500-errors

hawc/apps/animal/exports.py

@@ -115,16 +115,16 @@ def _get_data_rows(self):
             row.extend(Study.flat_complete_data_row(ser["animal_group"]["experiment"]["study"]))
             row.extend(models.Experiment.flat_complete_data_row(ser["animal_group"]["experiment"]))
             row.extend(models.AnimalGroup.flat_complete_data_row(ser["animal_group"]))
-            row.extend(
-                models.DosingRegime.flat_complete_data_row(ser["animal_group"]["dosing_regime"])
-            )
+            ser_dosing_regime = ser["animal_group"]["dosing_regime"]
+            row.extend(models.DosingRegime.flat_complete_data_row(ser_dosing_regime))
             row.extend(models.Endpoint.flat_complete_data_row(ser))
             for i, eg in enumerate(ser["groups"]):
                 row_copy = copy(row)
+                ser_doses = ser_dosing_regime["doses"] if ser_dosing_regime else None
                 row_copy.extend(
-                    models.DoseGroup.flat_complete_data_row(
-                        ser["animal_group"]["dosing_regime"]["doses"], self.doses, i
-                    )
+                    models.DoseGroup.flat_complete_data_row(ser_doses, self.doses, i)
+                    if ser_doses
+                    else [None for _ in self.doses]
                 )
                 row_copy.extend(models.EndpointGroup.flat_complete_data_row(eg, ser))
                 rows.append(row_copy)

hawc/apps/animal/models.py

@@ -318,7 +318,8 @@ def sex_symbol(self):
     def get_doses_json(self, json_encode=True):
         if not hasattr(self, "doses"):
             self.doses = [{"error": "no dosing regime"}]
-            self.doses = self.dosing_regime.get_doses_json(False)
+            if self.dosing_regime:
+                self.doses = self.dosing_regime.get_doses_json(False)
         if json_encode:
             return json.dumps(self.doses, cls=HAWCDjangoJSONEncoder)
         return self.doses
@@ -382,6 +383,12 @@ def delete_caches(cls, ids):
             Endpoint.objects.filter(animal_group__in=ids).values_list("id", flat=True)
         )
 
+    def can_delete(self) -> bool:
+        # can only be deleted if dosing regime is not associated with other animal groups
+        if not self.dosing_regime or self.dosing_regime.dosed_animals_id != self.id:
+            return True
+        return self.dosing_regime.can_delete()
+
     def copy_across_assessments(self, cw, skip_siblings: bool = False):
         children = list(self.endpoints.all().order_by("id"))
         old_id = self.id
@@ -544,18 +551,26 @@ def flat_complete_header_row():
     @staticmethod
     def flat_complete_data_row(ser):
         return (
-            ser["id"],
-            AnimalGroup.get_relation_id(ser["dosed_animals"]),
-            ser["route_of_exposure"],
-            ser["duration_exposure"],
-            ser["duration_exposure_text"],
-            ser["duration_observation"],
-            ser["num_dose_groups"],
-            ser["positive_control"],
-            ser["negative_control"],
-            cleanHTML(ser["description"]),
+            (
+                ser["id"],
+                AnimalGroup.get_relation_id(ser["dosed_animals"]),
+                ser["route_of_exposure"],
+                ser["duration_exposure"],
+                ser["duration_exposure_text"],
+                ser["duration_observation"],
+                ser["num_dose_groups"],
+                ser["positive_control"],
+                ser["negative_control"],
+                cleanHTML(ser["description"]),
+            )
+            if ser
+            else (None for _ in range(10))
         )
 
