Merge branch 'bugfix/API_refinement' into 'master'

REST API refinement

See merge request caimira/caimira!508

Author: lrdossan

.gitlab-ci.yml

@@ -87,6 +87,7 @@ test-cern-caimira-py39:
       - ./app-config/openshift/${CAIMIRA_INSTANCE}/expected
   only:
     - master
+    - live/caimira-test
 
 check_openshift_config_test:
   extends: .test_openshift_config

CHANGELOG.md

@@ -0,0 +1,9 @@
+# 4.17.2 (September 19, 2024)
+
+## Features Added
+- Initial commit with changelog file.
+- New project layout architecture.
+- Added CAiMIRA REST API features.
+
+## Bug Fixes
+- Virus and CO2 routes and controllers.

caimira/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "caimira"
-version = "4.17.0a2"
+version = "4.17.2"
 description = "CAiMIRA - CERN Airborne Model for Indoor Risk Assessment"
 license = { text = "Apache-2.0" }
 authors = [

caimira/src/caimira/api/controller/co2_report_controller.py

@@ -1,26 +1,27 @@
+import typing
+
 from caimira.calculator.validators.co2.co2_validator import CO2FormData
 from caimira.calculator.store.data_registry import DataRegistry
+from caimira.calculator.models.models import CO2DataModel
 
 
-def generate_form_obj(form_data, data_registry):
+def generate_form_obj(form_data: typing.Dict, data_registry: DataRegistry) -> CO2FormData:
     return CO2FormData.from_dict(form_data=form_data, data_registry=data_registry)
 
 
-def generate_model(form_obj, data_registry):
-    sample_size = data_registry.monte_carlo['sample_size']
-    return form_obj.build_model(sample_size=sample_size)
+def generate_model(form_obj: CO2FormData) -> CO2DataModel:
+    return form_obj.build_model()
 
 
-def generate_report(model):
+def generate_report(model: CO2DataModel) -> typing.Dict:
     return dict(model.CO2_fit_params())
 
 
-def submit_CO2_form(form_data):
-    data_registry = DataRegistry()
+def submit_CO2_form(form_data: typing.Dict) -> typing.Dict:
+    data_registry: DataRegistry = DataRegistry()
 
-    form_obj = generate_form_obj(
-        form_data=form_data, data_registry=data_registry)
-    model = generate_model(form_obj=form_obj, data_registry=data_registry)
-    report_data = generate_report(model=model)
+    form_obj: CO2FormData = generate_form_obj(form_data=form_data, data_registry=data_registry)
+    model: CO2DataModel = generate_model(form_obj=form_obj)
+    report_data: typing.Dict = generate_report(model=model)
 
     return report_data

caimira/src/caimira/api/controller/virus_report_controller.py

@@ -1,37 +1,37 @@
 import concurrent.futures
 import functools
+import typing
 
 from caimira.calculator.validators.virus.virus_validator import VirusFormData
 from caimira.calculator.store.data_registry import DataRegistry
+from caimira.calculator.models.models import ExposureModel
 import caimira.calculator.report.virus_report_data as rg
 
 
-def generate_form_obj(form_data, data_registry):
+def generate_form_obj(form_data: typing.Dict, data_registry: DataRegistry) -> VirusFormData:
     return VirusFormData.from_dict(
         form_data=form_data,
         data_registry=data_registry,
     )
 
 
-def generate_model(form_obj, data_registry):
-    sample_size = data_registry.monte_carlo['sample_size']
-    return form_obj.build_model(sample_size=sample_size)
-
-
-def generate_report_results(form_obj):
+def generate_report(form_obj: VirusFormData, report_generation_parallelism: typing.Optional[int]) -> typing.Dict:
     return rg.calculate_report_data(
         form=form_obj,
         executor_factory=functools.partial(
-            concurrent.futures.ThreadPoolExecutor, None,  # TODO define report_parallelism
+            concurrent.futures.ThreadPoolExecutor,
+            report_generation_parallelism,
         ),
     )
 
