UI updates

bmds_ui/__init__.py

@@ -1,7 +1,7 @@
 import os
 import sys
 
-__version__ = "24.1a5"
+__version__ = "24.1a6"
 
 
 def manage():

bmds_ui/analysis/schema.py

@@ -95,17 +95,4 @@ def add_schema_to_path(schema: dict, path: str, verb: str, name: str):
 
 
 class ApiSchemaGenerator(SchemaGenerator):
-    def get_schema(self, *args, **kwargs):
-        schema = super().get_schema(*args, **kwargs)
-        add_schemas(schema, [EditKeySchema, WrappedAnalysisSelectedSchema])
-        add_schema_to_path(schema, "/api/v1/analysis/{id}/execute/", "post", EditKeySchema.__name__)
-        add_schema_to_path(
-            schema, "/api/v1/analysis/{id}/execute-reset/", "post", EditKeySchema.__name__
-        )
-        add_schema_to_path(
-            schema,
-            "/api/v1/analysis/{id}/select-model/",
-            "post",
-            WrappedAnalysisSelectedSchema.__name__,
-        )
-        return schema
+    pass

bmds_ui/analysis/templates/analysis/desktop_home.html

@@ -7,7 +7,7 @@
   <div class="col-lg-8">
 
     <div class="d-flex">
-      <h3 class="flex-grow-1">Analyses</h3>
+      <h2 class="flex-grow-1">Analyses</h2>
 
       <div class="dropdown mr-2">
         <button class="btn btn-secondary dropdown-toggle" type="button" data-toggle="dropdown" aria-expanded="false">Collections</button>

bmds_ui/analysis/validators/options.py

@@ -36,6 +36,7 @@ class NestedDichotomousOption(BaseModel):
     litter_specific_covariate: LitterSpecificCovariate
     bootstrap_iterations: int
     bootstrap_seed: int
+    estimate_background: bool
 
 
 class DichotomousOptions(BaseModel):

bmds_ui/common/api.py

@@ -1,4 +1,4 @@
-from rest_framework import permissions, status, viewsets
+from rest_framework import status, viewsets
 from rest_framework.decorators import action
 from rest_framework.response import Response
 from rest_framework.throttling import UserRateThrottle
@@ -20,12 +20,3 @@ def worker(self, request):
         is_healthy = worker_healthcheck.healthy()
         status_code = status.HTTP_200_OK if is_healthy else status.HTTP_503_SERVICE_UNAVAILABLE
         return Response({"healthy": is_healthy}, status=status_code)
-
-    @action(
-        detail=False,
-        permission_classes=(permissions.IsAdminUser,),
-        throttle_classes=(FivePerMinuteThrottle,),
-    )
-    def throttle(self, request):
-        throttle = self.get_throttles()[0]
-        return Response({"identity": throttle.get_ident(request)})

bmds_ui/common/management/commands/scrub_db.py

@@ -4,7 +4,7 @@
 from django.contrib.auth.hashers import make_password
 from django.core.management.base import BaseCommand, CommandError
 from django.db import transaction
-from django.db.models import Value
+from django.db.models import CharField, Value
 from django.db.models.functions import Concat
 
 
@@ -41,10 +41,10 @@ def update_users(self):
 
         # save all programs
         get_user_model().objects.update(
-            first_name=Concat(Value("first-"), "id"),
-            last_name=Concat(Value("last-"), "id"),
-            username=Concat(Value("username-"), "id"),
-            email=Concat(Value("user-"), "id", Value("@bmdsonline.org")),
+            first_name=Concat(Value("f-"), "id", output_field=CharField()),
+            last_name=Concat(Value("l-"), "id", output_field=CharField()),
+            username=Concat(Value("u-"), "id", output_field=CharField()),
+            email=Concat(Value("e-"), "id", Value("@bmdsonline.org"), output_field=CharField()),
             password=hash_password,
         )
 

bmds_ui/static/css/epa/bmdsonline.css

@@ -83,3 +83,14 @@ a.dropdown-toggle:not([href])::after {
 .bmds-desktop,.footer__column{
   width: 100%;
 }
+
+/* reduce font size */
+h1 {
+  font-size: 2rem;
+}
+h2 {
+  font-size: 1.7rem;
+}
+h2 {
+  font-size: 1.5rem;
+}

