Assessment values update (#792)

* WIP modify fields based on sci feedback

* add adaf footnote to assessment detail and value detail templates

* lint

* fix imports

* update yaml

* Edit ADAF display

* change table column order and change to info icon

* Add changes from meeting feedback

* adjust help texts

* wip

* update adaf help text and footnote

* textual and layout updates

* ruff

---------

Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>

hawc/apps/assessment/constants.py

@@ -2,6 +2,13 @@
 
 from .permissions import AssessmentPermissions
 
+ADAF_FOOTNOTE = (
+    "Age-dependent ajustment factors (ADAFs) have not been applied to the value shown. "
+    "Application of ADAFs is recommended in combination with appropriate exposure data when "
+    "assessing risk associated with early-life exposure. More information is available in the "
+    "comments field for this value."
+)
+
 
 class AssessmentViewPermissions(models.IntegerChoices):
     PROJECT_MANAGER = 1

hawc/apps/assessment/forms.py

@@ -16,11 +16,7 @@
 from hawc.apps.study.models import Study
 from hawc.services.epa.dsstox import DssSubstance
 
-from ..common.autocomplete import (
-    AutocompleteSelectMultipleWidget,
-    AutocompleteSelectWidget,
-    AutocompleteTextWidget,
-)
+from ..common.autocomplete import AutocompleteSelectMultipleWidget, AutocompleteTextWidget
 from ..common.forms import (
     BaseFormHelper,
     QuillField,
@@ -44,6 +40,10 @@ class AssessmentForm(forms.ModelForm):
     class Meta:
         exclude = (
             "creator",
+            "noel_name",
+            "rob_name",
+            "vocabulary",
+            "modify_uncontrolled_vocabulary",
             "enable_literature_review",
             "enable_project_management",
             "enable_data_extraction",
@@ -119,7 +119,6 @@ def helper(self):
         helper.add_row("project_manager", 3, "col-md-4")
         helper.add_row("editable", 3, "col-md-4")
         helper.add_row("conflicts_of_interest", 2, "col-md-6")
-        helper.add_row("noel_name", 4, "col-md-3")
         helper.add_create_btn("dtxsids", reverse("assessment:dtxsid_create"), "Add new DTXSID")
         helper.attrs["novalidate"] = ""
         return helper
@@ -190,6 +189,9 @@ class Meta:
             "system": AutocompleteTextWidget(
                 autocomplete_class=autocomplete.AssessmentValueAutocomplete, field="system"
             ),
+            "species_studied": AutocompleteTextWidget(
+                autocomplete_class=autocomplete.AssessmentValueAutocomplete, field="species_studied"
+            ),
             "duration": AutocompleteTextWidget(
                 autocomplete_class=autocomplete.AssessmentValueAutocomplete, field="duration"
             ),
@@ -209,9 +211,6 @@ class Meta:
             "pod_unit": AutocompleteTextWidget(
                 autocomplete_class=autocomplete.AssessmentValueAutocomplete, field="pod_unit"
             ),
-            "species_studied": AutocompleteSelectWidget(
-                autocomplete_class=autocomplete.SpeciesAutocomplete
-            ),
             "pod_type": AutocompleteTextWidget(
                 autocomplete_class=autocomplete.AssessmentValueAutocomplete, field="pod_type"
             ),
@@ -265,11 +264,11 @@ def helper(self):
                 cancel_url=self.instance.assessment.get_absolute_url(),
             )
         helper.add_row("evaluation_type", 2, "col-md-6")
-        helper.add_row("value_type", 3, "col-md-4")
+        helper.add_row("value_type", 4, "col-md-3")
         helper.add_row("confidence", 3, "col-md-4")
         helper.add_row("pod_type", 4, "col-md-3")
         helper.add_row("species_studied", 3, "col-md-4")
-        helper.add_row("tumor_type", 4, "col-md-3")
+        helper.add_row("tumor_type", 2, "col-md-6")
         helper.add_row("comments", 2, "col-md-6")
 
