diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index eada20ee..e8626a3b 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -24,6 +24,7 @@ jobs: env: PROJECT_ROOT: ./ PROJECT_NAME: caimira + CAIMIRA_TESTS_CALCULATOR_TIMEOUT: 30 steps: - name: Checkout uses: actions/checkout@v2 diff --git a/.readthedocs.yaml b/.readthedocs.yaml index edd0ab51..c489761c 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -14,4 +14,4 @@ sphinx: python: install: - - requirements: caimira/docs/requirements.txt \ No newline at end of file + - requirements: caimira/docs/requirements.txt diff --git a/README.md b/README.md index 9a4a8346..fa66b893 100644 --- a/README.md +++ b/README.md @@ -103,25 +103,25 @@ pip install -e . # At the root of the repository ### Running the Calculator app in development mode ``` -python -m caimira.apps.calculator +python -m ui.apps.calculator ``` To run with a specific template theme created: ``` -python -m caimira.apps.calculator --theme=caimira/apps/templates/{theme} +python -m ui.apps.calculator --theme=ui/apps/templates/{theme} ``` To run the entire app in a different `APPLICATION_ROOT` path: ``` -python -m caimira.apps.calculator --app_root=/myroot +python -m ui.apps.calculator --app_root=/myroot ``` To run the calculator on a different URL path: ``` -python -m caimira.apps.calculator --prefix=/mycalc +python -m ui.apps.calculator --prefix=/mycalc ``` Each of these commands will start a local version of CAiMIRA, which can be visited at http://localhost:8080/. diff --git a/app-config/caimira-public-docker-image/run_caimira.sh b/app-config/caimira-public-docker-image/run_caimira.sh index 00a61542..86a994f9 100755 --- a/app-config/caimira-public-docker-image/run_caimira.sh +++ b/app-config/caimira-public-docker-image/run_caimira.sh @@ -7,4 +7,4 @@ nginx -c /opt/caimira/nginx.conf cd /opt/caimira/src/caimira # Run the calculator in the foreground. -/opt/caimira/app/bin/python -m caimira.apps.calculator --port 8081 --no-debug +/opt/caimira/app/bin/python -m ui.apps.calculator --port 8081 --no-debug diff --git a/app-config/calculator-app/app.sh b/app-config/calculator-app/app.sh index f3a05bd7..ec7beb8f 100755 --- a/app-config/calculator-app/app.sh +++ b/app-config/calculator-app/app.sh @@ -26,8 +26,8 @@ if [[ "$APP_NAME" == "calculator-app" ]]; then export "DATA_SERVICE_ENABLED"="${DATA_SERVICE_ENABLED:=0}" export "CAIMIRA_PROFILER_ENABLED"="${CAIMIRA_PROFILER_ENABLED:=0}" - echo "Starting the caimira webservice with: python -m caimira.apps.calculator ${args[@]}" - python -m caimira.apps.calculator "${args[@]}" + echo "Starting the caimira webservice with: python -m ui.apps.calculator ${args[@]}" + python -m ui.apps.calculator "${args[@]}" else echo "No APP_NAME specified" diff --git a/app-config/docker-compose.yml b/app-config/docker-compose.yml index b44ba2dd..329e886c 100644 --- a/app-config/docker-compose.yml +++ b/app-config/docker-compose.yml @@ -1,6 +1,5 @@ version: "3.8" services: - calculator-app: image: calculator-app environment: @@ -8,7 +7,7 @@ services: - APP_NAME=calculator-app - APPLICATION_ROOT=/ - CAIMIRA_CALCULATOR_PREFIX=/calculator-cern - - CAIMIRA_THEME=caimira/apps/templates/cern + - CAIMIRA_THEME=ui/apps/templates/cern - DATA_SERVICE_ENABLED=0 - CAIMIRA_PROFILER_ENABLED=0 user: ${CURRENT_UID} diff --git a/app-config/openshift/deploymentconfig.yaml b/app-config/openshift/deploymentconfig.yaml index ca2f363f..61c50e72 100644 --- a/app-config/openshift/deploymentconfig.yaml +++ b/app-config/openshift/deploymentconfig.yaml @@ -303,3 +303,4 @@ - name: PROJECT_NAME description: The name of this project, e.g. caimira-test required: true + \ No newline at end of file diff --git a/caimira/LICENSE b/caimira/LICENSE new file mode 100644 index 00000000..de49c2af --- /dev/null +++ b/caimira/LICENSE @@ -0,0 +1,13 @@ +Copyright 2020-2021 CERN. All rights not expressly granted are reserved. + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. diff --git a/caimira/store/__init__.py b/caimira/README.md similarity index 100% rename from caimira/store/__init__.py rename to caimira/README.md diff --git a/caimira/tests/__init__.py b/caimira/api/__init__.py similarity index 100% rename from caimira/tests/__init__.py rename to caimira/api/__init__.py diff --git a/caimira/api/app.py b/caimira/api/app.py new file mode 100644 index 00000000..db26c9d4 --- /dev/null +++ b/caimira/api/app.py @@ -0,0 +1,31 @@ +# """ +# Entry point for the CAiMIRA application +# """ + +import tornado.ioloop +import tornado.web +import tornado.log +from tornado.options import define, options +import logging + +from caimira.api.routes.report_routes import ReportHandler + +define("port", default=8088, help="Port to listen on", type=int) + +logging.basicConfig(format="%(message)s", level=logging.INFO) + +class Application(tornado.web.Application): + def __init__(self): + handlers = [ + (r"/report", ReportHandler), + ] + settings = dict( + debug=True, + ) + super(Application, self).__init__(handlers, **settings) + +if __name__ == "__main__": + app = Application() + app.listen(options.port) + logging.info(f"Tornado server is running on port {options.port}") + tornado.ioloop.IOLoop.current().start() diff --git a/caimira/tests/apps/__init__.py b/caimira/api/controller/__init__.py similarity index 100% rename from caimira/tests/apps/__init__.py rename to caimira/api/controller/__init__.py diff --git a/caimira/api/controller/report_controller.py b/caimira/api/controller/report_controller.py new file mode 100644 index 00000000..be151555 --- /dev/null +++ b/caimira/api/controller/report_controller.py @@ -0,0 +1,30 @@ +import concurrent.futures +import functools + +from caimira.calculator.validators.virus.virus_validator import VirusFormData +from caimira.calculator.store.data_registry import DataRegistry +import caimira.calculator.report.report_generator as rg + + +def generate_form_obj(form_data, data_registry): + return VirusFormData.from_dict(form_data, data_registry) + + +def generate_model(form_obj): + return form_obj.build_model(250_000) + + +def generate_report_results(form_obj, model): + return rg.calculate_report_data(form=form_obj, model=model, executor_factory=functools.partial( + concurrent.futures.ThreadPoolExecutor, None, # TODO define report_parallelism + ),) + + +def submit_virus_form(form_data): + data_registry = DataRegistry + + form_obj = generate_form_obj(form_data, data_registry) + model = generate_model(form_obj) + report_data = generate_report_results(form_obj, model=model) + + return report_data diff --git a/caimira/tests/apps/calculator/__init__.py b/caimira/api/routes/__init__.py similarity index 100% rename from caimira/tests/apps/calculator/__init__.py rename to caimira/api/routes/__init__.py diff --git a/caimira/api/routes/report_routes.py b/caimira/api/routes/report_routes.py new file mode 100644 index 00000000..7b6a51cb --- /dev/null +++ b/caimira/api/routes/report_routes.py @@ -0,0 +1,28 @@ +import json +import traceback +import tornado.web + +from caimira.api.controller.report_controller import submit_virus_form + +class ReportHandler(tornado.web.RequestHandler): + def set_default_headers(self): + self.set_header("Access-Control-Allow-Origin", "*") + self.set_header("Access-Control-Allow-Headers", "x-requested-with") + self.set_header("Access-Control-Allow-Methods", "POST, GET, OPTIONS") + + def post(self): + try: + form_data = json.loads(self.request.body) + report_data = submit_virus_form(form_data) + + response_data = { + "status": "success", + "message": "Results generated successfully", + "report_data": report_data, + } + + self.write(response_data) + except Exception as e: + traceback.print_exc() + self.set_status(400) + self.write({"message": str(e)}) diff --git a/caimira/apps/__init__.py b/caimira/apps/__init__.py deleted file mode 100644 index 26b7f5d3..00000000 --- a/caimira/apps/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from .expert import ExpertApplication -from .expert_co2 import CO2Application - -__all__ = ['ExpertApplication', 'CO2Application'] diff --git a/caimira/tests/data/__init__.py b/caimira/calculator/__init__.py similarity index 100% rename from caimira/tests/data/__init__.py rename to caimira/calculator/__init__.py diff --git a/caimira/docs/Makefile b/caimira/calculator/docs/Makefile similarity index 100% rename from caimira/docs/Makefile rename to caimira/calculator/docs/Makefile diff --git a/caimira/docs/UML-CAiMIRA.png b/caimira/calculator/docs/UML-CAiMIRA.png similarity index 100% rename from caimira/docs/UML-CAiMIRA.png rename to caimira/calculator/docs/UML-CAiMIRA.png diff --git a/caimira/docs/caimira.apps.calculator.rst b/caimira/calculator/docs/caimira.apps.calculator.rst similarity index 100% rename from caimira/docs/caimira.apps.calculator.rst rename to caimira/calculator/docs/caimira.apps.calculator.rst diff --git a/caimira/docs/caimira.apps.rst b/caimira/calculator/docs/caimira.apps.rst similarity index 100% rename from caimira/docs/caimira.apps.rst rename to caimira/calculator/docs/caimira.apps.rst diff --git a/caimira/docs/caimira.data.rst b/caimira/calculator/docs/caimira.data.rst similarity index 100% rename from caimira/docs/caimira.data.rst rename to caimira/calculator/docs/caimira.data.rst diff --git a/caimira/docs/caimira.monte_carlo.rst b/caimira/calculator/docs/caimira.monte_carlo.rst similarity index 100% rename from caimira/docs/caimira.monte_carlo.rst rename to caimira/calculator/docs/caimira.monte_carlo.rst diff --git a/caimira/docs/caimira.rst b/caimira/calculator/docs/caimira.rst similarity index 100% rename from caimira/docs/caimira.rst rename to caimira/calculator/docs/caimira.rst diff --git a/caimira/docs/caimira.tests.apps.calculator.rst b/caimira/calculator/docs/caimira.tests.apps.calculator.rst similarity index 100% rename from caimira/docs/caimira.tests.apps.calculator.rst rename to caimira/calculator/docs/caimira.tests.apps.calculator.rst diff --git a/caimira/docs/caimira.tests.apps.rst b/caimira/calculator/docs/caimira.tests.apps.rst similarity index 100% rename from caimira/docs/caimira.tests.apps.rst rename to caimira/calculator/docs/caimira.tests.apps.rst diff --git a/caimira/docs/caimira.tests.data.rst b/caimira/calculator/docs/caimira.tests.data.rst similarity index 100% rename from caimira/docs/caimira.tests.data.rst rename to caimira/calculator/docs/caimira.tests.data.rst diff --git a/caimira/docs/caimira.tests.models.rst b/caimira/calculator/docs/caimira.tests.models.rst similarity index 100% rename from caimira/docs/caimira.tests.models.rst rename to caimira/calculator/docs/caimira.tests.models.rst diff --git a/caimira/docs/caimira.tests.rst b/caimira/calculator/docs/caimira.tests.rst similarity index 100% rename from caimira/docs/caimira.tests.rst rename to caimira/calculator/docs/caimira.tests.rst diff --git a/caimira/docs/conf.py b/caimira/calculator/docs/conf.py similarity index 100% rename from caimira/docs/conf.py rename to caimira/calculator/docs/conf.py diff --git a/caimira/docs/full_diameter_dependence.rst b/caimira/calculator/docs/full_diameter_dependence.rst similarity index 100% rename from caimira/docs/full_diameter_dependence.rst rename to caimira/calculator/docs/full_diameter_dependence.rst diff --git a/caimira/docs/index.rst b/caimira/calculator/docs/index.rst similarity index 100% rename from caimira/docs/index.rst rename to caimira/calculator/docs/index.rst diff --git a/caimira/docs/make.bat b/caimira/calculator/docs/make.bat similarity index 100% rename from caimira/docs/make.bat rename to caimira/calculator/docs/make.bat diff --git a/caimira/docs/requirements.txt b/caimira/calculator/docs/requirements.txt similarity index 80% rename from caimira/docs/requirements.txt rename to caimira/calculator/docs/requirements.txt index 6074cd93..b1b732ea 100644 --- a/caimira/docs/requirements.txt +++ b/caimira/calculator/docs/requirements.txt @@ -3,4 +3,4 @@ sphinx-rtd-theme==1.2.2 pillow==5.4.1 mock==1.0.1 commonmark==0.9.1 -recommonmark==0.5.0 \ No newline at end of file +recommonmark==0.5.0 diff --git a/caimira/calculator/models/__init__.py b/caimira/calculator/models/__init__.py new file mode 100644 index 00000000..fd40e4db --- /dev/null +++ b/caimira/calculator/models/__init__.py @@ -0,0 +1,8 @@ +# This module is part of CAiMIRA. Please see the repository at +# https://gitlab.cern.ch/caimira/caimira for details of the license and terms of use. +""" +Documentation for the CAiMIRA package + +""" + +__version__ = "1.0.0" diff --git a/caimira/data/__init__.py b/caimira/calculator/models/data/__init__.py similarity index 98% rename from caimira/data/__init__.py rename to caimira/calculator/models/data/__init__.py index 8c0a1390..3d539df4 100644 --- a/caimira/data/__init__.py +++ b/caimira/calculator/models/data/__init__.py @@ -1,6 +1,6 @@ import numpy as np -from caimira import models -from caimira.data.weather import wx_data, nearest_wx_station +from caimira.calculator.models import models +from .weather import wx_data, nearest_wx_station MONTH_NAMES = [ 'January', 'February', 'March', 'April', 'May', 'June', 'July', diff --git a/caimira/data/global_weather_set.json b/caimira/calculator/models/data/global_weather_set.json similarity index 100% rename from caimira/data/global_weather_set.json rename to caimira/calculator/models/data/global_weather_set.json diff --git a/caimira/data/hadisd_station_fullinfo_v311_202001p.txt b/caimira/calculator/models/data/hadisd_station_fullinfo_v311_202001p.txt similarity index 100% rename from caimira/data/hadisd_station_fullinfo_v311_202001p.txt rename to caimira/calculator/models/data/hadisd_station_fullinfo_v311_202001p.txt diff --git a/caimira/data/weather.py b/caimira/calculator/models/data/weather.py similarity index 100% rename from caimira/data/weather.py rename to caimira/calculator/models/data/weather.py diff --git a/caimira/dataclass_utils.py b/caimira/calculator/models/dataclass_utils.py similarity index 100% rename from caimira/dataclass_utils.py rename to caimira/calculator/models/dataclass_utils.py diff --git a/caimira/enums.py b/caimira/calculator/models/enums.py similarity index 100% rename from caimira/enums.py rename to caimira/calculator/models/enums.py diff --git a/caimira/models.py b/caimira/calculator/models/models.py similarity index 99% rename from caimira/models.py rename to caimira/calculator/models/models.py index 88f9ffb1..b49f6692 100644 --- a/caimira/models.py +++ b/caimira/calculator/models/models.py @@ -40,7 +40,7 @@ import scipy.stats as sct from scipy.optimize import minimize -from caimira.store.data_registry import DataRegistry +from caimira.calculator.store.data_registry import DataRegistry if not typing.TYPE_CHECKING: from memoization import cached diff --git a/caimira/monte_carlo/__init__.py b/caimira/calculator/models/monte_carlo/__init__.py similarity index 100% rename from caimira/monte_carlo/__init__.py rename to caimira/calculator/models/monte_carlo/__init__.py diff --git a/caimira/monte_carlo/__init__.pyi b/caimira/calculator/models/monte_carlo/__init__.pyi similarity index 100% rename from caimira/monte_carlo/__init__.pyi rename to caimira/calculator/models/monte_carlo/__init__.pyi diff --git a/caimira/monte_carlo/data.py b/caimira/calculator/models/monte_carlo/data.py similarity index 98% rename from caimira/monte_carlo/data.py rename to caimira/calculator/models/monte_carlo/data.py index acca3207..7b503cb0 100644 --- a/caimira/monte_carlo/data.py +++ b/caimira/calculator/models/monte_carlo/data.py @@ -7,11 +7,11 @@ from scipy import special as sp from scipy.stats import weibull_min -from caimira.enums import ViralLoads +from ..enums import ViralLoads -import caimira.monte_carlo.models as mc -from caimira.monte_carlo.sampleable import LogCustom, LogNormal, Normal, LogCustomKernel, CustomKernel, Uniform, Custom -from caimira.store.data_registry import DataRegistry +import caimira.calculator.models.monte_carlo.models as mc +from caimira.calculator.models.monte_carlo.sampleable import LogCustom, LogNormal, Normal, LogCustomKernel, CustomKernel, Uniform, Custom +from caimira.calculator.store.data_registry import DataRegistry def evaluate_vl(root: typing.Dict, value: str, data_registry: DataRegistry): diff --git a/caimira/monte_carlo/models.py b/caimira/calculator/models/monte_carlo/models.py similarity index 78% rename from caimira/monte_carlo/models.py rename to caimira/calculator/models/monte_carlo/models.py index 7215db16..f4ad09e2 100644 --- a/caimira/monte_carlo/models.py +++ b/caimira/calculator/models/monte_carlo/models.py @@ -3,7 +3,7 @@ import sys import typing -import caimira.models +from caimira.calculator.models import models from .sampleable import SampleableDistribution, _VectorisedFloatOrSampleable @@ -57,7 +57,7 @@ def _build_mc_model(model: dataclass_instance) -> typing.Type[MCModelBase[_Model # Note: deepcopy not needed here as we aren't mutating entities beyond # the top level. new_field = copy.copy(field) - if field.type is caimira.models._VectorisedFloat: # noqa + if field.type is models._VectorisedFloat: # noqa new_field.type = _VectorisedFloatOrSampleable # type: ignore field_type: typing.Any = new_field.type @@ -65,30 +65,30 @@ def _build_mc_model(model: dataclass_instance) -> typing.Type[MCModelBase[_Model if getattr(field_type, '__origin__', None) in [typing.Union, typing.Tuple]: # It is challenging to generalise this code, so we provide specific transformations, # and raise for unforseen cases. - if new_field.type == typing.Tuple[caimira.models._VentilationBase, ...]: + if new_field.type == typing.Tuple[models._VentilationBase, ...]: VB = getattr(sys.modules[__name__], "_VentilationBase") - field_type = typing.Tuple[typing.Union[caimira.models._VentilationBase, VB], ...] - elif new_field.type == typing.Tuple[caimira.models._ExpirationBase, ...]: + field_type = typing.Tuple[typing.Union[models._VentilationBase, VB], ...] + elif new_field.type == typing.Tuple[models._ExpirationBase, ...]: EB = getattr(sys.modules[__name__], "_ExpirationBase") - field_type = typing.Tuple[typing.Union[caimira.models._ExpirationBase, EB], ...] - elif new_field.type == typing.Tuple[caimira.models.SpecificInterval, ...]: + field_type = typing.Tuple[typing.Union[models._ExpirationBase, EB], ...] + elif new_field.type == typing.Tuple[models.SpecificInterval, ...]: SI = getattr(sys.modules[__name__], "SpecificInterval") - field_type = typing.Tuple[typing.Union[caimira.models.SpecificInterval, SI], ...] + field_type = typing.Tuple[typing.Union[models.SpecificInterval, SI], ...] - elif new_field.type == typing.Union[int, caimira.models.IntPiecewiseConstant]: + elif new_field.type == typing.Union[int, models.IntPiecewiseConstant]: IPC = getattr(sys.modules[__name__], "IntPiecewiseConstant") - field_type = typing.Union[int, caimira.models.IntPiecewiseConstant, IPC] - elif new_field.type == typing.Union[caimira.models.Interval, None]: + field_type = typing.Union[int, models.IntPiecewiseConstant, IPC] + elif new_field.type == typing.Union[models.Interval, None]: I = getattr(sys.modules[__name__], "Interval") - field_type = typing.Union[None, caimira.models.Interval, I] + field_type = typing.Union[None, models.Interval, I] else: # Check that we don't need to do anything with this type. for item in new_field.type.__args__: - if getattr(item, '__module__', None) == 'caimira.models': + if getattr(item, '__module__', None) == 'source.models.models': raise ValueError( f"unsupported type annotation transformation required for {new_field.type}") - elif field_type.__module__ == 'caimira.models': + elif field_type.__module__ == 'source.models.models': mc_model = getattr(sys.modules[__name__], new_field.type.__name__) field_type = typing.Union[new_field.type, mc_model] @@ -119,7 +119,7 @@ def _build_mc_model(model: dataclass_instance) -> typing.Type[MCModelBase[_Model _MODEL_CLASSES = [ - cls for cls in vars(caimira.models).values() + cls for cls in vars(models).values() if dataclasses.is_dataclass(cls) ] diff --git a/caimira/monte_carlo/sampleable.py b/caimira/calculator/models/monte_carlo/sampleable.py similarity index 98% rename from caimira/monte_carlo/sampleable.py rename to caimira/calculator/models/monte_carlo/sampleable.py index 4bbc4c35..eddb4d24 100644 --- a/caimira/monte_carlo/sampleable.py +++ b/caimira/calculator/models/monte_carlo/sampleable.py @@ -3,7 +3,7 @@ import numpy as np from sklearn.neighbors import KernelDensity # type: ignore -import caimira.models +from caimira.calculator.models import models # Declare a float array type of a given size. # There is no better way to declare this currently, unfortunately. @@ -158,5 +158,5 @@ def generate_samples(self, size: int) -> float_array_size_n: _VectorisedFloatOrSampleable = typing.Union[ - SampleableDistribution, caimira.models._VectorisedFloat, + SampleableDistribution, models._VectorisedFloat, ] diff --git a/caimira/profiler.py b/caimira/calculator/models/profiler.py similarity index 100% rename from caimira/profiler.py rename to caimira/calculator/models/profiler.py diff --git a/caimira/utils.py b/caimira/calculator/models/utils.py similarity index 100% rename from caimira/utils.py rename to caimira/calculator/models/utils.py diff --git a/caimira/tests/models/__init__.py b/caimira/calculator/report/__init__.py similarity index 100% rename from caimira/tests/models/__init__.py rename to caimira/calculator/report/__init__.py diff --git a/caimira/apps/calculator/report_generator.py b/caimira/calculator/report/report_generator.py similarity index 54% rename from caimira/apps/calculator/report_generator.py rename to caimira/calculator/report/report_generator.py index 587c3b64..7c6f5cea 100644 --- a/caimira/apps/calculator/report_generator.py +++ b/caimira/calculator/report/report_generator.py @@ -1,26 +1,18 @@ import concurrent.futures import base64 import dataclasses -from datetime import datetime import io -import json import typing -import urllib -import zlib - -import jinja2 import numpy as np import matplotlib.pyplot as plt -from caimira import models -from caimira.apps.calculator import markdown_tools -from caimira.profiler import profile -from caimira.store.data_registry import DataRegistry -from ... import monte_carlo as mc -from .model_generator import VirusFormData -from ... import dataclass_utils -from caimira.enums import ViralLoads - +from caimira.calculator.models import models +# from caimira.apps.calculator import markdown_tools +# from caimira.profiler import profile +from caimira.calculator.store.data_registry import DataRegistry +from caimira.calculator.validators.virus.virus_validator import VirusFormData +from caimira.calculator.models import dataclass_utils +from caimira.calculator.models.enums import ViralLoads def model_start_end(model: models.ExposureModel): t_start = min(model.exposed.presence_interval().boundaries()[0][0], @@ -82,7 +74,6 @@ def walk_model(model, name=""): # such as PeriodicIntervals, which extend beyond the model itself). return sorted(time for time in change_times if (t_start <= time <= t_end)) - def interesting_times(model: models.ExposureModel, approx_n_pts: typing.Optional[int] = None) -> typing.List[float]: """ Pick approximately ``approx_n_pts`` time points which are interesting for the @@ -104,6 +95,7 @@ def interesting_times(model: models.ExposureModel, approx_n_pts: typing.Optional return nice_times + def concentrations_with_sr_breathing(form: VirusFormData, model: models.ExposureModel, times: typing.List[float], short_range_intervals: typing.List) -> typing.List[float]: lower_concentrations = [] for time in times: @@ -115,16 +107,20 @@ def concentrations_with_sr_breathing(form: VirusFormData, model: models.Exposure lower_concentrations.append(np.array(model.concentration_model.concentration(float(time))).mean()) return lower_concentrations + def _calculate_deposited_exposure(model, time1, time2, fn_name=None): return np.array(model.deposited_exposure_between_bounds(float(time1), float(time2))).mean(),fn_name + def _calculate_long_range_deposited_exposure(model, time1, time2, fn_name=None): return np.array(model.long_range_deposited_exposure_between_bounds(float(time1), float(time2))).mean(), fn_name + def _calculate_co2_concentration(CO2_model, time, fn_name=None): return np.array(CO2_model.concentration(float(time))).mean(), fn_name -@profile + +# @profile def calculate_report_data(form: VirusFormData, model: models.ExposureModel, executor_factory: typing.Callable[[], concurrent.futures.Executor]) -> typing.Dict[str, typing.Any]: times = interesting_times(model) short_range_intervals = [interaction.presence.boundaries()[0] for interaction in model.short_range] @@ -215,25 +211,6 @@ def calculate_report_data(form: VirusFormData, model: models.ExposureModel, exec } -def generate_permalink(base_url, get_root_url, get_root_calculator_url, form: VirusFormData): - form_dict = VirusFormData.to_dict(form, strip_defaults=True) - - # Generate the calculator URL arguments that would be needed to re-create this - # form. - args = urllib.parse.urlencode(form_dict) - - # Then zlib compress + base64 encode the string. To be inverted by the - # /_c/ endpoint. - compressed_args = base64.b64encode(zlib.compress(args.encode())).decode() - qr_url = f"{base_url}{get_root_url()}/_c/{compressed_args}" - url = f"{base_url}{get_root_calculator_url()}?