Treatment Related Effect (#681)

* created treatment effect * exports * arrows for constants * helptext, tests * fix popup * updates from review * remove hasData Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
shapiromatron · Aug 24, 2022 · 9ab8d21 · 9ab8d21
1 parent cb2655f
commit 9ab8d21
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Showing 16 changed files with 160 additions and 4 deletions.
diff --git a/frontend/animal/EndpointTable.js b/frontend/animal/EndpointTable.js
@@ -36,7 +36,7 @@ class EndpointTable {
             .map(function(d) {
                 return d[val];
             })
-            .some($.isNumeric)
+            .some(x => !_.isNil(x))
             .value();
     }
 
@@ -83,7 +83,10 @@ class EndpointTable {
             default:
                 throw "Unknown data type.";
         }
-
+        this.hasTreatmentColumn = this.hasValues("treatment_effect");
+        if (this.hasTreatmentColumn) {
+            tr.append("<th>Treatment Related Effect</th>");
+        }
         this.number_columns = tr.children().length;
         this.thead = $("<thead>").append(tr);
     }
@@ -113,6 +116,9 @@ class EndpointTable {
                     `<td>${self.endpoint._dichotomous_percent_change_incidence(v)}%</td>`
                 );
             }
+            if (self.hasTreatmentColumn) {
+                tr.append(`<td>${v.treatment_effect || "---"}</td>`);
+            }
             self.tbody.append(tr);
         });
     }

diff --git a/hawc/apps/animal/constants.py b/hawc/apps/animal/constants.py
@@ -150,6 +150,14 @@ class LitterEffect(models.TextChoices):
     O = "O", "Other"  # noqa: E741
 
 
+class TreatmentEffect(models.IntegerChoices):
+    NR = 0, "not reported"
+    YES_UP = 1, "yes ↑"
+    YES_DOWN = 2, "yes ↓"
+    YES = 3, "yes"
+    NO = 4, "no"
+
+
 # bool can't be subclassed with models.Choices
 POSITIVE_CONTROL_CHOICES = (
     (True, "Yes"),

diff --git a/hawc/apps/animal/exports.py b/hawc/apps/animal/exports.py
@@ -258,6 +258,7 @@ def _get_header_row(self):
             "upper_ci",
             "pairwise significant",
             "pairwise significant value",
+            "treatment related effect",
             "percent control mean",
             "percent control low",
             "percent control high",
@@ -358,6 +359,7 @@ def _get_data_rows(self):
                         eg["upper_ci"],
                         eg["significant"],
                         eg["significance_level"],
+                        eg["treatment_effect"],
                         eg["percentControlMean"],
                         eg["percentControlLow"],
                         eg["percentControlHigh"],
@@ -438,6 +440,7 @@ def _get_header_row(self):
         rng = range(1, num_doses + 1)
         header.extend([f"Dose {i}" for i in rng])
         header.extend([f"Significant {i}" for i in rng])
+        header.extend([f"Treatment Related Effect {i}" for i in rng])
         header.extend(list(self.rob_headers.values()))
 
         # distinct applied last so that queryset can add annotations above
@@ -585,9 +588,12 @@ def _get_data_rows(self):
 
             sigs = get_significance_and_direction(ser["data_type"], ser["groups"])
             sigs.extend([None] * (self.num_doses - len(sigs)))
-
             row.extend(sigs)
 
+            tres = [dose["treatment_effect"] for dose in ser["groups"]]
+            tres.extend([None] * (self.num_doses - len(tres)))
+            row.extend(tres)
+
             row.extend(
                 [self.rob_data[(ser["id"], metric_id)] for metric_id in self.rob_headers.keys()]
             )

diff --git a/hawc/apps/animal/migrations/0019_py3_unicode.py b/hawc/apps/animal/migrations/0019_py3_unicode.py
@@ -482,6 +482,7 @@ class Migration(migrations.Migration):
             field=models.FloatField(
                 blank=True,
                 default=None,
+                help_text="Enter statistical significance level for the effect. Typically this is as presented in the study. Indicate in the results comment field if it is based on statistical analysis conducted by the assessment team",
                 null=True,
                 validators=[
                     django.core.validators.MinValueValidator(0),

diff --git a/hawc/apps/animal/migrations/0031_tre.py b/hawc/apps/animal/migrations/0031_tre.py
@@ -0,0 +1,22 @@
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("animal", "0030_django31"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="endpointgroup",
+            name="treatment_effect",
+            field=models.PositiveSmallIntegerField(
+                blank=True,
+                choices=[(0, "not reported"), (1, "yes ↑"), (2, "yes ↓"), (3, "yes"), (4, "no")],
+                default=None,
+                help_text="Expert judgement based report of treatment related effects (add direction if known). Use when statistical analysis not available. In results comments, indicate whether it was author judgment or assessment team judgement",
+                null=True,
+            ),
+        )
+    ]
diff --git a/hawc/apps/animal/models.py b/hawc/apps/animal/models.py
@@ -1505,6 +1505,14 @@ class EndpointGroup(ConfidenceIntervalsMixin, models.Model):
         default=None,
         validators=[MinValueValidator(0), MaxValueValidator(1)],
         verbose_name="Statistical significance level",
+        help_text="Enter statistical significance level for the effect. Typically this is as presented in the study. Indicate in the results comment field if it is based on statistical analysis conducted by the assessment team",
+    )
+    treatment_effect = models.PositiveSmallIntegerField(
+        null=True,
+        blank=True,
+        default=None,
+        choices=constants.TreatmentEffect.choices,
+        help_text="Expert judgement based report of treatment related effects (add direction if known). Use when statistical analysis not available. In results comments, indicate whether it was author judgment or assessment team judgement",
     )
 
