(d['activity_start'][:2]) * 60 + int(d['activity_start'][3:])
+    activity_finish = int(d['activity_finish'][:2]) * 60 + int(d['activity_finish'][3:])
+    lunch_start = int(d['lunch_start'][:2]) * 60 + int(d['lunch_start'][3:])
+    lunch_finish = int(d['lunch_finish'][:2]) * 60 + int(d['lunch_finish'][3:])
+    coffee_duration = int(d['coffee_duration'])
+    coffee_breaks = int(d['coffee_breaks'])
+    coffee_period = (activity_finish - activity_start) // coffee_breaks + 1
+    leave_times = [lunch_start]
+    enter_times = [lunch_finish]
+    for minute in range(activity_start, activity_finish, coffee_period):
+        leave_times.append(minute)
+        enter_times.append(minute + coffee_duration)
+
+    # These lists represent the times where the infected person leaves or enters the room, respectively, sorted in
+    # reverse order. Note that these lists allows the person to "leave" when they should not even be present in the room
+    # The following loop handles this.
+    leave_times.sort(reverse=True)
+    enter_times.sort(reverse=True)
+
+    # This loop iterates through the lists above, populating present_intervals with (enter, leave) intervals
+    # representing the infected person entering and leaving the room. Note that if one of the evenly spaced coffee-
+    # breaks happens to coincide with the lunch-break, it is simply ignored.
+    is_present = True
+    present_intervals = []
+    time = activity_start
+    while time < activity_finish:
+        if is_present:
+            if not leave_times:
+                present_intervals.append((time / 60, activity_finish / 60))
+                break
+
+            if leave_times[-1] < time:
+                leave_times.pop()
+            else:
+                new_time = leave_times.pop()
+                present_intervals.append((time / 60, min(new_time, activity_finish) / 60))
+                is_present = False
+                time = new_time
+
+        else:
+            if not enter_times:
+                break
+
+            if enter_times[-1] < time:
+                enter_times.pop()
+            else:
+                is_present = True
+                time = enter_times.pop()
+
+    # Initializes a mask of type 1 if mask wearing is "continuous", otherwise instantiates the mask attribute as
+    # the "No mask"-mask
+    mask = models.Mask.types['Type I' if d['mask_wearing'] == "Continuous" else 'No mask']
+
+    # A dictionary containing the mapping of activities listed in the UI to the activity level and expiration level
+    # of the infected and exposed occupants respectively.
+    # I.e. (infected_activity, infected_expiration), (exposed_activity, exposed_expiration)
+
+    activity_dict = {'Office/Meeting': (('Seated', 'Talking'), ('Seated', 'Talking')),
+                     'Training': (('Light exercise', 'Talking'), ('Seated', 'Whispering')),
+                     'Workshop': (('Light exercise', 'Talking'), ('Light exercise', 'Talking'))}
+
+    (infected_activity, infected_expiration), (exposed_activity, exposed_expiration) = activity_dict[d['activity_type']]
+    # Converts these strings to Activity and Expiration instances
+    infected_activity, exposed_activity = models.Activity.types[infected_activity], models.Activity.types[exposed_activity]
+    infected_expiration, exposed_expiration = models.Expiration.types[infected_expiration], models.Expiration.types[exposed_expiration]
+
+    infected_occupants = int(d['infected_people'])
+    # Defines the number of exposed occupants as the total number of occupants minus the number of infected occupants
+    exposed_occupants = int(d['total_people']) - infected_occupants
+
+    # Initializes and returns a model with the attributes defined above
+    return models.Model(
+        room=room,
+        ventilation=ventilation,
+        infected=models.InfectedPerson(
+            virus=virus,
+            presence=models.SpecificInterval(tuple(present_intervals)),
+            mask=mask,
+            activity=infected_activity,
+            expiration=infected_expiration
+        ),
+        infected_occupants=infected_occupants,
+        exposed_occupants=exposed_occupants,
+        exposed_activity=exposed_activity
+    )
+
+
+def baseline_raw_form_data():
+    # Note: This isn't a special "baseline". It can be updated as required.
+    return {
+        'activity_finish': '17:00',
+        'activity_start': '09:00',
+        'activity_type': 'training',
+        'air_changes': '',
+        'air_supply': '',
+        'ceiling_height': '',
+        'coffee_breaks': '',
+        'coffee_duration': '1',
+        'coffee_option': '0',
+        'event_type': 'single_event',
+        'floor_area': '',
+        'infected_people': '1',
+        'lunch_finish': '13:30',
+        'lunch_option': '1',
+        'lunch_start': '12:30',
+        'mask_wearing': 'removed',
+        'opening_distance': '15',
+        'recurrent_event_month': 'January',
+        'room_number': 'baseline room',
+        'room_volume': '75',
+        'simulation_name': 'Baseline simulation',
+        'single_event_date': '11/02/2020',
+        'total_people': '10',
+        'ventilation_type': 'natural',
+        'volume_type': 'room_volume',
+        'window_height': '2',
+        'window_width': '2',
+        'windows_number': '1',
+        'windows_open': 'interval'
+    }