bmds_ui/templates/includes/epa/header.html

@@ -111,7 +111,7 @@
   {% endif %}
 </header>
 <nav class="bmds-header navbar justify-content-between">
-    <h2><a href="{% url 'home' %}">{% if IS_DESKTOP %}Benchmark Dose Tools (BMDS) Desktop{% else %}Benchmark Dose Tools (BMDS) Online{% endif %}</a></h2>
+    <h1><a href="{% url 'home' %}">{% if IS_DESKTOP %}Benchmark Dose Tools (BMDS) Desktop{% else %}Benchmark Dose Tools (BMDS) Online{% endif %}</a></h1>
     <ul class="nav text-right">
         {% if user.is_staff %}
         <li class="nav-item">

frontend/src/App.js

@@ -36,7 +36,7 @@ class App extends Component {
 
         return this.props.mainStore.isUpdateComplete ? (
             <HashRouter>
-                <h3>
+                <h2>
                     {getHeader()}
                     {isFuture ? (
                         <span
@@ -47,7 +47,7 @@ class App extends Component {
                             <Icon name="lightning-fill" />
                         </span>
                     ) : null}
-                </h3>
+                </h2>
                 <Navigation />
             </HashRouter>
         ) : null;

frontend/src/components/IndividualModel/ModelDetailModal.js

@@ -62,7 +62,7 @@ class ModelBody extends Component {
                         />
                     </Col>
                     <Col xl={4}>
-                        <Summary store={outputStore} />
+                        <Summary />
                     </Col>
                     <Col xl={8}>
                         <DoseResponsePlot
@@ -194,7 +194,7 @@ class MultitumorModalBody extends Component {
                         />
                     </Col>
                     <Col xl={4}>
-                        <Summary model={model} />
+                        <Summary />
                     </Col>
                     <Col xs={8}>
                         <DoseResponsePlot
@@ -250,7 +250,7 @@ class NestedDichotomousModalBody extends Component {
                         <ModelOptionsTable dtype={dtype} model={model} />
                     </Col>
                     <Col xs={6}>
-                        <Summary results={model.results} />
+                        <Summary />
                     </Col>
                     <Col xs={6}>
                         <DoseResponsePlot

frontend/src/components/IndividualModel/ModelOptionsTable.js

@@ -2,7 +2,7 @@ import {observer} from "mobx-react";
 import PropTypes from "prop-types";
 import React, {Component} from "react";
 
-import {getLabel} from "@/common";
+import {checkOrEmpty, getLabel} from "@/common";
 import TwoColumnTable from "@/components/common/TwoColumnTable";
 import {Dtype} from "@/constants/dataConstants";
 import {hasDegrees} from "@/constants/modelConstants";
@@ -70,19 +70,20 @@ class ModelOptionsTable extends Component {
                 ["BMR Type", getLabel(model.settings.bmr_type, dichotomousBmrOptions)],
                 ["BMR", ff(model.settings.bmr)],
                 ["Confidence Level (one sided)", ff(1 - model.settings.alpha)],
-                ["Bootstrap Seed", model.settings.bootstrap_seed],
-                ["Bootstrap Iterations", model.settings.bootstrap_iterations],
                 [
                     "Litter Specific Covariate",
-                    getLabel(
+                    `${getLabel(
                         model.settings.litter_specific_covariate,
                         litterSpecificCovariateOptions
-                    ),
+                    )} (${ff(model.results.fixed_lsc)})`,
                 ],
                 [
                     "Intralitter Correlation",
                     getLabel(model.settings.intralitter_correlation, intralitterCorrelation),
                 ],
+                ["Estimate Background", checkOrEmpty(model.settings.estimate_background)],
+                ["Bootstrap Iterations", model.settings.bootstrap_iterations],
+                ["Bootstrap Seed", model.settings.bootstrap_seed],
             ];
         } else {
             throw "Unknown dtype";

