Automatic report regeneration

cara/apps/calculator/README.md

@@ -33,7 +33,7 @@ A room number is included, if you do not wish to use a formal room number any re
 
 ### Room Data
 
-Please enter either the room volume (in m<sup>3</sup>) or both the floor area (m<sup>2</sup>) and the room height (m).
+Please enter either the room volume (in m³) or both the floor area (m²) and the room height (m).
 This information is available via GIS Portal (https://gis.cern.ch/gisportal/).
 
 ### Ventilation type
@@ -99,7 +99,6 @@ As an example, for a shared office with 4 people, where one person is infected,
 There are a few predefined activities in the tool at present.
 
 **Office ** = All persons seated, talking occasionally (1/3rd of the time, with normal breathing the other 2/3rds of the time). Everyone (exposed and infected occupants) is treated the same in this model.
-
 **Meeting** = All persons seated, having a conversation (approximately each occupant is 1/N % of the time talking, where N is the number of occupants). Everyone (exposed and infected occupants) is treated the same in this model.
 
 **Library** = All persons seated, breathing only (not talking), all the time.
@@ -191,9 +190,8 @@ It contains a summary of all the input data, which will allow the simulation to
 
 This part of the report shows the ``P(i)`` or probability of one exposed person getting infected.
 It is estimated based on the emission rate of virus into the simulated volume, and the amount which is inhaled by exposed individuals.
-This probability is valid for the simulation duration - i.e. if you have simulated one day and plan to work 5 days in these conditions and the infected person emits the same amount of virus each day, the cumulative probability of infection is ``(1-(1-P(i))^5)```.
+This probability is valid for the simulation duration - i.e. if you have simulated one day and plan to work 5 days in these conditions and the infected person emits the same amount of virus each day, the cumulative probability of infection is ``(1-(1-P(i))^5)``.
 If you are using the natural ventilation option, the simulation is only valid for the selected month, because the following or preceding month will have a different average temperature profile.
-
 The ``expected number of new cases`` for the simulation is calculated based on the probability of infection, multiplied by the number of exposed occupants.
 
 ### Exposure graph
@@ -207,6 +205,13 @@ It is determined by:
     * Under natural ventilation conditions, the effectiveness of ventilation relies upon the hourly temperature difference between the inside and outside air temperature.
     * A HEPA filter removes infectious quanta from the air at a constant rate and is modelled in the same way as mechanical ventilation, however air passed through a HEPA filter is recycled (i.e. it is not fresh air).
 
+### QR code
+
+At the end of the report you can find a unique QR code / hyperlink for this report. This provides an automatic way to review the calculator form with the corresponding specified parameters.
+This allows for:
+* sharing reports by either scanning or clicking on the QR code to obtain a shareable link.
+* easily regenerating reports with any new versions of the CARA model released in the future.
+
 # Conclusion
 
 This tool provides informative comparisons for COVID-19 (long-range) airborne risk only - see Disclaimer

cara/apps/calculator/__init__.py

@@ -55,7 +55,8 @@ class ConcentrationModel(BaseRequestHandler):
             self.finish(json.dumps(response_json))
             return
 
-        report = build_report(form.build_model(), form)
+        base_url = self.request.protocol + "://" + self.request.host
+        report = build_report(base_url, form.build_model(), form)
         self.finish(report)
 
 
@@ -63,7 +64,8 @@ class StaticModel(BaseRequestHandler):
     def get(self):
         form = model_generator.FormData.from_dict(model_generator.baseline_raw_form_data())
         model = form.build_model()
-        report = build_report(model, form)
+        base_url = self.request.protocol + "://" + self.request.host
+        report = build_report(base_url, model, form)
         self.finish(report)
 
 

cara/apps/calculator/model_generator.py

@@ -82,66 +82,29 @@ class FormData:
             if value == "":
                 form_data[key] = "0"
 
-        time_attributes = [
+        for attr_name in BOOLEAN_ATTRIBUTES:
-            'exposed_lunch_start', 'exposed_lunch_finish', 'exposed_start', 'exposed_finish',
+            form_data[attr_name] = form_data[attr_name] == '1'
-            'infected_lunch_start', 'infected_lunch_finish', 'infected_start', 'infected_finish',
+        for attr_name in FLOAT_ATTRIBUTES:
-        ]
+            form_data[attr_name] = float(form_data[attr_name])
-        for attr_name in time_attributes:
+        for attr_name in INT_ATTRIBUTES:
+            form_data[attr_name] = int(form_data[attr_name])
+        for attr_name in TIME_ATTRIBUTES:
             form_data[attr_name] = time_string_to_minutes(form_data[attr_name])
 