cara/apps/calculator/report_generator.py

@@ -0,0 +1,30 @@
+from datetime import datetime
+from pathlib import Path
+
+import jinja2
+
+from cara import models
+from .model_generator import FormData
+
+
+def build_report(model: models.Model, form: FormData):
+    now = datetime.now()
+    time = now.strftime("%d/%m/%Y %H:%M:%S")
+    request = {'the': 'form', 'request': 'data'}
+    context = {'model': model, 'request': request, 'creation_date': time, 'model_version': 'Beta v1.0.0', 
+            'simulation_name': 'SAMPLE', 'room_number': '40/1-02A', 'room_volume': 30, 'mechanical_ventilation': 'Yes', 
+            'air_supply': 1, 'air_changes': 2, 'windows_number': 5, 'window_height': 2, 'window_width': 1, 
+            'opening_distance': 0.05, 'windows_open': '20 minutes every 2 hours', 'hepa_filtration': 'No', 'total_people': 8,
+            'infected_people': 7, 'activity_type': 'Office work – typical scenario with all persons seated, talking',
+            'activity_start': '00:00', 'activity_finish': '01:15', 'exposure_start': '00:00', 'exposure_finish': '01:15',
+            'single_event_date': '5th November', 'lunch_option': 'Yes', 'lunch_start': '00:00', 'lunch_finish': '01:15', 
+            'coffee_option': 'Yes', 'coffee_number': 4,'coffee_duration': 15, 'coffee_start1': '00:00', 'coffee_finish1': '00:00',
+            'coffee_start2': '00:00','coffee_finish2': '00:00', 'coffee_start3': '00:00', 'coffee_finish3': '00:00', 
+            'coffee_start4': '00:00', 'coffee_finish4': '00:00', 'mask_wearing': 'Yes', 
+            'infection_probability': round(model.infection_probability(), 2), 'reproduction_rate': 2}
+
+    p = Path(__file__).parent / 'templates'
+    env = jinja2.Environment(
+        loader=jinja2.FileSystemLoader(Path(p)))
+    template = env.get_template('report.html.j2')
+    return template.render(**context)

cara/apps/calculator/static/css/report.css

@@ -0,0 +1,43 @@
+#body {
+    top: 10px;
+    left: 20px;
+    bottom: 20px;
+    right: 20px;
+    padding: 20px; 
+}
+
+.image {
+	display: flex; 
+	align-items: center; 
+	justify-content: center;
+	font-size: 13pt;
+}
+
+h1{
+	text-align: center;
+}
+
+.subtitle {
+	text-align: center;
+	font-size: 13pt;
+	padding-bottom: 15pt;
+}
+
+p.data_title {
+	font-weight: bold;
+}
+
+p.data_text {
+	padding-left: 30px;
+    padding-left:1em;
+}
+
+p.data_subtext {
+	padding-left: 60px;
+    margin-left:-3em;
+}
+
+p.result_title {
+	font-weight: bold;
+	font-size: 15pt;
+}