frontend/src/components/IndividualModel/Summary.js

@@ -11,47 +11,62 @@ import {ff, fractionalFormatter} from "@/utils/formatters";
 class Summary extends Component {
     render() {
         const {outputStore} = this.props,
-            model = outputStore.modalModel;
+            model = outputStore.modalModel,
+            {results} = model;
         let data;
         if (outputStore.isNestedDichotomous) {
             data = [
-                ["BMD", ff(model.results.bmd), model.results.bmd],
-                ["BMDL", ff(model.results.bmdl), model.results.bmdl],
-                ["BMDU", ff(model.results.bmdu), model.results.bmdu],
-                ["AIC", ff(model.results.aic), model.results.aic],
+                ["BMD", ff(results.bmd), results.bmd],
+                ["BMDL", ff(results.bmdl), results.bmdl],
+                ["BMDU", ff(results.bmdu), results.bmdu],
+                ["AIC", ff(results.aic), results.aic],
                 [
                     <span key={0}>
                         <i>P</i>-value
                     </span>,
-                    fractionalFormatter(model.results.combined_pvalue),
+                    fractionalFormatter(results.combined_pvalue),
+                    results.combined_pvalue,
                 ],
-                ["Model d.f.", ff(model.results.dof)],
-                [<span key={1}>Chi²</span>, ff(model.results.chi_squared)],
+                ["Model d.f.", ff(results.dof), results.dof],
+                [<span key={1}>Chi²</span>, ff(results.chi_squared), results.chi_squared],
+            ];
+        } else if (outputStore.getModelType === mc.MODEL_CONTINUOUS) {
+            data = [
+                ["BMD", ff(results.bmd), results.bmd],
+                ["BMDL", ff(results.bmdl), results.bmdl],
+                ["BMDU", ff(results.bmdu), results.bmdu],
+                ["AIC", ff(results.fit.aic), results.fit.aic],
+                [
+                    <span key={0}>
+                        <i>P</i>-value
+                    </span>,
+                    fractionalFormatter(results.tests.p_values[3]),
+                    results.tests.p_values[3],
+                ],
+                ["Model d.f.", ff(results.tests.dfs[3]), results.tests.dfs[3]],
+                ["Log-Likelihood", ff(results.fit.loglikelihood), results.fit.loglikelihood],
             ];
         } else {
-            const isContinuous = outputStore.getModelType === mc.MODEL_CONTINUOUS,
-                results = model.bmd ? model : model.results,
-                p_value = isContinuous ? results.tests.p_values[3] : results.gof.p_value,
-                df = isContinuous ? results.tests.dfs[3] : results.gof.df;
             data = [
                 ["BMD", ff(results.bmd), results.bmd],
                 ["BMDL", ff(results.bmdl), results.bmdl],
                 ["BMDU", ff(results.bmdu), results.bmdu],
+                outputStore.isMultiTumor
+                    ? ["Slope Factor", ff(results.slope_factor), results.slope_factor]
+                    : null,
                 ["AIC", ff(results.fit.aic), results.fit.aic],
-                ["Log-Likelihood", ff(results.fit.loglikelihood)],
                 [
                     <span key={0}>
                         <i>P</i>-value
                     </span>,
-                    fractionalFormatter(p_value),
+                    fractionalFormatter(results.gof.p_value),
+                    results.gof.p_value,
                 ],
-                ["Model d.f.", ff(df)],
+                ["Model d.f.", ff(results.gof.df), results.gof.df],
+                ["Log-Likelihood", ff(results.fit.loglikelihood), results.fit.loglikelihood],
+                ["Chi²", ff(results.fit.chisq), results.fit.chisq],
             ];
-            if (outputStore.isMultiTumor) {
-                data.splice(3, 0, ["Slope Factor", ff(results.slope_factor), results.slope_factor]);
-            }
         }
-
         return <TwoColumnTable data={data} label="Modeling Summary" />;
     }
 }

frontend/src/components/Logic/LogicRoot.js

@@ -23,6 +23,7 @@ class Logic extends Component {
         return (
             <div className="container-fluid">
                 <DecisionLogic />
+                <h3>Model Recommendation and Bin Placement Logic</h3>
                 <RuleTable />
             </div>
         );

frontend/src/components/Logic/RuleTable.js

@@ -18,9 +18,6 @@ class RuleList extends Component {
         return (
             <table id="rule-table" className="table table-sm">
                 <thead className="bg-custom">
-                    <tr>
-                        <th colSpan="5">Model Recommendation and Bin Placement Logic</th>
-                    </tr>
                     <tr>
                         <th>Test Description</th>
                         <th>Enabled</th>