Icf cpheapm79 observations animalv2

frontend/animal/EndpointForm/constants.js

@@ -62,14 +62,14 @@ const termUrlLookupMap = {
             endpoint_name_parent: "effect_subtype_term_id",
         },
         helpText: {
-            system_popup: `The health effect category/biological system an endpoint/outcome or group of related endpoints/outcomes within a health effect category. "Multi-system" is an option for widespread effects. If the Endpoint is measured in Blood, Urine, or biological media other than the affected system, extract the media term in the Effect Subtype field.`,
+            system_popup: `The health effect category/biological system an endpoint/outcome or group of related endpoints/outcomes within a health effect category. 'System' maps to 'endpoint_category' in ToxRefDB as the broadest descriptive term for an endpoint. Possible endpoint categories include: systemic, developmental, reproductive, and cholinesterase.`,
             system: `The health effect category/biological system an endpoint/outcome or group of related endpoints/outcomes within a health effect category. Please use a controlled vocabulary term if possible.`,
-            effect_popup: `A group of related outcomes considered as a health effect category and/or unit of analysis typically considered together during evidence synthesis.`,
+            effect_popup: `A group of related outcomes considered as a health effect category and/or unit of analysis typically considered together during evidence synthesis. 'Effect' maps to 'endpoint_type' in ToxRefDB as a subcategory for endpoint_category, which is more descriptive for a particular endpoint (e.g. pathology gross, clinical chemistry, reproductive performance, etc.`,
             effect: `Related outcomes (e.g., unit of analysis) considered together during evidence synthesis. Please use a controlled vocabulary term if possible.`,
-            effect_subtype_popup: `An outcome or measurement within an effect.`,
+            effect_subtype_popup: `An outcome or measurement within an effect. 'Effect_subtype' maps to 'Endpoint_target' in ToxRefDB indicating where or how the sample was collected to supply data for a particular endpoint. Typically describes an organ/tissue or metabolite/protein measured.`,
             effect_subtype: `Please use a controlled vocabulary term if possible.`,
             endpoint_name_popup: `An observable or measurable biological change used as an index of a potential health effect of an exposure. Endpoint may also be referred to as effect, outcome, or event. Search for the best match based on the author reported term. Use the field "Diagnostic (as reported)" to capture as reported by study authors. If no existing term matches, deselect use EHV for endpoint and enter the name as reported. Do not include units. If an endpoint is a repeated measure, indicate the time in parentheses, [e.g., running wheel activity (6 wk)], using the abbreviated format: seconds = sec, minutes = min, hours = h, days = d, weeks = wk, months = mon, years = y.`,
-            endpoint_name: `An observable or measurable biological change used as an index of a potential health effect of an exposure. Endpoint may also be referred to as effect or outcome. For a searchable list of ToxRefDB Vocabulary terms, see the <a href="/vocab/toxrefdb/">ToxRefDB.</a> Enter the term ID and all relationships to this term will automatically populate. Please use a controlled vocabulary term if possible.`,
+            endpoint_name: `An observable or measurable biological change used as an index of a potential health effect of an exposure. 'Endpoint_name' maps to 'Effect_desc' in ToxRefDB, detailing a specific condition associated with an endpoint_target (e.g. dysplasia, atrophy, necrosis, etc.`,
         },
     },
     defaultHelpText = {

frontend/animal/VocabBrowser/ToxRefDBBrowser/Table.js

@@ -44,28 +44,28 @@ class Table extends Component {
                         <thead>
                             <tr>
                                 <th>
-                                    Endpoint Category
+                                    System
                                     <HelpTextPopup
                                         title="Endpoint Category"
                                         content={helpText.system_popup}
                                     />
                                 </th>
                                 <th>
-                                    Endpoint Type
+                                    Effect
                                     <HelpTextPopup
                                         title="Endpoint Type"
                                         content={helpText.effect_popup}
                                     />
                                 </th>
                                 <th>
-                                    Endpoint Target
+                                    Effect Subtype
                                     <HelpTextPopup
                                         title="Endpoint Target"
                                         content={helpText.effect_subtype_popup}
                                     />
                                 </th>
                                 <th>
-                                    Effect Description
+                                    Endpoint/Outcome
                                     <HelpTextPopup
                                         title="Effect Description"
                                         content={helpText.endpoint_name_popup}