 
-def submit_virus_form(form_data):
-    data_registry = DataRegistry
+def submit_virus_form(form_data: typing.Dict, report_generation_parallelism: typing.Optional[int]) -> typing.Dict:
+    data_registry: DataRegistry = DataRegistry()
+
+    form_obj: VirusFormData = generate_form_obj(form_data=form_data, data_registry=data_registry)
+    report_data: typing.Dict = generate_report(form_obj=form_obj, report_generation_parallelism=report_generation_parallelism)
 
-    form_obj = generate_form_obj(form_data=form_data, data_registry=data_registry)
-    model = generate_model(form_obj=form_obj, data_registry=data_registry)
-    report_data = generate_report_results(form_obj=form_obj, model=model)
+    # Handle model representation
+    if report_data['model']: report_data['model'] = repr(report_data['model'])
 
     return report_data

caimira/src/caimira/api/routes/report_routes.py

@@ -7,7 +7,7 @@
 from caimira.api.controller.co2_report_controller import submit_CO2_form
 
 
-class BaseReportHandler(tornado.web.RedirectHandler):
+class BaseReportHandler(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")
@@ -22,7 +22,14 @@ class VirusReportHandler(BaseReportHandler):
     def post(self):
         try:
             form_data = json.loads(self.request.body)
-            report_data = submit_virus_form(form_data)
+            arguments = self.request.arguments
+            # Report generation parallelism argument
+            try:
+                report_generation_parallelism = int(arguments['report_generation_parallelism'][0])
+            except (ValueError, IndexError, KeyError):
+                report_generation_parallelism = None
+
+            report_data = submit_virus_form(form_data, report_generation_parallelism)
 
             response_data = {
                 "status": "success",
@@ -36,12 +43,7 @@ def post(self):
             self.write_error(status_code=400, exc_info=sys.exc_info())
 
 
-class CO2ReportHandler(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")
-
+class CO2ReportHandler(BaseReportHandler):
     def post(self):
         try:
             form_data = json.loads(self.request.body)

caimira/src/caimira/calculator/models/models.py

@@ -807,7 +807,7 @@ class SimplePopulation:
     number: typing.Union[int, IntPiecewiseConstant]
 
     #: The times in which the people are in the room.
-    presence: typing.Union[None, Interval]
+    presence: typing.Optional[Interval]
 
     #: The physical activity being carried out by the people.
     activity: Activity

caimira/src/caimira/calculator/validators/co2/co2_validator.py

@@ -193,8 +193,7 @@ def ventilation_transition_times(self) -> typing.Tuple[float]:
             vent_states.append(last_time_from_input)
         return tuple(vent_states)
 
-    def build_model(self, size=None) -> models.CO2DataModel: # type: ignore
-        size = size or self.data_registry.monte_carlo['sample_size']
+    def build_model(self, sample_size = None) -> models.CO2DataModel:
         # Build a simple infected and exposed population for the case when presence
         # intervals and number of people are dynamic. Activity type is not needed.
         if self.occupancy_format == 'dynamic':

caimira/src/caimira/calculator/validators/form_validator.py

@@ -206,7 +206,7 @@ def get_activity_mins(population):
     def validate(self):
         raise NotImplementedError("Subclass must implement")
 
-    def build_model(self, sample_size=None):
+    def build_model(self, sample_size: typing.Optional[int] = None):
         raise NotImplementedError("Subclass must implement")
 
     def _compute_breaks_in_interval(self, start, finish, n_breaks, duration) -> models.BoundarySequence_t:

cern_caimira/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cern-caimira"
-version = "4.17.1a1"
+version = "4.17.2"
 description = "CAiMIRA - CERN Airborne Model for Indoor Risk Assessment"
 license = { text = "Apache-2.0" }
 authors = [