Epi v2 metadata API endpoint

hawc/apps/animal/actions/model_metadata.py

@@ -1,9 +1,9 @@
 from pydantic import BaseModel
 
-from hawc.apps.animal import constants
-from hawc.apps.assessment.models import DoseUnits, Species, Strain
-from hawc.apps.common.actions import BaseApiAction
-from hawc.apps.study.constants import CoiReported
+from ...assessment.models import DoseUnits, Species, Strain
+from ...common.actions import BaseApiAction
+from ...study.models import Study
+from .. import constants
 
 
 class NoInput(BaseModel):
@@ -17,9 +17,6 @@ class AnimalMetadata(BaseApiAction):
 
     input_model = NoInput
 
-    def study_metadata(self):
-        return dict(coi_reported=dict(CoiReported.choices))
-
     def experiment_metadata(self):
         return dict(type=dict(constants.ExperimentType.choices))
 
@@ -53,9 +50,9 @@ def endpoint_metadata(self):
             trend_result=dict(constants.TrendResult.choices),
         )
 
-    def evaluate(self):
+    def evaluate(self) -> dict:
         return dict(
-            study=self.study_metadata(),
+            study=Study.metadata(),
             experiment=self.experiment_metadata(),
             animal_group=self.animal_group_metadata(),
             dosing_regime=self.dosing_regime_metadata(),

hawc/apps/common/actions.py

@@ -1,6 +1,6 @@
 import json
 from collections import defaultdict
-from typing import Any, ClassVar, Type, Union
+from typing import Any, ClassVar, Optional, Type, Union
 
 import pandas as pd
 import pydantic
@@ -24,8 +24,8 @@ class BaseApiAction:
 
     input_model: ClassVar[DataModel]  # should be defined
 
-    def __init__(self, data: dict):
-        self.data = data
+    def __init__(self, data: Optional[dict] = None):
+        self.data: dict = data or {}
         self.errors: dict[str, list] = defaultdict(list)
         self.inputs = None
 

hawc/apps/epi/actions/model_metadata.py

@@ -1,11 +1,11 @@
 from django.db.models.functions import Lower
 from pydantic import BaseModel
-from rest_framework.response import Response
 
-from hawc.apps.assessment.models import DoseUnits
-from hawc.apps.common.actions import BaseApiAction
-from hawc.apps.epi import constants
-from hawc.apps.epi.models import AdjustmentFactor, Country, Criteria, Ethnicity, ResultMetric
+from ...assessment.models import DoseUnits
+from ...common.actions import BaseApiAction
+from ...study.models import Study
+from .. import constants
+from ..models import AdjustmentFactor, Country, Criteria, Ethnicity, ResultMetric
 
 
 def get_all_model_objects(object_class, display_field="name", val_field="id"):
@@ -63,7 +63,7 @@ def result_metadata(self):
 
         metadata["assessment_specific_adjustment_factors"] = {
             af.id: af.description
-            for af in AdjustmentFactor.objects.filter(assessment=self.assessment).order_by(
+            for af in AdjustmentFactor.objects.filter(assessment=self.data["assessment"]).order_by(
                 Lower("description")
             )
         }
@@ -80,18 +80,18 @@ def study_population_metadata(self):
             design=dict(constants.Design.choices),
             countries=get_all_model_objects(Country, "name", "code"),
         )
-
         metadata["assessment_specific_criteria"] = {
             c.id: c.description
-            for c in Criteria.objects.filter(assessment=self.assessment).order_by(
+            for c in Criteria.objects.filter(assessment=self.data["assessment"]).order_by(
                 Lower("description")
             )
         }
 
         return metadata
 
-    def evaluate(self):
+    def evaluate(self) -> dict:
         return dict(
+            study=Study.metadata(),
             study_population=self.study_population_metadata(),
             outcome=self.outcome_metadata(),
             result=self.result_metadata(),
@@ -101,7 +101,3 @@ def evaluate(self):
             exposure=self.exposure_metadata(),
             central_tendency=self.central_tendency_metadata(),
         )
-
-    def handle_assessment_request(self, request, assessment):
-        self.assessment = assessment
-        return Response(self.evaluate())

hawc/apps/epi/api.py

@@ -545,8 +545,8 @@ def get_queryset(self, *args, **kwargs):
 
     def retrieve(self, request, *args, **kwargs):
         assessment = self.get_object()
-        if assessment.user_can_view_object(request.user):
-            eam = EpiAssessmentMetadata(None)
-            return eam.handle_assessment_request(request, assessment)
-        else:
+        if not assessment.user_can_view_object(request.user):
             raise PermissionDenied("Invalid permission to view assessment metadata")
+
+        action = EpiAssessmentMetadata(data={"assessment": assessment})
+        return Response(action.evaluate())

