From c0d41b4692b992cae4e8015d2c338bb074b53149 Mon Sep 17 00:00:00 2001
From: Matthew Munns <mmunns16@gmail.com>
Date: Tue, 9 Jul 2024 16:19:52 -0400
Subject: [PATCH 1/4] fix errors when loading read-only page in desktop mode

---
 frontend/src/components/Main/Actions/Actions.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend/src/components/Main/Actions/Actions.js b/frontend/src/components/Main/Actions/Actions.js
index d58b840f..87d5caa0 100644
--- a/frontend/src/components/Main/Actions/Actions.js
+++ b/frontend/src/components/Main/Actions/Actions.js
@@ -107,7 +107,7 @@ class Actions extends Component {
                     ) : (
                         <p className="text-muted pl-4 mb-0">Please save and execute analysis.</p>
                     )}
-                    {mainStore.isDesktop ? (
+                    {(mainStore.isDesktop && mainStore.canEdit) ? (
                         <>
                             <div className="dropdown-divider"></div>
                             <span className="dropdown-header">Collections</span>

From 29c7be3fe4bddbee7144a7f96e45f49837ccdb19 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Wed, 17 Jul 2024 21:22:26 -0400
Subject: [PATCH 2/4] fix text alignment on detail pages

---
 frontend/src/components/IndividualModel/CDFTable.js             | 2 +-
 frontend/src/components/IndividualModel/GoodnessFit.js          | 2 +-
 .../src/components/Output/NestedDichotomous/BootstrapRuns.js    | 1 +
 frontend/src/components/Output/NestedDichotomous/LitterData.js  | 2 +-
 frontend/src/components/common/Table.js                         | 2 +-
 5 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/frontend/src/components/IndividualModel/CDFTable.js b/frontend/src/components/IndividualModel/CDFTable.js
index 7653b47c..b20324e3 100644
--- a/frontend/src/components/IndividualModel/CDFTable.js
+++ b/frontend/src/components/IndividualModel/CDFTable.js
@@ -16,7 +16,7 @@ class CDFTable extends Component {
                     ff(bmd_dist[1][i]),
                     ff(bmd_dist[0][i]),
                 ]),
-                tblClasses: "table table-sm text-right col-l-1",
+                tblClasses: "table table-sm text-right",
             };
         return <Table data={data} />;
     }
diff --git a/frontend/src/components/IndividualModel/GoodnessFit.js b/frontend/src/components/IndividualModel/GoodnessFit.js
index 69a0711d..988c9843 100644
--- a/frontend/src/components/IndividualModel/GoodnessFit.js
+++ b/frontend/src/components/IndividualModel/GoodnessFit.js
@@ -106,7 +106,7 @@ class GoodnessFit extends Component {
         } else {
             data = getContinuousNormalData(dataset, dtype, model);
         }
-        data.tblClasses = "table table-sm text-right col-l-1";
+        data.tblClasses = "table table-sm text-right";
         data.subheader = "Goodness of Fit";
 
         return <Table data={data} />;
diff --git a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
index cecd54ab..a9f217eb 100644
--- a/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
+++ b/frontend/src/components/Output/NestedDichotomous/BootstrapRuns.js
@@ -37,6 +37,7 @@ const getData = function(model) {
             "99th",
         ],
         subheader: "Bootstrap Runs",
+        tblClasses: "table table-sm text-right",
         rows,
     };
 };
diff --git a/frontend/src/components/Output/NestedDichotomous/LitterData.js b/frontend/src/components/Output/NestedDichotomous/LitterData.js
index dd0f604e..f2588940 100644
--- a/frontend/src/components/Output/NestedDichotomous/LitterData.js
+++ b/frontend/src/components/Output/NestedDichotomous/LitterData.js
@@ -10,7 +10,7 @@ const getData = function(model) {
     const litter = model.results.litter,
         n = _.size(litter.lsc);
     return {
-        tblClasses: "table table-sm text-right col-l-1",
+        tblClasses: "table table-sm text-right",
         headers: [
             "Dose",
             "Litter Specific Covariance",
diff --git a/frontend/src/components/common/Table.js b/frontend/src/components/common/Table.js
index e9c167fe..569dd67a 100644
--- a/frontend/src/components/common/Table.js
+++ b/frontend/src/components/common/Table.js
@@ -23,7 +23,7 @@ class Table extends Component {
                 </colgroup>
                 <thead>
                     {data.subheader ? (
-                        <tr className="bg-custom sticky-top">
+                        <tr className="bg-custom sticky-top text-left">
                             <th colSpan={nCols}>{data.subheader}</th>
                         </tr>
                     ) : null}