         return helper
@@ -342,6 +341,9 @@ class Meta:
             "enable_risk_of_bias",
             "enable_bmd",
             "enable_summary_text",
+            "noel_name",
+            "rob_name",
+            "vocabulary",
             "epi_version",
         )
         model = models.Assessment
@@ -356,7 +358,7 @@ def __init__(self, *args, **kwargs):
     def helper(self):
         helper = BaseFormHelper(
             self,
-            legend_text="Update enabled modules",
+            legend_text="Update modules",
             help_text="""
                 HAWC is composed of multiple modules, each designed
                 to capture data and decisions related to specific components of a
@@ -367,6 +369,10 @@ def helper(self):
                 """,
             cancel_url=self.instance.get_absolute_url(),
         )
+        helper.add_row("enable_literature_review", 3, "col-lg-4")
+        helper.add_row("enable_risk_of_bias", 3, "col-lg-4")
+        helper.add_row("noel_name", 3, "col-lg-4")
+        helper.add_row("epi_version", 1, "col-lg-4")
         return helper
 
 

hawc/apps/assessment/migrations/0030_assessment_part1.py

@@ -129,7 +129,7 @@ class Migration(migrations.Migration):
             name="authors",
             field=models.TextField(
                 default="",
-                verbose_name="Assessment authors",
+                verbose_name="Assessment authors/organization",
                 help_text="""A publicly visible description of the assessment authors (if the assessment is made public). This could be an organization, a group, or the individual scientists involved.""",
             ),
             preserve_default=False,
@@ -149,7 +149,7 @@ class Migration(migrations.Migration):
             model_name="assessment",
             name="assessment_objective",
             field=models.TextField(
-                help_text="Describe the assessment objective(s), research questions, or clarification on the purpose of the assessment."
+                help_text="Describe the assessment objective(s), research questions, and purpose of this HAWC assessment. If a related peer-reviewed paper or journal article is available describing this work, please add a citation and hyperlink.",
             ),
         ),
         migrations.AddField(

hawc/apps/assessment/migrations/0032_assessment_epi_version.py

@@ -25,7 +25,8 @@ class Migration(migrations.Migration):
             field=models.PositiveSmallIntegerField(
                 choices=[(1, "v1"), (2, "v2")],
                 default=2,
-                help_text="Data extraction schema used for epidemiology studies",
+                verbose_name="Epidemiology schema version",
+                help_text="Data extraction schema version used for epidemiology studies",
             ),
         ),
         migrations.RunPython(set_epi_version, RunPython.noop),

hawc/apps/assessment/migrations/0034_assessmentdetail_assessmentvalue.py

@@ -58,7 +58,7 @@ class Migration(migrations.Migration):
                 (
                     "confidence",
                     models.CharField(
-                        blank=True, help_text="Overall confidence for the value.", max_length=64
+                        blank=True, help_text="Confidence in the toxicity value", max_length=64
                     ),
                 ),
                 (
@@ -163,15 +163,21 @@ class Migration(migrations.Migration):
                         verbose_name="Non-ADAF adjusted value",
                     ),
                 ),
-                ("comments", models.TextField(blank=True)),
+                (
+                    "comments",
+                    models.TextField(
+                        blank=True,
+                        help_text="General comments related to the derivation of this value",
+                    ),
+                ),
                 (
                     "extra",
                     models.JSONField(
                         blank=True,
                         default=dict,
-                        help_text='Any additional custom attributes; A <a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/JSON">JSON</a> object where keys are strings and values are strings or numbers. For example, <code>{"My Custom Field Name": "The Custom Value", "Extra ID": 12345}</code>.',
+                        help_text='Any additional custom fields; A <a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/JSON">JSON</a> object where keys are strings and values are strings or numbers. For example, <code>{"Player": "Michael Jordan", "Number": 23}</code>.',
                         validators=[hawc.apps.common.validators.FlatJSON.validate],
-                        verbose_name="Additional attributes",
+                        verbose_name="Additional fields",
                     ),
                 ),
                 ("created", models.DateTimeField(auto_now_add=True)),
@@ -289,8 +295,8 @@ class Migration(migrations.Migration):
                     "report_id",
                     models.CharField(
                         blank=True,
-                        help_text="A external report number or identifier, if any",
-                        max_length=16,
+                        help_text="A external report number or identifier (e.g., a DOI, publication number)",
+                        max_length=64,
                         verbose_name="Report identifier",
                     ),
                 ),
@@ -308,9 +314,9 @@ class Migration(migrations.Migration):
                     models.JSONField(
                         blank=True,
                         default=dict,
-                        help_text='Any additional custom attributes; A <a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/JSON">JSON</a> object where keys are strings and values are strings or numbers. For example, <code>{"My Custom Field Name": "The Custom Value", "Extra ID": 12345}</code>.',
+                        help_text='Any additional custom fields; A <a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/JSON">JSON</a> object where keys are strings and values are strings or numbers. For example, <code>{"Player": "Michael Jordan", "Number": 23}</code>.',
                         validators=[hawc.apps.common.validators.FlatJSON.validate],
-                        verbose_name="Additional attributes",
+                        verbose_name="Additional fields",
                     ),
                 ),
                 ("created", models.DateTimeField(auto_now_add=True)),