hawc/apps/animalv2/autocomplete.py

@@ -6,3 +6,10 @@
 class ChemicalAutocomplete(BaseAutocomplete):
     model = models.Chemical
     search_fields = ["name"]
+
+
+@register
+class ExperimentAutocomplete(BaseAutocomplete):
+    model = models.Experiment
+    search_fields = ["name"]
+    filter_fields = ["study_id", "study__assessment_id"]

hawc/apps/animalv2/filterset.py

@@ -0,0 +1,81 @@
+import django_filters as df
+from django.db.models import Q
+
+from ..common.autocomplete import AutocompleteTextWidget
+from ..common.filterset import (
+    BaseFilterSet,
+    InlineFilterForm,
+    PaginationFilter,
+)
+from . import autocomplete, models
+
+
+class ExperimentFilterSet(BaseFilterSet):
+    query = df.CharFilter(
+        method="filter_query",
+        label="Short Citation",
+        help_text="Filter citations (author, year, title, ID)",
+    )
+    name = df.CharFilter(
+        lookup_expr="icontains",
+        label="Experiment name",
+        widget=AutocompleteTextWidget(
+            autocomplete_class=autocomplete.ExperimentAutocomplete,
+            field="name",
+            attrs={
+                "data-placeholder": "Filter by name (ex: developmental)",
+                "class": "autocompletefilter",
+            },
+        ),
+    )
+    design = df.CharFilter(
+        lookup_expr="icontains",
+        label="Experiment design",
+        widget=AutocompleteTextWidget(
+            autocomplete_class=autocomplete.ExperimentAutocomplete,
+            field="design",
+            attrs={"data-placeholder": "Filter by design (ex: B)", "class": "autocompletefilter"},
+        ),
+    )
+    chemical = df.CharFilter(
+        field_name="v2_chemicals__name",
+        lookup_expr="icontains",
+        label="Chemical name",
+        widget=AutocompleteTextWidget(
+            autocomplete_class=autocomplete.ChemicalAutocomplete,
+            field="name",
+            attrs={"data-placeholder": "Chemical name", "class": "autocompletefilter"},
+        ),
+        help_text="ex: sodium",
+    )
+    cas = df.CharFilter(
+        field_name="v2_chemicals__cas",
+        lookup_expr="icontains",
+        label="CAS",
+        widget=AutocompleteTextWidget(
+            autocomplete_class=autocomplete.ChemicalAutocomplete,
+            field="cas",
+            attrs={"data-placeholder": "CAS", "class": "autocompletefilter"},
+        ),
+        help_text="ex: 107-02-8",
+    )
+    paginate_by = PaginationFilter()
+
+    class Meta:
+        model = models.Experiment
+        form = InlineFilterForm
+        fields = ["query", "name", "design", "paginate_by"]
+        main_field = "query"
+        appended_fields = ["name", "design", "chemical", "cas", "paginate_by"]
+
+    def __init__(self, *args, assessment, **kwargs):
+        super().__init__(*args, assessment=assessment, **kwargs)
+
+    def filter_queryset(self, queryset):
+        queryset = super().filter_queryset(queryset).prefetch_related("v2_chemicals")
+        queryset = queryset.filter(study__assessment=self.assessment, study__bioassay=True)
+        return queryset
+
+    def filter_query(self, queryset, name, value):
+        query = Q(study__short_citation__icontains=value)
+        return queryset.filter(query)

hawc/apps/animalv2/forms.py

@@ -6,6 +6,7 @@
 from ..assessment.autocomplete import DSSToxAutocomplete
 from ..common.autocomplete import AutocompleteSelectWidget, AutocompleteTextWidget
 from ..common.forms import BaseFormHelper
+from ..vocab.models import GuidelineProfile
 from . import autocomplete, constants, models
 