From 5657a26c0067bd772a0c18f59184306fa64dd66c Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Wed, 17 Jul 2024 22:54:48 -0400
Subject: [PATCH 3/4] rewrite model table implementation

---
 frontend/src/common.js                        |   8 +-
 .../Main/ModelsForm/ModelsCheckBox.js         |  19 +--
 .../Main/ModelsForm/ModelsCheckBoxHeader.js   | 151 +++++++++++-------
 .../Main/ModelsForm/ModelsCheckBoxList.js     |  11 +-
 frontend/src/components/common/Icon.js        |  10 +-
 frontend/src/stores/ModelsStore.js            |   5 -
 6 files changed, 116 insertions(+), 88 deletions(-)

diff --git a/frontend/src/common.js b/frontend/src/common.js
index 76d9c166..edb957d5 100644
--- a/frontend/src/common.js
+++ b/frontend/src/common.js
@@ -24,7 +24,13 @@ export const simulateClick = function(el) {
         };
     },
     checkOrEmpty = bool => {
-        return <Icon name={bool ? "check2-square" : "square"} classes="bi-lg" />;
+        return (
+            <Icon
+                title={bool ? "checked" : "unchecked"}
+                name={bool ? "check2-square" : "square"}
+                classes="bi-lg"
+            />
+        );
     },
     getLabel = function(value, mapping) {
         return _.find(mapping, d => d.value == value).label;
diff --git a/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js b/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
index d78fdfe5..37f2546e 100644
--- a/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
+++ b/frontend/src/components/Main/ModelsForm/ModelsCheckBox.js
@@ -77,41 +77,30 @@ const ModelsCheckBox = observer(props => {
                     <td className="text-left align-middle">Exponential</td>
                     <CheckBoxTd store={store} type={fr} model={"Exponential"} />
                     <td></td>
-                    <CheckBoxTd store={store} type={b} model={"Exponential"} disabled={true} />
-                    <PriorWeightTd store={store} model={"Exponential"} disabled={true} />
                 </tr>
                 <tr>
                     <td className="text-left align-middle">Hill</td>
                     <CheckBoxTd store={store} type={fr} model={"Hill"} />
                     <CheckBoxTd store={store} type={fu} model={"Hill"} />
-                    <CheckBoxTd store={store} type={b} model={"Hill"} disabled={true} />
-                    <PriorWeightTd store={store} model={"Hill"} disabled={true} />
                 </tr>
                 <tr>
                     <td className="text-left align-middle">Linear</td>
                     <td></td>
                     <CheckBoxTd store={store} type={fu} model={"Linear"} />
-                    <CheckBoxTd store={store} type={b} model={"Linear"} disabled={true} />
-                    <PriorWeightTd store={store} model={"Linear"} disabled={true} />
                 </tr>
                 <tr>
                     <td className="text-left align-middle">Polynomial</td>
                     <CheckBoxTd store={store} type={fr} model={"Polynomial"} />
                     <CheckBoxTd store={store} type={fu} model={"Polynomial"} />
-                    <CheckBoxTd store={store} type={b} model={"Polynomial"} disabled={true} />
-                    <PriorWeightTd store={store} model={"Polynomial"} disabled={true} />
                 </tr>
                 <tr>
                     <td className="text-left align-middle">Power</td>
                     <CheckBoxTd store={store} type={fr} model={"Power"} />
                     <CheckBoxTd store={store} type={fu} model={"Power"} />
-                    <CheckBoxTd store={store} type={b} model={"Power"} disabled={true} />
-                    <PriorWeightTd store={store} model={"Power"} disabled={true} />
                 </tr>
             </tbody>
         );
-    }
-    if (store.getModelType === mc.MODEL_DICHOTOMOUS) {
+    } else if (store.getModelType === mc.MODEL_DICHOTOMOUS) {
         return (
             <tbody>
                 <tr>
@@ -182,8 +171,7 @@ const ModelsCheckBox = observer(props => {
                 </tr>
             </tbody>
         );
-    }
-    if (store.getModelType === mc.MODEL_NESTED_DICHOTOMOUS) {
+    } else if (store.getModelType === mc.MODEL_NESTED_DICHOTOMOUS) {
         return (
             <tbody>
                 <tr>
@@ -198,8 +186,9 @@ const ModelsCheckBox = observer(props => {
                 </tr>
             </tbody>
         );
+    } else {
+        throw `Unknown modelType: ${store.getModelType}`;
     }
-    throw `Unknown modelType: ${store.getModelType}`;
 });
 ModelsCheckBox.propTypes = {
     store: PropTypes.any,
diff --git a/frontend/src/components/Main/ModelsForm/ModelsCheckBoxHeader.js b/frontend/src/components/Main/ModelsForm/ModelsCheckBoxHeader.js
index b00ae1bc..456c69ea 100644
--- a/frontend/src/components/Main/ModelsForm/ModelsCheckBoxHeader.js
+++ b/frontend/src/components/Main/ModelsForm/ModelsCheckBoxHeader.js
@@ -5,78 +5,119 @@ import React from "react";
 import * as mc from "@/constants/mainConstants";
 import {allModelOptions} from "@/constants/modelConstants";
 