cara/apps/calculator/static/form.html

@@ -12,11 +12,13 @@
 
 </head>
 
-<body onload="clear_form()">
+<body>
+
 
 Beta v1.0.0 <span style="float:right; font-weight:bold">Please send feedback to <a href="mailto:CARA-dev@cern.ch">CARA-dev@cern.ch</a></span>
 <h1> <p><b>CARA</b> Covid Airborne Risk Assessment tool</p></h1>
-<form id="covid_calculator" name="covid_calculator" onsubmit='return on_submit(this)'>
+<form id="covid_calculator" name="covid_calculator" action="/calculator/report" method="POST" onsubmit='return on_submit(this)'>
+
 <div style="width: 33%; float:left;">
 
     <!-- General Options -->
@@ -182,7 +184,7 @@ var request;
 function on_submit(form){
 
     // Prevent default posting of form - put here to work in case of errors
-    event.preventDefault();
+    // event.preventDefault();
 
     // Abort any pending request
     if (request)
@@ -191,6 +193,7 @@ function on_submit(form){
     // Let's select and cache all the fields
     var $inputs = $(form).find("input, select, button, textarea");
 
+<<<<<<< cara/apps/calculator/static/form.html
     // Serialize the data in the form
     var serializedData = objectifyForm($(form).serializeArray());
 
@@ -217,6 +220,33 @@ function on_submit(form){
             textStatus, errorThrown
         );
     });
+    
+    // // Serialize the data in the form
+    // var serializedData = objectifyForm($(form).serializeArray());
+
+    // console.log(['Sending over', JSON.stringify(serializedData)])
+
+    // // Fire off the request to the calculator.
+    // request = $.ajax({
+    //     url: "/calculator/report",
+    //     type: "post",
+    //     data: serializedData,
+    //     dataType: "json",       
+    // });
+
+    // // Callback handler that will be called on success
+    // request.done(function (response, textStatus, jqXHR){
+    //     build_report(response);
+    // });
+
+    // // Callback handler that will be called on failure
+    // request.fail(function (jqXHR, textStatus, errorThrown){
+    //     // Log the error to the console
+    //     console.error(
+    //         "The following error occurred: "+
+    //         textStatus, errorThrown
+    //     );
+    // });
 }
 