hawc/apps/assessment/migrations/0035_update_assessmentvalue.py

@@ -0,0 +1,69 @@
+# Generated by Django 3.2.18 on 2023-02-27 20:55
+
+
+from django.db import migrations, models
+
+
+def get_species_name(apps, schema_editor):
+    AssessmentValue = apps.get_model("assessment", "AssessmentValue")
+    Species = apps.get_model("assessment", "Species")
+    updates = []
+    for obj in AssessmentValue.objects.exclude(species_studied=""):
+        obj.species_studied = Species.objects.get(pk=int(obj.species_studied)).name
+        updates.append(obj)
+    if updates:
+        AssessmentValue.objects.bulk_update(updates, ["species_studied"])
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("assessment", "0034_assessmentdetail_assessmentvalue"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="assessmentvalue",
+            name="non_adaf_value",
+        ),
+        migrations.AlterField(
+            model_name="assessmentvalue",
+            name="adaf",
+            field=models.BooleanField(
+                default=False,
+                help_text="When checked, the ADAF note will appear as a footnote for the value. Add supporting information about ADAF in the comments.",
+                verbose_name="Apply ADAF?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="assessmentvalue",
+            name="duration",
+            field=models.CharField(
+                blank=True,
+                help_text="Duration associated with the value (e.g., Chronic, Subchronic)",
+                max_length=128,
+                verbose_name="Value duration",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="assessmentvalue",
+            name="species_studied",
+            field=models.TextField(
+                blank=True,
+                default="",
+                help_text="Provide information about the animal(s) studied, including species and strain information",
+                verbose_name="Species and strain",
+            ),
+            preserve_default=False,
+        ),
+        migrations.RunPython(get_species_name, migrations.RunPython.noop),
+        migrations.AlterField(
+            model_name="assessmentdetail",
+            name="report_id",
+            field=models.CharField(
+                blank=True,
+                help_text="A external report number or identifier (e.g., a DOI, publication number)",
+                max_length=128,
+                verbose_name="Report identifier",
+            ),
+        ),
+    ]