-        boolean_attributes = [
+        form_data.pop('_xsrf', None)
-            'hepa_option', 'exposed_lunch_option', 'infected_lunch_option', 'infected_dont_have_breaks_with_exposed',
+        instance = cls(**form_data)
-        ]
-        for attr_name in boolean_attributes:
-            form_data[attr_name] = form_data[attr_name] == '1'
-
-        instance = cls(
-            activity_type=form_data['activity_type'],
-            air_changes=float(form_data['air_changes']),
-            air_supply=float(form_data['air_supply']),
-            ceiling_height=float(form_data['ceiling_height']),
-            exposed_coffee_break_option=form_data['exposed_coffee_break_option'],
-            exposed_coffee_duration=int(form_data['exposed_coffee_duration']),
-            exposed_finish=form_data['exposed_finish'],
-            exposed_lunch_finish=form_data['exposed_lunch_finish'],
-            exposed_lunch_option=form_data['exposed_lunch_option'],
-            exposed_lunch_start=form_data['exposed_lunch_start'],
-            exposed_start=form_data['exposed_start'],
-            floor_area=float(form_data['floor_area']),
-            hepa_amount=float(form_data['hepa_amount']),
-            hepa_option=form_data['hepa_option'],
-            infected_coffee_break_option=form_data['infected_coffee_break_option'],
-            infected_coffee_duration=int(form_data['infected_coffee_duration']),
-            infected_dont_have_breaks_with_exposed=form_data['infected_dont_have_breaks_with_exposed'],
-            infected_finish=form_data['infected_finish'],
-            infected_lunch_finish=form_data['infected_lunch_finish'],
-            infected_lunch_option=form_data['infected_lunch_option'],
-            infected_lunch_start=form_data['infected_lunch_start'],
-            infected_people=int(form_data['infected_people']),
-            infected_start=form_data['infected_start'],
-            mask_type=form_data['mask_type'],
-            mask_wearing_option=form_data['mask_wearing_option'],
-            mechanical_ventilation_type=form_data['mechanical_ventilation_type'],
-            model_version=form_data['model_version'],
-            opening_distance=float(form_data['opening_distance']),
-            event_month=form_data['event_month'],
-            room_number=form_data['room_number'],
-            room_volume=float(form_data['room_volume']),
-            simulation_name=form_data['simulation_name'],
-            total_people=int(form_data['total_people']),
-            ventilation_type=form_data['ventilation_type'],
-            volume_type=form_data['volume_type'],
-            windows_duration=float(form_data['windows_duration']),
-            windows_frequency=float(form_data['windows_frequency']),
-            window_height=float(form_data['window_height']),
-            window_type=form_data['window_type'],
-            window_width=float(form_data['window_width']),
-            windows_number=int(form_data['windows_number']),
-            window_opening_regime=form_data['window_opening_regime'],
-        )
         instance.validate()
         return instance
 
+    @classmethod
+    def to_dict(self, form: "FormData") -> dict:
+        form_dict = form.__dict__.copy()
+        for attr_name in TIME_ATTRIBUTES:
+            form_dict[attr_name] = time_minutes_to_string(form_dict[attr_name])
+        for attr_name in BOOLEAN_ATTRIBUTES:
+            form_dict[attr_name] = form_dict[attr_name] & 1
+        return form_dict
+
     def validate(self):
         # Validate time intervals selected by user
         time_intervals = [
@@ -604,6 +567,12 @@ WINDOWS_TYPES = {'window_sliding', 'window_hinged', 'not-applicable'}
 
 COFFEE_OPTIONS_INT = {'coffee_break_0':0, 'coffee_break_1':1, 'coffee_break_2':2, 'coffee_break_4':4}
 
