From 250b7c0582ecedf58b3e90eb4d7b3f752dcbdd04 Mon Sep 17 00:00:00 2001 From: Luis Aleixo Date: Tue, 7 Sep 2021 06:43:22 +0200 Subject: [PATCH 01/12] Plot alternative scenarios in report using D3.js, speeding up the response time and improving user interactivity --- cara/apps/calculator/report_generator.py | 77 +----- cara/apps/calculator/static/js/report.js | 226 ++++++++++++++---- .../templates/base/calculator.report.html.j2 | 14 +- 3 files changed, 192 insertions(+), 125 deletions(-) diff --git a/cara/apps/calculator/report_generator.py b/cara/apps/calculator/report_generator.py index d1bff9dc..773481f3 100644 --- a/cara/apps/calculator/report_generator.py +++ b/cara/apps/calculator/report_generator.py @@ -9,11 +9,9 @@ import zlib import loky import jinja2 -import matplotlib -matplotlib.use('agg') -import matplotlib.pyplot as plt import numpy as np import qrcode +import json from cara import models from ... import monte_carlo as mc @@ -162,50 +160,13 @@ def _img2bytes(figure): return img_data -def _figure2bytes(figure): - # Draw the image - img_data = io.BytesIO() - figure.savefig(img_data, format='png', bbox_inches="tight", transparent=True) - return img_data - - def img2base64(img_data) -> str: - plt.close() img_data.seek(0) pic_hash = base64.b64encode(img_data.read()).decode('ascii') # A src suitable for a tag such as f'. return f'data:image/png;base64,{pic_hash}' -def plot(times, concentrations, model: models.ExposureModel): - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - datetimes = [datetime(1970, 1, 1) + timedelta(hours=time) for time in times] - ax.plot(datetimes, concentrations, lw=2, color='#1f77b4', label='Mean concentration') - ax.spines['right'].set_visible(False) - ax.spines['top'].set_visible(False) - - ax.set_xlabel('Time of day') - ax.set_ylabel('Mean concentration ($virions/m^{3}$)') - ax.set_title('Mean concentration of virions') - ax.xaxis.set_major_formatter(matplotlib.dates.DateFormatter("%H:%M")) - - # Plot presence of exposed person - for i, (presence_start, presence_finish) in enumerate(model.exposed.presence.boundaries()): - plt.fill_between( - datetimes, concentrations, 0, - where=(np.array(times) > presence_start) & (np.array(times) < presence_finish), - color="#1f77b4", alpha=0.1, - label="Presence of exposed person(s)" if i == 0 else "" - ) - - # Place a legend outside of the axes itself. - ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left') - ax.set_ylim(0) - - return fig - - def minutes_to_time(minutes: int) -> str: minute_string = str(minutes % 60) minute_string = "0" * (2 - len(minute_string)) + minute_string @@ -281,39 +242,7 @@ def manufacture_alternative_scenarios(form: FormData) -> typing.Dict[str, mc.Exp return scenarios -def comparison_plot(scenarios: typing.Dict[str, dict], sample_times: typing.List[float]): - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - - dash_styled_scenarios = [ - 'Base scenario with FFP2 masks', - 'Base scenario with HEPA filter', - 'Base scenario with HEPA and FFP2 masks', - ] - - sample_dts = [datetime(1970, 1, 1) + timedelta(hours=time) for time in sample_times] - for name, statistics in scenarios.items(): - concentrations = statistics['concentrations'] - - if name in dash_styled_scenarios: - ax.plot(sample_dts, concentrations, label=name, linestyle='--') - else: - ax.plot(sample_dts, concentrations, label=name, linestyle='-', alpha=0.5) - - # Place a legend outside of the axes itself. - ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left') - ax.spines['right'].set_visible(False) - ax.spines['top'].set_visible(False) - ax.xaxis.set_major_formatter(matplotlib.dates.DateFormatter("%H:%M")) - - ax.set_xlabel('Time of day') - ax.set_ylabel('Mean concentration ($virions/m^{3}$)') - ax.set_title('Mean concentration of virions') - - return fig - - -def scenario_statistics(mc_model: mc.ExposureModel, sample_times: typing.List[float]): +def scenario_statistics(mc_model: mc.ExposureModel, sample_times: np.ndarray): model = mc_model.build_model(size=_DEFAULT_MC_SAMPLE_SIZE) return { 'probability_of_infection': np.mean(model.infection_probability()), @@ -342,7 +271,6 @@ def comparison_report( for (name, model), model_stats in zip(scenarios.items(), results): statistics[name] = model_stats return { - 'plot': img2base64(_figure2bytes(comparison_plot(statistics, sample_times))), 'stats': statistics, } @@ -405,6 +333,7 @@ class ReportGenerator: env.filters['minutes_to_time'] = minutes_to_time env.filters['float_format'] = "{0:.2f}".format env.filters['int_format'] = "{:0.0f}".format + env.filters['JSONify'] = json.dumps return env def render(self, context: dict) -> str: diff --git a/cara/apps/calculator/static/js/report.js b/cara/apps/calculator/static/js/report.js index d1105bec..b815da2f 100644 --- a/cara/apps/calculator/static/js/report.js +++ b/cara/apps/calculator/static/js/report.js @@ -25,56 +25,16 @@ function draw_concentration_plot(svg_id, times, concentrations, exposed_presence yAxis = d3.axisLeft(yRange); // Plot tittle. - vis.append('svg:foreignObject') - .attr("background-color", "transparent") - .attr('width', width) - .attr('height', margins.top) - .style('text-align', 'center') - .html('Mean concentration of virions'); + plot_title(vis, width, margins.top, 'Mean concentration of virions'); // Line representing the mean concentration. - var lineFunc = d3.line() - .defined(d => !isNaN(d.concentration)) - .x(d => xTimeRange(d.time)) - .y(d => yRange(d.concentration)) - .curve(d3.curveBasis); + plot_scenario_data(vis, data, xTimeRange, yRange, '#1f77b4'); - vis.append('svg:path') - .attr('d', lineFunc(data)) - .attr('stroke', '#1f77b4') - .attr('stroke-width', 2) - .attr('fill', 'none'); + // X axis. + plot_x_axis(vis, height, width, margins, xAxis, 'Time of day'); - // X axis declaration. - vis.append('svg:g') - .attr('class', 'x axis') - .attr('transform', 'translate(0,' + (height - margins.bottom) + ')') - .call(xAxis); - - // X axis label. - vis.append('text') - .attr('class', 'x label') - .attr('fill', 'black') - .attr('text-anchor', 'middle') - .attr('x', (width + margins.right) / 2) - .attr('y', height * 0.97) - .text('Time of day') - - // Y axis declaration. - vis.append('svg:g') - .attr('class', 'y axis') - .attr('transform', 'translate(' + margins.left + ',0)') - .call(yAxis); - - // Y axis label. - vis.append('svg:text') - .attr('class', 'y label') - .attr('fill', 