Icf cpheapm73 79 add observations

hawc/apps/animal/exports.py

@@ -112,6 +112,7 @@ def get_value_map(self):
             "purity": "purity",
             "vehicle": "vehicle",
             "guideline_compliance": "guideline_compliance",
+            "guideline": "guideline",
             "description": "description",
         }
 

hawc/apps/animal/migrations/0032_experiment_guideline.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.1.1 on 2024-10-11 13:26
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("animal", "0031_tre"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="experiment",
+            name="guideline",
+            field=models.CharField(blank=True, max_length=128, null=True),
+        ),
+    ]

hawc/apps/animal/models.py

@@ -118,6 +118,7 @@ class Experiment(models.Model):
             414 and 412, 1981 versions). If not reported, then use state "not reported."
             """,
     )
+    guideline = models.CharField(max_length=128, blank=True, null=True)
     description = models.TextField(
         blank=True,
         verbose_name="Comments",

hawc/apps/animal/serializers.py

@@ -1,6 +1,7 @@
 import itertools
 import json
 
+from django.core.exceptions import ValidationError
 from django.db import transaction
 from rest_framework import serializers
 
@@ -13,6 +14,7 @@
 from ..study.models import Study
 from ..study.serializers import StudySerializer
 from ..vocab.constants import VocabularyTermType
+from ..vocab.serializers import GuidelineProfileSerializer
 from . import forms, models
 
 
@@ -47,6 +49,14 @@ def validate(self, data):
                     dict(dtxsid=f"DSSTox {dtxsid} does not exist")
                 ) from exc
 
+        # validate guideline profile
+        guideline = self.initial_data.get("guideline_profile")
+        if guideline:
+            valid_guidelines = GuidelineProfileSerializer._load_guideline_data()
+            names = [guideline["guideline_name"] for guideline in valid_guidelines]
+            if guideline not in names:
+                raise ValidationError(f"{guideline} is not a valid guideline")
+
         return data
 
     def create(self, validated_data):

hawc/apps/assessment/migrations/0047_assessment_enable_observations.py

@@ -0,0 +1,20 @@
+# Generated by Django 5.1.1 on 2024-10-17 14:16
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("assessment", "0046_assessmentvalue_value_type_qualifier"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="assessment",
+            name="enable_observations",
+            field=models.BooleanField(
+                default=True,
+                help_text="Observations can be used to identify negative effects in animal bioassay studies. The project must use the Toxicity Reference Database Vocabulary to use Observations.",
+            ),
+        ),
+    ]

hawc/apps/assessment/models.py

@@ -258,6 +258,10 @@ def get_rob_name_default():
         default=True,
         help_text="Show the downloads link on the assessment sidebar.",
     )
+    enable_observations = models.BooleanField(
+        default=True,
+        help_text="Observations can be used to identify negative effects in animal bioassay studies. The project must use the Toxicity Reference Database Vocabulary to use Observations.",
+    )
     conflicts_of_interest = models.TextField(
         blank=True,
         help_text="Describe any conflicts of interest by the assessment-team.",

hawc/apps/vocab/admin.py

@@ -74,3 +74,16 @@ def get_uid(self, obj):
     @admin.display(description="Related terms")
     def get_terms(self, obj):
         return ul_items(obj.terms.all(), lambda el: f"<a href={el.get_admin_edit_url()}>{el}</a>")
+
+
+@admin.register(models.GuidelineProfile)
+class GuidelineProfileAdmin(admin.ModelAdmin):
+    list_display = (
+        "id",
+        "guideline_id",
+        "endpoint",
+        "obs_status",
+        "description",
+    )
+    list_filter = ("guideline_id", "obs_status")
+    search_fields = ("guideline id", "obs_status")

hawc/apps/vocab/api.py

@@ -142,3 +142,23 @@ def bulk_update(self, request: Request) -> Response:
     def uids(self, request: Request) -> Response:
         qs = self.get_queryset().exclude(uid=None)
         return Response(qs.values_list("id", "uid"))
+
+
+class GuidelineProfileViewSet(viewsets.GenericViewSet):
+    serializer_class = serializers.GuidelineProfileSerializer
+    filename = "guideline_profiles"
+
+    def get_queryset(self, guideline=None) -> QuerySet:
+        guideline_id = models.GuidelineProfile.objects.get_guideline_id(guideline)
+        qs = models.GuidelineProfile.objects.all()
+        if guideline_id:
+            qs = qs.filter(guideline_id=guideline_id)
+        return qs
+
+    def get_df(self, guideline) -> pd.DataFrame:
+        qs = self.get_queryset(guideline).values()
+        return pd.DataFrame(list(qs))
+
+    @action(detail=True, renderer_classes=PandasRenderers, permission_classes=(AllowAny,))
+    def export(self, request: Request, pk: str):
+        return FlatExport.api_response(df=self.get_df(pk), filename=self.filename)

hawc/apps/vocab/constants.py

@@ -1,4 +1,4 @@
-from django.db.models import IntegerChoices
+from django.db.models import IntegerChoices, TextChoices
 from django.urls import reverse
 
 
@@ -70,3 +70,15 @@ class Ontology(IntegerChoices):
     """
 
     umls = 1, "UMLS"
+
+
+class ObservationStatus(TextChoices):
+    """
+    Guideline profile observation status
+    """
+
+    NM = "NM", "NM"
+    NR = "not required", "not required"
+    REC = "recommended", "recommended"
+    REQ = "required", "required"
+    TR = "triggered", "triggered"