{args}" - - return { - 'link': url, - 'shortened': qr_url, - } - - def conditional_prob_inf_given_vl_dist( data_registry: DataRegistry, infection_probability: models._VectorisedFloat, @@ -279,7 +256,7 @@ def uncertainties_plot(infection_probability: models._VectorisedFloat, lower_percentiles: models._VectorisedFloat, upper_percentiles: models._VectorisedFloat): - fig, axes = plt.subplots(2, 3, + fig, axes = plt.subplots(2, 3, gridspec_kw={'width_ratios': [5, 0.5] + [1], 'height_ratios': [3, 1], 'wspace': 0}, sharey='row', @@ -325,13 +302,6 @@ def uncertainties_plot(infection_probability: models._VectorisedFloat, return fig -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() @@ -344,249 +314,3 @@ def img2base64(img_data) -> str: 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 minutes_to_time(minutes: int) -> str: - minute_string = str(minutes % 60) - minute_string = "0" * (2 - len(minute_string)) + minute_string - hour_string = str(minutes // 60) - hour_string = "0" * (2 - len(hour_string)) + hour_string - - return f"{hour_string}:{minute_string}" - - -def readable_minutes(minutes: int) -> str: - time = float(minutes) - unit = " minute" - if time % 60 == 0: - time = minutes/60 - unit = " hour" - if time != 1: - unit += "s" - - if time.is_integer(): - time_str = "{:0.0f}".format(time) - else: - time_str = "{0:.2f}".format(time) - - return time_str + unit - - -def hour_format(hour: float) -> str: - # Convert float hour to HH:MM format - hours = int(hour) - minutes = int(hour % 1 * 60) - return f"{hours}:{minutes if minutes != 0 else '00'}" - - -def percentage(absolute: float) -> float: - return absolute * 100 - - -def non_zero_percentage(percentage: int) -> str: - if percentage < 0.01: - return "<0.01%" - elif percentage < 1: - return "{:0.2f}%".format(percentage) - elif percentage > 99.9 or np.isnan(percentage): - return ">99.9%" - else: - return "{:0.1f}%".format(percentage) - - -def manufacture_viral_load_scenarios_percentiles(model: mc.ExposureModel) -> typing.Dict[str, mc.ExposureModel]: - viral_load = model.concentration_model.infected.virus.viral_load_in_sputum - scenarios = {} - for percentil in (0.01, 0.05, 0.25, 0.5, 0.75, 0.95, 0.99): - vl = np.quantile(viral_load, percentil) - specific_vl_scenario = dataclass_utils.nested_replace(model, - {'concentration_model.infected.virus.viral_load_in_sputum': vl} - ) - scenarios[str(vl)] = np.mean(specific_vl_scenario.infection_probability()) - return scenarios - - -def manufacture_alternative_scenarios(form: VirusFormData) -> typing.Dict[str, mc.ExposureModel]: - scenarios = {} - if (form.short_range_option == "short_range_no"): - # Two special option cases - HEPA and/or FFP2 masks. - FFP2_being_worn = bool(form.mask_wearing_option == 'mask_on' and form.mask_type == 'FFP2') - if FFP2_being_worn and form.hepa_option: - FFP2andHEPAalternative = dataclass_utils.replace(form, mask_type='Type I') - if not (form.hepa_option and form.mask_wearing_option == 'mask_on' and form.mask_type == 'Type I'): - scenarios['Base scenario with HEPA filter and Type I masks'] = FFP2andHEPAalternative.build_mc_model() - if not FFP2_being_worn and form.hepa_option: - noHEPAalternative = dataclass_utils.replace(form, mask_type = 'FFP2') - noHEPAalternative = dataclass_utils.replace(noHEPAalternative, mask_wearing_option = 'mask_on') - noHEPAalternative = dataclass_utils.replace(noHEPAalternative, hepa_option=False) - if not (not form.hepa_option and FFP2_being_worn): - scenarios['Base scenario without HEPA filter, with FFP2 masks'] = noHEPAalternative.build_mc_model() - - # The remaining scenarios are based on Type I masks (possibly not worn) - # and no HEPA filtration. - form = dataclass_utils.replace(form, mask_type='Type I') - if form.hepa_option: - form = dataclass_utils.replace(form, hepa_option=False) - - with_mask = dataclass_utils.replace(form, mask_wearing_option='mask_on') - without_mask = dataclass_utils.replace(form, mask_wearing_option='mask_off') - - if form.ventilation_type == 'mechanical_ventilation': - #scenarios['Mechanical ventilation with Type I masks'] = with_mask.build_mc_model() - if not (form.mask_wearing_option == 'mask_off'): - scenarios['Mechanical ventilation without masks'] = without_mask.build_mc_model() - - elif form.ventilation_type == 'natural_ventilation': - #scenarios['Windows open with Type I masks'] = with_mask.build_mc_model() - if not (form.mask_wearing_option == 'mask_off'): - scenarios['Windows open without masks'] = without_mask.build_mc_model() - - # No matter the ventilation scheme, we include scenarios which don't have any ventilation. - with_mask_no_vent = dataclass_utils.replace(with_mask, ventilation_type='no_ventilation') - without_mask_or_vent = dataclass_utils.replace(without_mask, ventilation_type='no_ventilation') - - if not (form.mask_wearing_option == 'mask_on' and form.mask_type == 'Type I' and form.ventilation_type == 'no_ventilation'): - scenarios['No ventilation with Type I masks'] = with_mask_no_vent.build_mc_model() - if not (form.mask_wearing_option == 'mask_off' and form.ventilation_type == 'no_ventilation'): - scenarios['Neither ventilation nor masks'] = without_mask_or_vent.build_mc_model() - - else: - no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[], total_people=form.total_people - form.short_range_occupants) - scenarios['Base scenario without short-range interactions'] = no_short_range_alternative.build_mc_model() - - return scenarios - - -def scenario_statistics( - mc_model: mc.ExposureModel, - sample_times: typing.List[float], - compute_prob_exposure: bool -): - model = mc_model.build_model(size=mc_model.data_registry.monte_carlo['sample_size']) - if (compute_prob_exposure): - # It means we have data to calculate the total_probability_rule - prob_probabilistic_exposure = model.total_probability_rule() - else: - prob_probabilistic_exposure = 0. - - return { - 'probability_of_infection': np.mean(model.infection_probability()), - 'expected_new_cases': np.mean(model.expected_new_cases()), - 'concentrations': [ - np.mean(model.concentration(time)) - for time in sample_times - ], - 'prob_probabilistic_exposure': prob_probabilistic_exposure, - } - - -def comparison_report( - form: VirusFormData, - report_data: typing.Dict[str, typing.Any], - scenarios: typing.Dict[str, mc.ExposureModel], - sample_times: typing.List[float], - executor_factory: typing.Callable[[], concurrent.futures.Executor], -): - if (form.short_range_option == "short_range_no"): - statistics = { - 'Current scenario' : { - 'probability_of_infection': report_data['prob_inf'], - 'expected_new_cases': report_data['expected_new_cases'], - 'concentrations': report_data['concentrations'], - } - } - else: - statistics = {} - - if (form.short_range_option == "short_range_yes" and form.exposure_option == "p_probabilistic_exposure"): - compute_prob_exposure = True - else: - compute_prob_exposure = False - - with executor_factory() as executor: - results = executor.map( - scenario_statistics, - scenarios.values(), - [sample_times] * len(scenarios), - [compute_prob_exposure] * len(scenarios), - timeout=60, - ) - - for (name, model), model_stats in zip(scenarios.items(), results): - statistics[name] = model_stats - - return { - 'stats': statistics, - } - - -@dataclasses.dataclass -class ReportGenerator: - jinja_loader: jinja2.BaseLoader - get_root_url: typing.Any - get_root_calculator_url: typing.Any - - def build_report( - self, - base_url: str, - form: VirusFormData, - executor_factory: typing.Callable[[], concurrent.futures.Executor], - ) -> str: - model = form.build_model() - context = self.prepare_context(base_url, model, form, executor_factory=executor_factory) - return self.render(context) - - def prepare_context( - self, - base_url: str, - model: models.ExposureModel, - form: VirusFormData, - executor_factory: typing.Callable[[], concurrent.futures.Executor], - ) -> dict: - now = datetime.utcnow().astimezone() - time = now.strftime("%Y-%m-%d %H:%M:%S UTC") - - data_registry_version = f"v{model.data_registry.version}" if model.data_registry.version else None - context = { - 'model': model, - 'form': form, - 'creation_date': time, - 'data_registry_version': data_registry_version, - } - - scenario_sample_times = interesting_times(model) - report_data = calculate_report_data(form, model, executor_factory=executor_factory) - context.update(report_data) - - alternative_scenarios = manufacture_alternative_scenarios(form) - context['alternative_viral_load'] = manufacture_viral_load_scenarios_percentiles(model) if form.conditional_probability_viral_loads else None - context['alternative_scenarios'] = comparison_report( - form, report_data, alternative_scenarios, scenario_sample_times, executor_factory=executor_factory, - ) - context['permalink'] = generate_permalink(base_url, self.get_root_url, self.get_root_calculator_url, form) - context['get_url'] = self.get_root_url - context['get_calculator_url'] = self.get_root_calculator_url - - return context - - def _template_environment(self) -> jinja2.Environment: - env = jinja2.Environment( - loader=self.jinja_loader, - undefined=jinja2.StrictUndefined, - ) - env.globals["common_text"] = markdown_tools.extract_rendered_markdown_blocks( - env.get_template('common_text.md.j2') - ) - env.filters['non_zero_percentage'] = non_zero_percentage - env.filters['readable_minutes'] = readable_minutes - env.filters['minutes_to_time'] = minutes_to_time - env.filters['hour_format'] = hour_format - env.filters['float_format'] = "{0:.2f}".format - env.filters['int_format'] = "{:0.0f}".format - env.filters['percentage'] = percentage - env.filters['JSONify'] = json.dumps - return env - - def render(self, context: dict) -> str: - template = self._template_environment().get_template("calculator.report.html.j2") - return template.render(**context, text_blocks=template.globals["common_text"]) diff --git a/caimira/store/data_registry.py b/caimira/calculator/store/data_registry.py similarity index 99% rename from caimira/store/data_registry.py rename to caimira/calculator/store/data_registry.py index 570a4fd9..5b549858 100644 --- a/caimira/store/data_registry.py +++ b/caimira/calculator/store/data_registry.py @@ -1,4 +1,4 @@ -from caimira.enums import ViralLoads +from ..models.enums import ViralLoads class DataRegistry: diff --git a/caimira/store/data_service.py b/caimira/calculator/store/data_service.py similarity index 96% rename from caimira/store/data_service.py rename to caimira/calculator/store/data_service.py index 1ecbac82..7271e708 100644 --- a/caimira/store/data_service.py +++ b/caimira/calculator/store/data_service.py @@ -2,7 +2,7 @@ import typing import requests -from caimira.store.data_registry import DataRegistry +from ..store.data_registry import DataRegistry logger = logging.getLogger("DATA") diff --git a/caimira/calculator/tests/__init__.py b/caimira/calculator/tests/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/calculator/tests/apps/__init__.py b/caimira/calculator/tests/apps/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/calculator/tests/apps/calculator/__init__.py b/caimira/calculator/tests/apps/calculator/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/tests/apps/calculator/conftest.py b/caimira/calculator/tests/apps/calculator/conftest.py similarity index 65% rename from caimira/tests/apps/calculator/conftest.py rename to caimira/calculator/tests/apps/calculator/conftest.py index d774e333..d1aa1065 100644 --- a/caimira/tests/apps/calculator/conftest.py +++ b/caimira/calculator/tests/apps/calculator/conftest.py @@ -1,16 +1,16 @@ import pytest -from caimira.apps.calculator import model_generator +from caimira.calculator.validators.virus import virus_validator @pytest.fixture def baseline_form_data(): - return model_generator.baseline_raw_form_data() + return virus_validator.baseline_raw_form_data() @pytest.fixture def baseline_form(baseline_form_data, data_registry): - return model_generator.VirusFormData.from_dict(baseline_form_data, data_registry) + return virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) @pytest.fixture @@ -19,4 +19,4 @@ def baseline_form_with_sr(baseline_form_data, data_registry): form_data_sr['short_range_option'] = 'short_range_yes' form_data_sr['short_range_interactions'] = '[{"expiration": "Shouting", "start_time": "10:30", "duration": "30"}]' form_data_sr['short_range_occupants'] = 5 - return model_generator.VirusFormData.from_dict(form_data_sr, data_registry) \ No newline at end of file + return virus_validator.VirusFormData.from_dict(form_data_sr, data_registry) diff --git a/caimira/tests/apps/calculator/test_model_generator.py b/caimira/calculator/tests/apps/calculator/test_model_generator.py similarity index 89% rename from caimira/tests/apps/calculator/test_model_generator.py rename to caimira/calculator/tests/apps/calculator/test_model_generator.py index bcd9e064..435ecd39 100644 --- a/caimira/tests/apps/calculator/test_model_generator.py +++ b/caimira/calculator/tests/apps/calculator/test_model_generator.py @@ -6,24 +6,24 @@ import pytest from retry import retry -from caimira.apps.calculator import model_generator -from caimira.apps.calculator.form_data import (_hours2timestring, minutes_since_midnight, +from caimira.calculator.validators.virus import virus_validator +from caimira.calculator.validators.form_validator import (_hours2timestring, minutes_since_midnight, _CAST_RULES_FORM_ARG_TO_NATIVE, _CAST_RULES_NATIVE_TO_FORM_ARG) -from caimira import models -from caimira.monte_carlo.data import expiration_distributions -from caimira.apps.calculator.defaults import NO_DEFAULT -from caimira.store.data_registry import DataRegistry +from caimira.calculator.models import models +from caimira.calculator.models.monte_carlo.data import expiration_distributions +from caimira.calculator.validators.defaults import NO_DEFAULT +from caimira.calculator.store.data_registry import DataRegistry def test_model_from_dict(baseline_form_data, data_registry): - form = model_generator.VirusFormData.from_dict(baseline_form_data, data_registry) + form = virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) assert isinstance(form.build_model(), models.ExposureModel) def test_model_from_dict_invalid(baseline_form_data, data_registry): baseline_form_data['invalid_item'] = 'foobar' with pytest.raises(ValueError, match='Invalid argument "invalid_item" given'): - model_generator.VirusFormData.from_dict(baseline_form_data, data_registry) + virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) @retry(tries=10) @@ -39,14 +39,14 @@ def test_blend_expiration(data_registry, mask_type): SAMPLE_SIZE = 250000 TOLERANCE = 0.02 blend = {'Breathing': 2, 'Speaking': 1} - r = model_generator.build_expiration(data_registry, blend).build_model(SAMPLE_SIZE) + r = virus_validator.build_expiration(data_registry, blend).build_model(SAMPLE_SIZE) mask = models.Mask.types[mask_type] expected = (expiration_distributions(data_registry)['Breathing'].build_model(SAMPLE_SIZE).aerosols(mask).mean()*2/3. + expiration_distributions(data_registry)['Speaking'].build_model(SAMPLE_SIZE).aerosols(mask).mean()/3.) npt.assert_allclose(r.aerosols(mask).mean(), expected, rtol=TOLERANCE) -def test_ventilation_slidingwindow(data_registry: DataRegistry, baseline_form: model_generator.VirusFormData): +def test_ventilation_slidingwindow(data_registry: DataRegistry, baseline_form: virus_validator.VirusFormData): baseline_form.ventilation_type = 'natural_ventilation' baseline_form.windows_duration = 10 baseline_form.windows_frequency = 120 @@ -77,7 +77,7 @@ def test_ventilation_slidingwindow(data_registry: DataRegistry, baseline_form: m assert ventilation == baseline_vent -def test_ventilation_hingedwindow(baseline_form: model_generator.VirusFormData): +def test_ventilation_hingedwindow(baseline_form: virus_validator.VirusFormData): baseline_form.ventilation_type = 'natural_ventilation' baseline_form.windows_duration = 10 baseline_form.windows_frequency = 120 @@ -107,7 +107,7 @@ def test_ventilation_hingedwindow(baseline_form: model_generator.VirusFormData): assert ventilation == baseline_vent -def test_ventilation_mechanical(baseline_form: model_generator.VirusFormData): +def test_ventilation_mechanical(baseline_form: virus_validator.VirusFormData): room = models.Room(volume=75, inside_temp=models.PiecewiseConstant((0, 24), (293,))) mech = models.HVACMechanical( active=models.PeriodicInterval(period=120, duration=120), @@ -122,7 +122,7 @@ def test_ventilation_mechanical(baseline_form: model_generator.VirusFormData): np.array([baseline_form.ventilation().air_exchange(room, t) for t in ts])) -def test_ventilation_airchanges(baseline_form: model_generator.VirusFormData): +def test_ventilation_airchanges(baseline_form: virus_validator.VirusFormData): room = models.Room(75, inside_temp=models.PiecewiseConstant((0, 24), (293,))) airchange = models.AirChange( active=models.PeriodicInterval(period=120, duration=120), @@ -137,7 +137,7 @@ def test_ventilation_airchanges(baseline_form: model_generator.VirusFormData): np.array([baseline_form.ventilation().air_exchange(room, t) for t in ts])) -def test_ventilation_window_hepa(data_registry: DataRegistry, baseline_form: model_generator.VirusFormData): +def test_ventilation_window_hepa(data_registry: DataRegistry, baseline_form: virus_validator.VirusFormData): baseline_form.ventilation_type = 'natural_ventilation' baseline_form.windows_duration = 10 baseline_form.windows_frequency = 120 @@ -181,7 +181,7 @@ def test_ventilation_window_hepa(data_registry: DataRegistry, baseline_form: mod ] ) def test_infected_less_than_total_people(activity, total_people, infected_people, error, - baseline_form: model_generator.VirusFormData, + baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry): baseline_form.activity_type = activity baseline_form.total_people = total_people @@ -195,7 +195,7 @@ def present_times(interval: models.Interval) -> models.BoundarySequence_t: return interval.present_times -def test_infected_present_intervals(baseline_form: model_generator.VirusFormData): +def test_infected_present_intervals(baseline_form: virus_validator.VirusFormData): baseline_form.infected_dont_have_breaks_with_exposed = False baseline_form.exposed_coffee_duration = 15 baseline_form.exposed_coffee_break_option = 'coffee_break_2' @@ -209,7 +209,7 @@ def test_infected_present_intervals(baseline_form: model_generator.VirusFormData assert present_times(baseline_form.infected_present_interval()) == correct -def test_exposed_present_intervals(baseline_form: model_generator.VirusFormData): +def test_exposed_present_intervals(baseline_form: virus_validator.VirusFormData): baseline_form.exposed_coffee_duration = 15 baseline_form.exposed_coffee_break_option = 'coffee_break_2' baseline_form.exposed_start = minutes_since_midnight(9 * 60) @@ -220,7 +220,7 @@ def test_exposed_present_intervals(baseline_form: model_generator.VirusFormData) assert present_times(baseline_form.exposed_present_interval()) == correct -def test_present_intervals_common_breaks(baseline_form: model_generator.VirusFormData): +def test_present_intervals_common_breaks(baseline_form: virus_validator.VirusFormData): baseline_form.infected_dont_have_breaks_with_exposed = False baseline_form.infected_coffee_duration = baseline_form.exposed_coffee_duration = 15 baseline_form.infected_coffee_break_option = baseline_form.exposed_coffee_break_option = 'coffee_break_2' @@ -236,7 +236,7 @@ def test_present_intervals_common_breaks(baseline_form: model_generator.VirusFor assert present_times(baseline_form.infected_present_interval()) == correct_infected -def test_present_intervals_split_breaks(baseline_form: model_generator.VirusFormData): +def test_present_intervals_split_breaks(baseline_form: virus_validator.VirusFormData): baseline_form.infected_dont_have_breaks_with_exposed = True baseline_form.infected_coffee_duration = baseline_form.exposed_coffee_duration = 15 baseline_form.infected_coffee_break_option = baseline_form.exposed_coffee_break_option = 'coffee_break_2' @@ -252,7 +252,7 @@ def test_present_intervals_split_breaks(baseline_form: model_generator.VirusForm assert present_times(baseline_form.infected_present_interval()) == correct_infected -def test_exposed_present_intervals_starting_with_lunch(baseline_form: model_generator.VirusFormData): +def test_exposed_present_intervals_starting_with_lunch(baseline_form: virus_validator.VirusFormData): baseline_form.exposed_coffee_break_option = 'coffee_break_0' baseline_form.exposed_start = baseline_form.exposed_lunch_start = minutes_since_midnight(13 * 60) baseline_form.exposed_finish = minutes_since_midnight(18 * 60) @@ -261,7 +261,7 @@ def test_exposed_present_intervals_starting_with_lunch(baseline_form: model_gene assert