'black') - .attr('transform', 'rotate(-90, 0,' + height + ')') - .attr('text-anchor', 'middle') - .attr('x', (height + margins.bottom) / 2) - .attr('y', (height + margins.left) * 0.92) - .text('Mean concentration (virions/m³)'); + // Y axis + plot_y_axis(vis, height, width, margins, yAxis, 'Mean concentration (virions/m³)') // Area representing the presence of exposed person(s). exposed_presence_intervals.forEach(b => { @@ -181,4 +141,178 @@ function draw_concentration_plot(svg_id, times, concentrations, exposed_presence focus.select('#tooltip-time').text('x = ' + time_format(d.hour)); focus.select('#tooltip-concentration').text('y = ' + d.concentration.toFixed(2)); } +} + +// Generate the alternative scenarios plot using d3 library. +// 'alternative_scenarios' is a dictionary with all the alternative scenarios +// 'times' is a list of times for all the scenarios +function draw_alternative_scenarios_plot(svg_id, width, height, alternative_scenarios, times) { + // H:M format + var time_format = d3.timeFormat('%H:%M'); + // D3 array of ten categorical colors represented as RGB hexadecimal strings. + var colors = d3.schemeAccent; + + // Variable for the highest concentration for all the scenarios + var highest_concentration = 0. + + var data_for_scenarios = {} + for (scenario in alternative_scenarios) { + scenario_concentrations = alternative_scenarios[scenario].concentrations + + highest_concentration = Math.max(highest_concentration, Math.max(...scenario_concentrations)) + + var data = [] + times.map((time, index) => data.push({ 'time': time, 'hour': new Date().setHours(Math.trunc(time), (time - Math.trunc(time)) * 60), 'concentration': scenario_concentrations[index] })) + + // Add data into lines dictionary + data_for_scenarios[scenario] = data + } + + // We need one scenario to get the time range + var first_scenario = Object.values(data_for_scenarios)[0] + + var vis = d3.select(svg_id), + width = width, + height = height, + margins = { top: 30, right: 20, bottom: 50, left: 50 }, + + // H:M time format for x axis. + xRange = d3.scaleTime().range([margins.left, width - margins.right]).domain([first_scenario[0].hour, first_scenario[first_scenario.length - 1].hour]), + xTimeRange = d3.scaleLinear().range([margins.left, width - margins.right]).domain([times[0], times[times.length - 1]]), + + yRange = d3.scaleLinear().range([height - margins.bottom, margins.top]).domain([0., highest_concentration]), + + xAxis = d3.axisBottom(xRange).tickFormat(d => time_format(d)), + yAxis = d3.axisLeft(yRange); + + // Plot title. + plot_title(vis, width, margins.top, 'Mean concentration of virions'); + + // Line representing the mean concentration for each scenario. + for (const [scenario_name, data] of Object.entries(data_for_scenarios)) { + var scenario_index = Object.keys(data_for_scenarios).indexOf(scenario_name) + + // Line representing the mean concentration. + plot_scenario_data(vis, data, xTimeRange, yRange, colors[scenario_index]) + + // Legend for the plot elements - lines. + var size = 20 * (scenario_index + 1) + vis.append('rect') + .attr('x', width + 20) + .attr('y', margins.top + size) + .attr('width', 20) + .attr('height', 3) + .style('fill', colors[scenario_index]); + + vis.append('text') + .attr('x', width + 3 * 20) + .attr('y', margins.top + size) + .text(scenario_name) + .style('font-size', '15px') + .attr('alignment-baseline', 'central'); + + } + + // X axis. + plot_x_axis(vis, height, width, margins, xAxis, "Time of day"); + + // Y axis declaration. + vis.append('svg:g') + .attr('class', 'y axis') + .attr('transform', 'translate(' + margins.left + ',0)') + .call(yAxis); + + // Y axis label. + vis.append('svg:text') + .attr('class', 'y label') + .attr('fill', 'black') + .attr('transform', 'rotate(-90, 0,' + height + ')') + .attr('text-anchor', 'middle') + .attr('x', (height + margins.bottom) / 2) + .attr('y', (height + margins.left) * 0.92) + .text('Mean concentration (virions/m³)'); + + // Legend bounding box. + vis.append('rect') + .attr('width', 275) + .attr('height', 25 * (Object.keys(data_for_scenarios).length)) + .attr('x', width * 1.005) + .attr('y', margins.top + 5) + .attr('stroke', 'lightgrey') + .attr('stroke-width', '2') + .attr('rx', '5px') + .attr('ry', '5px') + .attr('stroke-linejoin', 'round') + .attr('fill', 'none'); +} + + +// Functions used to build the plots' components + +function plot_title(vis, width, margin_top, title) { + vis.append('svg:foreignObject') + .attr('width', width) + .attr('height', margin_top) + .attr('fill', 'none') + .append('xhtml:div') + .style('text-align', 'center') + .html(title); + + return vis; +} + +function plot_x_axis(vis, height, width, margins, xAxis, label) { + // X axis declaration + vis.append('svg:g') + .attr('class', 'x axis') + .attr('transform', 'translate(0,' + (height - margins.bottom) + ')') + .call(xAxis); + + // X axis label. + vis.append('text') + .attr('class', 'x label') + .attr('fill', 'black') + .attr('text-anchor', 'middle') + .attr('x', (width + margins.right) / 2) + .attr('y', height * 0.97) + .text(label); + + return vis; +} + +function plot_y_axis(vis, height, width, margins, yAxis, label) { + // Y axis declaration. + vis.append('svg:g') + .attr('class', 'y axis') + .attr('transform', 'translate(' + margins.left + ',0)') + .call(yAxis); + + // Y axis label. + vis.append('svg:text') + .attr('class', 'y label') + .attr('fill', 'black') + .attr('transform', 'rotate(-90, 0,' + height + ')') + .attr('text-anchor', 'middle') + .attr('x', (height + margins.bottom) / 2) + .attr('y', (height + margins.left) * 0.92) + .text(label); + + return vis; + +} + +function plot_scenario_data(vis, data, xTimeRange, yRange, line_color) { + var lineFunc = d3.line() + .defined(d => !isNaN(d.concentration)) + .x(d => xTimeRange(d.time)) + .y(d => yRange(d.concentration)) + .curve(d3.curveBasis); + + vis.append('svg:path') + .attr('d', lineFunc(data)) + .attr("stroke", line_color) + .attr('stroke-width', 2) + .attr('fill', 'none'); + + return vis; } \ No newline at end of file diff --git a/cara/apps/calculator/templates/base/calculator.report.html.j2 b/cara/apps/calculator/templates/base/calculator.report.html.j2 index ad04ffae..146478dc 100644 --- a/cara/apps/calculator/templates/base/calculator.report.html.j2 +++ b/cara/apps/calculator/templates/base/calculator.report.html.j2 @@ -88,9 +88,9 @@