hawc/apps/assessment/models.py

@@ -145,11 +145,10 @@ def get_rob_name_default():
         """,
     )
     assessment_objective = models.TextField(
-        help_text="Describe the assessment objective(s), research questions, "
-        "or clarification on the purpose of the assessment.",
+        help_text="Describe the assessment objective(s), research questions, and purpose of this HAWC assessment. If a related peer-reviewed paper or journal article is available describing this work, please add a citation and hyperlink.",
     )
     authors = models.TextField(
-        verbose_name="Assessment authors",
+        verbose_name="Assessment authors/organization",
         help_text="""A publicly visible description of the assessment authors (if the assessment is made public). This could be an organization, a group, or the individual scientists involved.""",
     )
     creator = models.ForeignKey(
@@ -274,7 +273,8 @@ def get_rob_name_default():
     epi_version = models.PositiveSmallIntegerField(
         choices=constants.EpiVersion.choices,
         default=constants.EpiVersion.V2,
-        help_text="Data extraction schema used for epidemiology studies",
+        verbose_name="Epidemiology schema version",
+        help_text="Data extraction schema version used for epidemiology studies",
     )
     admin_notes = models.TextField(
         blank=True,
@@ -525,10 +525,10 @@ class AssessmentDetail(models.Model):
         validators=[validate_hyperlink],
     )
     report_id = models.CharField(
-        max_length=16,
+        max_length=128,
         blank=True,
         verbose_name="Report identifier",
-        help_text="A external report number or identifier, if any",
+        help_text="A external report number or identifier (e.g., a DOI, publication number)",
     )
     report_url = models.URLField(
         blank=True,
@@ -540,8 +540,8 @@ class AssessmentDetail(models.Model):
         default=dict,
         validators=[FlatJSON.validate],
         blank=True,
-        verbose_name="Additional attributes",
-        help_text="Any additional custom attributes; " + FlatJSON.HELP_TEXT,
+        verbose_name="Additional fields",
+        help_text="Any additional custom fields; " + FlatJSON.HELP_TEXT,
     )
     created = models.DateTimeField(auto_now_add=True)
     last_updated = models.DateTimeField(auto_now=True)
@@ -580,15 +580,21 @@ class AssessmentValue(models.Model):
         help_text="The derived value",
     )
     value_unit = models.CharField(verbose_name="Value units", max_length=32)
+    adaf = models.BooleanField(
+        verbose_name="Apply ADAF?",
+        default=False,
+        help_text="When checked, the ADAF note will appear as a footnote for the value. Add supporting information about ADAF in the comments.",
+    )
     confidence = models.CharField(
         max_length=64,
         blank=True,
-        help_text="Overall confidence for the value.",
+        help_text="Confidence in the toxicity value",
     )
     duration = models.CharField(
         max_length=128,
         blank=True,
-        help_text="Duration of value",
+        verbose_name="Value duration",
+        help_text="Duration associated with the value (e.g., Chronic, Subchronic)",
     )
     basis = models.TextField(
         blank=True,
@@ -619,8 +625,10 @@ class AssessmentValue(models.Model):
         verbose_name="Uncertainty factor",
         help_text="Composite uncertainty factor applied to POD to derive the final value",
     )
-    species_studied = models.ForeignKey(
-        "assessment.Species", on_delete=models.SET_NULL, blank=True, null=True
+    species_studied = models.TextField(
+        blank=True,
+        verbose_name="Species and strain",
+        help_text="Provide information about the animal(s) studied, including species and strain information",
     )
     study = models.ForeignKey(
         "study.Study",
@@ -645,24 +653,15 @@ class AssessmentValue(models.Model):
         blank=True,
         help_text="Describe the statistical method(s) used to derive the cancer toxicity values (e.g., Time-to-tumor dose-response model with linear extrapolation from the POD (BMDL10(HED)) associated with 10% extra cancer risk)",
     )
-    adaf = models.BooleanField(
-        verbose_name="ADAF applied?",
-        default=False,
-        help_text="Has an Age Dependent Adjustment Factor (ADAF) been applied?",
-    )
-    non_adaf_value = models.FloatField(
-        verbose_name="Non-ADAF adjusted value",
-        blank=True,
-        null=True,
-        help_text="Value without ADAF adjustment (units the same as Value above)",
+    comments = models.TextField(
+        blank=True, help_text="General comments related to the derivation of this value"
     )
-    comments = models.TextField(blank=True)
     extra = models.JSONField(
         default=dict,
         blank=True,
         validators=[FlatJSON.validate],
-        verbose_name="Additional attributes",
-        help_text="Any additional custom attributes; " + FlatJSON.HELP_TEXT,
+        verbose_name="Additional fields",
+        help_text="Any additional custom fields; " + FlatJSON.HELP_TEXT,
     )
     created = models.DateTimeField(auto_now_add=True)
     last_updated = models.DateTimeField(auto_now=True)