Icf cpheapm71 72 add guidelines

hawc/apps/animal/exports.py

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

hawc/apps/animal/migrations/0032_experiment_guideline_profile.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_profile",
+            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_profile = 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/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"

hawc/apps/vocab/fixtures/guidelines.json

@@ -0,0 +1,128 @@
+[
+    {
+        "guideline_id": "1",
+        "guideline_number": "870.31",
+        "guideline_name": "90-day Oral Toxicity in Rodents",
+        "profile_name": "SUB_oral_rode",
+        "description": ""
+    },
+    {
+        "guideline_id": "2",
+        "guideline_number": "870.315",
+        "guideline_name": "90-day Oral Toxicity in Nonrodents",
+        "profile_name": "SUB_oral_nonr",
+        "description": ""
+    },
+    {
+        "guideline_id": "3",
+        "guideline_number": "870.325",
+        "guideline_name": "90-day Dermal Toxicity",
+        "profile_name": "SUB_sub_derm",
+        "description": ""
+    },
+    {
+        "guideline_id": "4",
+        "guideline_number": "870.3465",
+        "guideline_name": "90-Day Inhalation Toxicity",
+        "profile_name": "SUB_sub_inha",
+        "description": ""
+    },
+    {
+        "guideline_id": "5",
+        "guideline_number": "870.355",
+        "guideline_name": "Reproduction/Development Toxicity Screening Test",
+        "profile_name": "REP_rep_dev",
+        "description": ""
+    },
+    {
+        "guideline_id": "6",
+        "guideline_number": "870.37",
+        "guideline_name": "Prenatal Developmental Toxicity Study",
+        "profile_name": "DEV_pren_dev",
+        "description": ""
+    },
+    {
+        "guideline_id": "7",
+        "guideline_number": "870.38",
+        "guideline_name": "Reproduction and Fertility Effects post 1998",
+        "profile_name": "MGR_rep_fert",
+        "description": "MGR studies post 1998 (study_year 1996)"
+    },
+    {
+        "guideline_id": "8",
+        "guideline_number": "870.41",
+        "guideline_name": "Chronic Toxicity",
+        "profile_name": "CHR_chr_tox",
+        "description": ""
+    },
+    {
+        "guideline_id": "9",
+        "guideline_number": "870.42",
+        "guideline_name": "Carcinogenicty",
+        "profile_name": "CHR_carc",
+        "description": ""
+    },
+    {
+        "guideline_id": "10",
+        "guideline_number": "870.43",
+        "guideline_name": "Combined Chronic Toxicity/Carcinogenicity",
+        "profile_name": "CHR_chr_canc",
+        "description": ""
+    },
+    {
+        "guideline_id": "11",
+        "guideline_number": "870.62",
+        "guideline_name": "Neurotoxicity Screening Battery",
+        "profile_name": "NEU_neur_bat",
+        "description": ""
+    },
+    {
+        "guideline_id": "12",
+        "guideline_number": "870.63",
+        "guideline_name": "Developmental Neurotoxicity Study",
+        "profile_name": "DNT_dev_neur",
+        "description": ""
+    },
+    {
+        "guideline_id": "13",
+        "guideline_number": "870.38",
+        "guideline_name": "Reproduction and Fertility Effects pre 1998",
+        "profile_name": "MGR_rep_fert_pre98",
+        "description": "MGR studies pre 1998 (study year 1996)"
+    },
+    {
+        "guideline_id": "14",
+        "guideline_number": "870.305",
+        "guideline_name": "28-day Oral Toxicity in Rodents",
+        "profile_name": "SAC_oral_rode_28",
+        "description": ""
+    },
+    {
+        "guideline_id": "15",
+        "guideline_number": "NULL",
+        "guideline_name": "14-day Toxicity in Rodents",
+        "profile_name": "SAC_ntp",
+        "description": ""
+    },
+    {
+        "guideline_id": "16",
+        "guideline_number": "NULL",
+        "guideline_name": "13-Week Toxicity in Rodents",
+        "profile_name": "SUB_ntp",
+        "description": ""
+    },
+    {
+        "guideline_id": "17",
+        "guideline_number": "NULL",
+        "guideline_name": "2 - Year Toxicity",
+        "profile_name": "CHR_ntp",
+        "description": ""
+    },
+    {
+        "guideline_id": "18",
+        "guideline_number": "NULL",
+        "guideline_name": "Non-guideline",
+        "profile_name": "NON-GUIDE",
+        "description": ""
+    }
+]

