Update AssessmentValue global API

hawc/apps/assessment/exports.py

@@ -1,41 +1,108 @@
-import pandas as pd
-from django.conf import settings
+from ..common.exports import Exporter, ModelExport
+from ..common.models import sql_display, str_m2m
+from ..study.exports import StudyExport
+from . import constants
 
-from ..common.exports import ModelExport
-from ..common.helper import FlatFileExporter
-from ..common.models import sql_format
-from .models import AssessmentValue
 
+class AssessmentValueExport(ModelExport):
+    def get_value_map(self) -> dict:
+        return {
+            "evaluation_type": "evaluation_type_display",
+            "system": "system",
+            "value_type": "value_type_display",
+            "value": "value",
+            "value_unit": "value_unit",
+            "adaf": "adaf",
+            "confidence": "confidence",
+            "duration": "duration",
+            "basis": "basis",
+            "pod_type": "pod_type",
+            "pod_value": "pod_value",
+            "pod_unit": "pod_unit",
+            "uncertainty": "uncertainty_display",
+            "species_studied": "species_studied",
+            "evidence": "evidence",
+            "tumor_type": "tumor_type",
+            "extrapolation_method": "extrapolation_method",
+            "comments": "comments",
+            "extra": "extra",
+            "created": "created",
+            "last_updated": "last_updated",
+        }
 
-class DSSToxExport(ModelExport):
-    def get_value_map(self):
+    def get_annotation_map(self, query_prefix: str) -> dict:
         return {
-            "dtxsid": "dtxsid",
-            "dashboard_url": "dashboard_url",
-            "img_url": "img_url",
-            "content": "content",
+            "evaluation_type_display": sql_display(
+                query_prefix + "evaluation_type", constants.EvaluationType
+            ),
+            "value_type_display": sql_display(query_prefix + "value_type", constants.ValueType),
+            "uncertainty_display": sql_display(
+                query_prefix + "uncertainty", constants.UncertaintyChoices
+            ),
+        }
+
+    def prepare_df(self, df):
+        return self.format_time(df)
+
+
+class AssessmentExport(ModelExport):
+    def get_value_map(self) -> dict:
+        return {
+            "id": "id",
+            "name": "name",
+            "cas": "cas",
+            "dtxsids": "dtxsids__name",
+            "year": "year",
             "created": "created",
             "last_updated": "last_updated",
         }
 
     def get_annotation_map(self, query_prefix):
-        img_url_str = (
-            f"https://api-ccte.epa.gov/chemical/file/image/search/by-dtxsid/{{}}?x-api-key={settings.CCTE_API_KEY}"
-            if settings.CCTE_API_KEY
-            else "https://comptox.epa.gov/dashboard-api/ccdapp1/chemical-files/image/by-dtxsid/{}"
-        )
         return {
-            "dashboard_url": sql_format(
-                "https://comptox.epa.gov/dashboard/dsstoxdb/results?search={}",
-                query_prefix + "dtxsid",
-            ),
-            "img_url": sql_format(img_url_str, query_prefix + "dtxsid"),
+            "dtxsids__name": str_m2m(query_prefix + "dtxsids__dtxsid"),
         }
 
     def prepare_df(self, df):
         return self.format_time(df)
 
 
-class ValuesListExport(FlatFileExporter):
-    def build_df(self) -> pd.DataFrame:
-        return AssessmentValue.objects.get_df()
+class AssessmentDetailExport(ModelExport):
+    def get_value_map(self) -> dict:
+        return {
+            "project_type": "project_type",
+            "project_status": "project_status_display",
+            "project_url": "project_url",
+            "peer_review_status": "peer_review_status_display",
+            "qa_id": "qa_id",
+            "qa_url": "qa_url",
+            "report_id": "report_id",
+            "report_url": "report_url",
+            "extra": "extra",
+            "created": "created",
+            "last_updated": "last_updated",
+        }
+
+    def prepare_df(self, df):
+        return self.format_time(df)
+
+    def get_annotation_map(self, query_prefix: str) -> dict:
+        return {
+            "project_status_display": sql_display(
+                query_prefix + "project_status", constants.Status
+            ),
+            "peer_review_status_display": sql_display(
+                query_prefix + "peer_review_status", constants.PeerReviewType
+            ),
+        }
+
+
+class AssessmentExporter(Exporter):
+    def build_modules(self) -> list[ModelExport]:
+        return [
+            AssessmentExport("assessment", "assessment"),
+            AssessmentDetailExport("assessment_detail", "assessment__details"),
+            AssessmentValueExport("assessment_value", ""),
+            StudyExport(
+                "study", "study", include=("id", "short_citation", "hero_id", "pubmed_id", "doi")
+            ),
+        ]