* The results are based on the parameters and assumptions published in the CERN Open Report CERN-OPEN-2021-004.

@@ -108,8 +108,12 @@
- - + + {% block report_scenarios_summary_table %} From 9ed65a2b044448483dfc6b3de34047705cb0e3b2 Mon Sep 17 00:00:00 2001 From: Nicolas Mounet Date: Mon, 13 Sep 2021 12:00:06 +0200 Subject: [PATCH 02/12] Model optimisation: avoid computing before first presence time --- cara/models.py | 14 +++++++++++++- cara/tests/models/test_concentration_model.py | 4 ++++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/cara/models.py b/cara/models.py index 53cf52bc..86d2acb9 100644 --- a/cara/models.py +++ b/cara/models.py @@ -776,6 +776,14 @@ class ConcentrationModel: state_change_times.update(self.ventilation.transition_times()) return sorted(state_change_times) + @method_cache + def _first_presence_time(self) -> float: + """ + First presence time. Before that, the concentration is zero. + + """ + return self.infected.presence.boundaries()[0][0] + def last_state_change(self, time: float) -> float: """ Find the most recent/previous state change. @@ -823,7 +831,9 @@ class ConcentrationModel: Note that time is not vectorised. You can only pass a single float to this method. """ - if time == 0: + # The model always starts at t=0, but we avoid running concentration calculations + # before the first presence as an optimisation. + if time <= self._first_presence_time(): return 0.0 next_state_change_time = self._next_state_change(time) IVRR = self.infectious_virus_removal_rate(next_state_change_time) @@ -841,6 +851,8 @@ class ConcentrationModel: """ Get the integrated concentration dose between the times start and stop. """ + if stop <= self._first_presence_time(): + return 0.0 state_change_times = self.state_change_times() req_start, req_stop = start, stop total_concentration = 0. diff --git a/cara/tests/models/test_concentration_model.py b/cara/tests/models/test_concentration_model.py index 46e7e88e..9373d4a9 100644 --- a/cara/tests/models/test_concentration_model.py +++ b/cara/tests/models/test_concentration_model.py @@ -121,6 +121,10 @@ def test_next_state_change_time_out_of_range(simple_conc_model: models.Concentra simple_conc_model._next_state_change(3.1) +def test_first_presence_time(simple_conc_model): + assert simple_conc_model._first_presence_time() == 0.5 + + def test_integrated_concentration(simple_conc_model): c1 = simple_conc_model.integrated_concentration(0, 2) c2 = simple_conc_model.integrated_concentration(0, 1) From fdca7da53a0b8cd5866d688307681e8a11007356 Mon Sep 17 00:00:00 2001 From: jdevine Date: Mon, 13 Sep 2021 13:50:12 +0200 Subject: [PATCH 03/12] Changed default strain in calculator to Delta. Also applies retroactively to QR codes missing delta. The rational for the retrospective change is that old simulations (wild type) re-run need to be re-run with the current dominant strain. --- cara/apps/calculator/model_generator.py | 2 +- cara/apps/calculator/templates/calculator.form.html.j2 | 6 +++--- cara/apps/calculator/templates/userguide.html.j2 | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/cara/apps/calculator/model_generator.py b/cara/apps/calculator/model_generator.py index 06c29229..61f4e9fd 100644 --- a/cara/apps/calculator/model_generator.py +++ b/cara/apps/calculator/model_generator.py @@ -117,7 +117,7 @@ class FormData: 'simulation_name': _NO_DEFAULT, 'total_people': _NO_DEFAULT, 'ventilation_type': 'no_ventilation', - 'virus_type': 'SARS_CoV_2', + 'virus_type': 'SARS_CoV_2_B16172', 'volume_type': _NO_DEFAULT, 'window_type': 'window_sliding', 'window_height': 0., diff --git a/cara/apps/calculator/templates/calculator.form.html.j2 b/cara/apps/calculator/templates/calculator.form.html.j2 index c119d4e5..97209c98 100644 --- a/cara/apps/calculator/templates/calculator.form.html.j2 +++ b/cara/apps/calculator/templates/calculator.form.html.j2 @@ -62,10 +62,10 @@ v{{ calculator_version }} Please sen
@@ -344,13 +344,13 @@ v{{ calculator_version }} Please sen Quick Guide:
This tool simulates the long range airborne spread SARS-CoV-2 virus in a finite volume and estimates the risk of COVID-19 infection. It is based on current scientific data and can be used to compare the effectiveness of different mitigation measures.
Virus data:
- SARS-CoV-2 covers typical strains of the virus and three variants of concern (VOC):
+ SARS-CoV-2 covers the original wild strain of the virus and three variants of concern (VOC):
  • Alpha (also known as B.1.1.7, first identified in UK, Dec 2020),
  • Gamma (also known as P.1, first identified in Brazil/Japan, Jan 2021).
  • Delta (also known as B.1.617.2, first identified in India, Oct 2020).
- Choose variant according to local area prevalence, e.g. for Geneva + Modify the default (Delta) as necessary, according to local area prevalence e.g. for Geneva or Ain (France).
Ventilation data:
    diff --git a/cara/apps/calculator/templates/userguide.html.j2 b/cara/apps/calculator/templates/userguide.html.j2 index ede8c8e3..ac0e69ca 100644 --- a/cara/apps/calculator/templates/userguide.html.j2 +++ b/cara/apps/calculator/templates/userguide.html.j2 @@ -56,12 +56,12 @@ Changing this setting alters the properties of the virus which are used for the This has a significant effect on the probability of infection. The choices are:

      -
    • SARS-CoV-2 (nominal strain), covering typical strains and varaints which are not of concern from an epidemiologic point of view of the virus;
      • +
    • SARS-CoV-2 (nominal strain), covering typical strains and variants which are not of concern from an epidemiologic point of view of the virus;
    • SARS-CoV-2 (Alpha VOC), first identified in the UK at the end of 2020 which is found to be approximately 1.5x more transmissible compared to the non-VOCs;
    • SARS-CoV-2 (Gamma VOC), first identified in Brazil in January 2021 which is found to be approximately 2.2x more transmissible compared to the non-VOCs.
    • SARS-CoV-2 (Delta VOC), first identified in India towards the end of 2020 which is found to be approximately 60% more transmissible compared to the ALPHA VOC.
    -

    The user can base their choice according to the prevalence of the different variants in the local area. Access to this information can be found here:

    +

    The user can modify the selected variant from the default (Delta VOC), according to the prevalence of the different variants in the local area. Access to this information can be found here:

    • Geneva: https://www.covid19.admin.ch/fr/epidemiologic/virus-variants?detGeo=GE
    • Ain (France): https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/covid-19-cartographie-des-variants-en-france-donnees-par-region-et-par-departement
      • From 8fbe7856b98cd908934ee9798b1ac06039fb40ae Mon Sep 17 00:00:00 2001 From: jdevine Date: Tue, 14 Sep 2021 14:57:48 +0200 Subject: [PATCH 04/12] Addressed comments from Andre. --- cara/apps/calculator/__init__.py | 2 +- cara/apps/calculator/templates/calculator.form.html.j2 | 6 +++--- cara/apps/calculator/templates/userguide.html.j2 | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/cara/apps/calculator/__init__.py b/cara/apps/calculator/__init__.py index 1688d494..a60d5f74 100644 --- a/cara/apps/calculator/__init__.py +++ b/cara/apps/calculator/__init__.py @@ -33,7 +33,7 @@ from .user import AuthenticatedUser, AnonymousUser # calculator version. If the calculator needs to make breaking changes (e.g. change # form attributes) then it can also increase its MAJOR version without needing to # increase the overall CARA version (found at ``cara.__version__``). -__version__ = "3.0.0" +__version__ = "3.0.1" class BaseRequestHandler(RequestHandler): diff --git a/cara/apps/calculator/templates/calculator.form.html.j2 b/cara/apps/calculator/templates/calculator.form.html.j2 index 97209c98..65391454 100644 --- a/cara/apps/calculator/templates/calculator.form.html.j2 +++ b/cara/apps/calculator/templates/calculator.form.html.j2 @@ -62,10 +62,10 @@ v{{ calculator_version }} Please sen
      @@ -344,13 +344,13 @@ v{{ calculator_version }} Please sen Quick Guide:
      This tool simulates the long range airborne spread SARS-CoV-2 virus in a finite volume and estimates the risk of COVID-19 infection. It is based on current scientific data and can be used to compare the effectiveness of different mitigation measures.
      Virus data:
      - SARS-CoV-2 covers the original wild strain of the virus and three variants of concern (VOC):
      + SARS-CoV-2 covers the original "wild type" strain of the virus and three variants of concern (VOC):
      • Alpha (also known as B.1.1.7, first identified in UK, Dec 2020),
      • Gamma (also known as P.1, first identified in Brazil/Japan, Jan 2021).
      • Delta (also known as B.1.617.2, first identified in India, Oct 2020).
      - Modify the default (Delta) as necessary, according to local area prevalence e.g. for Geneva + Modify the default as necessary, according to local area prevalence e.g. for Geneva or Ain (France).
      Ventilation data:
        diff --git a/cara/apps/calculator/templates/userguide.html.j2 b/cara/apps/calculator/templates/userguide.html.j2 index ac0e69ca..f51cba61 100644 --- a/cara/apps/calculator/templates/userguide.html.j2 +++ b/cara/apps/calculator/templates/userguide.html.j2 @@ -61,7 +61,7 @@ The choices are:

      • SARS-CoV-2 (Gamma VOC), first identified in Brazil in January 2021 which is found to be approximately 2.2x more transmissible compared to the non-VOCs.
      • SARS-CoV-2 (Delta VOC), first identified in India towards the end of 2020 which is found to be approximately 60% more transmissible compared to the ALPHA VOC.
      -

      The user can modify the selected variant from the default (Delta VOC), according to the prevalence of the different variants in the local area. Access to this information can be found here:

      +

      The user can modify the selected variant from the default, according to the prevalence of the different variants in the local area. Access to this information can be found here:

      • Geneva: https://www.covid19.admin.ch/fr/epidemiologic/virus-variants?detGeo=GE
      • Ain (France): https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/covid-19-cartographie-des-variants-en-france-donnees-par-region-et-par-departement
        • From 92f9bce7e5c2de2de65ad13ea3d96139bb32c2b7 Mon Sep 17 00:00:00 2001 From: Nicolas Mounet Date: Tue, 14 Sep 2021 16:11:44 +0200 Subject: [PATCH 05/12] Normalization of the computation of the concentration --- cara/models.py | 94 ++++++++++++++-------- cara/tests/models/test_exposure_model.py | 16 ++-- cara/tests/test_monte_carlo_full_models.py | 2 +- 3 files changed, 70 insertions(+), 42 deletions(-) diff --git a/cara/models.py b/cara/models.py index 86d2acb9..98245997 100644 --- a/cara/models.py +++ b/cara/models.py @@ -701,11 +701,11 @@ class InfectedPopulation(Population): elif np.isinf(aerosols): ER = 970 * self.virus.infectious_dose - return ER + return ER * self.number - def individual_emission_rate(self, time) -> _VectorisedFloat: + def emission_rate(self, time) -> _VectorisedFloat: """ - The emission rate of a single individual in the population. + The emission rate of the population. """ # Note: The original model avoids time dependence on the emission rate @@ -721,13 +721,6 @@ class InfectedPopulation(Population): return self.emission_rate_when_present() - def emission_rate(self, time) -> _VectorisedFloat: - """ - The emission rate of the entire population. - - """ - return self.individual_emission_rate(time) * self.number - @dataclass(frozen=True) class ConcentrationModel: @@ -753,16 +746,22 @@ class ConcentrationModel: ) @method_cache - def _concentration_limit(self, time: float) -> _VectorisedFloat: + def _normed_concentration_limit(self, time: float) -> _VectorisedFloat: """ Provides a constant that represents the theoretical asymptotic value reached by the concentration when time goes to infinity, if all parameters were to stay time-independent. + This is normalized by the emission rate, the latter acting as a + multiplicative constant factor for the concentration model that + can be put back in front of the concentration after the time + dependence has been solved for. """ + if not self.infected.person_present(time): + return 0. V = self.room.volume IVRR = self.infectious_virus_removal_rate(time) - return (self.infected.emission_rate(time)) / (IVRR * V) + return 1. / (IVRR * V) @method_cache def state_change_times(self) -> typing.List[float]: @@ -815,15 +814,16 @@ class ConcentrationModel: ) @method_cache - def _concentration_cached(self, time: float) -> _VectorisedFloat: - # A cached version of the concentration method. Use this method if you - # expect that there may be multiple concentration calculations for the - # same time (e.g. at state change times). - return self.concentration(time) + def _normed_concentration_cached(self, time: float) -> _VectorisedFloat: + # A cached version of the _normed_concentration method. Use this + # method if you expect that there may be multiple concentration + # calculations for the same time (e.g. at state change times). + return self._normed_concentration(time) - def concentration(self, time: float) -> _VectorisedFloat: + def _normed_concentration(self, time: float) -> _VectorisedFloat: """ - Virus exposure concentration, as a function of time. + Virus exposure concentration, as a function of time, and + normalized by the emission rate. The formulas used here assume that all parameters (ventilation, emission rate) are constant between two state changes - only the value of these parameters at the next state change, are used. @@ -837,25 +837,36 @@ class ConcentrationModel: return 0.0 next_state_change_time = self._next_state_change(time) IVRR = self.infectious_virus_removal_rate(next_state_change_time) - concentration_limit = self._concentration_limit(next_state_change_time) + conc_limit = self._normed_concentration_limit(next_state_change_time) t_last_state_change = self.last_state_change(time) - concentration_at_last_state_change = self._concentration_cached(t_last_state_change) + conc_at_last_state_change = self._normed_concentration_cached(t_last_state_change) delta_time = time - t_last_state_change fac = np.exp(-IVRR * delta_time) - return concentration_limit * (1 - fac) + concentration_at_last_state_change * fac + return conc_limit * (1 - fac) + conc_at_last_state_change * fac + + def concentration(self, time: float) -> _VectorisedFloat: + """ + Virus exposure concentration, as a function of time. + + Note that time is not vectorised. You can only pass a single float + to this method. + """ + return (self._normed_concentration(time) * + self.infected.emission_rate_when_present()) @method_cache - def integrated_concentration(self, start: float, stop: float) -> _VectorisedFloat: + def normed_integrated_concentration(self, start: float, stop: float) -> _VectorisedFloat: """ - Get the integrated concentration dose between the times start and stop. + Get the integrated concentration dose between the times start and stop, + normalized by the emission rate. """ if stop <= self._first_presence_time(): return 0.0 state_change_times = self.state_change_times() req_start, req_stop = start, stop - total_concentration = 0. + total_normed_concentration = 0. for interval_start, interval_stop in zip(state_change_times[:-1], state_change_times[1:]): if req_start > interval_stop or req_stop < interval_start: continue @@ -863,17 +874,24 @@ class ConcentrationModel: start = max([interval_start, req_start]) stop = min([interval_stop, req_stop]) - conc_start = self._concentration_cached(start) + conc_start = self._normed_concentration_cached(start) next_conc_state = self._next_state_change(stop) - conc_limit = self._concentration_limit(next_conc_state) + conc_limit = self._normed_concentration_limit(next_conc_state) IVRR = self.infectious_virus_removal_rate(next_conc_state) delta_time = stop - start - total_concentration += ( + total_normed_concentration += ( conc_limit * delta_time + (conc_limit - conc_start) * (np.exp(-IVRR*delta_time)-1) / IVRR ) - return total_concentration + return total_normed_concentration + + def integrated_concentration(self, start: float, stop: float) -> _VectorisedFloat: + """ + Get the integrated concentration dose between the times start and stop. + """ + return (self.normed_integrated_concentration(start, stop) * + self.infected.emission_rate_when_present()) @dataclass(frozen=True) @@ -890,14 +908,22 @@ class ExposureModel: #: The fraction of viruses actually deposited in the respiratory tract fraction_deposited: _VectorisedFloat = 0.6 - def exposure(self) -> _VectorisedFloat: - """The number of virus per meter^3.""" - exposure = 0.0 + def _normed_exposure(self) -> _VectorisedFloat: + """ + The number of virus per meter^3, normalized by the emission rate + of the infected population. + """ + normed_exposure = 0.0 for start, stop in self.exposed.presence.boundaries(): - exposure += self.concentration_model.integrated_concentration(start, stop) + normed_exposure += self.concentration_model.normed_integrated_concentration(start, stop) - return exposure * self.repeats + return normed_exposure * self.repeats + + def exposure(self) -> _VectorisedFloat: + """The number of virus per meter^3.""" + return (self._normed_exposure() * + self.concentration_model.infected.emission_rate_when_present()) def infection_probability(self) -> _VectorisedFloat: exposure = self.exposure() diff --git a/cara/tests/models/test_exposure_model.py b/cara/tests/models/test_exposure_model.py index cf8cfb6e..11a135a1 100644 --- a/cara/tests/models/test_exposure_model.py +++ b/cara/tests/models/test_exposure_model.py @@ -11,20 +11,20 @@ from cara.dataclass_utils import replace @dataclass(frozen=True) -class KnownConcentrations(models.ConcentrationModel): +class KnownNormedconcentration(models.ConcentrationModel): """ A ConcentrationModel which is based on pre-known exposure concentrations and which therefore doesn't need other components. Useful for testing. """ - concentration_function: typing.Callable + normed_concentration_function: typing.Callable def infectious_virus_removal_rate(self, time: float) -> models._VectorisedFloat: # very large decay constant -> same as constant concentration return 1.e50 - def _concentration_limit(self, time: float) -> models._VectorisedFloat: - return self.concentration_function(time) + def _normed_concentration_limit(self, time: float) -> models._VectorisedFloat: + return self.normed_concentration_function(time) def state_change_times(self): return [0., 24.] @@ -32,8 +32,8 @@ class KnownConcentrations(models.ConcentrationModel): def _next_state_change(self, time: float): return 24. - def concentration(self, time: float) -> models._VectorisedFloat: # noqa - return self.concentration_function(time) + def _normed_concentration(self, time: float) -> models._VectorisedFloat: # noqa + return self.normed_concentration_function(time) halftime = models.PeriodicInterval(120, 60) @@ -67,7 +67,9 @@ def known_concentrations(func): virus=models.Virus.types['SARS_CoV_2_B117'], expiration=models.Expiration.types['Talking'] ) - return KnownConcentrations(dummy_room, dummy_ventilation, dummy_infected_population, func) + normed_func = lambda x: func(x) / dummy_infected_population.emission_rate_when_present() + return KnownNormedconcentration(dummy_room, dummy_ventilation, + dummy_infected_population, normed_func) @pytest.mark.parametrize( diff --git a/cara/tests/test_monte_carlo_full_models.py b/cara/tests/test_monte_carlo_full_models.py index 5cf88198..08bd2dad 100644 --- a/cara/tests/test_monte_carlo_full_models.py +++ b/cara/tests/test_monte_carlo_full_models.py @@ -238,7 +238,7 @@ def skagit_chorale_mc(): ["shared_office_mc", 10.7, 0.32, 57.24, 654], ["classroom_mc", 36.1, 6.85, 780.0, 28464], ["ski_cabin_mc", 16.3, 0.49, 35.94, 7404], - ["gym_mc", 2.25, 0.63, 0.7842, 984], + ["gym_mc", 2.25, 0.63, 0.7842, 1968], ["waiting_room_mc", 9.72, 1.36, 34.26, 3534], ["skagit_chorale_mc",29.9, 17.9, 190.0, 141400], ] From 5d4dc4b91d7b3c22bc30ded340e7a65f3cd2f3aa Mon Sep 17 00:00:00 2001 From: jdevine Date: Tue, 14 Sep 2021 16:22:49 +0200 Subject: [PATCH 06/12] reverted model_generator default virus type --- cara/apps/calculator/model_generator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cara/apps/calculator/model_generator.py b/cara/apps/calculator/model_generator.py index 61f4e9fd..06c29229 100644 --- a/cara/apps/calculator/model_generator.py +++ b/cara/apps/calculator/model_generator.py @@ -117,7 +117,7 @@ class FormData: 'simulation_name': _NO_DEFAULT, 'total_people': _NO_DEFAULT, 'ventilation_type': 'no_ventilation', - 'virus_type': 'SARS_CoV_2_B16172', + 'virus_type': 'SARS_CoV_2', 'volume_type': _NO_DEFAULT, 'window_type': 'window_sliding', 'window_height': 0., From af3ded7935f09eaa958cd624e12ad42a173281e9 Mon Sep 17 00:00:00 2001 From: Nicolas Mounet Date: Thu, 16 Sep 2021 13:55:04 +0200 Subject: [PATCH 07/12] Remove suprespreading event from the expiration types --- cara/models.py | 74 ++++++++++++++---------- cara/tests/conftest.py | 6 +- cara/tests/models/test_exposure_model.py | 6 +- cara/tests/test_known_quantities.py | 18 +++--- 4 files changed, 62 insertions(+), 42 deletions(-) diff --git a/cara/models.py b/cara/models.py index 98245997..296c260c 100644 --- a/cara/models.py +++ b/cara/models.py @@ -620,7 +620,6 @@ _ExpirationBase.types = { 'Talking': Expiration((1., 1., 1.)), 'Shouting': Expiration((1., 5., 5.)), 'Singing': Expiration((1., 5., 5.)), - 'Superspreading event': Expiration((np.inf, 0., 0.)), } @@ -669,44 +668,21 @@ class Population: @dataclass(frozen=True) -class InfectedPopulation(Population): +class _PopulationWithVirus(Population): #: The virus with which the population is infected. virus: Virus - #: The type of expiration that is being emitted whilst doing the activity. - expiration: _ExpirationBase - @method_cache def emission_rate_when_present(self) -> _VectorisedFloat: """ - The emission rate if the infected population is present. - - Note that the rate is not currently time-dependent. - + The emission rate if the infected population is present + (in virions / h). It should not be a function of time. """ - # Emission Rate (virions / h) - # Note on units: exhalation rate is in m^3/h, aerosols in mL/cm^3 - # and viral load in virus/mL -> 1e6 conversion factor - aerosols = self.expiration.aerosols(self.mask) - - ER = (self.virus.viral_load_in_sputum * - self.activity.exhalation_rate * - 10 ** 6 * - aerosols) - - # For superspreading event, where ejection_factor is infinite we fix the ER - # based on Miller et al. (2020). - if isinstance(aerosols, np.ndarray): - ER[np.isinf(aerosols)] = 970 * self.virus.infectious_dose - elif np.isinf(aerosols): - ER = 970 * self.virus.infectious_dose - - return ER * self.number + raise NotImplementedError("Subclass must implement") def emission_rate(self, time) -> _VectorisedFloat: """ - The emission rate of the population. - + The emission rate of the population vs time. """ # Note: The original model avoids time dependence on the emission rate # at the cost of implementing a piecewise (on time) concentration function. @@ -722,11 +698,49 @@ class InfectedPopulation(Population): return self.emission_rate_when_present() +@dataclass(frozen=True) +class EmittingPopulation(_PopulationWithVirus): + #: The emission rate of a single individual, in virions / h. + known_individual_emission_rate: float + + @method_cache + def emission_rate_when_present(self) -> _VectorisedFloat: + """ + The emission rate if the infected population is present. + """ + return self.known_individual_emission_rate * self.number + + +@dataclass(frozen=True) +class InfectedPopulation(_PopulationWithVirus): + #: The type of expiration that is being emitted whilst doing the activity. + expiration: _ExpirationBase + + @method_cache + def emission_rate_when_present(self) -> _VectorisedFloat: + """ + The emission rate if the infected population is present. + Note that the rate is not currently time-dependent. + """ + # Emission Rate (virions / h) + # Note on units: exhalation rate is in m^3/h, aerosols in mL/cm^3 + # and viral load in virus/mL -> 1e6 conversion factor + + aerosols = self.expiration.aerosols(self.mask) + + ER = (self.virus.viral_load_in_sputum * + self.activity.exhalation_rate * + 10 ** 6 * + aerosols) + + return ER * self.number + + @dataclass(frozen=True) class ConcentrationModel: room: Room ventilation: _VentilationBase - infected: InfectedPopulation + infected: _PopulationWithVirus @property def virus(self): diff --git a/cara/tests/conftest.py b/cara/tests/conftest.py index 9499dfcf..e828e0cd 100644 --- a/cara/tests/conftest.py +++ b/cara/tests/conftest.py @@ -13,13 +13,15 @@ def baseline_model(): active=models.SpecificInterval(((0., 24.), )), air_exch=30., ), - infected=models.InfectedPopulation( + infected=models.EmittingPopulation( number=1, virus=models.Virus.types['SARS_CoV_2'], presence=models.SpecificInterval(((0., 4.), (5., 8.))), mask=models.Mask.types['No mask'], activity=models.Activity.types['Light activity'], - expiration=models.Expiration.types['Superspreading event'], + known_individual_emission_rate=970 * 50, + # superspreading event, where ejection factor is fixed based + # on Miller et al. (2020) - 50 represents the infectious dose. ), ) return model diff --git a/cara/tests/models/test_exposure_model.py b/cara/tests/models/test_exposure_model.py index 