present_times(baseline_form.exposed_present_interval()) == correct -def test_exposed_present_intervals_ending_with_lunch(baseline_form: model_generator.VirusFormData): +def test_exposed_present_intervals_ending_with_lunch(baseline_form: virus_validator.VirusFormData): baseline_form.exposed_coffee_break_option = 'coffee_break_0' baseline_form.exposed_start = minutes_since_midnight(11 * 60) baseline_form.exposed_finish = baseline_form.exposed_lunch_start = minutes_since_midnight(13 * 60) @@ -270,7 +270,7 @@ def test_exposed_present_intervals_ending_with_lunch(baseline_form: model_genera assert present_times(baseline_form.exposed_present_interval()) == correct -def test_exposed_present_lunch_end_before_beginning(baseline_form: model_generator.VirusFormData, data_registry: DataRegistry): +def test_exposed_present_lunch_end_before_beginning(baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry): baseline_form.exposed_coffee_break_option = 'coffee_break_0' baseline_form.exposed_lunch_start = minutes_since_midnight(14 * 60) baseline_form.exposed_lunch_finish = minutes_since_midnight(13 * 60) @@ -287,7 +287,7 @@ def test_exposed_present_lunch_end_before_beginning(baseline_form: model_generat [9, 20], # lunch_finish after the presence finishing ], ) -def test_exposed_presence_lunch_break(baseline_form: model_generator.VirusFormData, data_registry: DataRegistry, exposed_lunch_start, exposed_lunch_finish): +def test_exposed_presence_lunch_break(baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry, exposed_lunch_start, exposed_lunch_finish): baseline_form.exposed_lunch_start = minutes_since_midnight(exposed_lunch_start * 60) baseline_form.exposed_lunch_finish = minutes_since_midnight(exposed_lunch_finish * 60) with pytest.raises(ValueError, match='exposed lunch break must be within presence times.'): @@ -303,14 +303,14 @@ def test_exposed_presence_lunch_break(baseline_form: model_generator.VirusFormDa [9, 20], # lunch_finish after the presence finishing ], ) -def test_infected_presence_lunch_break(baseline_form: model_generator.VirusFormData, data_registry: DataRegistry, infected_lunch_start, infected_lunch_finish): +def test_infected_presence_lunch_break(baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry, infected_lunch_start, infected_lunch_finish): baseline_form.infected_lunch_start = minutes_since_midnight(infected_lunch_start * 60) baseline_form.infected_lunch_finish = minutes_since_midnight(infected_lunch_finish * 60) with pytest.raises(ValueError, match='infected lunch break must be within presence times.'): baseline_form.validate() -def test_exposed_breaks_length(baseline_form: model_generator.VirusFormData, data_registry: DataRegistry): +def test_exposed_breaks_length(baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry): baseline_form.exposed_coffee_break_option = 'coffee_break_4' baseline_form.exposed_coffee_duration = 30 baseline_form.exposed_start = minutes_since_midnight(10 * 60) @@ -320,7 +320,7 @@ def test_exposed_breaks_length(baseline_form: model_generator.VirusFormData, dat baseline_form.validate() -def test_infected_breaks_length(baseline_form: model_generator.VirusFormData, data_registry: DataRegistry): +def test_infected_breaks_length(baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry): baseline_form.infected_start = minutes_since_midnight(9 * 60) baseline_form.infected_finish = minutes_since_midnight(12 * 60) baseline_form.infected_lunch_start = minutes_since_midnight(10 * 60) @@ -332,7 +332,7 @@ def test_infected_breaks_length(baseline_form: model_generator.VirusFormData, da @pytest.fixture -def coffee_break_between_1045_and_1115(baseline_form: model_generator.VirusFormData): +def coffee_break_between_1045_and_1115(baseline_form: virus_validator.VirusFormData): baseline_form.exposed_coffee_break_option = 'coffee_break_1' baseline_form.exposed_coffee_duration = 30 baseline_form.exposed_start = minutes_since_midnight(10 * 60) @@ -390,7 +390,7 @@ def assert_boundaries(interval, boundaries_in_time_string_form): @pytest.fixture -def breaks_every_25_mins_for_20_mins(baseline_form: model_generator.VirusFormData): +def breaks_every_25_mins_for_20_mins(baseline_form: virus_validator.VirusFormData): baseline_form.exposed_coffee_break_option = 'coffee_break_4' baseline_form.exposed_coffee_duration = 20 baseline_form.exposed_start = time2mins("10:00") @@ -435,7 +435,7 @@ def test_present_only_during_second_break(breaks_every_25_mins_for_20_mins): assert_boundaries(interval, []) -def test_valid_no_lunch(baseline_form: model_generator.VirusFormData, data_registry: DataRegistry): +def test_valid_no_lunch(baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry): # Check that it is valid to have a 0 length lunch if no lunch is selected. baseline_form.exposed_lunch_option = False baseline_form.exposed_lunch_start = minutes_since_midnight(0) @@ -443,7 +443,7 @@ def test_valid_no_lunch(baseline_form: model_generator.VirusFormData, data_regis assert baseline_form.validate() is None -def test_no_breaks(baseline_form: model_generator.VirusFormData): +def test_no_breaks(baseline_form: virus_validator.VirusFormData): # Check that the times are correct in the absence of breaks. baseline_form.infected_dont_have_breaks_with_exposed = False baseline_form.exposed_lunch_option = False @@ -458,7 +458,7 @@ def test_no_breaks(baseline_form: model_generator.VirusFormData): assert present_times(baseline_form.infected_present_interval()) == infected_correct -def test_coffee_lunch_breaks(baseline_form: model_generator.VirusFormData): +def test_coffee_lunch_breaks(baseline_form: virus_validator.VirusFormData): baseline_form.exposed_coffee_duration = 30 baseline_form.exposed_coffee_break_option = 'coffee_break_4' baseline_form.exposed_start = minutes_since_midnight(9 * 60) @@ -470,7 +470,7 @@ def test_coffee_lunch_breaks(baseline_form: model_generator.VirusFormData): np.testing.assert_allclose(present_times(baseline_form.exposed_present_interval()), correct, rtol=1e-14) -def test_coffee_lunch_breaks_unbalance(baseline_form: model_generator.VirusFormData): +def test_coffee_lunch_breaks_unbalance(baseline_form: virus_validator.VirusFormData): baseline_form.exposed_coffee_duration = 30 baseline_form.exposed_coffee_break_option = 'coffee_break_2' baseline_form.exposed_start = minutes_since_midnight(9 * 60) @@ -481,7 +481,7 @@ def test_coffee_lunch_breaks_unbalance(baseline_form: model_generator.VirusFormD np.testing.assert_allclose(present_times(baseline_form.exposed_present_interval()), correct, rtol=1e-14) -def test_coffee_breaks(baseline_form: model_generator.VirusFormData): +def test_coffee_breaks(baseline_form: virus_validator.VirusFormData): baseline_form.exposed_coffee_duration = 10 baseline_form.exposed_coffee_break_option = 'coffee_break_4' baseline_form.exposed_start = minutes_since_midnight(9 * 60) @@ -494,24 +494,24 @@ def test_coffee_breaks(baseline_form: model_generator.VirusFormData): def test_key_validation(baseline_form_data, data_registry): baseline_form_data['activity_type'] = 'invalid key' with pytest.raises(ValueError): - model_generator.VirusFormData.from_dict(baseline_form_data, data_registry) + virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) def test_key_validation_natural_ventilation_window_type_na(baseline_form_data, data_registry): baseline_form_data['ventilation_type'] = 'natural_ventilation' baseline_form_data['window_type'] = 'not-applicable' with pytest.raises(ValueError, match='window_type cannot be \'not-applicable\''): - model_generator.VirusFormData.from_dict(baseline_form_data, data_registry) + virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) def test_key_validation_natural_ventilation_window_opening_regime_na(baseline_form_data, data_registry): baseline_form_data['ventilation_type'] = 'natural_ventilation' baseline_form_data['window_opening_regime'] = 'not-applicable' with pytest.raises(ValueError, match='window_opening_regime cannot be \'not-applicable\''): - model_generator.VirusFormData.from_dict(baseline_form_data, data_registry) + virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) -def test_natural_ventilation_window_opening_periodically(baseline_form: model_generator.VirusFormData, data_registry: DataRegistry): +def test_natural_ventilation_window_opening_periodically(baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry): baseline_form.window_opening_regime = 'windows_open_periodically' baseline_form.windows_duration = 20 baseline_form.windows_frequency = 10 @@ -523,20 +523,20 @@ def test_key_validation_mech_ventilation_type_na(baseline_form_data, data_regist baseline_form_data['ventilation_type'] = 'mechanical_ventilation' baseline_form_data['mechanical_ventilation_type'] = 'not-applicable' with pytest.raises(ValueError, match='mechanical_ventilation_type cannot be \'not-applicable\''): - model_generator.VirusFormData.from_dict(baseline_form_data, data_registry) + virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) def test_key_validation_event_month(baseline_form_data, data_registry): baseline_form_data['event_month'] = 'invalid month' with pytest.raises(ValueError, match='invalid month is not a valid value for event_month'): - model_generator.VirusFormData.from_dict(baseline_form_data, data_registry) + virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) def test_default_types(): # Validate that VirusFormData._DEFAULTS are complete and of the correct type. # Validate that we have the right types and matching attributes to the DEFAULTS. - fields = {field.name: field for field in dataclasses.fields(model_generator.VirusFormData)} - for field, value in model_generator.VirusFormData._DEFAULTS.items(): + fields = {field.name: field for field in dataclasses.fields(virus_validator.VirusFormData)} + for field, value in virus_validator.VirusFormData._DEFAULTS.items(): if field not in fields: raise ValueError(f"Unmatched default {field}") @@ -557,7 +557,7 @@ def test_default_types(): for field in fields.values(): if field.name == "data_registry": continue # Skip the assertion for the "data_registry" field - assert field.name in model_generator.VirusFormData._DEFAULTS, f"No default set for field name {field.name}" + assert field.name in virus_validator.VirusFormData._DEFAULTS, f"No default set for field name {field.name}" def test_form_to_dict(baseline_form): @@ -566,7 +566,7 @@ def test_form_to_dict(baseline_form): assert 1 < len(stripped) < len(full) assert 'exposed_coffee_break_option' in stripped # If we set the value to the default one, it should no longer turn up in the dictionary. - baseline_form.exposed_coffee_break_option = model_generator.VirusFormData._DEFAULTS['exposed_coffee_break_option'] + baseline_form.exposed_coffee_break_option = virus_validator.VirusFormData._DEFAULTS['exposed_coffee_break_option'] assert 'exposed_coffee_break_option' not in baseline_form.to_dict(baseline_form, strip_defaults=True) @@ -584,7 +584,7 @@ def test_form_timezone(baseline_form_data, data_registry, longitude, latitude, m baseline_form_data['location_latitude'] = latitude baseline_form_data['location_longitude'] = longitude baseline_form_data['event_month'] = month - form = model_generator.VirusFormData.from_dict(baseline_form_data, data_registry) + form = virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) name, offset = form.tz_name_and_utc_offset() assert name == expected_tz_name assert offset == expected_offset diff --git a/caimira/tests/apps/calculator/test_specific_model_generator.py b/caimira/calculator/tests/apps/calculator/test_specific_model_generator.py similarity index 93% rename from caimira/tests/apps/calculator/test_specific_model_generator.py rename to caimira/calculator/tests/apps/calculator/test_specific_model_generator.py index e8a6b977..6945a2c1 100644 --- a/caimira/tests/apps/calculator/test_specific_model_generator.py +++ b/caimira/calculator/tests/apps/calculator/test_specific_model_generator.py @@ -2,8 +2,8 @@ import numpy as np import pytest -from caimira.apps.calculator import model_generator -from caimira.store.data_registry import DataRegistry +from caimira.calculator.validators.virus import virus_validator +from caimira.calculator.store.data_registry import DataRegistry @pytest.mark.parametrize( @@ -14,7 +14,7 @@ [{"exposed_breaks": [], "ifected_breaks": []}, 'Unable to fetch "infected_breaks" key. Got "ifected_breaks".'], ] ) -def test_specific_break_structure(break_input, error, baseline_form: model_generator.VirusFormData, data_registry: DataRegistry): +def test_specific_break_structure(break_input, error, baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry): baseline_form.specific_breaks = break_input with pytest.raises(TypeError, match=error): baseline_form.validate() @@ -31,7 +31,7 @@ def test_specific_break_structure(break_input, error, baseline_form: model_gener [[{"start_time": "10:00", "finish_time": "11"}], 'Wrong time format - "HH:MM". Got "11".'], ] ) -def test_specific_population_break_data_structure(population_break_input, error, baseline_form: model_generator.VirusFormData, data_registry: DataRegistry): +def test_specific_population_break_data_structure(population_break_input, error, baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry): baseline_form.specific_breaks = {'exposed_breaks': population_break_input, 'infected_breaks': population_break_input} with pytest.raises(TypeError, match=error): baseline_form.validate() @@ -46,7 +46,7 @@ def test_specific_population_break_data_structure(population_break_input, error, [{'exposed_breaks': [], 'infected_breaks': [{"start_time": "08:00", "finish_time": "11:00"}, {"start_time": "14:00", "finish_time": "15:00"}, ]}, "All breaks should be within the simulation time. Got 08:00."], ] ) -def test_specific_break_time(break_input, error, baseline_form: model_generator.VirusFormData): +def test_specific_break_time(break_input, error, baseline_form: virus_validator.VirusFormData): with pytest.raises(ValueError, match=error): baseline_form.generate_specific_break_times(breaks_dict=break_input, target='exposed') baseline_form.generate_specific_break_times(breaks_dict=break_input, target='infected') @@ -65,7 +65,7 @@ def test_specific_break_time(break_input, error, baseline_form: model_generator. [{"physical_activity": "Light activity", "respiratory_activity": [{"type": "Breathing", "percentag": 50}, {"type": "Speaking", "percentage": 50}]}, 'Unable to fetch "percentage" key. Got "percentag".'], ] ) -def test_precise_activity_structure(precise_activity_input, error, baseline_form: model_generator.VirusFormData, data_registry: DataRegistry): +def test_precise_activity_structure(precise_activity_input, error, baseline_form: virus_validator.VirusFormData, data_registry: DataRegistry): baseline_form.precise_activity = precise_activity_input with pytest.raises(TypeError, match=error): baseline_form.validate() @@ -80,7 +80,7 @@ def test_precise_activity_structure(precise_activity_input, error, baseline_form [{"physical_activity": "Light activity", "respiratory_activity": [{"type": "Breathing", "percentage": 50}]}, 'The sum of all respiratory activities should be 100. Got 50.'], ] ) -def test_sum_precise_activity(precise_activity_input, error, baseline_form: model_generator.VirusFormData): +def test_sum_precise_activity(precise_activity_input, error, baseline_form: virus_validator.VirusFormData): baseline_form.precise_activity = precise_activity_input with pytest.raises(ValueError, match=error): baseline_form.validate() diff --git a/caimira/tests/conftest.py b/caimira/calculator/tests/conftest.py similarity index 86% rename from caimira/tests/conftest.py rename to caimira/calculator/tests/conftest.py index 4142ff79..f9391901 100644 --- a/caimira/tests/conftest.py +++ b/caimira/calculator/tests/conftest.py @@ -1,10 +1,10 @@ -from caimira import models -import caimira.data -import caimira.dataclass_utils +from caimira.calculator.models import models +import caimira.calculator.models.data +import caimira.calculator.models.dataclass_utils import pytest -from caimira.store.data_registry import DataRegistry +from caimira.calculator.store.data_registry import DataRegistry @pytest.fixture @@ -61,12 +61,12 @@ def baseline_exposure_model(data_registry, baseline_concentration_model, baselin @pytest.fixture def exposure_model_w_outside_temp_changes(data_registry, baseline_exposure_model: models.ExposureModel): - exp_model = caimira.dataclass_utils.nested_replace( + exp_model = caimira.calculator.models.dataclass_utils.nested_replace( baseline_exposure_model, { 'concentration_model.ventilation': models.SlidingWindow( data_registry=data_registry, active=models.PeriodicInterval(2.2 * 60, 1.8 * 60), - outside_temp=caimira.data.GenevaTemperatures['Jan'], + outside_temp=caimira.calculator.models.data.GenevaTemperatures['Jan'], window_height=1.6, opening_length=0.6, ) diff --git a/caimira/calculator/tests/data/__init__.py b/caimira/calculator/tests/data/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/tests/data/test_weather.py b/caimira/calculator/tests/data/test_weather.py similarity index 98% rename from caimira/tests/data/test_weather.py rename to caimira/calculator/tests/data/test_weather.py index 03eb29c3..7cdab2a8 100644 --- a/caimira/tests/data/test_weather.py +++ b/caimira/calculator/tests/data/test_weather.py @@ -5,7 +5,7 @@ import numpy.testing import pytest -import caimira.data.weather as wx +import caimira.calculator.models.data.weather as wx def test_nearest_wx_station(): diff --git a/caimira/calculator/tests/models/__init__.py b/caimira/calculator/tests/models/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/tests/models/test_co2_concentration_model.py b/caimira/calculator/tests/models/test_co2_concentration_model.py similarity index 96% rename from caimira/tests/models/test_co2_concentration_model.py rename to caimira/calculator/tests/models/test_co2_concentration_model.py index ce57110b..d6010032 100644 --- a/caimira/tests/models/test_co2_concentration_model.py +++ b/caimira/calculator/tests/models/test_co2_concentration_model.py @@ -1,7 +1,7 @@ import numpy.testing as npt import pytest -from caimira import models +from caimira.calculator.models import models @pytest.fixture diff --git a/caimira/tests/models/test_concentration_model.py b/caimira/calculator/tests/models/test_concentration_model.py similarity index 98% rename from caimira/tests/models/test_concentration_model.py rename to caimira/calculator/tests/models/test_concentration_model.py index 88d796d7..d2d5020c 100644 --- a/caimira/tests/models/test_concentration_model.py +++ b/caimira/calculator/tests/models/test_concentration_model.py @@ -5,8 +5,8 @@ import pytest from dataclasses import dataclass -from caimira import models -from caimira.store.data_registry import DataRegistry +from caimira.calculator.models import models +from caimira.calculator.store.data_registry import DataRegistry @dataclass(frozen=True) class KnownConcentrationModelBase(models._ConcentrationModelBase): diff --git a/caimira/tests/models/test_dynamic_population.py b/caimira/calculator/tests/models/test_dynamic_population.py similarity index 99% rename from caimira/tests/models/test_dynamic_population.py rename to caimira/calculator/tests/models/test_dynamic_population.py index 79c89980..daffdd56 100644 --- a/caimira/tests/models/test_dynamic_population.py +++ b/caimira/calculator/tests/models/test_dynamic_population.py @@ -4,8 +4,8 @@ import numpy.testing as npt import pytest -from caimira import models -import caimira.dataclass_utils as dc_utils +from caimira.calculator.models import models +import caimira.calculator.models.dataclass_utils as dc_utils @pytest.fixture def full_exposure_model(data_registry): diff --git a/caimira/tests/models/test_exposure_model.py b/caimira/calculator/tests/models/test_exposure_model.py similarity index 98% rename from caimira/tests/models/test_exposure_model.py rename to caimira/calculator/tests/models/test_exposure_model.py index 99e7ca1e..37fc7450 100644 --- a/caimira/tests/models/test_exposure_model.py +++ b/caimira/calculator/tests/models/test_exposure_model.py @@ -5,11 +5,11 @@ import pytest from dataclasses import dataclass -from caimira import models -from caimira.models import ExposureModel -from caimira.dataclass_utils import replace -from caimira.monte_carlo.data import expiration_distributions -from caimira.store.data_registry import DataRegistry +from caimira.calculator.models import models +from caimira.calculator.models.models import ExposureModel +from caimira.calculator.models.dataclass_utils import replace +from caimira.calculator.models.monte_carlo.data import expiration_distributions +from caimira.calculator.store.data_registry import DataRegistry @dataclass(frozen=True) class KnownNormedconcentration(models.ConcentrationModel): diff --git a/caimira/tests/models/test_fitting_algorithm.py b/caimira/calculator/tests/models/test_fitting_algorithm.py similarity index 97% rename from caimira/tests/models/test_fitting_algorithm.py rename to caimira/calculator/tests/models/test_fitting_algorithm.py index 65b6f447..bb4886de 100644 --- a/caimira/tests/models/test_fitting_algorithm.py +++ b/caimira/calculator/tests/models/test_fitting_algorithm.py @@ -2,7 +2,7 @@ import numpy.testing as npt import pytest -from caimira import models +from caimira.calculator.models import models @pytest.mark.parametrize( diff --git a/caimira/tests/models/test_mask.py b/caimira/calculator/tests/models/test_mask.py similarity index 95% rename from caimira/tests/models/test_mask.py rename to caimira/calculator/tests/models/test_mask.py index 5d87ac61..3c32a8dc 100644 --- a/caimira/tests/models/test_mask.py +++ b/caimira/calculator/tests/models/test_mask.py @@ -2,7 +2,7 @@ import numpy.testing as npt import pytest -from caimira import models +from caimira.calculator.models import models @pytest.mark.parametrize( diff --git a/caimira/tests/models/test_piecewiseconstant.py b/caimira/calculator/tests/models/test_piecewiseconstant.py similarity index 96% rename from caimira/tests/models/test_piecewiseconstant.py rename to caimira/calculator/tests/models/test_piecewiseconstant.py index 74c8a056..93347bf4 100644 --- a/caimira/tests/models/test_piecewiseconstant.py +++ b/caimira/calculator/tests/models/test_piecewiseconstant.py @@ -1,8 +1,8 @@ import numpy as np import pytest -from caimira import models -from caimira import data +from caimira.calculator.models import models +from caimira.calculator.models import data def test_piecewiseconstantfunction_wrongarguments(): diff --git a/caimira/tests/models/test_short_range_model.py b/caimira/calculator/tests/models/test_short_range_model.py similarity index 96% rename from caimira/tests/models/test_short_range_model.py rename to caimira/calculator/tests/models/test_short_range_model.py index 7bf5f429..0382369a 100644 --- a/caimira/tests/models/test_short_range_model.py +++ b/caimira/calculator/tests/models/test_short_range_model.py @@ -3,10 +3,10 @@ import numpy as np import pytest -from caimira import models -import caimira.monte_carlo as mc_models -from caimira.apps.calculator.model_generator import build_expiration -from caimira.monte_carlo.data import short_range_expiration_distributions,\ +from caimira.calculator.models import models +import caimira.calculator.models.monte_carlo as mc_models +from caimira.calculator.validators.virus.virus_validator import build_expiration +from caimira.calculator.models.monte_carlo.data import short_range_expiration_distributions,\ expiration_distributions, short_range_distances, activity_distributions SAMPLE_SIZE = 250_000 diff --git a/caimira/calculator/tests/test_caimira.py b/caimira/calculator/tests/test_caimira.py new file mode 100644 index 00000000..e9f43c36 --- /dev/null +++ b/caimira/calculator/tests/test_caimira.py @@ -0,0 +1,10 @@ +""" +High-level tests for the package. + +""" + +import caimira.calculator.models + + +def test_version(): + assert caimira.calculator.models.