+BOOLEAN_ATTRIBUTES = {'hepa_option', 'exposed_lunch_option', 'infected_lunch_option', 'infected_dont_have_breaks_with_exposed'}
+FLOAT_ATTRIBUTES = {'air_changes', 'air_supply', 'ceiling_height', 'floor_area', 'hepa_amount', 'opening_distance', 
+        'room_volume', 'windows_duration', 'windows_frequency', 'window_height', 'window_width'}
+INT_ATTRIBUTES = {'exposed_coffee_duration', 'infected_coffee_duration', 'infected_people', 'total_people', 'windows_number'}
+TIME_ATTRIBUTES = {'exposed_lunch_start', 'exposed_lunch_finish', 'exposed_start', 'exposed_finish',
+                'infected_lunch_start', 'infected_lunch_finish', 'infected_start', 'infected_finish'}        
 
 def time_string_to_minutes(time: str) -> minutes_since_midnight:
     """
@@ -612,3 +581,11 @@ def time_string_to_minutes(time: str) -> minutes_since_midnight:
     :return: The number of minutes between 'time' and 00:00
     """
     return minutes_since_midnight(60 * int(time[:2]) + int(time[3:]))
+
+def time_minutes_to_string(time: int) -> str:
+    """
+    Converts time from an integer number of minutes after 00:00 to string-format
+    :param time: The number of minutes between 'time' and 00:00
+    :return: A string of the form "HH:MM" representing a time of day
+    """
+    return "{0:0=2d}".format(int(time/60)) + ":" + "{0:0=2d}".format(time%60)

cara/apps/calculator/report_generator.py

@@ -5,6 +5,8 @@ import io
 from pathlib import Path
 import typing
 
+import qrcode
+import urllib
 import jinja2
 import matplotlib
 matplotlib.use('agg')
@@ -61,16 +63,46 @@ def calculate_report_data(model: models.ExposureModel):
         "emission_rate": er,
         "exposed_occupants": exposed_occupants,
         "expected_new_cases": expected_new_cases,
-        "scenario_plot_src": embed_figure(plot(times, concentrations, model)),
+        "scenario_plot_src": img2base64(_figure2bytes(plot(times, concentrations, model))),
         "repeated_events": repeated_events,
     }
 
 
-def embed_figure(figure) -> str:
+def generate_qr_code(prefix, form: FormData):
-    # Draw the scenario graph.
+    form_dict = FormData.to_dict(form)
-    img_data = io.BytesIO()
+    url = prefix + "?" + urllib.parse.urlencode(form_dict)
 
+    qr = qrcode.QRCode(
+        version=1,
+        error_correction=qrcode.constants.ERROR_CORRECT_H,
+        box_size=10,
+        border=4,
+    )
+    qr.add_data(url)
+    qr.make(fit=True)
+    img = qr.make_image(fill_color="black", back_color="white").convert('RGB')
+
+    return {
+        'image': img2base64(_img2bytes(img)),
+        'link': url,
+    }
+
+
+def _img2bytes(figure):
+    # Draw the image
+    img_data = io.BytesIO()
+    figure.save(img_data, format='png', bbox_inches="tight")
+    return img_data
+
+
+def _figure2bytes(figure):
+    # Draw the image
+    img_data = io.BytesIO()
     figure.savefig(img_data, format='png', bbox_inches="tight")
+    return img_data
+
+
+def img2base64(img_data) -> str:
     plt.close()
     img_data.seek(0)
     pic_hash = base64.b64encode(img_data.read()).decode('ascii')
@@ -220,12 +252,12 @@ def comparison_report(scenarios: typing.Dict[str, models.ExposureModel]):
             'expected_new_cases': model.expected_new_cases(),
         }
     return {
-        'plot': embed_figure(comparison_plot(scenarios)),
+        'plot': img2base64(_figure2bytes(comparison_plot(scenarios))),
         'stats': statistics,
     }
 
 
-def build_report(model: models.ExposureModel, form: FormData):
+def build_report(base_url: str, model: models.ExposureModel, form: FormData):
     now = datetime.now()
     time = now.strftime("%d/%m/%Y %H:%M:%S")
     request = {"the": "form", "request": "data"}
@@ -240,6 +272,7 @@ def build_report(model: models.ExposureModel, form: FormData):
     context.update(calculate_report_data(model))
     alternative_scenarios = manufacture_alternative_scenarios(form)
     context['alternative_scenarios'] = comparison_report(alternative_scenarios)
+    context['qr_code'] = generate_qr_code(f'{base_url}/calculator', form)
 
     cara_templates = Path(__file__).parent.parent / "templates"
     calculator_templates = Path(__file__).parent / "templates"

cara/apps/calculator/static/js/form.js

@@ -231,7 +231,7 @@ function on_ventilation_type_change() {
       unrequire_fields(this);
 