hawc/apps/epiv2/actions/model_metadata.py

@@ -0,0 +1,62 @@
+from ...common.actions import BaseApiAction
+from ...epi.actions.model_metadata import NoInput, get_all_model_objects
+from ...epi.models import Country
+from ...study.models import Study
+from .. import constants
+
+
+class EpiV2Metadata(BaseApiAction):
+    """
+    Generate a dictionary of field choices for all epiv2 models.
+    """
+
+    input_model = NoInput
+
+    def design_metadata(self):
+        return dict(
+            study_design=dict(constants.StudyDesign.choices),
+            source=dict(constants.Source.choices),
+            age_profile=dict(constants.AgeProfile.choices),
+            sex=dict(constants.Sex.choices),
+            countries=get_all_model_objects(Country, "name", "code"),
+        )
+
+    def exposure_metadata(self):
+        metadata = dict(
+            measurement_type=dict(constants.MeasurementType.choices),
+            biomonitoring_matrix=dict(constants.BiomonitoringMatrix.choices),
+            biomonitoring_source=dict(constants.BiomonitoringSource.choices),
+            exposure_route=dict(constants.ExposureRoute.choices),
+        )
+        return metadata
+
+    def exposure_level_metadata(self):
+        return dict(
+            variance_type=dict(constants.VarianceType.choices),
+            ci_type=dict(constants.ConfidenceIntervalType.choices),
+        )
+
+    def outcome_metadata(self):
+        metadata = dict(
+            system=dict(constants.HealthOutcomeSystem.choices),
+        )
+        return metadata
+
+    def data_extraction_metadata(self):
+        return dict(
+            effect_estimate_type=dict(constants.EffectEstimateType.choices),
+            ci_type=dict(constants.ConfidenceIntervalType.choices),
+            variance_type=dict(constants.VarianceType.choices),
+            significant=dict(constants.Significant.choices),
+            transforms=dict(constants.DataTransforms.choices),
+        )
+
+    def evaluate(self) -> dict:
+        return dict(
+            study=Study.metadata(),
+            design=self.design_metadata(),
+            exposure=self.exposure_metadata(),
+            exposure_level=self.exposure_level_metadata(),
+            outcome=self.outcome_metadata(),
+            data_extraction=self.data_extraction_metadata(),
+        )

hawc/apps/epiv2/admin.py

@@ -44,6 +44,7 @@ class DesignAdmin(admin.ModelAdmin):
         "last_updated",
     )
     list_filter = ("study_design", "created")
+    raw_id_fields = ("study",)
     inlines = [
         ChemicalInline,
         ExposureInline,

hawc/apps/epiv2/api.py

@@ -1,3 +1,4 @@
+from rest_framework import viewsets
 from rest_framework.decorators import action
 from rest_framework.response import Response
 
@@ -6,6 +7,7 @@
 from ..common.api.viewsets import EditPermissionsCheckMixin
 from ..common.renderers import PandasRenderers
 from . import exports, models, serializers
+from .actions.model_metadata import EpiV2Metadata
 
 
 class EpiAssessmentViewset(BaseAssessmentViewset):
@@ -35,3 +37,8 @@ class Design(EditPermissionsCheckMixin, AssessmentEditViewset):
 
     def get_queryset(self, *args, **kwargs):
         return self.model.objects.all()
+
+
+class Metadata(viewsets.ViewSet):
+    def list(self, request):
+        return EpiV2Metadata.handle_request(request)

hawc/apps/epiv2/forms.py

@@ -1,15 +1,13 @@
 from django import forms
 from django.urls import reverse
 
-from hawc.apps.common.forms import BaseFormHelper
-
 from ..assessment.autocomplete import DSSToxAutocomplete
 from ..common.autocomplete import (
     AutocompleteSelectMultipleWidget,
     AutocompleteSelectWidget,
     AutocompleteTextWidget,
 )
-from ..common.forms import ArrayCheckboxSelectMultiple, QuillField
+from ..common.forms import ArrayCheckboxSelectMultiple, BaseFormHelper, QuillField
 from ..common.widgets import SelectMultipleOtherWidget, SelectOtherWidget
 from ..epi.autocomplete import CountryAutocomplete
 from . import autocomplete, constants, models

hawc/apps/epiv2/urls.py

@@ -6,6 +6,7 @@
 router = SimpleRouter()
 router.register(r"assessment", api.EpiAssessmentViewset, basename="assessment")
 router.register(r"design", api.Design, basename="design")
+router.register(r"metadata", api.Metadata, basename="metadata")
 
 app_name = "epiv2"
 urlpatterns = [

hawc/apps/study/models.py

@@ -140,6 +140,11 @@ def save_new_from_reference(cls, reference, attrs):
             study.set_communications(internal_communications)
         return study
 
+    @classmethod
+    def metadata(cls) -> dict:
+        # return schema metadata for choice fields
+        return dict(coi_reported=dict(constants.CoiReported.choices))
+
     def __str__(self):
         return self.short_citation