+    def can_delete(self) -> bool:
+        # can delete only if no animals others than those dosed are related
+        return self.animalgroup_set.exclude(id=self.dosed_animals_id).count() == 0
+
     def get_doses_json(self, json_encode=True):
         doses = []
         dgs = self.dose_groups.order_by("dose_units_id", "dose_group_id")

hawc/apps/animal/templates/animal/animalgroup_confirm_delete.html

@@ -2,5 +2,10 @@
 
 {% block content %}
   {{ block.super }}
-  {% include "hawc/_delete_block.html" with name="animal-group" notes="This will remove all data associated with the animal-group, including dose-regimes, endpoints, and BMD modeling runs." %}
+
+  {% if object.can_delete %}
+    {% include "hawc/_delete_block.html" with name="animal-group" notes="This will remove all data associated with the animal-group, including dose-regimes, endpoints, and BMD modeling runs." %}
+  {% else %}
+    <div class="alert alert-danger" role="alert">Cannot be deleted. The dosing regime is associated with at least one more animal group; please delete associated animal groups before continuing.</div>
+  {% endif %}
 {% endblock content %}

hawc/apps/animal/templates/animal/animalgroup_detail.html

@@ -38,12 +38,12 @@ <h2 id="animal-group-header" class="d-inline-block">{{object}}</h2>
 window.app.startup("animalStartup", function(animal){
     const data = window.app.getConfig();
     animal.AnimalGroup.get_object(data.id, function(d){
-        $('h2#animal-group-header')
-          .after(
-              d.build_details_table(),
-              $("<h3>Dosing regime</h3>"),
-              d.build_dr_details_table()
-          );
+      inserts = [d.build_details_table()];
+      if (data.has_dosing_regime){
+        inserts.push($("<h3>Dosing regime</h3>"));
+        inserts.push(d.build_dr_details_table());
+      }
+      $('h2#animal-group-header').after(inserts);
     });
     animal.startupAnimalGroupTable(document.getElementById("animalGroupTableMain"), data);
   });

hawc/apps/animal/templates/animal/endpoint_form.html

@@ -4,8 +4,11 @@
 {% load crispy_forms_tags %}
 
 {% block content %}
-
-  {% crispy form %}
+  {% if animal_group.dosing_regime %}
+    {% crispy form %}
+  {% else %}
+    <div class="alert alert-danger" role="alert">Cannot create or modify an endpoint. The animal group has no dose regime. Please update the animal group to add a dosing regime before continuing.</div>
+  {% endif %}
 
   {# extra stuff that JS will move to correct location #}
   <div id="extra" class="hidden">

hawc/apps/animal/views.py

@@ -201,6 +201,7 @@ def get_context_data(self, **kwargs):
         )
         context["config"] = dict(
             id=self.object.id,
+            has_dosing_regime=self.object.dosing_regime is not None,
             endpoints=[endpoint.get_json(json_encode=False) for endpoint in endpoints],
         )
         return context
@@ -239,6 +240,8 @@ class AnimalGroupDelete(BaseDelete):
     model = models.AnimalGroup
 
     def get_success_url(self):
+        if not self.object.can_delete():
+            raise ValueError("Cannot be deleted")
         return self.object.experiment.get_absolute_url()
 
 
@@ -332,11 +335,12 @@ def get_form_kwargs(self):
         return kwargs
 
     def build_initial_formset_factory(self):
+        num_groups = self.parent.dosing_regime.num_dose_groups if self.parent.dosing_regime else 1
         Formset = modelformset_factory(
             models.EndpointGroup,
             form=forms.EndpointGroupForm,
             formset=forms.BaseEndpointGroupFormSet,
-            extra=self.parent.dosing_regime.num_dose_groups,
+            extra=num_groups,
         )
         return Formset(queryset=models.EndpointGroup.objects.none())
 
@@ -365,6 +369,7 @@ def post_object_save(self, form, formset):
 
     def get_context_data(self, **kwargs):
         context = super().get_context_data(**kwargs)
+        context["animal_group"] = self.parent
         context["vocabulary"] = self.model.get_vocabulary_settings(self.assessment, context["form"])
         return context
 

hawc/apps/lit/api.py

@@ -299,9 +299,11 @@ def reference_search(self, request, pk):
     def excel_to_json(self, request, pk):
         self.get_object()  # permissions check
 
-        file_ = request.data["file"]
+        file_ = request.data.get("file")
 