+import Button from "../../common/Button";
 import CheckboxInput from "../../common/CheckboxInput";
-import HelpTextPopover from "../../common/HelpTextPopover";
+import LabelInput from "../../common/LabelInput";
 
 const areAllModelsChecked = function(modelType, type, models) {
         return type in models && models[type].length === allModelOptions[modelType][type].length;
     },
     SelectAllComponent = observer(props => {
-        const {store, type, disabled} = props;
-        return store.canEdit ? (
-            <th>
-                <label className="m-0">
-                    <CheckboxInput
-                        id={`select_all_${type}`}
-                        disabled={disabled}
-                        onChange={value => store.enableAll(type, value)}
-                        checked={areAllModelsChecked(store.getModelType, type, store.models)}
-                    />
-                    &nbsp;Select all
-                </label>
-            </th>
-        ) : (
-            <th></th>
+        const {store, type, disabled, label} = props,
+            id = `select_all_${type}`;
+        return (
+            <>
+                <CheckboxInput
+                    id={id}
+                    disabled={disabled}
+                    onChange={value => store.enableAll(type, value)}
+                    checked={areAllModelsChecked(store.getModelType, type, store.models)}
+                />
+                &nbsp;
+                <LabelInput label={label} htmlFor={id} />
+            </>
+        );
+    }),
+    ModelColGroup = observer(props => {
+        const {hasBayesianModels} = props,
+            cols = hasBayesianModels ? [20, 20, 20, 20, 20] : [33, 33, 34];
+        return (
+            <colgroup>
+                {cols.map((d, i) => (
+                    <col key={i} width={`${d}%`} />
+                ))}
+            </colgroup>
         );
     });
 
 const ModelsCheckBoxHeader = observer(props => {
     const {store} = props,
-        content = "Models were previewed in BMDS Excel 3.2 and will be formally peer reviewed.",
-        title = "Bayesian Model Averaging",
-        {hasBayesianModels} = store,
-        isContinuous = store.getModelType === mc.MODEL_CONTINUOUS,
-        isMultiTumor = store.getModelType === mc.MODEL_MULTI_TUMOR;
+        {canEdit} = store,
+        hasBayesianModels = store.getModelType === mc.MODEL_DICHOTOMOUS;
     return (
-        <thead className="bg-custom">
-            <tr>
-                <th rowSpan="3">Models</th>
-                <th colSpan="2">Maximum Likelihood Estimate</th>
-                {hasBayesianModels ? (
-                    <th colSpan="3" rowSpan="2">
-                        Bayesian Model Averaging
-                        {isContinuous ? (
-                            <HelpTextPopover title={title} content={content}></HelpTextPopover>
+        <>
+            <ModelColGroup hasBayesianModels={hasBayesianModels} />
+            <thead className="bg-custom">
+                <tr>
+                    <th className="align-top" rowSpan="2">
+                        Model
+                        {canEdit ? (
+                            <>
+                                <Button
+                                    className="mt-4 btn btn-sm btn-block btn-info"
+                                    onClick={store.resetModelSelection}
+                                    text="Reset Selection"
+                                />
+                            </>
                         ) : null}
                     </th>
-                ) : null}
-            </tr>
-            <tr>
-                <th>Restricted</th>
-                <th>Unrestricted</th>
-            </tr>
-            <tr>
-                <SelectAllComponent store={store} type={"frequentist_restricted"} />
-                <SelectAllComponent
-                    store={store}
-                    type={"frequentist_unrestricted"}
-                    disabled={isMultiTumor}
-                />
-                {hasBayesianModels ? (
-                    <>
-                        <SelectAllComponent
-                            store={store}
-                            type={"bayesian"}
-                            disabled={isContinuous}
-                        />
-                        <th>Prior Weights</th>
-                    </>
-                ) : null}
-            </tr>
-        </thead>
+                    <th colSpan="2">Maximum Likelihood Estimate</th>
+                    {hasBayesianModels ? <th colSpan="2">Bayesian Model Averaging</th> : null}
+                </tr>
+                <tr>
+                    <th>
+                        Restricted
+                        {canEdit ? (
+                            <>
+                                <br />
+                                <SelectAllComponent
+                                    store={store}
+                                    type={"frequentist_restricted"}
+                                    label="Select All"
+                                />
+                            </>
+                        ) : null}
+                    </th>
+                    <th>
+                        Unrestricted
+                        {canEdit ? (
+                            <>
+                                <br />
+                                <SelectAllComponent
+                                    store={store}
+                                    type={"frequentist_unrestricted"}
+                                    label="Select All"
+                                />
+                            </>
+                        ) : null}
+                    </th>
+                    {hasBayesianModels ? (
+                        <>
+                            <th>
+                                Include
+                                {canEdit ? (
+                                    <>
+                                        <br />
+                                        <SelectAllComponent
+                                            store={store}
+                                            type={"bayesian"}
+                                            label="Select All"
+                                        />
+                                    </>
+                                ) : null}
+                            </th>
+                            <th>
+                                <span className="mb-1">Prior Weight</span>
+                            </th>
+                        </>
+                    ) : null}
+                </tr>
+            </thead>
+        </>
     );
 });
 ModelsCheckBoxHeader.propTypes = {
     store: PropTypes.object,
 };
+
 export default ModelsCheckBoxHeader;
diff --git a/frontend/src/components/Main/ModelsForm/ModelsCheckBoxList.js b/frontend/src/components/Main/ModelsForm/ModelsCheckBoxList.js
index e4bfc3f5..e651eb7f 100644
--- a/frontend/src/components/Main/ModelsForm/ModelsCheckBoxList.js
+++ b/frontend/src/components/Main/ModelsForm/ModelsCheckBoxList.js
@@ -4,7 +4,6 @@ import React, {Component} from "react";
 