__version__ is not None diff --git a/caimira/tests/test_conditional_probability.py b/caimira/calculator/tests/test_conditional_probability.py similarity index 89% rename from caimira/tests/test_conditional_probability.py rename to caimira/calculator/tests/test_conditional_probability.py index 0e616ae7..447a8fe3 100644 --- a/caimira/tests/test_conditional_probability.py +++ b/caimira/calculator/tests/test_conditional_probability.py @@ -2,11 +2,11 @@ import pytest from retry import retry -import caimira.monte_carlo as mc -from caimira import models -from caimira.dataclass_utils import nested_replace -from caimira.apps.calculator import report_generator -from caimira.monte_carlo.data import activity_distributions, virus_distributions, expiration_distributions +import caimira.calculator.models.monte_carlo as mc +from caimira.calculator.models import models +from caimira.calculator.models.dataclass_utils import nested_replace +from caimira.calculator.report import report_generator +from caimira.calculator.models.monte_carlo.data import activity_distributions, virus_distributions, expiration_distributions @pytest.fixture diff --git a/caimira/tests/test_data_service.py b/caimira/calculator/tests/test_data_service.py similarity index 95% rename from caimira/tests/test_data_service.py rename to caimira/calculator/tests/test_data_service.py index c6c21343..d6c5025b 100644 --- a/caimira/tests/test_data_service.py +++ b/caimira/calculator/tests/test_data_service.py @@ -1,7 +1,7 @@ import unittest from unittest.mock import Mock, patch -from caimira.store.data_service import DataService +from caimira.calculator.store.data_service import DataService class DataServiceTests(unittest.TestCase): diff --git a/caimira/tests/test_dataclass_utils.py b/caimira/calculator/tests/test_dataclass_utils.py similarity index 90% rename from caimira/tests/test_dataclass_utils.py rename to caimira/calculator/tests/test_dataclass_utils.py index ac575052..14088018 100644 --- a/caimira/tests/test_dataclass_utils.py +++ b/caimira/calculator/tests/test_dataclass_utils.py @@ -1,6 +1,6 @@ import dataclasses -from caimira.dataclass_utils import nested_replace, walk_dataclass +from caimira.calculator.models.dataclass_utils import nested_replace, walk_dataclass @dataclasses.dataclass(frozen=True) diff --git a/caimira/tests/test_expiration.py b/caimira/calculator/tests/test_expiration.py similarity index 93% rename from caimira/tests/test_expiration.py rename to caimira/calculator/tests/test_expiration.py index 0cda581b..03842149 100644 --- a/caimira/tests/test_expiration.py +++ b/caimira/calculator/tests/test_expiration.py @@ -5,8 +5,8 @@ import pytest from retry import retry -from caimira import models -from caimira.monte_carlo.data import expiration_distribution +from caimira.calculator.models import models +from caimira.calculator.models.monte_carlo.data import expiration_distribution def test_multiple_wrong_weight_size(): diff --git a/caimira/tests/test_full_algorithm.py b/caimira/calculator/tests/test_full_algorithm.py similarity index 99% rename from caimira/tests/test_full_algorithm.py rename to caimira/calculator/tests/test_full_algorithm.py index 112b1082..adb93df0 100644 --- a/caimira/tests/test_full_algorithm.py +++ b/caimira/calculator/tests/test_full_algorithm.py @@ -8,11 +8,11 @@ import pytest from retry import retry -import caimira.monte_carlo as mc -from caimira import models -from caimira.utils import method_cache -from caimira.models import _VectorisedFloat,Interval,SpecificInterval -from caimira.monte_carlo.data import (expiration_distributions, +import caimira.calculator.models.monte_carlo as mc +from caimira.calculator.models import models +from caimira.calculator.models.utils import method_cache +from caimira.calculator.models.models import _VectorisedFloat,Interval,SpecificInterval +from caimira.calculator.models.monte_carlo.data import (expiration_distributions, expiration_BLO_factors,short_range_expiration_distributions, short_range_distances,virus_distributions,activity_distributions) diff --git a/caimira/tests/test_infected_population.py b/caimira/calculator/tests/test_infected_population.py similarity index 69% rename from caimira/tests/test_infected_population.py rename to caimira/calculator/tests/test_infected_population.py index 192441e4..2a48e8df 100644 --- a/caimira/tests/test_infected_population.py +++ b/caimira/calculator/tests/test_infected_population.py @@ -1,7 +1,7 @@ import numpy as np import pytest -import caimira.models +import caimira.calculator.models.models @pytest.mark.parametrize( @@ -17,26 +17,26 @@ def test_infected_population_vectorisation(override_params, data_registry): } defaults.update(override_params) - office_hours = caimira.models.SpecificInterval(present_times=[(8,17)]) - infected = caimira.models.InfectedPopulation( + office_hours = caimira.calculator.models.models.SpecificInterval(present_times=[(8,17)]) + infected = caimira.calculator.models.models.InfectedPopulation( data_registry=data_registry, number=1, presence=office_hours, - mask=caimira.models.Mask( + mask=caimira.calculator.models.models.Mask( factor_exhale=0.95, η_inhale=0.3, ), - activity=caimira.models.Activity( + activity=caimira.calculator.models.models.Activity( 0.51, defaults['exhalation_rate'], ), - virus=caimira.models.SARSCoV2( + virus=caimira.calculator.models.models.SARSCoV2( viral_load_in_sputum=defaults['viral_load_in_sputum'], infectious_dose=50., viable_to_RNA_ratio = 0.5, transmissibility_factor=1.0, ), - expiration=caimira.models._ExpirationBase.types['Breathing'], + expiration=caimira.calculator.models.models._ExpirationBase.types['Breathing'], host_immunity=0., ) emission_rate = infected.emission_rate(10) diff --git a/caimira/tests/test_known_quantities.py b/caimira/calculator/tests/test_known_quantities.py similarity index 99% rename from caimira/tests/test_known_quantities.py rename to caimira/calculator/tests/test_known_quantities.py index ba7e451a..c3943157 100644 --- a/caimira/tests/test_known_quantities.py +++ b/caimira/calculator/tests/test_known_quantities.py @@ -2,8 +2,8 @@ import numpy.testing as npt import pytest -import caimira.models as models -import caimira.data as data +import caimira.calculator.models.models as models +import caimira.calculator.models.data as data def test_no_mask_superspeading_emission_rate(baseline_concentration_model): diff --git a/caimira/tests/test_model.py b/caimira/calculator/tests/test_model.py similarity index 87% rename from caimira/tests/test_model.py rename to caimira/calculator/tests/test_model.py index eec01921..956d0c92 100644 --- a/caimira/tests/test_model.py +++ b/caimira/calculator/tests/test_model.py @@ -1,5 +1,4 @@ -import caimira.models -from caimira.dataclass_utils import nested_replace +from caimira.calculator.models.dataclass_utils import nested_replace def test_exposure_r0(baseline_exposure_model): diff --git a/caimira/calculator/tests/test_monte_carlo.py b/caimira/calculator/tests/test_monte_carlo.py new file mode 100644 index 00000000..ece38bd7 --- /dev/null +++ b/caimira/calculator/tests/test_monte_carlo.py @@ -0,0 +1,102 @@ +import dataclasses + +import numpy as np +import pytest + +import caimira.calculator.models +import caimira.calculator.models.models +import caimira.calculator.models.monte_carlo.sampleable + +MODEL_CLASSES = [ + cls for cls in vars(caimira.calculator.models).values() + if dataclasses.is_dataclass(cls) +] + + +def test_type_annotations(): + # Check that there are appropriate type annotations for all of the model + # classes in caimira.models. Note that these must be statically defined in + # caimira.monte_carlo, rather than being dynamically generated, in order to + # allow the type system to be able to see their definition without needing + # runtime execution. + missing = [] + for cls in MODEL_CLASSES: + if not hasattr(caimira.calculator.models.monte_carlo, cls.__name__): + missing.append(cls.__name__) + continue + mc_cls = getattr(caimira.calculator.models.monte_carlo, cls.__name__) + assert issubclass(mc_cls, caimira.calculator.models.monte_carlo.MCModelBase) + + if missing: + msg = ( + 'There are missing model implementations in caimira.monte_carlo. ' + 'The following definitions are needed:\n ' + + '\n '.join([f'{model} = build_mc_model(caimira.models.{model})' for model in missing]) + ) + pytest.fail(msg) + + +@pytest.fixture +def baseline_mc_concentration_model(data_registry) -> caimira.calculator.models.monte_carlo.ConcentrationModel: + mc_model = caimira.calculator.models.monte_carlo.ConcentrationModel( + data_registry=data_registry, + room=caimira.calculator.models.monte_carlo.Room(volume=caimira.calculator.models.monte_carlo.sampleable.Normal(75, 20), + inside_temp=caimira.calculator.models.models.PiecewiseConstant((0., 24.), (293,))), + ventilation=caimira.calculator.models.monte_carlo.SlidingWindow( + data_registry=data_registry, + active=caimira.calculator.models.models.PeriodicInterval(period=120, duration=120), + outside_temp=caimira.calculator.models.models.PiecewiseConstant((0., 24.), (283,)), + window_height=1.6, opening_length=0.6, + ), + infected=caimira.calculator.models.models.InfectedPopulation( + data_registry=data_registry, + number=1, + virus=caimira.calculator.models.models.Virus.types['SARS_CoV_2'], + presence=caimira.calculator.models.models.SpecificInterval(((0., 4.), (5., 8.))), + mask=caimira.calculator.models.models.Mask.types['No mask'], + activity=caimira.calculator.models.models.Activity.types['Light activity'], + expiration=caimira.calculator.models.models.Expiration.types['Breathing'], + host_immunity=0., + ), + evaporation_factor=0.3, + ) + return mc_model + + +@pytest.fixture +def baseline_mc_sr_model() -> caimira.calculator.models.monte_carlo.ShortRangeModel: + return () + + +@pytest.fixture +def baseline_mc_exposure_model(data_registry, baseline_mc_concentration_model, baseline_mc_sr_model) -> caimira.calculator.models.monte_carlo.ExposureModel: + return caimira.calculator.models.monte_carlo.ExposureModel( + data_registry, + baseline_mc_concentration_model, + baseline_mc_sr_model, + exposed=caimira.calculator.models.models.Population( + number=10, + presence=baseline_mc_concentration_model.infected.presence, + activity=baseline_mc_concentration_model.infected.activity, + mask=baseline_mc_concentration_model.infected.mask, + host_immunity=0., + ), + geographical_data=caimira.calculator.models.models.Cases(), + ) + + +def test_build_concentration_model(baseline_mc_concentration_model: caimira.calculator.models.monte_carlo.ConcentrationModel): + model = baseline_mc_concentration_model.build_model(7) + assert isinstance(model, caimira.calculator.models.models.ConcentrationModel) + assert isinstance(model.concentration(time=0.), float) + conc = model.concentration(time=1.) + assert isinstance(conc, np.ndarray) + assert conc.shape == (7, ) + + +def test_build_exposure_model(baseline_mc_exposure_model: caimira.calculator.models.monte_carlo.ExposureModel): + model = baseline_mc_exposure_model.build_model(7) + assert isinstance(model, caimira.calculator.models.models.ExposureModel) + prob = model.deposited_exposure() + assert isinstance(prob, np.ndarray) + assert prob.shape == (7, ) diff --git a/caimira/tests/test_monte_carlo_full_models.py b/caimira/calculator/tests/test_monte_carlo_full_models.py similarity index 97% rename from caimira/tests/test_monte_carlo_full_models.py rename to caimira/calculator/tests/test_monte_carlo_full_models.py index ec4f6496..948ce45e 100644 --- a/caimira/tests/test_monte_carlo_full_models.py +++ b/caimira/calculator/tests/test_monte_carlo_full_models.py @@ -3,10 +3,10 @@ import pytest from retry import retry -import caimira.monte_carlo as mc -from caimira import models,data -from caimira.monte_carlo.data import activity_distributions, virus_distributions, expiration_distributions, infectious_dose_distribution, viable_to_RNA_ratio_distribution -from caimira.apps.calculator.model_generator import build_expiration +import caimira.calculator.models.monte_carlo as mc +from caimira.calculator.models import models, data +from caimira.calculator.models.monte_carlo.data import activity_distributions, virus_distributions, expiration_distributions, infectious_dose_distribution, viable_to_RNA_ratio_distribution +from caimira.calculator.validators.virus.virus_validator import build_expiration SAMPLE_SIZE = 500_000 TOLERANCE = 0.05 diff --git a/caimira/tests/test_predefined_distributions.py b/caimira/calculator/tests/test_predefined_distributions.py similarity index 92% rename from caimira/tests/test_predefined_distributions.py rename to caimira/calculator/tests/test_predefined_distributions.py index b75e4ce5..c0248b17 100644 --- a/caimira/tests/test_predefined_distributions.py +++ b/caimira/calculator/tests/test_predefined_distributions.py @@ -2,8 +2,7 @@ import numpy.testing as npt import pytest -from caimira.monte_carlo.data import activity_distributions, virus_distributions -from caimira.store import data_registry +from caimira.calculator.models.monte_carlo.data import activity_distributions, virus_distributions # Mean & std deviations from https://doi.org/10.1101/2021.10.14.21264988 (Table 3) diff --git a/caimira/tests/test_sampleable_distribution.py b/caimira/calculator/tests/test_sampleable_distribution.py similarity index 98% rename from caimira/tests/test_sampleable_distribution.py rename to caimira/calculator/tests/test_sampleable_distribution.py index 98f0a9ca..add9dba2 100644 --- a/caimira/tests/test_sampleable_distribution.py +++ b/caimira/calculator/tests/test_sampleable_distribution.py @@ -3,7 +3,7 @@ import pytest from retry import retry -from caimira.monte_carlo import sampleable +from caimira.calculator.models.monte_carlo import sampleable @retry(tries=10) diff --git a/caimira/tests/test_ventilation.py b/caimira/calculator/tests/test_ventilation.py similarity index 99% rename from caimira/tests/test_ventilation.py rename to caimira/calculator/tests/test_ventilation.py index 4d322cfa..82c9f682 100644 --- a/caimira/tests/test_ventilation.py +++ b/caimira/calculator/tests/test_ventilation.py @@ -4,7 +4,7 @@ import numpy.testing as npt import pytest -from caimira import models +from caimira.calculator.models import models @pytest.fixture diff --git a/caimira/calculator/validators/__init__.py b/caimira/calculator/validators/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/calculator/validators/co2/__init__.py b/caimira/calculator/validators/co2/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/apps/calculator/co2_model_generator.py b/caimira/calculator/validators/co2/co2_validator.py similarity index 97% rename from caimira/apps/calculator/co2_model_generator.py rename to caimira/calculator/validators/co2/co2_validator.py index a4a6a9c2..a630e774 100644 --- a/caimira/apps/calculator/co2_model_generator.py +++ b/caimira/calculator/validators/co2/co2_validator.py @@ -6,11 +6,11 @@ import matplotlib.pyplot as plt import re -from caimira import models -from caimira.store.data_registry import DataRegistry -from .form_data import FormData, cast_class_fields -from .defaults import NO_DEFAULT -from .report_generator import img2base64, _figure2bytes +from ..form_validator import FormData, cast_class_fields +from ..defaults import NO_DEFAULT +from ...store.data_registry import DataRegistry +from ...models import models +from ...report.report_generator import img2base64, _figure2bytes minutes_since_midnight = typing.NewType('minutes_since_midnight', int) diff --git a/caimira/apps/calculator/defaults.py b/caimira/calculator/validators/defaults.py similarity index 100% rename from caimira/apps/calculator/defaults.py rename to caimira/calculator/validators/defaults.py diff --git a/caimira/apps/calculator/form_data.py b/caimira/calculator/validators/form_validator.py similarity index 79% rename from caimira/apps/calculator/form_data.py rename to caimira/calculator/validators/form_validator.py index a0a96b67..94cf32b4 100644 --- a/caimira/apps/calculator/form_data.py +++ b/caimira/calculator/validators/form_validator.py @@ -7,9 +7,9 @@ import numpy as np -from caimira import models -from caimira.store.data_registry import DataRegistry from .defaults import DEFAULTS, NO_DEFAULT, COFFEE_OPTIONS_INT +from ..models import models +from ..store.data_registry import DataRegistry LOG = logging.getLogger(__name__) @@ -26,13 +26,16 @@ class FormData: exposed_lunch_option: bool exposed_lunch_start: minutes_since_midnight exposed_start: minutes_since_midnight - infected_coffee_break_option: str #Used if infected_dont_have_breaks_with_exposed - infected_coffee_duration: int #Used if infected_dont_have_breaks_with_exposed + # Used if infected_dont_have_breaks_with_exposed + infected_coffee_break_option: str + infected_coffee_duration: int # Used if infected_dont_have_breaks_with_exposed infected_dont_have_breaks_with_exposed: bool infected_finish: minutes_since_midnight - infected_lunch_finish: minutes_since_midnight #Used if infected_dont_have_breaks_with_exposed - infected_lunch_option: bool #Used if infected_dont_have_breaks_with_exposed - infected_lunch_start: minutes_since_midnight #Used if infected_dont_have_breaks_with_exposed + # Used if infected_dont_have_breaks_with_exposed + infected_lunch_finish: minutes_since_midnight + infected_lunch_option: bool # Used if infected_dont_have_breaks_with_exposed + # Used if infected_dont_have_breaks_with_exposed + infected_lunch_start: minutes_since_midnight infected_people: int infected_start: minutes_since_midnight room_volume: float @@ -47,7 +50,6 @@ def from_dict(cls, form_data: typing.Dict, data_registry: DataRegistry): # Take a copy of the form data so that we can mutate it. form_data = form_data.copy() form_data.pop('_xsrf', None) - # Don't let arbitrary unescaped HTML through the net. for key, value in form_data.items(): if isinstance(value, str): @@ -64,7 +66,8 @@ def from_dict(cls, form_data: typing.Dict, data_registry: DataRegistry): form_data[key] = _CAST_RULES_FORM_ARG_TO_NATIVE[key](value) if key not in cls._DEFAULTS: - raise ValueError(f'Invalid argument "{html.escape(key)}" given') + raise ValueError( + f'Invalid argument "{html.escape(key)}" given') instance = cls(**form_data, data_registry=data_registry) instance.validate() @@ -93,7 +96,8 @@ def to_dict(cls, form: "FormData", strip_defaults: bool = False) -> dict: def validate_population_parameters(self): # Validate number of infected <= number of total people if self.infected_people >= self.total_people: - raise ValueError('Number of infected people cannot be greater or equal to the number of total people.') + raise ValueError( + 'Number of infected people cannot be greater or equal to the number of total people.') # Validate time intervals selected by user time_intervals = [ @@ -101,9 +105,11 @@ def validate_population_parameters(self): ['infected_start', 'infected_finish'], ] if self.exposed_lunch_option: - time_intervals.append(['exposed_lunch_start', 'exposed_lunch_finish']) + time_intervals.append( + ['exposed_lunch_start', 'exposed_lunch_finish']) if self.infected_dont_have_breaks_with_exposed and self.infected_lunch_option: - time_intervals.append(['infected_lunch_start', 'infected_lunch_finish']) + time_intervals.append( + ['infected_lunch_start', 'infected_lunch_finish']) for start_name, end_name in time_intervals: start = getattr(self, start_name) @@ -116,29 +122,33 @@ def validate_lunch(start, finish): lunch_start = getattr(self, f'{population}_lunch_start') lunch_finish = getattr(self, f'{population}_lunch_finish') return (start <= lunch_start <= finish and - start <= lunch_finish <= finish) + start <= lunch_finish <= finish) def get_lunch_mins(population): lunch_mins = 0 if getattr(self, f'{population}_lunch_option'): - lunch_mins = getattr(self, f'{population}_lunch_finish') - getattr(self, f'{population}_lunch_start') + lunch_mins = getattr( + self, f'{population}_lunch_finish') - getattr(self, f'{population}_lunch_start') return lunch_mins def get_coffee_mins(population): coffee_mins = 0 if getattr(self, f'{population}_coffee_break_option') != 'coffee_break_0': - coffee_mins = COFFEE_OPTIONS_INT[getattr(self, f'{population}_coffee_break_option')] * getattr(self, f'{population}_coffee_duration') + coffee_mins = COFFEE_OPTIONS_INT[getattr( + self, f'{population}_coffee_break_option')] * getattr(self, f'{population}_coffee_duration') return coffee_mins def get_activity_mins(population): return getattr(self, f'{population}_finish') - getattr(self, f'{population}_start') - populations = ['exposed', 'infected'] if self.infected_dont_have_breaks_with_exposed else ['exposed'] + populations = [ + 'exposed', 'infected'] if self.infected_dont_have_breaks_with_exposed else ['exposed'] for population in populations: # Validate lunch time within the activity times. if (getattr(self, f'{population}_lunch_option') and - not validate_lunch(getattr(self, f'{population}_start'), getattr(self, f'{population}_finish')) - ): + not validate_lunch(getattr(self, f'{population}_start'), getattr( + self, f'{population}_finish')) + ): raise ValueError( f"{population} lunch break must be within presence times." ) @@ -152,7 +162,8 @@ def get_activity_mins(population): for attr_name, valid_set in [('exposed_coffee_break_option', COFFEE_OPTIONS_INT), ('infected_coffee_break_option', COFFEE_OPTIONS_INT)]: if getattr(self, attr_name) not in valid_set: - raise ValueError(f"{getattr(self, attr_name)} is not a valid value for {attr_name}") + raise ValueError( + f"{getattr(self, attr_name)} is not a valid value for {attr_name}") def validate(self): raise NotImplementedError("Subclass must implement") @@ -161,7 +172,8 @@ def build_model(self, sample_size=None): raise NotImplementedError("Subclass must implement") def _compute_breaks_in_interval(self, start, finish, n_breaks, duration) -> models.BoundarySequence_t: - break_delay = ((finish - start) - (n_breaks * duration)) // (n_breaks+1) + break_delay = ((finish - start) - + (n_breaks * duration)) // (n_breaks+1) break_times = [] end = start for n in range(n_breaks): @@ -173,14 +185,16 @@ def _compute_breaks_in_interval(self, start, finish, n_breaks, duration) -> mode def exposed_lunch_break_times(self) -> models.BoundarySequence_t: result = [] if self.exposed_lunch_option: - result.append((self.exposed_lunch_start, self.exposed_lunch_finish)) + result.append((self.exposed_lunch_start, + self.exposed_lunch_finish)) return tuple(result) def infected_lunch_break_times(self) -> models.BoundarySequence_t: if self.infected_dont_have_breaks_with_exposed: result = [] if self.infected_lunch_option: - result.append((self.infected_lunch_start, self.infected_lunch_finish)) + result.append((self.infected_lunch_start, + self.infected_lunch_finish)) return tuple(result) else: return self.exposed_lunch_break_times() @@ -194,7 +208,8 @@ def infected_number_of_coffee_breaks(self) -> int: def _coffee_break_times(self, activity_start, activity_finish, coffee_breaks, coffee_duration, lunch_start, lunch_finish) -> models.BoundarySequence_t: time_before_lunch = lunch_start - activity_start time_after_lunch = activity_finish - lunch_finish - before_lunch_frac = time_before_lunch / (time_before_lunch + time_after_lunch) + before_lunch_frac = time_before_lunch / \ + (time_before_lunch + time_after_lunch) n_morning_breaks = round(coffee_breaks * before_lunch_frac) breaks = ( self._compute_breaks_in_interval( @@ -211,9 +226,11 @@ def exposed_coffee_break_times(self) -> models.BoundarySequence_t: if exposed_coffee_breaks == 0: return () if self.exposed_lunch_option: - breaks = self._coffee_break_times(self.exposed_start, self.exposed_finish, exposed_coffee_breaks, self.exposed_coffee_duration, self.exposed_lunch_start, self.exposed_lunch_finish) + breaks = self._coffee_break_times(self.exposed_start, self.exposed_finish, exposed_coffee_breaks, + self.exposed_coffee_duration, self.exposed_lunch_start, self.exposed_lunch_finish) else: - breaks = self._compute_breaks_in_interval(self.exposed_start, self.exposed_finish, exposed_coffee_breaks, self.exposed_coffee_duration) + breaks = self._compute_breaks_in_interval( + self.exposed_start, self.exposed_finish, exposed_coffee_breaks, self.exposed_coffee_duration) return breaks def infected_coffee_break_times(self) -> models.BoundarySequence_t: @@ -222,9 +239,11 @@ def infected_coffee_break_times(self) -> models.BoundarySequence_t: if infected_coffee_breaks == 0: return () if self.infected_lunch_option: - breaks = self._coffee_break_times(self.infected_start, self.infected_finish, infected_coffee_breaks, self.infected_coffee_duration, self.infected_lunch_start, self.infected_lunch_finish) + breaks = self._coffee_break_times(self.infected_start, self.infected_finish, infected_coffee_breaks, + self.infected_coffee_duration, self.infected_lunch_start, self.infected_lunch_finish) else: - breaks = self._compute_breaks_in_interval(self.infected_start, self.infected_finish, infected_coffee_breaks, self.infected_coffee_duration) + breaks = self._compute_breaks_in_interval( + self.infected_start, self.infected_finish, infected_coffee_breaks, self.infected_coffee_duration) return breaks else: return self.exposed_coffee_break_times() @@ -232,13 +251,14 @@ def infected_coffee_break_times(self) -> models.BoundarySequence_t: def generate_specific_break_times(self, breaks_dict: dict, target: str) -> models.BoundarySequence_t: break_times = [] for n in breaks_dict[f'{target}_breaks']: - # Parse break times. + # Parse break times. begin = time_string_to_minutes(n["start_time"]) end = time_string_to_minutes(n["finish_time"]) for time in [begin, end]: # For a specific break, the infected and exposed presence is the same. if not getattr(self, f'{target}_start') < time < getattr(self, f'{target}_finish'): - raise ValueError(f'All breaks should be within the simulation time. Got {time_minutes_to_string(time)}.') + raise ValueError( + f'All breaks should be within the simulation time. Got {time_minutes_to_string(time)}.') break_times.append((begin, end)) return tuple(break_times) @@ -260,7 +280,8 @@ def present_interval( # Order the breaks by their start-time, and ensure that they are monotonic # and that the start of one break happens after the end of another. - break_boundaries: models.BoundarySequence_t = tuple(sorted(breaks, key=lambda break_pair: break_pair[0])) + break_boundaries: models.BoundarySequence_t = tuple( + sorted(breaks, key=lambda break_pair: break_pair[0])) for break_start, break_end in break_boundaries: if break_start >= break_end: @@ -269,13 +290,15 @@ def present_interval( prev_break_end = break_boundaries[0][1] for break_start, break_end in break_boundaries[1:]: if prev_break_end >= break_start: - raise ValueError(f"A break starts before another ends ({break_start}, {break_end}, {prev_break_end}).") + raise ValueError( + f"A break starts before another ends ({break_start}, {break_end}, {prev_break_end}).") prev_break_end = break_end present_intervals = [] current_time = start - LOG.debug(f"starting time march at {_hours2timestring(current_time/60)} to {_hours2timestring(finish/60)}") + LOG.debug( + f"starting time march at {_hours2timestring(current_time/60)} to {_hours2timestring(finish/60)}") # As we step through the breaks. For each break there are 6 important cases # we must cover. Let S=start; E=end; Bs=Break start; Be=Break end: @@ -336,8 +359,9 @@ def present_interval( return models.SpecificInterval(tuple(present_intervals)) def infected_present_interval(self) -> models.Interval: - if self.specific_breaks != {}: # It means the breaks are specific and not predefined - breaks = self.generate_specific_break_times(breaks_dict=self.specific_breaks, target='exposed') + if self.specific_breaks != {}: # It means the breaks are specific and not predefined + breaks = self.generate_specific_break_times( + breaks_dict=self.specific_breaks, target='exposed') else: breaks = self.infected_lunch_break_times() + self.infected_coffee_break_times() return self.present_interval( @@ -346,14 +370,17 @@ def infected_present_interval(self) -> models.Interval: ) def population_present_interval(self) -> models.Interval: - state_change_times = set(self.infected_present_interval().transition_times()) - state_change_times.update(self.exposed_present_interval().transition_times()) + state_change_times = set( + self.infected_present_interval().transition_times()) + state_change_times.update( + self.exposed_present_interval().transition_times()) all_state_changes = sorted(state_change_times) return models.SpecificInterval(tuple(zip(all_state_changes[:-1], all_state_changes[1:]))) def exposed_present_interval(self) -> models.Interval: - if self.specific_breaks != {}: # It means the breaks are specific and not predefined - breaks = self.generate_specific_break_times(breaks_dict=self.specific_breaks, target='exposed') + if self.specific_breaks != {}: # It means the breaks are specific and not predefined + breaks = self.generate_specific_break_times( + breaks_dict=self.specific_breaks, target='exposed') else: breaks = self.exposed_lunch_break_times() + self.exposed_coffee_break_times() return self.present_interval( @@ -382,7 +409,7 @@ def time_minutes_to_string(time: int) -> str: :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) + return "{0:0=2d}".format(int(time/60)) + ":" + "{0:0=2d}".format(time % 60) def string_to_list(s: str) -> list: @@ -409,7 +436,8 @@ def _safe_int_cast(value) -> int: elif isinstance(value, str) and value.isdecimal(): return int(value) else: - raise TypeError(f"Unable to safely cast {value} ({type(value)} type) to int") + raise TypeError( + f"Unable to safely cast {value} ({type(value)} type) to int") #: Mapping of field name to a callable which can convert values from form @@ -420,6 +448,7 @@ def _safe_int_cast(value) -> int: #: that can be encoded to URL arguments. _CAST_RULES_NATIVE_TO_FORM_ARG: typing.Dict[str, typing.Callable] = {} + def cast_class_fields(cls): for _field in dataclasses.fields(cls): if _field.type is minutes_since_midnight: @@ -439,4 +468,5 @@ def cast_class_fields(cls): _CAST_RULES_FORM_ARG_TO_NATIVE[_field.name] = string_to_dict _CAST_RULES_NATIVE_TO_FORM_ARG[_field.name] = dict_to_string + cast_class_fields(FormData) diff --git a/caimira/calculator/validators/virus/__init__.py b/caimira/calculator/validators/virus/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/apps/calculator/model_generator.py b/caimira/calculator/validators/virus/virus_validator.py similarity index 78% rename from caimira/apps/calculator/model_generator.py rename to caimira/calculator/validators/virus/virus_validator.py index aa35ba1e..74f10427 100644 --- a/caimira/apps/calculator/model_generator.py +++ b/caimira/calculator/validators/virus/virus_validator.py @@ -6,17 +6,13 @@ import numpy as np -from caimira import models -from caimira import data -import caimira.data.weather -import caimira.monte_carlo as mc -from .. import calculator -from .form_data import FormData, cast_class_fields, time_string_to_minutes -from caimira.monte_carlo.data import activity_distributions, virus_distributions, mask_distributions, short_range_distances -from caimira.monte_carlo.data import expiration_distribution, expiration_BLO_factors, expiration_distributions, short_range_expiration_distributions -from .defaults import (DEFAULTS, CONFIDENCE_LEVEL_OPTIONS, - MECHANICAL_VENTILATION_TYPES, MASK_WEARING_OPTIONS, MONTH_NAMES, VACCINE_BOOSTER_TYPE, VACCINE_TYPE, - VENTILATION_TYPES, VOLUME_TYPES, WINDOWS_OPENING_REGIMES, WINDOWS_TYPES) +from ..form_validator import FormData, cast_class_fields, time_string_to_minutes +from ..defaults import (DEFAULTS, CONFIDENCE_LEVEL_OPTIONS, + MECHANICAL_VENTILATION_TYPES, MASK_WEARING_OPTIONS, MONTH_NAMES, VACCINE_BOOSTER_TYPE, VACCINE_TYPE, + VENTILATION_TYPES, VOLUME_TYPES, WINDOWS_OPENING_REGIMES, WINDOWS_TYPES) +from ...models import models, data, monte_carlo as mc +from ...models.monte_carlo.data import activity_distributions, virus_distributions, mask_distributions, short_range_distances +from ...models.monte_carlo.data import expiration_distribution, expiration_BLO_factors, expiration_distributions, short_range_expiration_distributions LOG = logging.getLogger("MODEL") @@ -77,15 +73,17 @@ class VirusFormData(FormData): _DEFAULTS: typing.ClassVar[typing.Dict[str, typing.Any]] = DEFAULTS def validate(self): - # Validate population parameters self.validate_population_parameters() validation_tuples = [('activity_type', self.data_registry.population_scenario_activity.keys()), - ('mechanical_ventilation_type', MECHANICAL_VENTILATION_TYPES), - ('mask_type', list(mask_distributions(self.data_registry).keys())), + ('mechanical_ventilation_type', + MECHANICAL_VENTILATION_TYPES), + ('mask_type', list(mask_distributions( + self.data_registry).keys())), ('mask_wearing_option', MASK_WEARING_OPTIONS), ('ventilation_type', VENTILATION_TYPES), - ('virus_type', list(virus_distributions(self.data_registry).keys())), + ('virus_type', list(virus_distributions( + self.data_registry).keys())), ('volume_type', VOLUME_TYPES), ('window_opening_regime', WINDOWS_OPENING_REGIMES), ('window_type', WINDOWS_TYPES), @@ -96,11 +94,13 @@ def validate(self): for attr_name, valid_set in validation_tuples: if getattr(self, attr_name) not in valid_set: - raise ValueError(f"{getattr(self, attr_name)} is not a valid value for {attr_name}") + raise ValueError( + f"{getattr(self, attr_name)} is not a valid value for {attr_name}") # Validate number of infected people == 1 when activity is Conference/Training. if self.activity_type == 'training' and self.infected_people > 1: - raise ValueError('Conference/Training activities are limited to 1 infected.') + raise ValueError( + 'Conference/Training activities are limited to 1 infected.') # Validate ventilation parameters if self.ventilation_type == 'natural_ventilation': @@ -115,7 +115,7 @@ def validate(self): "ventilation_type is 'natural_ventilation'" ) if (self.window_opening_regime == 'windows_open_periodically' and - self.windows_duration > self.windows_frequency): + self.windows_duration > self.windows_frequency): raise ValueError( 'Duration cannot be bigger than frequency.' ) @@ -128,61 +128,78 @@ def validate(self): # Validate specific inputs - breaks (exposed and infected) if self.specific_breaks != {}: if type(self.specific_breaks) is not dict: - raise TypeError('The specific breaks should be in a dictionary.') + raise TypeError( + 'The specific breaks should be in a dictionary.') dict_keys = list(self.specific_breaks.keys()) if "exposed_breaks" not in dict_keys: - raise TypeError(f'Unable to fetch "exposed_breaks" key. Got "{dict_keys[0]}".') + raise TypeError( + f'Unable to fetch "exposed_breaks" key. Got "{dict_keys[0]}".') if "infected_breaks" not in dict_keys: - raise TypeError(f'Unable to fetch "infected_breaks" key. Got "{dict_keys[1]}".') + raise TypeError( + f'Unable to fetch "infected_breaks" key. Got "{dict_keys[1]}".') for population_breaks in ['exposed_breaks', 'infected_breaks']: if self.specific_breaks[population_breaks] != []: if type(self.specific_breaks[population_breaks]) is not list: - raise TypeError(f'All breaks should be in a list. Got {type(self.specific_breaks[population_breaks])}.') + raise TypeError( + f'All breaks should be in a list. Got {type(self.specific_breaks[population_breaks])}.') for input_break in self.specific_breaks[population_breaks]: # Input validations. if type(input_break) is not dict: - raise TypeError(f'Each break should be a dictionary. Got {type(input_break)}.') + raise TypeError( + f'Each break should be a dictionary. Got {type(input_break)}.') dict_keys = list(input_break.keys()) if "start_time" not in input_break: - raise TypeError(f'Unable to fetch "start_time" key. Got "{dict_keys[0]}".') + raise TypeError( + f'Unable to fetch "start_time" key. Got "{dict_keys[0]}".') if "finish_time" not in input_break: - raise TypeError(f'Unable to fetch "finish_time" key. Got "{dict_keys[1]}".') + raise TypeError( + f'Unable to fetch "finish_time" key. Got "{dict_keys[1]}".') for time in input_break.values(): if not re.compile("^(2[0-3]|[01]?[0-9]):([0-5]?[0-9])$").match(time): - raise TypeError(f'Wrong time format - "HH:MM". Got "{time}".') + raise TypeError( + f'Wrong time format - "HH:MM". Got "{time}".') # Validate specific inputs - precise activity if self.precise_activity != {}: if type(self.precise_activity) is not dict: - raise TypeError('The precise activities should be in a dictionary.') + raise TypeError( + 'The precise activities should be in a dictionary.') dict_keys = list(self.precise_activity.keys()) if "physical_activity" not in dict_keys: - raise TypeError(f'Unable to fetch "physical_activity" key. Got "{dict_keys[0]}".') + raise TypeError( + f'Unable to fetch "physical_activity" key. Got "{dict_keys[0]}".') if "respiratory_activity" not in dict_keys: - raise TypeError(f'Unable to fetch "respiratory_activity" key. Got "{dict_keys[1]}".') + raise TypeError( + f'Unable to fetch "respiratory_activity" key. Got "{dict_keys[1]}".') if type(self.precise_activity['physical_activity']) is not str: - raise TypeError('The physical activities should be a single string.') + raise TypeError( + 'The physical activities should be a single string.') if type(self.precise_activity['respiratory_activity']) is not list: - raise TypeError('The respiratory activities should be in a list.') + raise TypeError( + 'The respiratory activities should be in a list.') total_percentage = 0 for respiratory_activity in self.precise_activity['respiratory_activity']: if type(respiratory_activity) is not dict: - raise TypeError('Each respiratory activity should be defined in a dictionary.') + raise TypeError( + 'Each respiratory activity should be defined in a dictionary.') dict_keys = list(respiratory_activity.keys()) if "type" not in dict_keys: - raise TypeError(f'Unable to fetch "type" key. Got "{dict_keys[0]}".') + raise TypeError( + f'Unable to fetch "type" key. Got "{dict_keys[0]}".') if "percentage" not in dict_keys: - raise TypeError(f'Unable to fetch "percentage" key. Got "{dict_keys[1]}".') + raise TypeError( + f'Unable to fetch "percentage" key. Got "{dict_keys[1]}".') total_percentage += respiratory_activity['percentage'] if total_percentage != 100: - raise ValueError(f'The sum of all respiratory activities should be 100. Got {total_percentage}.') + raise ValueError( + f'The sum of all respiratory activities should be 100. Got {total_percentage}.') # Validate number of people with short-range interactions max_occupants_for_sr = self.total_people - self.infected_people @@ -219,7 +236,8 @@ def build_mc_model(self) -> mc.ExposureModel: for interaction in self.short_range_interactions: short_range.append(mc.ShortRangeModel( data_registry=self.data_registry, - expiration=short_range_expiration_distributions(self.data_registry)[interaction['expiration']], + expiration=short_range_expiration_distributions( + self.data_registry)[interaction['expiration']], activity=infected_population.activity, presence=self.short_range_interval(interaction), distance=short_range_distances(self.data_registry), @@ -234,7 +252,7 @@ def build_mc_model(self) -> mc.ExposureModel: infected=infected_population, evaporation_factor=0.3, ), - short_range = tuple(short_range), + short_range=tuple(short_range), exposed=self.exposed_population(), geographical_data=mc.Cases( geographic_population=self.geographic_population, @@ -250,11 +268,14 @@ def build_model(self, sample_size=None) -> models.ExposureModel: def build_CO2_model(self, sample_size=None) -> models.CO2ConcentrationModel: sample_size = sample_size or self.data_registry.monte_carlo['sample_size'] - infected_population: models.InfectedPopulation = self.infected_population().build_model(sample_size) + infected_population: models.InfectedPopulation = self.infected_population( + ).build_model(sample_size) exposed_population: models.Population = self.exposed_population().build_model(sample_size) - state_change_times = set(infected_population.presence_interval().transition_times()) - state_change_times.update(exposed_population.presence_interval().transition_times()) + state_change_times = set( + infected_population.presence_interval().transition_times()) + state_change_times.update( + exposed_population.presence_interval().transition_times()) transition_times = sorted(state_change_times) total_people = [infected_population.people_present(stop) + exposed_population.people_present(stop) @@ -263,10 +284,12 @@ def build_CO2_model(self, sample_size=None) -> models.CO2ConcentrationModel: if (self.activity_type == 'precise'): activity_defn, _ = self.generate_precise_activity_expiration() else: - activity_defn = self.data_registry.population_scenario_activity[self.activity_type]['activity'] + activity_defn = self.data_registry.population_scenario_activity[ + self.activity_type]['activity'] population = mc.SimplePopulation( - number=models.IntPiecewiseConstant(transition_times=tuple(transition_times), values=tuple(total_people)), + number=models.IntPiecewiseConstant(transition_times=tuple( + transition_times), values=tuple(total_people)), presence=None, activity=activity_distributions(self.data_registry)[activity_defn], ) @@ -286,7 +309,7 @@ def tz_name_and_utc_offset(self) -> typing.Tuple[str, float]: """ month = MONTH_NAMES.index(self.event_month) + 1 - timezone = caimira.data.weather.timezone_at( + timezone = data.weather.timezone_at( latitude=self.location_latitude, longitude=self.location_longitude, ) # We choose the first of the month for the current year. @@ -307,7 +330,8 @@ def outside_temp(self) -> models.PiecewiseConstant: month = MONTH_NAMES.index(self.event_month) + 1 wx_station = self.nearest_weather_station() - temp_profile = caimira.data.weather.mean_hourly_temperatures(wx_station = wx_station[0], month = MONTH_NAMES.index(self.event_month) + 1) + temp_profile = data.weather.mean_hourly_temperatures( + wx_station=wx_station[0], month=MONTH_NAMES.index(self.event_month) + 1) _, utc_offset = self.tz_name_and_utc_offset() @@ -315,13 +339,14 @@ def outside_temp(self) -> models.PiecewiseConstant: # result the first data value may no longer be a midnight, and the hours # no longer ordered modulo 24). source_times = np.arange(24) + utc_offset - times, temp_profile = caimira.data.weather.refine_hourly_data( + times, temp_profile = data.weather.refine_hourly_data( source_times, temp_profile, npts=24*10, # 10 steps per hour => 6 min steps ) outside_temp = models.PiecewiseConstant( - tuple(float(t) for t in times), tuple(float(t) for t in temp_profile), + tuple(float(t) for t in times), tuple(float(t) + for t in temp_profile), ) return outside_temp @@ -337,7 +362,8 @@ def ventilation(self) -> models._VentilationBase: ventilations.append(models.AirChange(active=models.SpecificInterval(present_times=((start, stop), )), air_exch=self.CO2_fitting_result['ventilation_values'][index])) else: - ventilations.append(models.AirChange(active=always_on, air_exch=self.CO2_fitting_result['ventilation_values'][0])) + ventilations.append(models.AirChange( + active=always_on, air_exch=self.CO2_fitting_result['ventilation_values'][0])) return models.MultipleVentilation(tuple(ventilations)) # Initializes a ventilation instance as a window if 'natural_ventilation' is selected, or as a HEPA-filter otherwise @@ -373,7 +399,8 @@ def ventilation(self) -> models._VentilationBase: ventilation = models.AirChange(active=always_on, air_exch=0.) else: if self.mechanical_ventilation_type == 'mech_type_air_changes': - ventilation = models.AirChange(active=always_on, air_exch=self.air_changes) + ventilation = models.AirChange( + active=always_on, air_exch=self.air_changes) else: ventilation = models.HVACMechanical( active=always_on, q_air_mech=self.air_supply) @@ -382,16 +409,18 @@ def ventilation(self) -> models._VentilationBase: # to the air infiltration from the outside. # See CERN-OPEN-2021-004, p. 12. residual_vent: float = self.data_registry.ventilation['infiltration_ventilation'] # type: ignore - infiltration_ventilation = models.AirChange(active=always_on, air_exch=residual_vent) + infiltration_ventilation = models.AirChange( + active=always_on, air_exch=residual_vent) if self.hepa_option: - hepa = models.HEPAFilter(active=always_on, q_air_mech=self.hepa_amount) + hepa = models.HEPAFilter( + active=always_on, q_air_mech=self.hepa_amount) return models.MultipleVentilation((ventilation, hepa, infiltration_ventilation)) else: return models.MultipleVentilation((ventilation, infiltration_ventilation)) - def nearest_weather_station(self) -> caimira.data.weather.WxStationRecordType: + def nearest_weather_station(self) -> data.weather.WxStationRecordType: """Return the nearest weather station (which has valid data) for this form""" - return caimira.data.weather.nearest_wx_station( + return data.weather.nearest_wx_station( longitude=self.location_longitude, latitude=self.location_latitude ) @@ -405,11 +434,13 @@ def mask(self) -> models.Mask: return mask def generate_precise_activity_expiration(self) -> typing.Tuple[typing.Any, ...]: - if self.precise_activity == {}: # It means the precise activity is not defined by a specific input. + # It means the precise activity is not defined by a specific input. + if self.precise_activity == {}: return () respiratory_dict = {} for respiratory_activity in self.precise_activity['respiratory_activity']: - respiratory_dict[respiratory_activity['type']] = respiratory_activity['percentage'] + respiratory_dict[respiratory_activity['type'] + ] = respiratory_activity['percentage'] return (self.precise_activity['physical_activity'], respiratory_dict) @@ -417,11 +448,14 @@ def infected_population(self) -> mc.InfectedPopulation: # Initializes the virus virus = virus_distributions(self.data_registry)[self.virus_type] - activity_defn = self.data_registry.population_scenario_activity[self.activity_type]['activity'] - expiration_defn = self.data_registry.population_scenario_activity[self.activity_type]['expiration'] + activity_defn = self.data_registry.population_scenario_activity[ + self.activity_type]['activity'] + expiration_defn = self.data_registry.population_scenario_activity[ + self.activity_type]['expiration'] if (self.activity_type == 'smallmeeting'): # Conversation of N people is approximately 1/N% of the time speaking. - expiration_defn = {'Speaking': 1, 'Breathing': self.total_people - 1} + expiration_defn = {'Speaking': 1, + 'Breathing': self.total_people - 1} elif (self.activity_type == 'precise'): activity_defn, expiration_defn = self.generate_precise_activity_expiration() @@ -438,7 +472,8 @@ def infected_population(self) -> mc.InfectedPopulation: mask=self.mask(), activity=activity, expiration=expiration, - host_immunity=0., # Vaccination status does not affect the infected population (for now) + # Vaccination status does not affect the infected population (for now) + host_immunity=0., ) return infected @@ -456,8 +491,8 @@ def exposed_population(self) -> mc.Population: if (self.vaccine_option): if (self.vaccine_booster_option and self.vaccine_booster_type != 'Other'): host_immunity = [vaccine['VE'] for vaccine in data.vaccine_booster_host_immunity if - vaccine['primary series vaccine'] == self.vaccine_type and - vaccine['booster vaccine'] == self.vaccine_booster_type][0] + vaccine['primary series vaccine'] == self.vaccine_type and + vaccine['booster vaccine'] == self.vaccine_booster_type][0] else: host_immunity = data.vaccine_primary_host_immunity[self.vaccine_type] else: @@ -484,9 +519,10 @@ def build_expiration(data_registry, expiration_definition) -> mc._ExpirationBase elif isinstance(expiration_definition, dict): total_weight = sum(expiration_definition.values()) BLO_factors = np.sum([ - np.array(expiration_BLO_factors(data_registry)[exp_type]) * weight/total_weight + np.array(expiration_BLO_factors(data_registry) + [exp_type]) * weight/total_weight for exp_type, weight in expiration_definition.items() - ], axis=0) + ], axis=0) return expiration_distribution(data_registry=data_registry, BLO_factors=tuple(BLO_factors)) @@ -529,7 +565,7 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]: 'mask_type': 'Type I', 'mask_wearing_option': 'mask_off', 'mechanical_ventilation_type': '', - 'calculator_version': calculator.