-        if not file_.name.endswith(".xlsx"):
+        if file_ is None:
+            raise ValidationError({"file": "A file is required"})
+        elif not file_.name.endswith(".xlsx"):
             raise ValidationError({"file": "File extension must be .xlsx"})
 
         try:

tests/data/api/api-animal-assessment-full-export-missing-dr.json

@@ -0,0 +1 @@
+[]

tests/hawc/apps/animal/test_api.py

@@ -7,6 +7,7 @@
 from rest_framework.test import APIClient
 
 from hawc.apps.animal import forms, models
+from hawc.apps.assessment.models import Species, Strain
 
 from ..test_utils import check_details_of_last_log_entry
 
@@ -56,6 +57,30 @@ def test_full_export(self, rewrite_data_files: bool, db_keys):
         )
         self._test_flat_export(rewrite_data_files, fn, url)
 
+    def test_missing_dosing_regime(self, rewrite_data_files: bool, db_keys):
+        # create an animal group/endpoint with no dosing regime and make sure the export doesn't cause a 500 error
+        fn = "api-animal-assessment-full-export-missing-dr.json"
+        experiment = models.Experiment.objects.get(pk=1)
+        species = Species.objects.get(pk=1)
+        strain = Strain.objects.get(pk=1)
+        animal_group = models.AnimalGroup(
+            experiment=experiment,
+            species=species,
+            strain=strain,
+            sex="C",
+        )
+        animal_group.save()
+        endpoint = models.Endpoint(
+            assessment_id=db_keys.assessment_working,
+            animal_group=animal_group,
+        )
+        endpoint.save()
+        url = (
+            reverse("animal:api:assessment-full-export", args=(db_keys.assessment_working,))
+            + "?format=json"
+        )
+        self._test_flat_export(rewrite_data_files, fn, url)
+
     def test_endpoint_export(self, rewrite_data_files: bool, db_keys):
         fn = "api-animal-assessment-endpoint-export.json"
         url = (

tests/hawc/apps/animal/test_models.py

@@ -1,6 +1,52 @@
 import pytest
 
 from hawc.apps.animal import models
+from hawc.apps.assessment.models import Species, Strain
+from hawc.apps.study.models import Study
+
+
+@pytest.mark.django_db
+class TestAnimalGroup:
+    def test_can_delete(self):
+        study = Study.objects.get(pk=1)
+        experiment = models.Experiment(
+            study=study,
+            name="test",
+            type="Rp",
+        )
+        experiment.save()
+        species = Species.objects.get(pk=1)
+        strain = Strain.objects.get(pk=1)
+        dr = models.DosingRegime(route_of_exposure="OR")
+        dr.save()
+        parent = models.AnimalGroup(
+            experiment=experiment,
+            name="parent",
+            sex="C",
+            dosing_regime=dr,
+            species=species,
+            strain=strain,
+        )
+        dr.dosed_animals = parent
+        parent.save()
+        dr.save()
+        child = models.AnimalGroup(
+            experiment=experiment,
+            name="child",
+            sex="C",
+            dosing_regime=dr,
+            species=species,
+            strain=strain,
+        )
+        child.save()
+        assert parent.can_delete() is False
+        assert child.can_delete() is True
+        child.delete()
+        assert parent.can_delete() is True
+
+        # animal group with no dosing regime can be deleted
+        parent.dosing_regime = None
+        assert parent.can_delete() is True
 
 
 @pytest.mark.django_db

tests/hawc/apps/lit/test_api.py

@@ -271,6 +271,10 @@ def test_excel_to_json(self, db_keys):
             "detail": "Missing filename. Request should include a Content-Disposition header with a filename parameter."
         }
 
+        # invalid; no file returns an error
+        resp = c.post(url)
+        assert resp.status_code == 400 and resp.json() == {"file": "A file is required"}
+
         # invalid; non excel files return an error
         resp = c.post(url, {"file": csv}, HTTP_CONTENT_DISPOSITION="attachment; filename=test.csv")
         assert resp.status_code == 400 and resp.json() == {"file": "File extension must be .xlsx"}