11a135a1..ac82dae3 100644 --- a/cara/tests/models/test_exposure_model.py +++ b/cara/tests/models/test_exposure_model.py @@ -144,13 +144,15 @@ def conc_model(): return models.ConcentrationModel( models.Room(25), models.AirChange(always, 5), - models.InfectedPopulation( + models.EmittingPopulation( number=1, presence=interesting_times, mask=models.Mask.types['No mask'], activity=models.Activity.types['Seated'], virus=models.Virus.types['SARS_CoV_2'], - expiration=models.Expiration.types['Superspreading event'], + known_individual_emission_rate=970 * 50, + # superspreading event, where ejection factor is fixed based + # on Miller et al. (2020) - 50 represents the infectious dose. ) ) diff --git a/cara/tests/test_known_quantities.py b/cara/tests/test_known_quantities.py index 89c0268d..d1db42c2 100644 --- a/cara/tests/test_known_quantities.py +++ b/cara/tests/test_known_quantities.py @@ -66,13 +66,15 @@ def build_model(interval_duration): active=models.PeriodicInterval(period=120, duration=interval_duration), q_air_mech=500., ), - infected=models.InfectedPopulation( + infected=models.EmittingPopulation( number=1, virus=models.Virus.types['SARS_CoV_2'], presence=models.SpecificInterval(((0., 4.), (5., 8.))), mask=models.Mask.types['No mask'], activity=models.Activity.types['Light activity'], - expiration=models.Expiration.types['Superspreading event'], + known_individual_emission_rate=970 * 50, + # superspreading event, where ejection factor is fixed based + # on Miller et al. (2020) - 50 represents the infectious dose. ), ) return model @@ -226,13 +228,13 @@ def build_hourly_dependent_model( outside_temp=outside_temp, window_height=1.6, opening_length=0.6, ), - infected=models.InfectedPopulation( + infected=models.EmittingPopulation( number=1, virus=models.Virus.types['SARS_CoV_2'], presence=models.SpecificInterval(intervals_presence_infected), mask=models.Mask.types['No mask'], activity=models.Activity.types['Light activity'], - expiration=models.Expiration.types['Superspreading event'], + known_individual_emission_rate=970 * 50, ), ) return model @@ -247,13 +249,13 @@ def build_constant_temp_model(outside_temp, intervals_open=((7.5, 8.5),)): outside_temp=models.PiecewiseConstant((0., 24.), (outside_temp,)), window_height=1.6, opening_length=0.6, ), - infected=models.InfectedPopulation( + infected=models.EmittingPopulation( number=1, virus=models.Virus.types['SARS_CoV_2'], presence=models.SpecificInterval(((0., 4.), (5., 7.5))), mask=models.Mask.types['No mask'], activity=models.Activity.types['Light activity'], - expiration=models.Expiration.types['Superspreading event'], + known_individual_emission_rate=970 * 50, ), ) return model @@ -275,13 +277,13 @@ def build_hourly_dependent_model_multipleventilation(month, intervals_open=((7.5 model = models.ConcentrationModel( room=models.Room(volume=75), ventilation=vent, - infected=models.InfectedPopulation( + infected=models.EmittingPopulation( number=1, virus=models.Virus.types['SARS_CoV_2'], presence=models.SpecificInterval(((0., 4.), (5., 7.5))), mask=models.Mask.types['No mask'], activity=models.Activity.types['Light activity'], - expiration=models.Expiration.types['Superspreading event'], + known_individual_emission_rate=970 * 50, ), ) return model From 480e5237c976dff48f628e12e3950a66c4eee4c5 Mon Sep 17 00:00:00 2001 From: Luis Aleixo Date: Tue, 28 Sep 2021 09:48:26 +0200 Subject: [PATCH 08/12] ipympl (Matplotlib Jupyter Extension) version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9e5eb596..6be0d0f9 100644 --- a/setup.py +++ b/setup.py @@ -20,7 +20,7 @@ REQUIREMENTS: dict = { 'core': [ 'dataclasses; python_version < "3.7"', 'ipykernel', - 'ipympl', + 'ipympl != 0.8.0', 'ipywidgets', 'Jinja2', 'loky', From dfc66991f4efe2bfec0b8564c3de431fd8ec6dcf Mon Sep 17 00:00:00 2001 From: Phil Elson Date: Tue, 10 Aug 2021 17:34:37 +0200 Subject: [PATCH 09/12] Move QR generation to the browser, saving some time and effort on the server. --- cara/apps/calculator/report_generator.py | 23 ++++----------- cara/apps/calculator/static/js/pdf.js | 29 ------------------- .../templates/base/calculator.report.html.j2 | 16 ++++++---- cara/tests/apps/calculator/test_webapp.py | 16 +++++----- requirements.txt | 1 - setup.py | 1 - 6 files changed, 24 insertions(+), 62 deletions(-) delete mode 100644 cara/apps/calculator/static/js/pdf.js diff --git a/cara/apps/calculator/report_generator.py b/cara/apps/calculator/report_generator.py index 773481f3..2f55e3eb 100644 --- a/cara/apps/calculator/report_generator.py +++ b/cara/apps/calculator/report_generator.py @@ -1,17 +1,15 @@ import concurrent.futures import base64 import dataclasses -from datetime import datetime, timedelta +from datetime import datetime import io +import json import typing import urllib import zlib -import loky import jinja2 import numpy as np -import qrcode -import json from cara import models from ... import monte_carlo as mc @@ -123,7 +121,7 @@ def calculate_report_data(model: models.ExposureModel): } -def generate_qr_code(base_url, calculator_prefix, form: FormData): +def generate_permalink(base_url, calculator_prefix, form: FormData): form_dict = FormData.to_dict(form, strip_defaults=True) # Generate the calculator URL arguments that would be needed to re-create this @@ -136,20 +134,9 @@ def generate_qr_code(base_url, calculator_prefix, form: FormData): qr_url = f"{base_url}/_c/{compressed_args}" url = f"{base_url}{calculator_prefix}?{args}" - qr = qrcode.QRCode( - version=1, - error_correction=qrcode.constants.ERROR_CORRECT_H, - box_size=10, - border=4, - ) - qr.add_data(qr_url) - qr.make(fit=True) - img = qr.make_image(fill_color="black", back_color="white").convert('RGB') - return { - 'image': img2base64(_img2bytes(img)), 'link': url, - 'qr_url': qr_url, + 'shortened': qr_url, } @@ -313,7 +300,7 @@ class ReportGenerator: context['alternative_scenarios'] = comparison_report( alternative_scenarios, scenario_sample_times, executor_factory=executor_factory, ) - context['qr_code'] = generate_qr_code(base_url, self.calculator_prefix, form) + context['permalink'] = generate_permalink(base_url, self.calculator_prefix, form) context['calculator_prefix'] = self.calculator_prefix context['scale_warning'] = { 'level': 'yellow-2', diff --git a/cara/apps/calculator/static/js/pdf.js b/cara/apps/calculator/static/js/pdf.js deleted file mode 100644 index 6afb4fea..00000000 --- a/cara/apps/calculator/static/js/pdf.js +++ /dev/null @@ -1,29 +0,0 @@ -function generate_pdf_version(qr_link) { - const pdf_version = this.document.getElementById("body"); - - // PDF styling - var opt = { - filename: 'myfile.pdf', - image: { type: 'jpeg', quality: 0.98 }, - html2canvas: { scale: 2, width: 1200, windowWidth: 1200 }, - enableLinks: false, - jsPDF: { - unit: 'pt', - format: 'letter', - orientation: 'portrait', - }, - pagebreak: { mode: '', avoid: '.break-avoid' }, - }; - html2pdf().set(opt).from(pdf_version).toPdf().get('pdf').then(function(pdf) { - var totalPages = pdf.internal.getNumberOfPages(); - pdf.setPage(1); - pdf.link(530, 25, 60, 60, { url: qr_link }); //Hyperlink to reproduce results - - for (i = 1; i <= totalPages; i++) { - pdf.setPage(i); - pdf.setFontSize(10); - pdf.setTextColor(150); - pdf.text('Page ' + i + ' of ' + totalPages, (pdf.internal.pageSize.getWidth() / 2.25), (pdf.internal.pageSize.getHeight() - 10)); - } - }).save(); -}; \ No newline at end of file diff --git a/cara/apps/calculator/templates/base/calculator.report.html.j2 b/cara/apps/calculator/templates/base/calculator.report.html.j2 index 146478dc..128dd21d 100644 --- a/cara/apps/calculator/templates/base/calculator.report.html.j2 +++ b/cara/apps/calculator/templates/base/calculator.report.html.j2 @@ -24,8 +24,6 @@