 
@@ -66,6 +67,9 @@ def __init__(self, *args, **kwargs):
         self.fields["has_multiple_generations"].widget = forms.Select(
             choices=((True, "Yes"), (False, "No"))
         )
+        self.fields["guideline"].widget = forms.Select(
+            choices=GuidelineProfile.objects.get_guideline_choices()
+        )
 
     @property
     def helper(self):

hawc/apps/animalv2/migrations/0003_experiment_guideline.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.1.6 on 2025-02-09 22:39
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("animalv2", "0002_studylevelvalue"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="experiment",
+            name="guideline",
+            field=models.CharField(blank=True, max_length=128, null=True),
+        ),
+    ]

hawc/apps/animalv2/models.py

@@ -31,6 +31,7 @@ class Experiment(models.Model):
         blank=True,
         help_text="""Description of any compliance methods used (i.e. use of EPA OECD, NTP, or other guidelines; conducted under GLP guideline conditions, non-GLP but consistent with guideline study, etc.). This field response should match any description used in study evaluation in the reporting quality domain, e.g., GLP study (OECD guidelines 414 and 412, 1981 versions). If not reported, then use state \"not reported.\"""",
     )
+    guideline = models.CharField(max_length=128, blank=True, null=True)
     comments = models.TextField(
         blank=True,
         help_text="Additional comments (eg., description, animal husbandry, etc.)",

hawc/apps/animalv2/templates/animalv2/experiment_detail.html

@@ -8,6 +8,10 @@ <h2>{{object.name}}</h2>
         <span class="dropdown-header">Experiment editing</span>
         <a class="dropdown-item" href="{{object.get_update_url}}">Update</a>
         <a class="dropdown-item" href="{{object.get_delete_url}}">Delete</a>
+        <a class="dropdown-item" href="{% url 'vocab:api:guideline_profile-export' object.guideline %}?format=csv">View guideline profiles</a>
+        {% if assessment.enable_observations and object.guideline %}
+          <a class="dropdown-item" href="{% url 'vocab:observation-list' object.pk %}?order_by=system">View observations</a>
+        {% endif %}
       {% endactions %}
     {% endif %}
   </div>

hawc/apps/animalv2/templates/animalv2/experiment_list.html

@@ -0,0 +1,39 @@
+{% extends 'assessment-rooted.html' %}
+
+{% block content %}
+  <div class="d-flex">
+    <h2>Available bioassay experiments ({{page_obj.paginator.count}} found)</h2>
+  </div>
+
+  {% include 'common/inline_filter_form.html' %}
+
+  <table id="mainTbl" class="table table-sm table-striped">
+    {% bs4_colgroup '25,25,50' %}
+    {% bs4_thead 'Short citation,Experiment name,Experiment design' %}
+    <tbody>
+      {% for object in object_list %}
+        <tr>
+          <td>
+            <a href="{% url 'vocab:observation-list' object.pk %}?order_by=system">{{ object.study.short_citation }}</a>
+            {% debug_badge object.id %}
+          </td>
+          <td>
+            <a href="{% url 'study:detail' object.pk %}">{{ object.name }}</a>
+          </td>
+          <td>
+            <a href="{% url 'study:detail' object.pk %}">{{ object.design }}</a>
+          </td>
+        </tr>
+      {% empty %}
+        <tr>
+          <td colspan="7">
+            No experiments available
+          </td>
+        </tr>
+      {% endfor %}
+    </tbody>
+  </table>
+
+  {% include 'includes/paginator.html' with plural_object_name='experiments' %}
+
+{% endblock %}