hawc/apps/vocab/migrations/00010_load_guideline_profile.py

@@ -0,0 +1,24 @@
+from pathlib import Path
+
+from django.core.management import call_command
+from django.db import migrations
+
+
+def load_fixture(apps, schema_editor):
+    here = Path(__file__).parent
+    fixtures = (here / "../fixtures").resolve()
+    call_command("loaddata", str(fixtures / "guideline_profile.jsonl"), app_label="vocab")
+
+
+def unload_fixture(apps, schema_editor):
+    apps.get_model("vocab", "GuidelineProfile").objects.all().delete()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("vocab", "0009_guideline_profile"),
+    ]
+
+    operations = [
+        migrations.RunPython(load_fixture, reverse_code=unload_fixture),
+    ]

hawc/apps/vocab/migrations/0009_guideline_profile.py

@@ -0,0 +1,54 @@
+# Generated by Django 5.1.1 on 2024-10-11 14:36
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("vocab", "0008_alter_term_namespace"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="GuidelineProfile",
+            fields=[
+                (
+                    "guideline_profile_id",
+                    models.PositiveIntegerField(
+                        primary_key=True, serialize=False, unique=True, verbose_name="ID"
+                    ),
+                ),
+                ("guideline_id", models.PositiveIntegerField()),
+                (
+                    "endpoint",
+                    models.ForeignKey(
+                        blank=True,
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        to="vocab.term",
+                    ),
+                ),
+                ("endpoint_category", models.CharField(max_length=256)),
+                ("endpoint_type", models.CharField(max_length=256)),
+                ("endpoint_target", models.CharField(max_length=256)),
+                (
+                    "obs_status",
+                    models.CharField(
+                        choices=[
+                            ("NM", "NM"),
+                            ("not required", "not required"),
+                            ("recommended", "recommended"),
+                            ("required", "required"),
+                            ("triggered", "triggered"),
+                        ],
+                        null=True,
+                    ),
+                ),
+                ("description", models.TextField(blank=True)),
+            ],
+            options={
+                "ordering": ("guideline_profile_id",),
+            },
+        ),
+    ]

hawc/apps/vocab/models.py

@@ -202,6 +202,26 @@ def __str__(self) -> str:
         return f"{self.term} -> {self.entity}"
 
 
+class GuidelineProfile(models.Model):
+    guideline_profile_id = models.PositiveIntegerField(
+        unique=True, primary_key=True, verbose_name="ID"
+    )
+    guideline_id = models.PositiveIntegerField()
+    endpoint = models.ForeignKey("Term", on_delete=models.CASCADE, blank=True, null=True)
+    endpoint_category = models.CharField(max_length=256)
+    endpoint_type = models.CharField(max_length=256)
+    endpoint_target = models.CharField(max_length=256)
+    obs_status = models.CharField(choices=constants.ObservationStatus, null=True)
+    description = models.TextField(blank=True)
+
+    class Meta:
+        ordering = ("guideline_profile_id",)
+
+    def __str__(self) -> str:
+        return f"{self.guideline_id}::{self.profile_id}::{self.endpoint_id}"
+
+
 reversion.register(Term)
 reversion.register(Entity)
 reversion.register(EntityTermRelation)
+reversion.register(GuidelineProfile)

hawc/apps/vocab/serializers.py

@@ -1,3 +1,8 @@
+import json
+from pathlib import Path
+
+from django.conf import settings
+from django.core.exceptions import ValidationError
 from django.utils import timezone
 from rest_framework import serializers
 
@@ -43,3 +48,24 @@ def get_unique_together_validators(self):
     class Meta:
         model = models.Entity
         fields = ("id", "ontology", "uid")
+
+
+class GuidelineProfileSerializer(serializers.ModelSerializer):
+    class Meta:
+        model = models.GuidelineProfile
+        fields = "_all_"
+
+    def validate_guideline_profile_id(self, guideline_id):
+        # validate guideline profile
+        if guideline_id:
+            valid_guidelines = self._load_guideline_data()
+            ids = [guideline["guideline_id"] for guideline in valid_guidelines]
+            if guideline_id not in ids:
+                raise ValidationError(f"{guideline_id} is not a valid guideline")
+
+        return guideline_id
+
+    def _load_guideline_data() -> dict:
+        """Return guideline fixture data."""
+        p = Path(settings.PROJECT_PATH) / "apps/vocab/fixtures/guidelines.json"
+        return json.loads(p.read_text())