        Created {{ creation_date }} using CARA calculator version v{{ form.calculator_version }}

        - {# To be replaced by "Generate PDF" #} - {% endblock report_header %} @@ -162,10 +160,10 @@
        - +

        - Click the QR code to regenerate the report and get a shareable link.
        Alternatively, scan to regenerate the report.
        Mobile-friendly app coming soon! + Click the QR code to regenerate the report and get a shareable link.
        Alternatively, scan to regenerate the report.
        @@ -433,11 +431,19 @@
        {% endblock disclaimer_container %} - + + + diff --git a/cara/tests/apps/calculator/test_webapp.py b/cara/tests/apps/calculator/test_webapp.py index 40b75595..09bc104c 100644 --- a/cara/tests/apps/calculator/test_webapp.py +++ b/cara/tests/apps/calculator/test_webapp.py @@ -4,7 +4,7 @@ import pytest import tornado.testing import cara.apps.calculator -from cara.apps.calculator.report_generator import generate_qr_code +from cara.apps.calculator.report_generator import generate_permalink _TIMEOUT = 20. @@ -97,26 +97,26 @@ class TestOpenApp(tornado.testing.AsyncHTTPTestCase): assert response.code == 404 -async def test_qrcode_urls(http_server_client, baseline_form): +async def test_permalink_urls(http_server_client, baseline_form): base_url = 'proto://hostname/prefix' - qr_data = generate_qr_code(base_url, "/calculator", baseline_form) + permalink_data = generate_permalink(base_url, "/calculator", baseline_form) expected = f'{base_url}/calculator?exposed_coffee_break_option={baseline_form.exposed_coffee_break_option}&' - assert qr_data['link'].startswith(expected) + assert permalink_data['link'].startswith(expected) # We should get a 200 for the link. - response = await http_server_client.fetch(qr_data['link'].replace(base_url, '')) + response = await http_server_client.fetch(permalink_data['link'].replace(base_url, '')) assert response.code == 200 # And a 302 for the QR url itself. The redirected URL should be the same as # in the link. - assert qr_data['qr_url'].startswith(base_url) + assert permalink_data['shortened'].startswith(base_url) response = await http_server_client.fetch( - qr_data['qr_url'].replace(base_url, ''), + permalink_data['shortened'].replace(base_url, ''), max_redirects=0, raise_error=False, ) assert response.code == 302 - assert response.headers['Location'] == qr_data['link'].replace(base_url, '') + assert response.headers['Location'] == permalink_data['link'].replace(base_url, '') async def test_invalid_compressed_url(http_server_client, baseline_form): diff --git a/requirements.txt b/requirements.txt index 457a69b7..724bf5cc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -62,7 +62,6 @@ pyparsing==2.4.7 pyrsistent==0.18.0 python-dateutil==2.8.2 pyzmq==22.1.0 -qrcode==7.2 requests==2.26.0 requests-unixsocket==0.2.0 scikit-learn==0.24.2 diff --git a/setup.py b/setup.py index 6be0d0f9..704f923c 100644 --- a/setup.py +++ b/setup.py @@ -30,7 +30,6 @@ REQUIREMENTS: dict = { 'numpy', 'psutil', 'python-dateutil', - 'qrcode[pil]', 'scipy', 'sklearn', 'timezonefinder', From ea3f4abe0b8877ba5c3630774575aba4a1efc22b Mon Sep 17 00:00:00 2001 From: Luis Aleixo Date: Fri, 10 Sep 2021 13:06:27 +0200 Subject: [PATCH 10/12] Create a new QRcode for the PDF version --- cara/apps/calculator/static/css/report.css | 12 ++---------- .../templates/base/calculator.report.html.j2 | 8 +++++++- 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/cara/apps/calculator/static/css/report.css b/cara/apps/calculator/static/css/report.css index 0e0a7cf7..c9b2b3ab 100644 --- a/cara/apps/calculator/static/css/report.css +++ b/cara/apps/calculator/static/css/report.css @@ -56,7 +56,7 @@ p.notes { margin: 1% } -#pdf-qr-code { +#pdf_qrcode_aref { margin-right: 1%; width: 100pt; } @@ -102,11 +102,6 @@ p.notes { border-radius: 5px; } -.print-button { - margin-left: auto; - margin-right: 1%; -} - /* @media (width: 1200px) { */ @media print { /* #body { @@ -120,7 +115,7 @@ p.notes { #link_reproduce_results { display: none!important; } - #pdf-qr-code { + #pdf_qrcode_aref { visibility: inherit!important; } .collapse { @@ -138,9 +133,6 @@ p.notes { .icon_button { display: none!important; } - .print-button { - display: none!important; - } .card { page-break-inside: avoid; } diff --git a/cara/apps/calculator/templates/base/calculator.report.html.j2 b/cara/apps/calculator/templates/base/calculator.report.html.j2 index 128dd21d..a6180770 100644 --- a/cara/apps/calculator/templates/base/calculator.report.html.j2 +++ b/cara/apps/calculator/templates/base/calculator.report.html.j2 @@ -23,7 +23,8 @@

        CARA - CALCULATOR REPORT

        Created {{ creation_date }} using CARA calculator version v{{ form.calculator_version }}

        - + + {% endblock report_header %} @@ -443,6 +444,11 @@ width: 330, height: 330} ); + new QRCode(document.getElementById("pdf_qrcode"), { + text: "{{ permalink.shortened }}", + width: 133, + height: 133} + ); From fcfaee2b4afad53ce5871fd919eb39ff5f05d0c5 Mon Sep 17 00:00:00 2001 From: Phil Elson Date: Wed, 6 Oct 2021 11:55:27 +0200 Subject: [PATCH 11/12] Handle the case where the URL being encoded by qrcodejs is causing an error with the library (e.g. https://github.com/davidshimjs/qrcodejs/issues/78). --- .../templates/base/calculator.report.html.j2 | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/cara/apps/calculator/templates/base/calculator.report.html.j2 b/cara/apps/calculator/templates/base/calculator.report.html.j2 index a6180770..d06a21bc 100644 --- a/cara/apps/calculator/templates/base/calculator.report.html.j2 +++ b/cara/apps/calculator/templates/base/calculator.report.html.j2 @@ -442,13 +442,15 @@ new QRCode(document.getElementById("qrcode"), { text: "{{ permalink.shortened }}", width: 330, - height: 330} - ); - new QRCode(document.getElementById("pdf_qrcode"), { + height: 330, + correctLevel : QRCode.CorrectLevel.L + }); + new QRCode(document.getElementById("pdf_qrcode"), { text: "{{ permalink.shortened }}", width: 133, - height: 133} - ); + height: 133, + correctLevel : QRCode.CorrectLevel.L + }); From 0840dc43ef45b9654dd78ed860debd9eb3cd4565 Mon Sep 17 00:00:00 2001 From: Luis Aleixo Date: Wed, 6 Oct 2021 11:58:36 +0200 Subject: [PATCH 12/12] Update concentration docstring --- cara/models.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cara/models.py b/cara/models.py index 296c260c..b7885768 100644 --- a/cara/models.py +++ b/cara/models.py @@ -873,7 +873,7 @@ class ConcentrationModel: @method_cache def normed_integrated_concentration(self, start: float, stop: float) -> _VectorisedFloat: """ - Get the integrated concentration dose between the times start and stop, + Get the integrated concentration of viruses in the air between the times start and stop, normalized by the emission rate. """ if stop <= self._first_presence_time(): @@ -902,7 +902,7 @@ class ConcentrationModel: def integrated_concentration(self, start: float, stop: float) -> _VectorisedFloat: """ - Get the integrated concentration dose between the times start and stop. + Get the integrated concentration of viruses in the air between the times start and stop. """ return (self.normed_integrated_concentration(start, stop) * self.infected.emission_rate_when_present())