hawc/apps/animalv2/templates/animalv2/fragments/_experiment_table.html

@@ -5,6 +5,7 @@
     {% optional_table_row "Design" object.get_design_display %}
     {% optional_table_row "Multiple generations" object.get_has_multiple_generations_display %}
     {% optional_table_row "Guideline compliance" object.guideline_compliance %}
+    {% optional_table_row "Guideline" object.guideline %}
     {% optional_table_row "Comments" object.comments %}
   </tbody>
 </table>

hawc/apps/animalv2/urls.py

@@ -20,6 +20,7 @@
         views.ExperimentDetail.as_view(),
         name="experiment_detail",
     ),
+    path("assessment/<int:pk>/", views.ExperimentFilterList.as_view(), name="experiment_list"),
     path(
         "experiment/<int:pk>/delete/",
         views.ExperimentDelete.as_view(),

hawc/apps/animalv2/views.py

@@ -4,20 +4,22 @@
 from django.http import HttpRequest
 from django.shortcuts import render
 
+from ..assessment.models import Assessment
 from ..common.forms import FormsetGenericFormHelper
 from ..common.htmx import HtmxViewSet, Item, action, can_edit, can_view
 from ..common.views import (
     BaseCreate,
     BaseDelete,
     BaseDetail,
+    BaseFilterList,
     BaseList,
     BaseUpdate,
     FormsetConfiguration,
     create_object_log,
 )
 from ..mgmt.views import EnsureExtractionStartedMixin
 from ..study.models import Study
-from . import forms, models
+from . import filterset, forms, models
 
 # TODO - make sure HTML views efficiently query database, HTMX views lower priority
 
@@ -258,6 +260,17 @@ def get_context_data(self, **kwargs):
         return context
 
 
+class ExperimentFilterList(BaseFilterList):
+    template_name = "animalv2/experiment_list.html"
+    parent_model = Assessment
+    model = models.Experiment
+    filterset_class = filterset.ExperimentFilterSet
+    paginate_by = 50
+
+    def get_queryset(self):
+        return super().get_queryset()
+
+
 class ChemicalViewSet(ExperimentChildViewSet):
     model = models.Chemical
     form_class = forms.ChemicalForm

hawc/apps/assessment/forms.py

@@ -319,6 +319,7 @@ class Meta:
             "enable_summary_tables",
             "enable_visuals",
             "enable_downloads",
+            "enable_observations",
             "noel_name",
             "rob_name",
             "vocabulary",
@@ -354,13 +355,27 @@ def helper(self):
         )
         helper.add_row("enable_literature_review", 3, "col-lg-4")
         helper.add_row("enable_risk_of_bias", 3, "col-lg-4")
-        helper.add_row("enable_visuals", 2, "col-lg-6")
+        helper.add_row("enable_visuals", 3, "col-lg-4")
         helper.add_row("noel_name", 3, "col-lg-4")
         helper.add_row(
             "epi_version", 2 if settings.HAWC_FEATURES.ENABLE_BIOASSAY_V2 else 1, "col-lg-4"
         )
         return helper
 
+    def clean(self):
+        cleaned_data = super().clean()
+
+        obs_enabled = cleaned_data.get("enable_observations")
+        vocabulary = cleaned_data.get("vocabulary")
+
+        if obs_enabled and vocabulary != VocabularyNamespace.ToxRefDB:
+            self.add_error(
+                "enable_observations",
+                "Toxicity Reference Database Vocabulary must be selected to enable observations.",
+            )
+
+        return cleaned_data
+
 
 class AttachmentForm(forms.ModelForm):
     class Meta:

hawc/apps/assessment/migrations/0049_assessment_enable_observations.py

@@ -0,0 +1,20 @@
+# Generated by Django 5.1.6 on 2025-02-09 23:39
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("assessment", "0048_assessment_animal_version"),
+    ]
+
+    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

@@ -29,3 +29,16 @@ def get_queryset(self, request):
 
     def has_delete_permission(self, request, obj=None):
         return False
+
+
+@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")