       //Clear invalid inputs for this newly hidden child element
-      removeInvalid(getChildElement($(this)).find('input').not('input[type=radio]').attr('id'));
+      removeInvalid("#"+getChildElement($(this)).find('input').not('input[type=radio]').attr('id'));
     }
   });
 }
@@ -456,6 +456,32 @@ function parseTimeToMins(cTime) {
 
 /* -------On Load------- */
 $(document).ready(function () {
+
+  //Pre-fill form with known values
+  (new URL(decodeURIComponent(window.location.href))).searchParams.forEach((value, name) => {
+
+    //If element exists
+    if(document.getElementsByName(name).length > 0) {
+      var elemObj = document.getElementsByName(name)[0];
+
+      //Pre-select checked radios
+      if (elemObj.type === 'radio') {
+        if (value !== 'not-applicable') {
+          $('[name="'+name+'"][value="'+value+'"]').prop('checked',true);
+        }
+      }
+      //Pre-select checkboxes
+      else if (elemObj.type === 'checkbox') {
+        elemObj.checked = (value==1);
+      }
+      //Ignore 0 (default) values from server side
+      else if (!(elemObj.classList.contains("non_zero") || elemObj.classList.contains("remove_zero")) || (value != "0.0" && value != "0")) {
+        elemObj.value = value;
+        validateValue(elemObj);
+      }
+    }
+  });
+
   // 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.

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

@@ -1,6 +1,6 @@
 {% extends "layout.html.j2" %}
 
-{% set MODEL_VERSION="v1.4.0" %}
+{% set MODEL_VERSION="v1.4.1" %}
 {% set DEBUG=False %}
 {% set active_page="calculator/" %}
 
@@ -92,8 +92,8 @@
           <label for="windows_open_permanently">Permanently</label><br>
         <span class="tabbed"><input type="radio" id="windows_open_periodically" name="window_opening_regime" value="windows_open_periodically" onclick="require_fields(this)"></span>
           <label for="windows_open_periodically">Periodically:</label>&nbsp;&nbsp;
-        <input type="number" step="any" id="windows_duration" class="disabled" name="windows_duration" placeholder="Duration (min)" min="1" data-has-radio="#windows_open_periodically"> / 
+        <input type="number" step="any" id="windows_duration" class="non_zero disabled" name="windows_duration" placeholder="Duration (min)" min="1" data-has-radio="#windows_open_periodically"> / 
-        <input type="number" step="any" id="windows_frequency" class="disabled" name="windows_frequency" placeholder="Frequency (min)" min="1" data-has-radio="#windows_open_periodically">
+        <input type="number" step="any" id="windows_frequency" class="non_zero disabled" name="windows_frequency" placeholder="Frequency (min)" min="1" data-has-radio="#windows_open_periodically">
         <br>
     </div>
     

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

@@ -265,7 +265,6 @@ In this scenario, the estimated probability of one exposed occupant getting infe
             {% endfor %}
             </tbody>
         </table>
-
     </p>
     <div style="clear: both;">
 
@@ -287,11 +286,15 @@ In this scenario, the estimated probability of one exposed occupant getting infe
 	    	<li>Limitation - the personal doses have to be kept below the legal limits (in this case the CERN exposure limits)</li>
 	    	<li>Optimisation - the personal doses and collective doses have to be kept as low as reasonably achievable (ALARA).</li>
 	    </ol>
-    For more information, please refer to <a href="https://cds.cern.ch/record/1533023/files/CERN-2013-001-p415.pdf"> this document from CERN HSE </a> and <a href="https://www.cdc.gov/nceh/radiation/safety.html#:~:text=ALARA%20stands%20for%20%E2%80%9Cas%20low,time%2C%20distance%2C%20and%20shielding."> this publication from the CDC.</a> <br>
+	    For more information, please refer to <a href="https://cds.cern.ch/record/1533023/files/CERN-2013-001-p415.pdf"> this document from CERN HSE </a> and <a href="https://www.cdc.gov/nceh/radiation/safety.html#:~:text=ALARA%20stands%20for%20%E2%80%9Cas%20low,time%2C%20distance%2C%20and%20shielding."> this publication from the CDC.</a> 
-
+	    <br><br>
-<br>
 	</p>
 