hawc/apps/assessment/filterset.py

@@ -8,6 +8,8 @@
     BaseFilterSet,
     ExpandableFilterForm,
     InlineFilterForm,
+    OrderingFilter,
+    PaginationFilter,
 )
 from ..common.helper import new_window_a
 from ..myuser.models import HAWCUser
@@ -165,3 +167,36 @@ def create_form(self):
 
 class EffectTagFilterSet(df.FilterSet):
     name = df.CharFilter(lookup_expr="icontains")
+
+
+class AssessmentValueFilterSet(df.FilterSet):
+    name = df.CharFilter(
+        field_name="assessment__name",
+        lookup_expr="icontains",
+        label="Assessment name",
+    )
+    cas = df.CharFilter(
+        field_name="assessment__cas",
+        label="Assessment CAS",
+    )
+    dtxsid = df.CharFilter(
+        field_name="assessment__dtxsids__dtxsid",
+        label="Assessment DTXSID",
+    )
+    project_type = df.CharFilter(
+        field_name="assessment__details__project_type",
+        lookup_expr="icontains",
+        label="Assessment project type",
+    )
+    year = df.CharFilter(field_name="assessment__year", label="Assessment year")
+
+    order_by = OrderingFilter(
+        fields=(("assessment__name", "name"), ("assessment__id", "assessment_id")),
+        initial="name",
+    )
+
+    paginate_by = PaginationFilter()
+
+    class Meta:
+        model = models.AssessmentValue
+        fields = ("value_type",)

hawc/apps/assessment/managers.py

@@ -8,7 +8,7 @@
 from django.db.models import Case, Exists, OuterRef, Q, QuerySet, Value, When
 from reversion.models import Version
 
-from ..common.helper import HAWCDjangoJSONEncoder, map_enum
+from ..common.helper import HAWCDjangoJSONEncoder
 from ..common.models import BaseManager, replace_null, str_m2m
 from . import constants
 
@@ -202,54 +202,6 @@ class DatasetManager(BaseManager):
 class AssessmentValueManager(BaseManager):
     assessment_relation = "assessment"
 
-    def get_df(self) -> pd.DataFrame:
-        """Get a dataframe of Assessment Values from given Queryset of Values."""
-        mapping: dict[str, str] = {
-            "assessment_id": "assessment_id",
-            "assessment__name": "assessment_name",
-            "assessment__created": "assessment_created",
-            "assessment__last_updated": "assessment_last_updated",
-            "assessment__details__project_type": "project_type",
-            "assessment__details__project_status": "project_status",
-            "assessment__details__project_url": "project_url",
-            "assessment__details__peer_review_status": "peer_review_status",
-            "assessment__details__qa_id": "qa_id",
-            "assessment__details__qa_url": "qa_url",
-            "assessment__details__report_id": "report_id",
-            "assessment__details__report_url": "report_url",
-            "assessment__details__extra": "assessment_extra",
-            "evaluation_type": "evaluation_type",
-            "id": "value_id",
-            "system": "system",
-            "value_type": "value_type",
-            "value": "value",
-            "value_unit": "value_unit",
-            "basis": "basis",
-            "pod_value": "pod_value",
-            "pod_unit": "pod_unit",
-            "species_studied": "species_studied",
-            "duration": "duration",
-            "study_id": "study_id",
-            "study__short_citation": "study_citation",
-            "confidence": "confidence",
-            "uncertainty": "uncertainty",
-            "tumor_type": "tumor_type",
-            "extrapolation_method": "extrapolation_method",
-            "evidence": "evidence",
-            "comments": "comments",
-            "extra": "extra",
-        }
-        data = self.select_related("assessment__details").values_list(*list(mapping.keys()))
-        df = pd.DataFrame(data=data, columns=list(mapping.values())).sort_values(
-            ["assessment_id", "value_id"]
-        )
-        map_enum(df, "project_status", constants.Status, replace=True)
-        map_enum(df, "peer_review_status", constants.PeerReviewType, replace=True)
-        map_enum(df, "evaluation_type", constants.EvaluationType, replace=True)
-        map_enum(df, "value_type", constants.ValueType, replace=True)
-        map_enum(df, "confidence", constants.Confidence, replace=True)
-        return df
-
 