__version__, + 'calculator_version': '4.17.0', #TODO different version for API and calculator form? 'opening_distance': '0.2', 'event_month': 'January', 'room_heating_option': '0', @@ -555,4 +591,5 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]: 'short_range_interactions': '[]', } + cast_class_fields(VirusFormData) diff --git a/caimira/core_requirements.txt b/caimira/core_requirements.txt new file mode 100644 index 00000000..e69de29b diff --git a/caimira/dev_requirements.txt b/caimira/dev_requirements.txt new file mode 100644 index 00000000..e69de29b diff --git a/caimira/pyproject.toml b/caimira/pyproject.toml new file mode 100644 index 00000000..1b68d94e --- /dev/null +++ b/caimira/pyproject.toml @@ -0,0 +1,3 @@ +[build-system] +requires = ["setuptools>=42", "wheel"] +build-backend = "setuptools.build_meta" \ No newline at end of file diff --git a/caimira/setup.cfg b/caimira/setup.cfg new file mode 100644 index 00000000..5d55bc97 --- /dev/null +++ b/caimira/setup.cfg @@ -0,0 +1,2 @@ +[tool:pytest] +addopts = --mypy diff --git a/caimira/tests/apps/calculator/test_report_json.py b/caimira/tests/apps/calculator/test_report_json.py deleted file mode 100644 index 95cb60a1..00000000 --- a/caimira/tests/apps/calculator/test_report_json.py +++ /dev/null @@ -1,32 +0,0 @@ -import json - -import tornado.testing - -import caimira.apps.calculator -from caimira.apps.calculator import model_generator - -_TIMEOUT = 40. - - -class TestCalculatorJsonResponse(tornado.testing.AsyncHTTPTestCase): - def setUp(self): - super().setUp() - self.http_client.defaults['request_timeout'] = _TIMEOUT - - def get_app(self): - return caimira.apps.calculator.make_app() - - @tornado.testing.gen_test(timeout=_TIMEOUT) - def test_json_response(self): - response = yield self.http_client.fetch( - request=self.get_url("/calculator/report-json"), - method="POST", - headers={'content-type': 'application/json'}, - body=json.dumps(model_generator.baseline_raw_form_data()) - ) - self.assertEqual(response.code, 200) - - data = json.loads(response.body) - self.assertIsInstance(data['prob_inf'], float) - self.assertIsInstance(data['expected_new_cases'], float) - diff --git a/caimira/tests/models/test_virus.py b/caimira/tests/models/test_virus.py deleted file mode 100644 index 060ae6af..00000000 --- a/caimira/tests/models/test_virus.py +++ /dev/null @@ -1,25 +0,0 @@ -import numpy as np -import numpy.testing as npt -import pytest - -from caimira import models - - -@pytest.mark.parametrize( - "inside_temp, humidity, expected_halflife, expected_decay_constant", - [ - [293.15, 0.5, 0.5947447349860315, 1.1654532436949188], - [272.15, 0.7, 1.6070844193207476, 0.4313072619127947], - [300.15, 1., 0.17367078830147223, 3.9911558376571805], - [300.15, 0., 6.43, 0.10779893943389507], - [np.array([272.15, 300.15]), np.array([0.7, 0.]), - np.array([1.60708442, 6.43]), np.array([0.43130726, 0.10779894])], - [np.array([293.15, 300.15]), np.array([0.5, 1.]), - np.array([0.59474473, 0.17367079]), np.array([1.16545324, 3.99115584])] - ], -) -def test_decay_constant(inside_temp, humidity, expected_halflife, expected_decay_constant): - npt.assert_almost_equal(models.Virus.types['SARS_CoV_2'].halflife(humidity, inside_temp), - expected_halflife) - npt.assert_almost_equal(models.Virus.types['SARS_CoV_2'].decay_constant(humidity, inside_temp), - expected_decay_constant) \ No newline at end of file diff --git a/caimira/tests/test_caimira.py b/caimira/tests/test_caimira.py deleted file mode 100644 index c99882be..00000000 --- a/caimira/tests/test_caimira.py +++ /dev/null @@ -1,10 +0,0 @@ -""" -High-level tests for the package. - -""" - -import caimira - - -def test_version(): - assert caimira.__version__ is not None diff --git a/caimira/tests/test_monte_carlo.py b/caimira/tests/test_monte_carlo.py deleted file mode 100644 index 656450ea..00000000 --- a/caimira/tests/test_monte_carlo.py +++ /dev/null @@ -1,102 +0,0 @@ -import dataclasses - -import numpy as np -import pytest - -import caimira.models -import caimira.monte_carlo.models as mc_models -import caimira.monte_carlo.sampleable - -MODEL_CLASSES = [ - cls for cls in vars(caimira.models).values() - if dataclasses.is_dataclass(cls) -] - - -def test_type_annotations(): - # Check that there are appropriate type annotations for all of the model - # classes in caimira.models. Note that these must be statically defined in - # caimira.monte_carlo, rather than being dynamically generated, in order to - # allow the type system to be able to see their definition without needing - # runtime execution. - missing = [] - for cls in MODEL_CLASSES: - if not hasattr(caimira.monte_carlo, cls.__name__): - missing.append(cls.__name__) - continue - mc_cls = getattr(caimira.monte_carlo, cls.__name__) - assert issubclass(mc_cls, caimira.monte_carlo.MCModelBase) - - if missing: - msg = ( - 'There are missing model implementations in caimira.monte_carlo. ' - 'The following definitions are needed:\n ' + - '\n '.join([f'{model} = build_mc_model(caimira.models.{model})' for model in missing]) - ) - pytest.fail(msg) - - -@pytest.fixture -def baseline_mc_concentration_model(data_registry) -> caimira.monte_carlo.ConcentrationModel: - mc_model = caimira.monte_carlo.ConcentrationModel( - data_registry=data_registry, - room=caimira.monte_carlo.Room(volume=caimira.monte_carlo.sampleable.Normal(75, 20), - inside_temp=caimira.models.PiecewiseConstant((0., 24.), (293,))), - ventilation=caimira.monte_carlo.SlidingWindow( - data_registry=data_registry, - active=caimira.models.PeriodicInterval(period=120, duration=120), - outside_temp=caimira.models.PiecewiseConstant((0., 24.), (283,)), - window_height=1.6, opening_length=0.6, - ), - infected=caimira.models.InfectedPopulation( - data_registry=data_registry, - number=1, - virus=caimira.models.Virus.types['SARS_CoV_2'], - presence=caimira.models.SpecificInterval(((0., 4.), (5., 8.))), - mask=caimira.models.Mask.types['No mask'], - activity=caimira.models.Activity.types['Light activity'], - expiration=caimira.models.Expiration.types['Breathing'], - host_immunity=0., - ), - evaporation_factor=0.3, - ) - return mc_model - - -@pytest.fixture -def baseline_mc_sr_model() -> caimira.monte_carlo.ShortRangeModel: - return () - - -@pytest.fixture -def baseline_mc_exposure_model(data_registry, baseline_mc_concentration_model, baseline_mc_sr_model) -> caimira.monte_carlo.ExposureModel: - return caimira.monte_carlo.ExposureModel( - data_registry, - baseline_mc_concentration_model, - baseline_mc_sr_model, - exposed=caimira.models.Population( - number=10, - presence=baseline_mc_concentration_model.infected.presence, - activity=baseline_mc_concentration_model.infected.activity, - mask=baseline_mc_concentration_model.infected.mask, - host_immunity=0., - ), - geographical_data=caimira.models.Cases(), - ) - - -def test_build_concentration_model(baseline_mc_concentration_model: caimira.monte_carlo.ConcentrationModel): - model = baseline_mc_concentration_model.build_model(7) - assert isinstance(model, caimira.models.ConcentrationModel) - assert isinstance(model.concentration(time=0.), float) - conc = model.concentration(time=1.) - assert isinstance(conc, np.ndarray) - assert conc.shape == (7, ) - - -def test_build_exposure_model(baseline_mc_exposure_model: caimira.monte_carlo.ExposureModel): - model = baseline_mc_exposure_model.build_model(7) - assert isinstance(model, caimira.models.ExposureModel) - prob = model.deposited_exposure() - assert isinstance(prob, np.ndarray) - assert prob.shape == (7, ) diff --git a/ui/__init__.py b/ui/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/ui/apps/__.init__.py b/ui/apps/__.init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/apps/calculator/__init__.py b/ui/apps/calculator/__init__.py similarity index 93% rename from caimira/apps/calculator/__init__.py rename to ui/apps/calculator/__init__.py index 98f75762..b16b7c7a 100644 --- a/caimira/apps/calculator/__init__.py +++ b/ui/apps/calculator/__init__.py @@ -25,14 +25,17 @@ from tornado.web import Application, RequestHandler, StaticFileHandler from tornado.httpclient import AsyncHTTPClient, HTTPRequest import tornado.log -from caimira.profiler import CaimiraProfiler, Profilers -from caimira.store.data_registry import DataRegistry +from caimira.calculator.models.profiler import CaimiraProfiler, Profilers +from caimira.calculator.store.data_registry import DataRegistry +from caimira.calculator.store.data_service import DataService -from caimira.store.data_service import DataService +from caimira.api.controller.report_controller import generate_form_obj, generate_model, generate_report_results +from caimira.calculator.report.report_generator import calculate_report_data +from caimira.calculator.validators.virus import virus_validator +from caimira.calculator.validators.co2 import co2_validator +from .report import ReportGenerator from . import markdown_tools -from . import model_generator, co2_model_generator -from .report_generator import ReportGenerator, calculate_report_data from .user import AuthenticatedUser, AnonymousUser # The calculator version is based on a combination of the model version and the @@ -42,7 +45,7 @@ # 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 CAiMIRA version (found at ``caimira.__version__``). -__version__ = "4.16.1" +__version__ = "4.17.0" LOG = logging.getLogger("Calculator") @@ -177,27 +180,27 @@ async def post(self) -> None: LOG.debug(pformat(requested_model_config)) try: - form = model_generator.VirusFormData.from_dict(requested_model_config, data_registry) + form = generate_form_obj(requested_model_config, data_registry) + model = generate_model(form) + report_data = generate_report_results(form, model) + except Exception as err: LOG.exception(err) response_json = {'code': 400, 'error': f'Your request was invalid {html.escape(str(err))}'} self.set_status(400) self.finish(json.dumps(response_json)) return - + base_url = self.request.protocol + "://" + self.request.host report_generator: ReportGenerator = self.settings['report_generator'] executor = loky.get_reusable_executor( max_workers=self.settings['handler_worker_pool_size'], timeout=300, ) - # Re-generate the report with the conditional probability of infection plot - if self.get_cookie('conditional_plot'): - form.conditional_probability_plot = True if self.get_cookie('conditional_plot') == '1' else False - self.clear_cookie('conditional_plot') # Clears cookie after changing the form value. report_task = executor.submit( report_generator.build_report, base_url, form, + model, report_data, executor_factory=functools.partial( concurrent.futures.ThreadPoolExecutor, self.settings['report_generation_parallelism'], @@ -231,7 +234,7 @@ async def post(self) -> None: LOG.debug(pformat(requested_model_config)) try: - form = model_generator.VirusFormData.from_dict(requested_model_config, data_registry) + form = generate_form_obj(requested_model_config, data_registry) except Exception as err: LOG.exception(err) response_json = {'code': 400, 'error': f'Your request was invalid {html.escape(str(err))}'} @@ -243,7 +246,7 @@ async def post(self) -> None: max_workers=self.settings['handler_worker_pool_size'], timeout=300, ) - model = form.build_model() + model = generate_model(form) report_data_task = executor.submit(calculate_report_data, form, model, executor_factory=functools.partial( concurrent.futures.ThreadPoolExecutor, @@ -262,14 +265,17 @@ async def get(self) -> None: if data_service: data_service.update_registry(data_registry) - form = model_generator.VirusFormData.from_dict(model_generator.baseline_raw_form_data(), data_registry) + form = generate_form_obj(virus_validator.baseline_raw_form_data(), data_registry) + model = generate_model(form) + report_data = generate_report_results(form, model) + base_url = self.request.protocol + "://" + self.request.host report_generator: ReportGenerator = self.settings['report_generator'] executor = loky.get_reusable_executor(max_workers=self.settings['handler_worker_pool_size']) report_task = executor.submit( report_generator.build_report, base_url, form, - executor_factory=functools.partial( + model, report_data, executor_factory=functools.partial( concurrent.futures.ThreadPoolExecutor, self.settings['report_generation_parallelism'], ), @@ -442,7 +448,7 @@ async def post(self, endpoint: str) -> None: requested_model_config = tornado.escape.json_decode(self.request.body) try: - form = co2_model_generator.CO2FormData.from_dict(requested_model_config, data_registry) + form = co2_validator.CO2FormData.from_dict(requested_model_config, data_registry) except Exception as err: if self.settings.get("debug", False): import traceback @@ -453,8 +459,8 @@ async def post(self, endpoint: str) -> None: return if endpoint.rstrip('/') == 'plot': - transition_times = co2_model_generator.CO2FormData.find_change_points_with_pelt(form.CO2_data) - self.finish({'CO2_plot': co2_model_generator.CO2FormData.generate_ventilation_plot(form.CO2_data, transition_times), + transition_times = co2_validator.CO2FormData.find_change_points_with_pelt(form.CO2_data) + self.finish({'CO2_plot': co2_validator.CO2FormData.generate_ventilation_plot(form.CO2_data, transition_times), 'transition_times': [round(el, 2) for el in transition_times]}) else: executor = loky.get_reusable_executor( @@ -462,7 +468,7 @@ async def post(self, endpoint: str) -> None: timeout=300, ) report_task = executor.submit( - co2_model_generator.CO2FormData.build_model, form, + co2_validator.CO2FormData.build_model, form, ) report = await asyncio.wrap_future(report_task) @@ -471,7 +477,7 @@ async def post(self, endpoint: str) -> None: result['fitting_ventilation_type'] = form.fitting_ventilation_type result['transition_times'] = ventilation_transition_times - result['CO2_plot'] = co2_model_generator.CO2FormData.generate_ventilation_plot(CO2_data=form.CO2_data, + result['CO2_plot'] = co2_validator.CO2FormData.generate_ventilation_plot(CO2_data=form.CO2_data, transition_times=ventilation_transition_times[:-1], predictive_CO2=result['predictive_CO2']) self.finish(result) diff --git a/caimira/apps/calculator/__main__.py b/ui/apps/calculator/__main__.py similarity index 100% rename from caimira/apps/calculator/__main__.py rename to ui/apps/calculator/__main__.py diff --git a/caimira/apps/calculator/markdown_tools.py b/ui/apps/calculator/markdown_tools.py similarity index 100% rename from caimira/apps/calculator/markdown_tools.py rename to ui/apps/calculator/markdown_tools.py diff --git a/ui/apps/calculator/report.py b/ui/apps/calculator/report.py new file mode 100644 index 00000000..428f7fdb --- /dev/null +++ b/ui/apps/calculator/report.py @@ -0,0 +1,379 @@ +from datetime import datetime +import dataclasses + +import concurrent.futures +import json +import typing +import jinja2 +import numpy as np +import urllib +import base64 +import zlib + +from . import markdown_tools + +from caimira.calculator.validators.virus.virus_validator import VirusFormData +from caimira.calculator.models import dataclass_utils, models, monte_carlo as mc + + +def generate_permalink(base_url, get_root_url, get_root_calculator_url, form: VirusFormData): + form_dict = VirusFormData.to_dict(form, strip_defaults=True) + + # Generate the calculator URL arguments that would be needed to re-create this + # form. + args = urllib.parse.urlencode(form_dict) + + # Then zlib compress + base64 encode the string. To be inverted by the + # /_c/ endpoint. + compressed_args = base64.b64encode(zlib.compress(args.encode())).decode() + qr_url = f"{base_url}{get_root_url()}/_c/{compressed_args}" + url = f"{base_url}{get_root_calculator_url()}?{args}" + + return { + 'link': url, + 'shortened': qr_url, + } + + +def model_start_end(model: models.ExposureModel): + t_start = min(model.exposed.presence_interval().boundaries()[0][0], + model.concentration_model.infected.presence_interval().boundaries()[0][0]) + t_end = max(model.exposed.presence_interval().boundaries()[-1][1], + model.concentration_model.infected.presence_interval().boundaries()[-1][1]) + return t_start, t_end + + +def fill_big_gaps(array, gap_size): + """ + Insert values into the given sorted list if there is a gap of more than ``gap_size``. + All values in the given array are preserved, even if they are within the ``gap_size`` of one another. + + >>> fill_big_gaps([1, 2, 4], gap_size=0.75) + [1, 1.75, 2, 2.75, 3.5, 4] + + """ + result = [] + if len(array) == 0: + raise ValueError("Input array must be len > 0") + + last_value = array[0] + for value in array: + while value - last_value > gap_size + 1e-15: + last_value = last_value + gap_size + result.append(last_value) + result.append(value) + last_value = value + return result + + +def non_temp_transition_times(model: models.ExposureModel): + """ + Return the non-temperature (and PiecewiseConstant) based transition times. + + """ + def walk_model(model, name=""): + # Extend walk_dataclass to handle lists of dataclasses + # (e.g. in MultipleVentilation). + for name, obj in dataclass_utils.walk_dataclass(model, name=name): + if name.endswith('.ventilations') and isinstance(obj, (list, tuple)): + for i, item in enumerate(obj): + fq_name_i = f'{name}[{i}]' + yield fq_name_i, item + if dataclasses.is_dataclass(item): + yield from dataclass_utils.walk_dataclass(item, name=fq_name_i) + else: + yield name, obj + + t_start, t_end = model_start_end(model) + + change_times = {t_start, t_end} + for name, obj in walk_model(model, name="exposure"): + if isinstance(obj, models.Interval): + change_times |= obj.transition_times() + + # Only choose times that are in the range of the model (removes things + # such as PeriodicIntervals, which extend beyond the model itself). + return sorted(time for time in change_times if (t_start <= time <= t_end)) + + +def interesting_times(model: models.ExposureModel, approx_n_pts: typing.Optional[int] = None) -> typing.List[float]: + """ + Pick approximately ``approx_n_pts`` time points which are interesting for the + given model. If not provided by argument, ``approx_n_pts`` is set to be 15 times + the number of hours of the simulation. + + Initially the times are seeded by important state change times (excluding + outside temperature), and the times are then subsequently expanded to ensure + that the step size is at most ``(t_end - t_start) / approx_n_pts``. + + """ + times = non_temp_transition_times(model) + sim_duration = max(times) - min(times) + if not approx_n_pts: + approx_n_pts = sim_duration * 15 + + # Expand the times list to ensure that we have a maximum gap size between + # the key times. + nice_times = fill_big_gaps(times, gap_size=(sim_duration) / approx_n_pts) + return nice_times + + +def manufacture_viral_load_scenarios_percentiles(model: mc.ExposureModel) -> typing.Dict[str, mc.ExposureModel]: + viral_load = model.concentration_model.infected.virus.viral_load_in_sputum + scenarios = {} + for percentil in (0.01, 0.05, 0.25, 0.5, 0.75, 0.95, 0.99): + vl = np.quantile(viral_load, percentil) + specific_vl_scenario = dataclass_utils.nested_replace(model, + {'concentration_model.infected.virus.viral_load_in_sputum': vl} + ) + scenarios[str(vl)] = np.mean( + specific_vl_scenario.infection_probability()) + return scenarios + +def manufacture_alternative_scenarios(form: VirusFormData) -> typing.Dict[str, mc.ExposureModel]: + scenarios = {} + if (form.short_range_option == "short_range_no"): + # Two special option cases - HEPA and/or FFP2 masks. + FFP2_being_worn = bool(form.mask_wearing_option == + 'mask_on' and form.mask_type == 'FFP2') + if FFP2_being_worn and form.hepa_option: + FFP2andHEPAalternative = dataclass_utils.replace( + form, mask_type='Type I') + if not (form.hepa_option and form.mask_wearing_option == 'mask_on' and form.mask_type == 'Type I'): + scenarios['Base scenario with HEPA filter and Type I masks'] = FFP2andHEPAalternative.build_mc_model() + if not FFP2_being_worn and form.hepa_option: + noHEPAalternative = dataclass_utils.replace(form, mask_type='FFP2') + noHEPAalternative = dataclass_utils.replace( + noHEPAalternative, mask_wearing_option='mask_on') + noHEPAalternative = dataclass_utils.replace( + noHEPAalternative, hepa_option=False) + if not (not form.hepa_option and FFP2_being_worn): + scenarios['Base scenario without HEPA filter, with FFP2 masks'] = noHEPAalternative.build_mc_model() + + # The remaining scenarios are based on Type I masks (possibly not worn) + # and no HEPA filtration. + form = dataclass_utils.replace(form, mask_type='Type I') + if form.hepa_option: + form = dataclass_utils.replace(form, hepa_option=False) + + with_mask = dataclass_utils.replace( + form, mask_wearing_option='mask_on') + without_mask = dataclass_utils.replace( + form, mask_wearing_option='mask_off') + + if form.ventilation_type == 'mechanical_ventilation': + # scenarios['Mechanical ventilation with Type I masks'] = with_mask.build_mc_model() + if not (form.mask_wearing_option == 'mask_off'): + scenarios['Mechanical ventilation without masks'] = without_mask.build_mc_model( + ) + + elif form.ventilation_type == 'natural_ventilation': + # scenarios['Windows open with Type I masks'] = with_mask.build_mc_model() + if not (form.mask_wearing_option == 'mask_off'): + scenarios['Windows open without masks'] = without_mask.build_mc_model() + + # No matter the ventilation scheme, we include scenarios which don't have any ventilation. + with_mask_no_vent = dataclass_utils.replace( + with_mask, ventilation_type='no_ventilation') + without_mask_or_vent = dataclass_utils.replace( + without_mask, ventilation_type='no_ventilation') + + if not (form.mask_wearing_option == 'mask_on' and form.mask_type == 'Type I' and form.ventilation_type == 'no_ventilation'): + scenarios['No ventilation with Type I masks'] = with_mask_no_vent.build_mc_model() + if not (form.mask_wearing_option == 'mask_off' and form.ventilation_type == 'no_ventilation'): + scenarios['Neither ventilation nor masks'] = without_mask_or_vent.build_mc_model() + + else: + no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[], + total_people=form.total_people - form.short_range_occupants) + scenarios['Base scenario without short-range interactions'] = no_short_range_alternative.build_mc_model() + + return scenarios + + +def scenario_statistics( + mc_model: mc.ExposureModel, + sample_times: typing.List[float], + compute_prob_exposure: bool +): + model = mc_model.build_model( + size=mc_model.data_registry.monte_carlo['sample_size']) + if (compute_prob_exposure): + # It means we have data to calculate the total_probability_rule + prob_probabilistic_exposure = model.total_probability_rule() + else: + prob_probabilistic_exposure = 0. + + return { + 'probability_of_infection': np.mean(model.infection_probability()), + 'expected_new_cases': np.mean(model.expected_new_cases()), + 'concentrations': [ + np.mean(model.concentration(time)) + for time in sample_times + ], + 'prob_probabilistic_exposure': prob_probabilistic_exposure, + } + + +def comparison_report( + form: VirusFormData, + report_data: typing.Dict[str, typing.Any], + scenarios: typing.Dict[str, mc.ExposureModel], + sample_times: typing.List[float], + executor_factory: typing.Callable[[], concurrent.futures.Executor], +): + if (form.short_range_option == "short_range_no"): + statistics = { + 'Current scenario': { + 'probability_of_infection': report_data['prob_inf'], + 'expected_new_cases': report_data['expected_new_cases'], + 'concentrations': report_data['concentrations'], + } + } + else: + statistics = {} + + if (form.short_range_option == "short_range_yes" and form.exposure_option == "p_probabilistic_exposure"): + compute_prob_exposure = True + else: + compute_prob_exposure = False + + with executor_factory() as executor: + results = executor.map( + scenario_statistics, + scenarios.values(), + [sample_times] * len(scenarios), + [compute_prob_exposure] * len(scenarios), + timeout=60, + ) + + for (name, model), model_stats in zip(scenarios.items(), results): + statistics[name] = model_stats + + return { + 'stats': statistics, + } + + +def minutes_to_time(minutes: int) -> str: + minute_string = str(minutes % 60) + minute_string = "0" * (2 - len(minute_string)) + minute_string + hour_string = str(minutes // 60) + hour_string = "0" * (2 - len(hour_string)) + hour_string + + return f"{hour_string}:{minute_string}" + + +def readable_minutes(minutes: int) -> str: + time = float(minutes) + unit = " minute" + if time % 60 == 0: + time = minutes/60 + unit = " hour" + if time != 1: + unit += "s" + + if time.is_integer(): + time_str = "{:0.0f}".format(time) + else: + time_str = "{0:.2f}".format(time) + + return time_str + unit + + +def hour_format(hour: float) -> str: + # Convert float hour to HH:MM format + hours = int(hour) + minutes = int(hour % 1 * 60) + return f"{hours}:{minutes if minutes != 0 else '00'}" + + +def percentage(absolute: float) -> float: + return absolute * 100 + + +def non_zero_percentage(percentage: int) -> str: + if percentage < 0.01: + return "<0.01%" + elif percentage < 1: + return "{:0.2f}%".format(percentage) + elif percentage > 99.9 or np.isnan(percentage): + return ">99.9%" + else: + return "{:0.1f}%".format(percentage) + + +@dataclasses.dataclass +class ReportGenerator: + jinja_loader: jinja2.BaseLoader + get_root_url: typing.Any + get_root_calculator_url: typing.Any + + def build_report( + self, + base_url: str, + form: VirusFormData, + model: models.ExposureModel, + report_data: dict, + executor_factory: typing.Callable[[], concurrent.futures.Executor], + ) -> str: + context = self.prepare_context( + base_url, form, model, report_data, executor_factory=executor_factory) + return self.render(context) + + def prepare_context( + self, + base_url: str, + form: VirusFormData, + model: models.ExposureModel, + report_data: dict, + executor_factory: typing.Callable[[], concurrent.futures.Executor], + ) -> dict: + now = datetime.utcnow().astimezone() + time = now.strftime("%Y-%m-%d %H:%M:%S UTC") + + data_registry_version = f"v{model.data_registry.version}" if model.data_registry.version else None + context = { + 'model': model, + 'form': form, + 'creation_date': time, + 'data_registry_version': data_registry_version, + } + + scenario_sample_times = interesting_times(model) + context.update(report_data) + + alternative_scenarios = manufacture_alternative_scenarios(form) + context['alternative_viral_load'] = manufacture_viral_load_scenarios_percentiles( + model) if form.conditional_probability_viral_loads else None + context['alternative_scenarios'] = comparison_report( + form, report_data, alternative_scenarios, scenario_sample_times, executor_factory=executor_factory, + ) + context['permalink'] = generate_permalink( + base_url, self.get_root_url, self.get_root_calculator_url, form) + context['get_url'] = self.get_root_url + context['get_calculator_url'] = self.get_root_calculator_url + + return context + + def _template_environment(self) -> jinja2.Environment: + env = jinja2.Environment( + loader=self.jinja_loader, + undefined=jinja2.StrictUndefined, + ) + env.globals["common_text"] = markdown_tools.extract_rendered_markdown_blocks( + env.get_template('common_text.md.j2') + ) + env.filters['non_zero_percentage'] = non_zero_percentage + env.filters['readable_minutes'] = readable_minutes + env.filters['minutes_to_time'] = minutes_to_time + env.filters['hour_format'] = hour_format + env.filters['float_format'] = "{0:.2f}".format + env.filters['int_format'] = "{:0.0f}".format + env.filters['percentage'] = percentage + env.filters['JSONify'] = json.dumps + return env + + def render(self, context: dict) -> str: + template = self._template_environment().get_template("calculator.report.html.j2") + return template.render(**context, text_blocks=template.globals["common_text"]) diff --git a/caimira/apps/calculator/static/css/form.css b/ui/apps/calculator/static/css/form.css similarity index 100% rename from caimira/apps/calculator/static/css/form.css rename to ui/apps/calculator/static/css/form.css diff --git a/caimira/apps/calculator/static/css/report.css b/ui/apps/calculator/static/css/report.css similarity index 100% rename from caimira/apps/calculator/static/css/report.css rename to ui/apps/calculator/static/css/report.css diff --git a/caimira/apps/calculator/static/icons/favicon.ico b/ui/apps/calculator/static/icons/favicon.ico similarity index 100% rename from caimira/apps/calculator/static/icons/favicon.ico rename to ui/apps/calculator/static/icons/favicon.ico diff --git a/caimira/apps/calculator/static/images/disclaimer.jpg b/ui/apps/calculator/static/images/disclaimer.jpg similarity index 100% rename from caimira/apps/calculator/static/images/disclaimer.jpg rename to ui/apps/calculator/static/images/disclaimer.jpg diff --git a/caimira/apps/calculator/static/images/warning_scale/green-1.png b/ui/apps/calculator/static/images/warning_scale/green-1.png similarity index 100% rename from caimira/apps/calculator/static/images/warning_scale/green-1.png rename to ui/apps/calculator/static/images/warning_scale/green-1.png diff --git a/caimira/apps/calculator/static/images/warning_scale/orange-3.png b/ui/apps/calculator/static/images/warning_scale/orange-3.png similarity index 100% rename from caimira/apps/calculator/static/images/warning_scale/orange-3.png rename to ui/apps/calculator/static/images/warning_scale/orange-3.png diff --git a/caimira/apps/calculator/static/images/warning_scale/red-4.png b/ui/apps/calculator/static/images/warning_scale/red-4.png similarity index 100% rename from caimira/apps/calculator/static/images/warning_scale/red-4.png rename to ui/apps/calculator/static/images/warning_scale/red-4.png diff --git a/caimira/apps/calculator/static/images/warning_scale/yellow-2.png b/ui/apps/calculator/static/images/warning_scale/yellow-2.png similarity index 100% rename from caimira/apps/calculator/static/images/warning_scale/yellow-2.png rename to ui/apps/calculator/static/images/warning_scale/yellow-2.png diff --git a/caimira/apps/calculator/static/images/window_opening.png b/ui/apps/calculator/static/images/window_opening.png similarity index 100% rename from caimira/apps/calculator/static/images/window_opening.png rename to ui/apps/calculator/static/images/window_opening.png diff --git a/caimira/apps/calculator/static/images/window_type.PNG b/ui/apps/calculator/static/images/window_type.PNG similarity index 100% rename from caimira/apps/calculator/static/images/window_type.PNG rename to ui/apps/calculator/static/images/window_type.PNG diff --git a/caimira/apps/calculator/static/js/co2_form.js b/ui/apps/calculator/static/js/co2_form.js similarity index 100% rename from caimira/apps/calculator/static/js/co2_form.js rename to ui/apps/calculator/static/js/co2_form.js diff --git a/caimira/apps/calculator/static/js/form.js b/ui/apps/calculator/static/js/form.js similarity index 100% rename from caimira/apps/calculator/static/js/form.js rename to ui/apps/calculator/static/js/form.js diff --git a/caimira/apps/calculator/static/js/report.js b/ui/apps/calculator/static/js/report.js similarity index 100% rename from caimira/apps/calculator/static/js/report.js rename to ui/apps/calculator/static/js/report.js diff --git a/ui/apps/calculator/tests/__init__.py b/ui/apps/calculator/tests/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/ui/apps/calculator/tests/conftest.py b/ui/apps/calculator/tests/conftest.py new file mode 100644 index 00000000..a611f7bc --- /dev/null +++ b/ui/apps/calculator/tests/conftest.py @@ -0,0 +1,87 @@ +from caimira.calculator.models import models +import caimira.calculator.models.data +import caimira.calculator.models.dataclass_utils + +import pytest + +from caimira.calculator.validators.virus import virus_validator +from caimira.calculator.store.data_registry import DataRegistry + + +@pytest.fixture +def baseline_form_data(): + return virus_validator.baseline_raw_form_data() + + +@pytest.fixture +def baseline_form(baseline_form_data, data_registry): + return virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry) + + +@pytest.fixture +def data_registry(): + return DataRegistry() + + +@pytest.fixture +def baseline_concentration_model(data_registry): + model = models.ConcentrationModel( + data_registry=data_registry, + room=models.Room( + volume=75, inside_temp=models.PiecewiseConstant((0., 24.), (293,))), + ventilation=models.AirChange( + active=models.SpecificInterval(((0., 24.), )), + air_exch=30., + ), + infected=models.EmittingPopulation( + data_registry=data_registry, + 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'], + known_individual_emission_rate=970 * 50, + host_immunity=0., + # Superspreading event, where ejection factor is fixed based + # on Miller et al. (2020) - 50 represents the infectious dose. + ), + evaporation_factor=0.3, + ) + return model + + +@pytest.fixture +def baseline_sr_model(): + return () + + +@pytest.fixture +def baseline_exposure_model(data_registry, baseline_concentration_model, baseline_sr_model): + return models.ExposureModel( + data_registry=data_registry, + concentration_model=baseline_concentration_model, + short_range=baseline_sr_model, + exposed=models.Population( + number=1000, + presence=baseline_concentration_model.infected.presence, + activity=baseline_concentration_model.infected.activity, + mask=baseline_concentration_model.infected.mask, + host_immunity=0., + ), + geographical_data=models.Cases(), + ) + + +@pytest.fixture +def exposure_model_w_outside_temp_changes(data_registry, baseline_exposure_model: models.ExposureModel): + exp_model = caimira.calculator.models.dataclass_utils.nested_replace( + baseline_exposure_model, { + 'concentration_model.ventilation': models.SlidingWindow( + data_registry=data_registry, + active=models.PeriodicInterval(2.2 * 60, 1.8 * 60), + outside_temp=caimira.calculator.models.data.GenevaTemperatures['Jan'], + window_height=1.6, + opening_length=0.6, + ) + }) + return exp_model diff --git a/caimira/tests/apps/calculator/test_markdown_tools.py b/ui/apps/calculator/tests/test_markdown_tools.py similarity index 91% rename from caimira/tests/apps/calculator/test_markdown_tools.py rename to ui/apps/calculator/tests/test_markdown_tools.py index 9dfe0781..f05c1cfb 100644 --- a/caimira/tests/apps/calculator/test_markdown_tools.py +++ b/ui/apps/calculator/tests/test_markdown_tools.py @@ -3,7 +3,7 @@ import jinja2 import pytest -import caimira.apps.calculator.markdown_tools as md_tools +import ui.apps.calculator.markdown_tools as md_tools @pytest.fixture diff --git a/caimira/tests/apps/calculator/test_report_generator.py b/ui/apps/calculator/tests/test_report_generator.py similarity index 76% rename from caimira/tests/apps/calculator/test_report_generator.py rename to ui/apps/calculator/tests/test_report_generator.py index ba0295eb..ec4494b1 100644 --- a/caimira/tests/apps/calculator/test_report_generator.py +++ b/ui/apps/calculator/tests/test_report_generator.py @@ -6,11 +6,12 @@ import numpy as np import pytest -from caimira.apps.calculator import make_app +from ui.apps.calculator import make_app +from caimira.api.controller.report_controller import generate_model, generate_report_results from caimira.apps.calculator.model_generator import VirusFormData from caimira.apps.calculator.report_generator import (ReportGenerator, readable_minutes, calculate_report_data, manufacture_alternative_scenarios, interesting_times, comparison_report) -import caimira.apps.calculator.report_generator as rep_gen +import caimira.calculator.report.report_generator as rep_gen def test_generate_report(baseline_form) -> None: @@ -18,17 +19,24 @@ def test_generate_report(baseline_form) -> None: # generate a report for it. Because this is what happens in the caimira # calculator, we confirm that the generation happens within a reasonable # time threshold. - time_limit: float = float(os.environ.get("CAIMIRA_TESTS_CALCULATOR_TIMEOUT", 10.)) + time_limit: float = float(os.environ.get( + "CAIMIRA_TESTS_CALCULATOR_TIMEOUT", 10.)) start = time.perf_counter() generator: ReportGenerator = make_app().settings['report_generator'] - report = generator.build_report("", baseline_form, partial( + + model = generate_model(baseline_form) + report_data = generate_report_results(baseline_form, model) + + report = generator.build_report("", baseline_form, model, report_data, partial( concurrent.futures.ThreadPoolExecutor, 1, )) + end = time.perf_counter() total = end-start - print(f"Time limit: {time_limit} | Time taken: {end} - {start} = {total} < {time_limit}") + print( + f"Time limit: {time_limit} | Time taken: {end} - {start} = {total} < {time_limit}") assert report != "" assert end - start < time_limit @@ -54,8 +62,10 @@ def test_fill_big_gaps(): def test_fill_big_gaps__float_tolerance(): # Ensure that there is some float tolerance to the gap size check. - assert rep_gen.fill_big_gaps([0, 2 + 1e-15, 4], gap_size=2) == [0, 2 + 1e-15, 4] - assert rep_gen.fill_big_gaps([0, 2 + 1e-14, 4], gap_size=2) == [0, 2, 2 + 1e-14, 4] + assert rep_gen.fill_big_gaps( + [0, 2 + 1e-15, 4], gap_size=2) == [0, 2 + 1e-15, 4] + assert rep_gen.fill_big_gaps( + [0, 2 + 1e-14, 4], gap_size=2) == [0, 2, 2 + 1e-14, 4] def test_non_temp_transition_times(baseline_exposure_model): @@ -65,7 +75,8 @@ def test_non_temp_transition_times(baseline_exposure_model): def test_interesting_times_many(baseline_exposure_model): - result = rep_gen.interesting_times(baseline_exposure_model, approx_n_pts=100) + result = rep_gen.interesting_times( + baseline_exposure_model, approx_n_pts=100) assert 100 <= len(result) <= 120 assert np.abs(np.diff(result)).max() < 8.1/100. @@ -73,7 +84,8 @@ def test_interesting_times_many(baseline_exposure_model): def test_interesting_times_small(baseline_exposure_model): expected = [0.0, 0.8, 1.6, 2.4, 3.2, 4.0, 4.8, 5.0, 5.8, 6.6, 7.4, 8.0] # Ask for more data than there is in the transition times. - result = rep_gen.interesting_times(baseline_exposure_model, approx_n_pts=10) + result = rep_gen.interesting_times( + baseline_exposure_model, approx_n_pts=10) np.testing.assert_allclose(result, expected, atol=1e-04) @@ -81,12 +93,14 @@ def test_interesting_times_small(baseline_exposure_model): def test_interesting_times_w_temp(exposure_model_w_outside_temp_changes): # Ensure that the state change times are returned (minus the temperature changes) by # requesting n_points=1. - result = rep_gen.interesting_times(exposure_model_w_outside_temp_changes, approx_n_pts=1) + result = rep_gen.interesting_times( + exposure_model_w_outside_temp_changes, approx_n_pts=1) expected = [0., 1.8, 2.2, 4., 4.4, 5., 6.2, 6.6, 8.] np.testing.assert_allclose(result, expected) # Now request more than the state-change times. - result = rep_gen.interesting_times(exposure_model_w_outside_temp_changes, approx_n_pts=20) + result = rep_gen.interesting_times( + exposure_model_w_outside_temp_changes, approx_n_pts=20) expected = [ 0., 0.4, 0.8, 1.2, 1.6, 1.8, 2.2, 2.6, 3., 3.4, 3.8, 4., 4.4, 4.8, 5., 5.4, 5.8, 6.2, 6.6, 7., 7.4, 7.8, 8. @@ -115,3 +129,4 @@ def test_expected_new_cases(baseline_form_with_sr: VirusFormData): lr_expected_new_cases = alternative_statistics['stats']['Base scenario without short-range interactions']['expected_new_cases'] np.testing.assert_almost_equal(sr_lr_expected_new_cases, lr_expected_new_cases + sr_lr_prob_inf * baseline_form_with_sr.short_range_occupants, 2) + \ No newline at end of file diff --git a/caimira/tests/apps/calculator/test_webapp.py b/ui/apps/calculator/tests/test_webapp.py similarity index 83% rename from caimira/tests/apps/calculator/test_webapp.py rename to ui/apps/calculator/tests/test_webapp.py index a9fd52f3..ce78037e 100644 --- a/caimira/tests/apps/calculator/test_webapp.py +++ b/ui/apps/calculator/tests/test_webapp.py @@ -4,15 +4,15 @@ import pytest import tornado.testing -import caimira.apps.calculator -from caimira.apps.calculator.report_generator import generate_permalink +import ui.apps.calculator +from ui.apps.calculator.report import generate_permalink _TIMEOUT = float(os.environ.get("CAIMIRA_TESTS_CALCULATOR_TIMEOUT", 10.)) @pytest.fixture def app(): - return caimira.apps.calculator.make_app() + return ui.apps.calculator.make_app() async def test_homepage(http_server_client): @@ -36,7 +36,7 @@ async def test_404(http_server_client): class TestBasicApp(tornado.testing.AsyncHTTPTestCase): def get_app(self): - return caimira.apps.calculator.make_app() + return ui.app.make_app() @tornado.testing.gen_test(timeout=_TIMEOUT) def test_report(self): @@ -64,8 +64,8 @@ def end_time(resp): class TestCernApp(tornado.testing.AsyncHTTPTestCase): def get_app(self): - cern_theme = Path(caimira.apps.calculator.__file__).parent.parent / 'themes' / 'cern' - return caimira.apps.calculator.make_app(theme_dir=cern_theme) + cern_theme = Path(ui.app.__file__).parent.parent / 'themes' / 'cern' + return ui.app.make_app(theme_dir=cern_theme) @tornado.testing.gen_test(timeout=_TIMEOUT) def test_report(self): @@ -76,7 +76,7 @@ def test_report(self): class TestOpenApp(tornado.testing.AsyncHTTPTestCase): def get_app(self): - return caimira.apps.calculator.make_app(calculator_prefix="/mycalc") + return ui.app.make_app(calculator_prefix="/mycalc") @tornado.testing.gen_test(timeout=_TIMEOUT) def test_report(self): @@ -121,10 +121,10 @@ async def test_invalid_compressed_url(http_server_client, baseline_form): class TestError500(tornado.testing.AsyncHTTPTestCase): def get_app(self): - class ProcessingErrorPage(caimira.apps.calculator.BaseRequestHandler): + class ProcessingErrorPage(ui.app.BaseRequestHandler): def get(self): raise ValueError('some unexpected error') - app = caimira.apps.calculator.make_app() + app = ui.app.make_app() page = [ (r'/', ProcessingErrorPage), ] @@ -138,11 +138,11 @@ def test_500(self): class TestCERNGenericPage(tornado.testing.AsyncHTTPTestCase): def get_app(self): - cern_theme = Path(caimira.apps.calculator.__file__).parent.parent / 'themes' / 'cern' - app = caimira.apps.calculator.make_app(theme_dir=cern_theme) + cern_theme = Path(ui.app.