+	<div>
+		<a href="{{ qr_code.link }}"><img style="width:250pt;" id="qr_code" src="{{ qr_code.image }}"/></a>
+		<i style="position:absolute; margin-top:3.5cm">Click the QR code to regenerate the report and get a shareable link.<br>Alternatively, scan to regenerate the report.<br> Mobile-friendly app coming soon!</i>
+	</div>
+
 	<br><br><br>
 	<div style="border: 2px solid black; padding: 15px;">
 		<p class="image"> <img <img align="middle" src="/calculator/static/images/disclaimer.jpg" width="40" height="40"><b>Disclaimer:</b><br><br></p>

cara/tests/apps/calculator/test_report_generator.py

@@ -17,7 +17,7 @@ def baseline_form(baseline_form_data):
 def test_generate_report(baseline_form):
     model = baseline_form.build_model()
 
-    report = report_generator.build_report(model, baseline_form)
+    report = report_generator.build_report("", model, baseline_form)
     assert report != ""
 
 

requirements.txt

@@ -3,64 +3,73 @@
 #    pip freeze | grep -v cara >> requirements.txt
 
 .[app]
+anyio==2.1.0
+appnope==0.1.2
 argon2-cffi==20.1.0
 async-generator==1.10
-attrs==20.2.0
+attrs==20.3.0
 backcall==0.2.0
-bleach==3.2.1
+bleach==3.3.0
-certifi==2020.6.20
+certifi==2020.12.5
-cffi==1.14.3
+cffi==1.14.5
+contextvars==2.4
 cycler==0.10.0
-dataclasses==0.7
+dataclasses==0.8
 decorator==4.4.2
 defusedxml==0.6.0
 entrypoints==0.3
-importlib-metadata==2.0.0
+idna==3.1
-ipykernel==5.3.4
+immutables==0.15
-ipympl==0.5.8
+importlib-metadata==3.5.0
+ipykernel==5.5.0
+ipympl==0.6.3
 ipython==7.16.1
 ipython-genutils==0.2.0
-ipywidgets==7.5.1
+ipywidgets==7.6.3
-jedi==0.17.2
+jedi==0.18.0
-Jinja2==2.11.2
+Jinja2==2.11.3
 jsonschema==3.2.0
-jupyter-client==6.1.7
+jupyter-client==6.1.11
-jupyter-core==4.6.3
+jupyter-core==4.7.1
-jupyter-server==1.0.5
+jupyter-server==1.4.1
 jupyterlab-pygments==0.1.2
-kiwisolver==1.2.0
+jupyterlab-widgets==1.0.0
+kiwisolver==1.3.1
 MarkupSafe==1.1.1
-matplotlib==3.3.2
+matplotlib==3.3.4
 mistune==0.8.4
-nbclient==0.5.1
+nbclient==0.5.2
 nbconvert==6.0.7
-nbformat==5.0.8
+nbformat==5.1.2
-nest-asyncio==1.4.1
+nest-asyncio==1.5.1
-notebook==6.1.4
+notebook==6.2.0
-numpy==1.19.2
+numpy==1.19.5
-packaging==20.4
+packaging==20.9
-pandocfilters==1.4.2
+pandocfilters==1.4.3
-parso==0.7.1
+parso==0.8.1
 pexpect==4.8.0
 pickleshare==0.7.5
-Pillow==8.0.0
+Pillow==8.1.0
-prometheus-client==0.8.0
+prometheus-client==0.9.0
-prompt-toolkit==3.0.8
+prompt-toolkit==3.0.16
-ptyprocess==0.6.0
+ptyprocess==0.7.0
 pycparser==2.20
-Pygments==2.7.1
+Pygments==2.8.0
 pyparsing==2.4.7
 pyrsistent==0.17.3
 python-dateutil==2.8.1
-pyzmq==19.0.2
+pyzmq==22.0.3
+qrcode==6.1
 Send2Trash==1.5.0
 six==1.15.0
-terminado==0.9.1
+sniffio==1.2.0
+terminado==0.9.2
 testpath==0.4.4
-tornado==6.0.4
+tornado==6.1
 traitlets==4.3.3
-voila==0.2.4
+typing-extensions==3.7.4.3
+voila==0.2.7
 wcwidth==0.2.5
 webencodings==0.5.1
 widgetsnbextension==3.5.1
-zipp==3.3.1
+zipp==3.4.0

setup.cfg

@@ -16,3 +16,6 @@ ignore_missing_imports = True
 
 [mypy-mistune.*]
 ignore_missing_imports = True
+
+[mypy-qrcode.*]
+ignore_missing_imports = True

setup.py

@@ -24,6 +24,7 @@ REQUIREMENTS: dict = {
         'matplotlib',
         'mistune',
         'numpy',
+        'qrcode[pil]',
         'tornado',
         'voila >=0.2.4',
     ],