 class AssessmentDetailManager(BaseManager):
     assessment_relation = "assessment"

hawc/apps/common/api/filters.py

@@ -1,4 +1,8 @@
+from django.db.models import QuerySet
+from django_filters.filterset import FilterSet
+from django_filters.utils import translate_validation
 from rest_framework import exceptions, filters
+from rest_framework.request import Request
 
 from ..helper import try_parse_list_ints
 
@@ -30,3 +34,24 @@ def filter_queryset(self, request, queryset, view):
                 raise exceptions.PermissionDenied()
 
         return queryset
+
+
+def filtered_qs(
+    queryset: QuerySet, filterset_cls: type[FilterSet], request: Request, **kw
+) -> QuerySet:
+    """
+    Filter a queryset based on a FilterSet and a DRF request.
+
+    This is a utility method to add filtering to custom ViewSet actions, it is adapted from the
+    `django_filters.rest_framework.FilterSet` used for standard ViewSet operations.
+
+    Args:
+        queryset (QuerySet): the queryset to filter
+        filterset_cls (type[filters.FilterSet]): a FilterSet class
+        request (Request): a rest framework request
+        **kw: any additional arguments provided to FilterSet class constructor
+    """
+    filterset = filterset_cls(data=request.query_params, queryset=queryset, request=request, **kw)
+    if not filterset.is_valid():
+        raise translate_validation(filterset.errors)
+    return filterset.qs

hawc/apps/hawc_admin/api.py

@@ -1,12 +1,14 @@
 from django.utils import timezone
-from rest_framework import permissions, status, viewsets
+from rest_framework import permissions, viewsets
 from rest_framework.decorators import action
 from rest_framework.renderers import JSONRenderer
 from rest_framework.response import Response
 
-from ..assessment.exports import ValuesListExport
+from ..assessment import exports
+from ..assessment.filterset import AssessmentValueFilterSet
 from ..assessment.models import AssessmentValue
 from ..common.api import FivePerMinuteThrottle
+from ..common.api.filters import filtered_qs
 from ..common.helper import FlatExport
 from ..common.renderers import PandasRenderers
 from .actions import media_metadata_report
@@ -40,7 +42,8 @@ class ReportsViewSet(viewsets.ViewSet):
     @action(detail=False, renderer_classes=PandasRenderers)
     def values(self, request):
         """Gets all value data across all assessments."""
-        export = ValuesListExport(
-            queryset=AssessmentValue.objects.all(), filename="hawc-assessment-values"
-        ).build_export()
-        return Response(export, status=status.HTTP_200_OK)
+        qs = AssessmentValue.objects.all()
+        exporter = exports.AssessmentExporter.flat_export(
+            filtered_qs(qs, AssessmentValueFilterSet, request), filename="assessment-values"
+        )
+        return Response(exporter)

tests/hawc/apps/hawc_admin/test_api.py

@@ -82,7 +82,7 @@ def test_assessment_values(self):
         resp = client.get(url)
         assert resp.status_code == 200
         df = pd.read_json(StringIO(resp.content.decode()))
-        assert df.shape == (3, 33)
+        assert df.shape == (3, 44)
 
 
 @pytest.mark.django_db