     COPY_NAME = "groups"
@@ -1550,6 +1558,7 @@ def flat_complete_header_row():
             "endpoint_group-upper_ci",
             "endpoint_group-significant",
             "endpoint_group-significance_level",
+            "endpoint_group-treatment_effect",
             "endpoint_group-NOEL",
             "endpoint_group-LOEL",
             "endpoint_group-FEL",
@@ -1568,6 +1577,7 @@ def flat_complete_data_row(ser, endpoint):
             ser["upper_ci"],
             ser["significant"],
             ser["significance_level"],
+            ser["treatment_effect"],
             ser["dose_group_id"] == endpoint["NOEL"],
             ser["dose_group_id"] == endpoint["LOEL"],
             ser["dose_group_id"] == endpoint["FEL"],

diff --git a/hawc/apps/animal/serializers.py b/hawc/apps/animal/serializers.py
@@ -232,6 +232,7 @@ def to_representation(self, instance):
         ret = super().to_representation(instance)
         ret["hasVariance"] = instance.hasVariance
         ret["isReported"] = instance.isReported
+        ret["treatment_effect"] = instance.get_treatment_effect_display()
         return ret
 
     def validate(self, data):

diff --git a/hawc/apps/animal/templates/animal/endpoint_form.html b/hawc/apps/animal/templates/animal/endpoint_form.html
@@ -55,7 +55,12 @@
                 <th id="varianceHeader" class="c_only">Variance (SD or SE)</th>
                 <th class="p_only">Low CI (%)</th>
                 <th class="p_only">High CI (%)</th>
-                <th>Significance<br>Level<br>(if significant)</th>
+                <th>Significance<br>Level<br>(if significant)
+                  {% include "common/helptext_popup.html" with text=formset.0.significance_level.help_text %}
+                </th>
+                <th>Treatment Related Effect
+                  {% include "common/helptext_popup.html" with text=formset.0.treatment_effect.help_text %}
+                </th>
               </tr>
             </thead>
             <tbody>
@@ -77,6 +82,7 @@
                   <th class="p_only">{{form.lower_ci}}{{form.lower_ci.errors|add_class:"alert alert-danger"}}</th>
                   <th class="p_only">{{form.upper_ci}}{{form.upper_ci.errors|add_class:"alert alert-danger"}}</th>
                   <td>{{form.significance_level}}</td>
+                  <td>{{form.treatment_effect}}</td>
                 </tr>
               {% endfor %}
             </tbody>
@@ -134,4 +140,5 @@
     });
   });
   </script>
+  {% include "common/helptext_popup_js.html" %}
 {% endblock %}
diff --git a/hawc/apps/common/templates/common/helptext_popup.html b/hawc/apps/common/templates/common/helptext_popup.html
@@ -0,0 +1,3 @@
+<i class="ml-1 fa fa-fw fa-question-circle"
+    aria-hidden="true" data-html="true" data-toggle="popover"
+    title="{{title}}" data-content="{{text}}"></i>
diff --git a/hawc/apps/common/templates/common/helptext_popup_js.html b/hawc/apps/common/templates/common/helptext_popup_js.html
@@ -0,0 +1,9 @@
+<script type="text/javascript">
+    $(document).ready(() => {
+            $('[data-toggle="popover"]').popover({
+                placement: "auto",
+                trigger: "hover",
+                delay: { show: 100, hide: 1000 },
+            })
+    });
+</script>
diff --git a/tests/data/api/api-animal-assessment-full-export.json b/tests/data/api/api-animal-assessment-full-export.json
@@ -70,6 +70,7 @@
     "endpoint_group-response": 15.0,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 15.7956244909,
     "endpoint_group-variance": 1.7,
     "experiment-cas": "1163-19-5",
@@ -178,6 +179,7 @@
     "endpoint_group-response": 11.0,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 11.8892273722,
     "endpoint_group-variance": 1.9,
     "experiment-cas": "1163-19-5",
@@ -286,6 +288,7 @@
     "endpoint_group-response": 15.0,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 16.0764331348,
     "endpoint_group-variance": 2.3,
     "experiment-cas": "1163-19-5",
@@ -394,6 +397,7 @@
     "endpoint_group-response": 12.0,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 13.0296316941,
     "endpoint_group-variance": 2.2,
     "experiment-cas": "1163-19-5",
@@ -502,6 +506,7 @@
     "endpoint_group-response": 9.0,
     "endpoint_group-significance_level": 0.05,
     "endpoint_group-significant": true,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 9.5616172877,
     "endpoint_group-variance": 1.2,
     "experiment-cas": "1163-19-5",
@@ -610,6 +615,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": null,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",
@@ -718,6 +724,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": null,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",
@@ -826,6 +833,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": null,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",
@@ -934,6 +942,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": null,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",
@@ -1042,6 +1051,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": null,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",
@@ -1150,6 +1160,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 0.3408051366,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",
@@ -1258,6 +1269,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 0.3408051366,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",
@@ -1366,6 +1378,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 0.4871743473,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",
@@ -1474,6 +1487,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 0.4171011516,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",
@@ -1582,6 +1596,7 @@
     "endpoint_group-response": null,
     "endpoint_group-significance_level": null,
     "endpoint_group-significant": false,
+    "endpoint_group-treatment_effect": null,
     "endpoint_group-upper_ci": 0.7265646156,
     "endpoint_group-variance": null,
     "experiment-cas": "1163-19-5",