 // Convert all type int in form

cara/apps/calculator/templates/report.html.j2

@@ -0,0 +1,91 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+	<meta charset="UTF-8">  
+	<meta name="viewport" content="width=device-width, initial-scale=1">
+
+	<link rel="stylesheet" type="text/css" href="/calculator/static/css/report.css"> 
+</head>
+
+<body id="body">
+
+	<p class=image> <img src="/calculator/static/images/disclaimer.jpg" width="40" height="40">
+	VERY IMPORTANT DISCLAIMER</p>
+
+	<h1>Output from CARA - COVID Airborne Risk Assessment tool</h1>
+
+	<p class=subtitle> Created {{ creation_date }} using model version {{ model_version }}</p><br>
+
+	<p>Simulation Name: {{ simulation_name }}</p>
+	<p>Room Number: {{ room_number }}</p>
+
+	<p class="data_title">Input data:</p>
+	<ul>
+		<li><p class="data_text">Room Volume: {{ room_volume }} m³</p></li>
+	</ul>
+
+	<p class="data_title">Ventilation data:</p>
+	<ul>
+		<li><p class="data_text">Mechanical ventilation: {{ mechanical_ventilation }}</p></li>
+		<!--If mechanical ventialtion is yes {-->
+		<ul>
+			<li><p class="data_subtext">Air supply flow rate: {{ air_supply }}</p></li>
+			<li><p class="data_subtext">Air changes per hour: {{ air_changes }}</p></li>
+		</ul>
+		<!--}-->
+		<li><p class="data_text">Natural ventilation: No</li>
+		<!--If natural ventialtion is yes {
+		<ul>
+			<li><p class="data_subtext">Number of windows: {{ windows_number }}</p></li>
+			<li><p class="data_subtext">Height of window: {{ window_height }}</p></li>
+			<li><p class="data_subtext">Width of window: {{ window_width }}</p></li>
+			<li><p class="data_subtext">Opening distance: {{ opening_distance }}</p></li>
+			<li><p class="data_subtext">Windows open: {{ windows_open }}</p></li>
+		</ul>
+		}-->
+		<li><p class="data_text">HEPA Filtration: {{ hepa_filtration }}</li>
+		<!--If HEPA filtration is yes {
+			X type of filter with y flow rate (default model assumption) ?
+		}-->
+	</ul>
+
+	<p class="data_title">Event data:</p>
+	<ul>
+		<li><p class="data_text">Number of attendees and infected people: {{ total_people }} in attendance, of whom {{ infected_people }} are infected.</p></li>
+		<li><p class="data_text">Activity type: {{ activity_type }}</p></li>
+		<ul>
+				<li><p class="data_subtext">Start time: {{ activity_start }}		End time: {{ activity_finish }}</p></li>
+			</ul>
+		<li><p class="data_text">Exposure time (presence of infected person):</p></li>
+		<ul>
+			<li><p class="data_subtext">Start time: {{ exposure_start }}		End time: {{ exposure_finish }}</p></li>
+		</ul>
+		<li><p class="data_text">Single event on {{ single_event_date }}</p></li>
+	</ul>
+
+	<p class="data_title">Break data:</p>
+	<ul>
+		<li><p class="data_text">Lunchbreak: {{ lunch_option }}	Start: {{ lunch_start }} End: {{ lunch_end }}</p></li>
+		<li><p class="data_text">Coffee breaks: {{ coffee_option }}	Number: {{ coffee_number }}		Duration: {{ coffee_duration }}</p></li>
+		<ul>
+			<li><p class="data_subtext">Coffee break 1: Start: {{ coffee_start1 }} 	End: {{ coffee_finish1 }}</p></li>
+			<li><p class="data_subtext">Coffee break 2: Start: {{ coffee_start2 }} 	End: {{ coffee_finish2 }}</p></li>
+			<li><p class="data_subtext">Coffee break 3: Start: {{ coffee_start3 }} 	End: {{ coffee_finish3 }}</p></li>
+			<li><p class="data_subtext">Coffee break 4: Start: {{ coffee_start4 }} 	End: {{ coffee_finish4 }}</p></li>
+		</ul>
+	</ul>
+
+	<!--or Recurrent for months of X, Y and Z…-->
+
+	<p class="data_title">Mask wearing:</p>
+	<ul>
+		<li><p class="data_text">Masks worn at workstations? {{ mask_wearing }}</p></li>
+		<li><p class="data_text">Mask type: Type 1 (default, for now)</p></li>
+	</ul>
+
+	<p class="result_title">Results:</p>
+		<p class="data_text"> In this scenario, the estimated probability of one exposed occupant getting infected (Pi) is {{ infection_probability }} % and the estimated basic reproduction rate (R0) rate is {{ reproduction_rate }}. If you have selected a recurrent event, this is the probability per day, and is cumulative over the number of days.<p>
+	<p class="data_title">Exposure graph:
+
+</body>
+</html>

cara/tests/apps/calculator/test_model_generator.py

@@ -0,0 +1,25 @@
+import pytest
+
+from cara.apps.calculator import model_generator
+
+
+@pytest.fixture
+def baseline_form_data():
+    return model_generator.baseline_raw_form_data()
+
+
+@pytest.fixture
+def baseline_form(baseline_form_data):
+    return model_generator.FormData.from_dict(baseline_form_data)
+
+
+def test_model_from_dict(baseline_form_data):
+    model = model_generator.FormData.from_dict(baseline_form_data)
+    # TODO:
+    # assert model.ventilation == cara.models.Ventilation()
+
+
+def test_ventilation(baseline_form):
+    ventilation = baseline_form.ventilation()
+    # TODO:
+    # assert ventilation == cara.models.Ventilation()