 import {MODEL_MULTI_TUMOR} from "@/constants/mainConstants";
 
-import Button from "../../common/Button";
 import ModelsCheckBox from "./ModelsCheckBox";
 import ModelsCheckBoxHeader from "./ModelsCheckBoxHeader";
 
@@ -12,8 +11,7 @@ import ModelsCheckBoxHeader from "./ModelsCheckBoxHeader";
 @observer
 class ModelsCheckBoxList extends Component {
     render() {
-        const {modelsStore} = this.props,
-            mainStore = modelsStore.rootStore.mainStore;
+        const {modelsStore} = this.props;
         if (modelsStore.getModelType === MODEL_MULTI_TUMOR) {
             return (
                 <div className="alert alert-info my-3">
@@ -29,13 +27,6 @@ class ModelsCheckBoxList extends Component {
         }
         return (
             <div className="mt-2">
-                {mainStore.canEdit ? (
-                    <Button
-                        className="btn btn-sm btn-warning"
-                        onClick={mainStore.resetModelSelection}
-                        text="Reset Model Selection"
-                    />
-                ) : null}
                 <table className="table table-sm">
                     <ModelsCheckBoxHeader store={modelsStore} />
                     <ModelsCheckBox store={modelsStore} />
diff --git a/frontend/src/components/common/Icon.js b/frontend/src/components/common/Icon.js
index 09c36bea..2950bc71 100644
--- a/frontend/src/components/common/Icon.js
+++ b/frontend/src/components/common/Icon.js
@@ -3,9 +3,14 @@ import React, {Component} from "react";
 
 class Icon extends Component {
     render() {
-        const {name, classes, text} = this.props,
+        const {name, classes, text, title} = this.props,
             extra = text ? " mr-1 " : " ",
-            icon = <span className={`bi bi-${name}${extra}${classes}`} aria-hidden="true"></span>;
+            icon = (
+                <span
+                    title={title}
+                    className={`bi bi-${name}${extra}${classes}`}
+                    aria-hidden="true"></span>
+            );
         if (text) {
             return (
                 <>
@@ -21,6 +26,7 @@ Icon.propTypes = {
     name: PropTypes.string.isRequired,
     classes: PropTypes.string,
     text: PropTypes.string,
+    title: PropTypes.string,
 };
 Icon.defaultProps = {
     classes: "",
diff --git a/frontend/src/stores/ModelsStore.js b/frontend/src/stores/ModelsStore.js
index 3c63b9bd..ed5265c5 100644
--- a/frontend/src/stores/ModelsStore.js
+++ b/frontend/src/stores/ModelsStore.js
@@ -34,11 +34,6 @@ class ModelsStore {
         return this.rootStore.mainStore.model_type;
     }
 
-    @computed get hasBayesianModels() {
-        const modelType = this.getModelType;
-        return modelType === mc.MODEL_DICHOTOMOUS || modelType === mc.MODEL_CONTINUOUS;
-    }
-
     @action.bound setModels(models) {
         this.models = models;
         this.setDefaultsByDatasetType();