__file__).parent.parent / 'themes' / 'cern' + app = ui.app.make_app(theme_dir=cern_theme) pages = [ - (r'/calculator/user-guide', caimira.apps.calculator.GenericExtraPage, {'active_page': 'calculator/user-guide', 'filename': 'userguide.html.j2'}), - (r'/about', caimira.apps.calculator.GenericExtraPage, {'active_page': 'about', 'filename': 'about.html.j2'}), + (r'/calculator/user-guide', ui.app.GenericExtraPage, {'active_page': 'calculator/user-guide', 'filename': 'userguide.html.j2'}), + (r'/about', ui.app.GenericExtraPage, {'active_page': 'about', 'filename': 'about.html.j2'}), ] return tornado.web.Application(pages, **app.settings) diff --git a/caimira/apps/calculator/user.py b/ui/apps/calculator/user.py similarity index 100% rename from caimira/apps/calculator/user.py rename to ui/apps/calculator/user.py diff --git a/ui/apps/expert_apps/__init__.py b/ui/apps/expert_apps/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/caimira/apps/expert.py b/ui/apps/expert_apps/expert.py similarity index 99% rename from caimira/apps/expert.py rename to ui/apps/expert_apps/expert.py index 79c64c2b..d60e33e4 100644 --- a/caimira/apps/expert.py +++ b/ui/apps/expert_apps/expert.py @@ -14,8 +14,11 @@ import pandas as pd import logging -from caimira import data, models, state -from caimira.store.data_registry import DataRegistry +from . import state +from caimira.calculator.models import data, models +from caimira.calculator.store.data_registry import DataRegistry + +LOG = logging.getLogger(__name__) LOG = logging.getLogger(__name__) @@ -935,7 +938,7 @@ def __init__(self) -> None: LOG.warning( "ExpertApplication is currently deactivated and will no longer be maintained. It remains in the codebase for legacy purposes." ) - + self._data_registry = DataRegistry() #: A list of scenario name and ModelState instances. This is intended to be #: mutated. Any mutation should notify the appropriate Views for handling. diff --git a/caimira/apps/expert/caimira.ipynb b/ui/apps/expert_apps/expert/caimira.ipynb similarity index 100% rename from caimira/apps/expert/caimira.ipynb rename to ui/apps/expert_apps/expert/caimira.ipynb diff --git a/caimira/apps/expert/static/images/header_image.png b/ui/apps/expert_apps/expert/static/images/header_image.png similarity index 100% rename from caimira/apps/expert/static/images/header_image.png rename to ui/apps/expert_apps/expert/static/images/header_image.png diff --git a/caimira/apps/expert_co2.py b/ui/apps/expert_apps/expert_co2.py similarity index 99% rename from caimira/apps/expert_co2.py rename to ui/apps/expert_apps/expert_co2.py index 29964bf9..4a0a9ba5 100644 --- a/caimira/apps/expert_co2.py +++ b/ui/apps/expert_apps/expert_co2.py @@ -4,13 +4,17 @@ import numpy as np import logging -from caimira import data, models, state -from caimira.store.data_registry import DataRegistry +from . import state +from .expert import generate_presence_widget, collapsible, ipympl_canvas, WidgetGroup, CAIMIRAStateBuilder +from caimira.calculator.models import data, models +from caimira.calculator.store.data_registry import DataRegistry + import matplotlib import matplotlib.figure import matplotlib.lines as mlines import matplotlib.patches as patches -from .expert import generate_presence_widget, collapsible, ipympl_canvas, WidgetGroup, CAIMIRAStateBuilder + +LOG = logging.getLogger(__name__) LOG = logging.getLogger(__name__) @@ -194,7 +198,7 @@ def __init__(self) -> None: LOG.warning( "CO2Application is currently deactivated and will no longer be maintained. It remains in the codebase for legacy purposes." ) - + self._data_registry = DataRegistry() # self._debug_output = widgets.Output() diff --git a/caimira/apps/expert_co2/caimira.ipynb b/ui/apps/expert_apps/expert_co2/caimira.ipynb similarity index 100% rename from caimira/apps/expert_co2/caimira.ipynb rename to ui/apps/expert_apps/expert_co2/caimira.ipynb diff --git a/caimira/apps/expert_co2/static/images/header_image.png b/ui/apps/expert_apps/expert_co2/static/images/header_image.png similarity index 100% rename from caimira/apps/expert_co2/static/images/header_image.png rename to ui/apps/expert_apps/expert_co2/static/images/header_image.png diff --git a/caimira/state.py b/ui/apps/expert_apps/state.py similarity index 100% rename from caimira/state.py rename to ui/apps/expert_apps/state.py diff --git a/caimira/apps/static/css/style.css b/ui/apps/static/css/style.css similarity index 100% rename from caimira/apps/static/css/style.css rename to ui/apps/static/css/style.css diff --git a/caimira/apps/static/icons/calculator.svg b/ui/apps/static/icons/calculator.svg similarity index 100% rename from caimira/apps/static/icons/calculator.svg rename to ui/apps/static/icons/calculator.svg diff --git a/caimira/apps/static/icons/expert.svg b/ui/apps/static/icons/expert.svg similarity index 100% rename from caimira/apps/static/icons/expert.svg rename to ui/apps/static/icons/expert.svg diff --git a/caimira/apps/static/icons/favicon.ico b/ui/apps/static/icons/favicon.ico similarity index 100% rename from caimira/apps/static/icons/favicon.ico rename to ui/apps/static/icons/favicon.ico diff --git a/caimira/apps/static/images/CAiMIRA_1_Vs3_Colour.jpg b/ui/apps/static/images/CAiMIRA_1_Vs3_Colour.jpg similarity index 100% rename from caimira/apps/static/images/CAiMIRA_1_Vs3_Colour.jpg rename to ui/apps/static/images/CAiMIRA_1_Vs3_Colour.jpg diff --git a/caimira/apps/static/images/caimira_full_logo.png b/ui/apps/static/images/caimira_full_logo.png similarity index 100% rename from caimira/apps/static/images/caimira_full_logo.png rename to ui/apps/static/images/caimira_full_logo.png diff --git a/caimira/apps/static/images/caimira_full_text.png b/ui/apps/static/images/caimira_full_text.png similarity index 100% rename from caimira/apps/static/images/caimira_full_text.png rename to ui/apps/static/images/caimira_full_text.png diff --git a/caimira/apps/static/images/caimira_logo.200x200.png b/ui/apps/static/images/caimira_logo.200x200.png similarity index 100% rename from caimira/apps/static/images/caimira_logo.200x200.png rename to ui/apps/static/images/caimira_logo.200x200.png diff --git a/caimira/apps/static/images/caimira_logo_white_text.png b/ui/apps/static/images/caimira_logo_white_text.png similarity index 100% rename from caimira/apps/static/images/caimira_logo_white_text.png rename to ui/apps/static/images/caimira_logo_white_text.png diff --git a/caimira/apps/static/images/long_range_anim.png b/ui/apps/static/images/long_range_anim.png similarity index 100% rename from caimira/apps/static/images/long_range_anim.png rename to ui/apps/static/images/long_range_anim.png diff --git a/caimira/apps/static/images/masks/cloth.png b/ui/apps/static/images/masks/cloth.png similarity index 100% rename from caimira/apps/static/images/masks/cloth.png rename to ui/apps/static/images/masks/cloth.png diff --git a/caimira/apps/static/images/masks/ffp2.png b/ui/apps/static/images/masks/ffp2.png similarity index 100% rename from caimira/apps/static/images/masks/ffp2.png rename to ui/apps/static/images/masks/ffp2.png diff --git a/caimira/apps/static/images/masks/t1.png b/ui/apps/static/images/masks/t1.png similarity index 100% rename from caimira/apps/static/images/masks/t1.png rename to ui/apps/static/images/masks/t1.png diff --git a/caimira/apps/static/images/nat_vent_dimensions.png b/ui/apps/static/images/nat_vent_dimensions.png similarity index 100% rename from caimira/apps/static/images/nat_vent_dimensions.png rename to ui/apps/static/images/nat_vent_dimensions.png diff --git a/caimira/apps/static/images/short_range_anim.png b/ui/apps/static/images/short_range_anim.png similarity index 100% rename from caimira/apps/static/images/short_range_anim.png rename to ui/apps/static/images/short_range_anim.png diff --git a/caimira/apps/static/js/ScrollMagic.min.js b/ui/apps/static/js/ScrollMagic.min.js similarity index 100% rename from caimira/apps/static/js/ScrollMagic.min.js rename to ui/apps/static/js/ScrollMagic.min.js diff --git a/caimira/apps/static/js/jquery.colorbox-min.js b/ui/apps/static/js/jquery.colorbox-min.js similarity index 100% rename from caimira/apps/static/js/jquery.colorbox-min.js rename to ui/apps/static/js/jquery.colorbox-min.js diff --git a/caimira/apps/static/js/js_packaged_for_theme.js b/ui/apps/static/js/js_packaged_for_theme.js similarity index 100% rename from caimira/apps/static/js/js_packaged_for_theme.js rename to ui/apps/static/js/js_packaged_for_theme.js diff --git a/caimira/apps/static/js/usage-tracking.js b/ui/apps/static/js/usage-tracking.js similarity index 100% rename from caimira/apps/static/js/usage-tracking.js rename to ui/apps/static/js/usage-tracking.js diff --git a/caimira/apps/templates/about.html.j2 b/ui/apps/templates/about.html.j2 similarity index 100% rename from caimira/apps/templates/about.html.j2 rename to ui/apps/templates/about.html.j2 diff --git a/caimira/apps/templates/base/calculator.form.html.j2 b/ui/apps/templates/base/calculator.form.html.j2 similarity index 100% rename from caimira/apps/templates/base/calculator.form.html.j2 rename to ui/apps/templates/base/calculator.form.html.j2 diff --git a/caimira/apps/templates/base/calculator.report.html.j2 b/ui/apps/templates/base/calculator.report.html.j2 similarity index 99% rename from caimira/apps/templates/base/calculator.report.html.j2 rename to ui/apps/templates/base/calculator.report.html.j2 index 041cf3ef..b47aa63a 100644 --- a/caimira/apps/templates/base/calculator.report.html.j2 +++ b/ui/apps/templates/base/calculator.report.html.j2 @@ -615,11 +615,11 @@ diff --git a/caimira/apps/templates/base/index.html.j2 b/ui/apps/templates/base/index.html.j2 similarity index 100% rename from caimira/apps/templates/base/index.html.j2 rename to ui/apps/templates/base/index.html.j2 diff --git a/caimira/apps/templates/base/layout.html.j2 b/ui/apps/templates/base/layout.html.j2 similarity index 96% rename from caimira/apps/templates/base/layout.html.j2 rename to ui/apps/templates/base/layout.html.j2 index e64664bd..9e743f72 100644 --- a/caimira/apps/templates/base/layout.html.j2 +++ b/ui/apps/templates/base/layout.html.j2 @@ -45,8 +45,8 @@ diff --git a/caimira/apps/templates/base/userguide.html.j2 b/ui/apps/templates/base/userguide.html.j2 similarity index 100% rename from caimira/apps/templates/base/userguide.html.j2 rename to ui/apps/templates/base/userguide.html.j2 diff --git a/caimira/apps/templates/calculator.form.html.j2 b/ui/apps/templates/calculator.form.html.j2 similarity index 100% rename from caimira/apps/templates/calculator.form.html.j2 rename to ui/apps/templates/calculator.form.html.j2 diff --git a/caimira/apps/templates/calculator.report.html.j2 b/ui/apps/templates/calculator.report.html.j2 similarity index 100% rename from caimira/apps/templates/calculator.report.html.j2 rename to ui/apps/templates/calculator.report.html.j2 diff --git a/caimira/apps/templates/cern/calculator.form.html.j2 b/ui/apps/templates/cern/calculator.form.html.j2 similarity index 100% rename from caimira/apps/templates/cern/calculator.form.html.j2 rename to ui/apps/templates/cern/calculator.form.html.j2 diff --git a/caimira/apps/templates/cern/calculator.report.html.j2 b/ui/apps/templates/cern/calculator.report.html.j2 similarity index 100% rename from caimira/apps/templates/cern/calculator.report.html.j2 rename to ui/apps/templates/cern/calculator.report.html.j2 diff --git a/caimira/apps/templates/cern/index.html.j2 b/ui/apps/templates/cern/index.html.j2 similarity index 100% rename from caimira/apps/templates/cern/index.html.j2 rename to ui/apps/templates/cern/index.html.j2 diff --git a/caimira/apps/templates/cern/layout.html.j2 b/ui/apps/templates/cern/layout.html.j2 similarity index 100% rename from caimira/apps/templates/cern/layout.html.j2 rename to ui/apps/templates/cern/layout.html.j2 diff --git a/caimira/apps/templates/cern/userguide.html.j2 b/ui/apps/templates/cern/userguide.html.j2 similarity index 100% rename from caimira/apps/templates/cern/userguide.html.j2 rename to ui/apps/templates/cern/userguide.html.j2 diff --git a/caimira/apps/templates/common_text.md.j2 b/ui/apps/templates/common_text.md.j2 similarity index 100% rename from caimira/apps/templates/common_text.md.j2 rename to ui/apps/templates/common_text.md.j2 diff --git a/caimira/apps/templates/error.html.j2 b/ui/apps/templates/error.html.j2 similarity index 100% rename from caimira/apps/templates/error.html.j2 rename to ui/apps/templates/error.html.j2 diff --git a/caimira/apps/templates/expert-app.html.j2 b/ui/apps/templates/expert-app.html.j2 similarity index 97% rename from caimira/apps/templates/expert-app.html.j2 rename to ui/apps/templates/expert-app.html.j2 index 5e18a638..93c81e47 100644 --- a/caimira/apps/templates/expert-app.html.j2 +++ b/ui/apps/templates/expert-app.html.j2 @@ -15,4 +15,4 @@ For any query, please let us know by sending an email to Some text

\n' + assert 'Another header' in blocks + assert blocks['Another header'] == '

Some more text.

\n' diff --git a/ui/apps/tests/test_report_generator.py b/ui/apps/tests/test_report_generator.py new file mode 100644 index 00000000..f9fd6d37 --- /dev/null +++ b/ui/apps/tests/test_report_generator.py @@ -0,0 +1,132 @@ +import concurrent.futures +from functools import partial +import os +import time + +import numpy as np +import pytest + +from ui.apps.calculator import make_app +from caimira.apps.calculator.model_generator import VirusFormData +from caimira.apps.calculator.report_generator import (ReportGenerator, readable_minutes, calculate_report_data, + manufacture_alternative_scenarios, interesting_times, comparison_report) +import caimira.calculator.report.report_generator as rep_gen +from caimira.api.controller.report_controller import generate_model, generate_report_results + + +def test_generate_report(baseline_form) -> None: + # This is a simple test that confirms that given a model, we can actually + # generate a report for it. Because this is what happens in the caimira + # calculator, we confirm that the generation happens within a reasonable + # time threshold. + time_limit: float = float(os.environ.get( + "CAIMIRA_TESTS_CALCULATOR_TIMEOUT", 10.)) + + start = time.perf_counter() + + generator: ReportGenerator = make_app().settings['report_generator'] + + model = generate_model(baseline_form) + report_data = generate_report_results(baseline_form, model) + + report = generator.build_report("", baseline_form, model, report_data, partial( + concurrent.futures.ThreadPoolExecutor, 1, + )) + + end = time.perf_counter() + total = end-start + print( + f"Time limit: {time_limit} | Time taken: {end} - {start} = {total} < {time_limit}") + assert report != "" + assert end - start < time_limit + + +@pytest.mark.parametrize( + ["test_input", "expected"], + [ + [1, '1 minute'], + [2, '2 minutes'], + [60, '1 hour'], + [120, '2 hours'], + [150, '150 minutes'], + ], +) +def test_readable_minutes(test_input, expected): + assert readable_minutes(test_input) == expected + + +def test_fill_big_gaps(): + expected = [1, 1.75, 2, 2.75, 3.5, 4] + assert rep_gen.fill_big_gaps([1, 2, 4], gap_size=0.75) == expected + + +def test_fill_big_gaps__float_tolerance(): + # Ensure that there is some float tolerance to the gap size check. + assert rep_gen.fill_big_gaps( + [0, 2 + 1e-15, 4], gap_size=2) == [0, 2 + 1e-15, 4] + assert rep_gen.fill_big_gaps( + [0, 2 + 1e-14, 4], gap_size=2) == [0, 2, 2 + 1e-14, 4] + + +def test_non_temp_transition_times(baseline_exposure_model): + expected = [0.0, 4.0, 5.0, 8.0] + result = rep_gen.non_temp_transition_times(baseline_exposure_model) + assert result == expected + + +def test_interesting_times_many(baseline_exposure_model): + result = rep_gen.interesting_times( + baseline_exposure_model, approx_n_pts=100) + assert 100 <= len(result) <= 120 + assert np.abs(np.diff(result)).max() < 8.1/100. + + +def test_interesting_times_small(baseline_exposure_model): + expected = [0.0, 0.8, 1.6, 2.4, 3.2, 4.0, 4.8, 5.0, 5.8, 6.6, 7.4, 8.0] + # Ask for more data than there is in the transition times. + result = rep_gen.interesting_times( + baseline_exposure_model, approx_n_pts=10) + + np.testing.assert_allclose(result, expected, atol=1e-04) + + +def test_interesting_times_w_temp(exposure_model_w_outside_temp_changes): + # Ensure that the state change times are returned (minus the temperature changes) by + # requesting n_points=1. + result = rep_gen.interesting_times( + exposure_model_w_outside_temp_changes, approx_n_pts=1) + expected = [0., 1.8, 2.2, 4., 4.4, 5., 6.2, 6.6, 8.] + np.testing.assert_allclose(result, expected) + + # Now request more than the state-change times. + result = rep_gen.interesting_times( + exposure_model_w_outside_temp_changes, approx_n_pts=20) + expected = [ + 0., 0.4, 0.8, 1.2, 1.6, 1.8, 2.2, 2.6, 3., 3.4, 3.8, 4., 4.4, 4.8, + 5., 5.4, 5.8, 6.2, 6.6, 7., 7.4, 7.8, 8. + ] + np.testing.assert_allclose(result, expected) + + +def test_expected_new_cases(baseline_form_with_sr: VirusFormData): + model = baseline_form_with_sr.build_model() + + executor_factory = partial( + concurrent.futures.ThreadPoolExecutor, 1, + ) + + # Short- and Long-range contributions + report_data = calculate_report_data(baseline_form_with_sr, model, executor_factory) + sr_lr_expected_new_cases = report_data['expected_new_cases'] + sr_lr_prob_inf = report_data['prob_inf']/100 + + # Long-range contributions alone + scenario_sample_times = interesting_times(model) + alternative_scenarios = manufacture_alternative_scenarios(baseline_form_with_sr) + alternative_statistics = comparison_report( + baseline_form_with_sr, report_data, alternative_scenarios, scenario_sample_times, executor_factory=executor_factory, + ) + + lr_expected_new_cases = alternative_statistics['stats']['Base scenario without short-range interactions']['expected_new_cases'] + np.testing.assert_almost_equal(sr_lr_expected_new_cases, lr_expected_new_cases + sr_lr_prob_inf * baseline_form_with_sr.short_range_occupants, 2) + \ No newline at end of file diff --git a/caimira/tests/test_state.py b/ui/apps/tests/test_state.py similarity index 99% rename from caimira/tests/test_state.py rename to ui/apps/tests/test_state.py index ac0341fe..11eb08e6 100644 --- a/caimira/tests/test_state.py +++ b/ui/apps/tests/test_state.py @@ -4,7 +4,7 @@ import pytest -from caimira import state +from ui.apps.expert_apps.expert import state @dataclass diff --git a/ui/apps/tests/test_webapp.py b/ui/apps/tests/test_webapp.py new file mode 100644 index 00000000..4add88c8 --- /dev/null +++ b/ui/apps/tests/test_webapp.py @@ -0,0 +1,162 @@ +import os +from pathlib import Path + +import pytest +import tornado.testing + +import ui.apps.calculator +from ui.apps.calculator.report import generate_permalink + +_TIMEOUT = float(os.environ.get("CAIMIRA_TESTS_CALCULATOR_TIMEOUT", 10.)) + + +@pytest.fixture +def app(): + return ui.apps.calculator.make_app() + + +async def test_homepage(http_server_client): + response = await http_server_client.fetch('/') + assert response.code == 200 + + +async def test_calculator_form(http_server_client): + # Both with and without a trailing slash. + response = await http_server_client.fetch('/calculator') + assert response.code == 200 + + response = await http_server_client.fetch('/calculator/') + assert response.code == 200 + + +async def test_404(http_server_client): + resp = await http_server_client.fetch('/doesnt-exist', raise_error=False) + assert resp.code == 404 + + +class TestBasicApp(tornado.testing.AsyncHTTPTestCase): + def get_app(self): + return ui.apps.calculator.make_app() + + @tornado.testing.gen_test(timeout=_TIMEOUT) + def test_report(self): + requests = [ + self.http_client.fetch(self.get_url('/calculator/baseline-model/result'), request_timeout=_TIMEOUT), + # At the same time, request a non-report page (to check whether the report is blocking). + self.http_client.fetch(self.get_url('/calculator/')), + ] + response = yield requests[0] + other_response = yield requests[1] + + def end_time(resp): + return resp.start_time + resp.request_time + + # The start time is before the other request, + # but the end time is after the other request (because it takes longer + # to process a report than a simple page). + assert response.start_time < other_response.start_time + assert end_time(response) > end_time(other_response) + + self.assertEqual(response.code, 200) + assert 'CERN HSE' not in response.body.decode() + assert 'expected number of new cases is' in response.body.decode() + + +class TestCernApp(tornado.testing.AsyncHTTPTestCase): + def get_app(self): + cern_theme = Path(ui.apps.calculator.__file__).parent.parent / 'themes' / 'cern' + return ui.apps.calculator.make_app(theme_dir=cern_theme) + + @tornado.testing.gen_test(timeout=_TIMEOUT) + def test_report(self): + response = yield self.http_client.fetch(self.get_url('/calculator/baseline-model/result'), request_timeout=_TIMEOUT) + self.assertEqual(response.code, 200) + assert 'expected number of new cases is' in response.body.decode() + + +class TestOpenApp(tornado.testing.AsyncHTTPTestCase): + def get_app(self): + return ui.apps.calculator.make_app(calculator_prefix="/mycalc") + + @tornado.testing.gen_test(timeout=_TIMEOUT) + def test_report(self): + response = yield self.http_client.fetch(self.get_url('/mycalc/baseline-model/result'), request_timeout=_TIMEOUT) + self.assertEqual(response.code, 200) + + def test_calculator_404(self): + response = self.fetch('/calculator') + assert response.code == 404 + + +async def test_permalink_urls(http_server_client, baseline_form): + base_url = 'proto://hostname/prefix' + permalink_data = generate_permalink(base_url, lambda: "", lambda: "/calculator", baseline_form) + expected = f'{base_url}/calculator?exposed_coffee_break_option={baseline_form.exposed_coffee_break_option}&' + assert permalink_data['link'].startswith(expected) + + # We should get a 200 for the link. + 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 permalink_data['shortened'].startswith(base_url) + response = await http_server_client.fetch( + permalink_data['shortened'].replace(base_url, ''), + max_redirects=0, + raise_error=False, + ) + assert response.code == 302 + assert response.headers['Location'] == permalink_data['link'].replace(base_url, '') + + +async def test_invalid_compressed_url(http_server_client, baseline_form): + response = await http_server_client.fetch( + '/_c/invalid-data', + max_redirects=0, + raise_error=False, + ) + assert response.code == 400 + + +class TestError500(tornado.testing.AsyncHTTPTestCase): + def get_app(self): + class ProcessingErrorPage(ui.apps.calculator.BaseRequestHandler): + def get(self): + raise ValueError('some unexpected error') + app = ui.apps.calculator.make_app() + page = [ + (r'/', ProcessingErrorPage), + ] + return tornado.web.Application(page, **app.settings) + + def test_500(self): + response = self.fetch('/') + assert response.code == 500 + assert 'Unfortunately an error occurred when processing your request' in response.body.decode() + + +class TestCERNGenericPage(tornado.testing.AsyncHTTPTestCase): + def get_app(self): + cern_theme = Path(ui.apps.calculator.__file__).parent.parent / 'themes' / 'cern' + app = ui.apps.calculator.make_app(theme_dir=cern_theme) + pages = [ + (r'/calculator/user-guide', ui.apps.calculator.GenericExtraPage, {'active_page': 'calculator/user-guide', 'filename': 'userguide.html.j2'}), + (r'/about', ui.apps.calculator.GenericExtraPage, {'active_page': 'about', 'filename': 'about.html.j2'}), + ] + + return tornado.web.Application(pages, **app.settings) + + @tornado.testing.gen_test(timeout=_TIMEOUT) + def test_user_guide(self): + response = yield self.http_client.fetch(self.get_url('/calculator/user-guide')) + self.assertEqual(response.code, 200) + + @tornado.testing.gen_test(timeout=_TIMEOUT) + def test_about(self): + response = yield self.http_client.fetch(self.get_url('/about')) + self.assertEqual(response.code, 200) + + def test_calculator_404(self): + response = self.fetch('/calculator') + assert response.code == 404