From 8f7ff90b411f0497a0490c1551e7b6be7dfc2892 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiromatron@gmail.com>
Date: Wed, 17 Jul 2024 23:37:34 -0400
Subject: [PATCH 4/4] fix layout of option and model options

---
 bmds_ui/static/css/site.css                                 | 4 ++++
 frontend/src/components/Main/Actions/Actions.js             | 2 +-
 .../Main/DatasetModelOptionList/DatasetModelOption.js       | 2 +-
 .../Main/DatasetModelOptionList/DatasetModelOptionList.js   | 6 +++---
 frontend/src/components/Main/OptionsForm/OptionsFormList.js | 4 ++--
 5 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/bmds_ui/static/css/site.css b/bmds_ui/static/css/site.css
index a83c0058..1bc78975 100644
--- a/bmds_ui/static/css/site.css
+++ b/bmds_ui/static/css/site.css
@@ -63,6 +63,10 @@ input[type=number] {
   visibility: visible;
 }
 
+.table-fixed {
+  table-layout: fixed;
+}
+
 /* table column text alignment */
 .col-r-1 td:nth-child(1),
 .col-r-1 th:nth-child(1),
diff --git a/frontend/src/components/Main/Actions/Actions.js b/frontend/src/components/Main/Actions/Actions.js
index 87d5caa0..ba2cfe66 100644
--- a/frontend/src/components/Main/Actions/Actions.js
+++ b/frontend/src/components/Main/Actions/Actions.js
@@ -107,7 +107,7 @@ class Actions extends Component {
                     ) : (
                         <p className="text-muted pl-4 mb-0">Please save and execute analysis.</p>
                     )}
-                    {(mainStore.isDesktop && mainStore.canEdit) ? (
+                    {mainStore.isDesktop && mainStore.canEdit ? (
                         <>
                             <div className="dropdown-divider"></div>
                             <span className="dropdown-header">Collections</span>
diff --git a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js
index 1215faa2..4f89e8a9 100644
--- a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js
+++ b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOption.js
@@ -64,7 +64,7 @@ class DatasetModelOption extends Component {
             </tr>
         ) : (
             <tr>
-                <td className="text-center">{checkOrEmpty(option.enabled)}</td>
+                <td>{checkOrEmpty(option.enabled)}</td>
                 <td>{dataset.metadata.name}</td>
                 {option.degree !== undefined ? (
                     <td>{getDegreeText(dtype, option.degree)}</td>
diff --git a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOptionList.js b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOptionList.js
index c5269b99..90775d5b 100644
--- a/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOptionList.js
+++ b/frontend/src/components/Main/DatasetModelOptionList/DatasetModelOptionList.js
@@ -26,14 +26,14 @@ class DatasetModelOptionList extends Component {
         }
 
         return (
-            <table className="table table-sm">
+            <table className="table table-sm table-fixed">
                 <thead>
                     {dtype == Dtype.CONTINUOUS || dtype == Dtype.CONTINUOUS_INDIVIDUAL ? (
                         <tr className="bg-custom">
                             <th>Enabled</th>
                             <th>Dataset</th>
                             <th>
-                                Maximum polynomial degree&nbsp;
+                                Maximum Polynomial Degree&nbsp;
                                 <HelpTextPopover content={maxDegreeText} />
                             </th>
                             <th>Adverse Direction</th>
@@ -54,7 +54,7 @@ class DatasetModelOptionList extends Component {
                             <th>Enabled</th>
                             <th>Dataset</th>
                             <th>
-                                Maximum multistage degree
+                                Maximum Multistage Degree
                                 <HelpTextPopover content={maxDegreeText} />
                             </th>
                         </tr>
diff --git a/frontend/src/components/Main/OptionsForm/OptionsFormList.js b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
index 4c18e667..3c36d018 100644
--- a/frontend/src/components/Main/OptionsForm/OptionsFormList.js
+++ b/frontend/src/components/Main/OptionsForm/OptionsFormList.js
@@ -29,7 +29,7 @@ class OptionsFormList extends Component {
             <div>
                 <div className="panel panel-default">
                     <form className="form-horizontal">
-                        <table className="table table-sm text-center">
+                        <table className="table table-sm table-fixed">
                             <thead className="bg-custom">
                                 <tr>
                                     <th>Option Set #</th>
@@ -78,7 +78,7 @@ class OptionsFormList extends Component {
                                         </>
                                     ) : null}
                                     {optionsStore.canEdit ? (
-                                        <th>
+                                        <th style={{width: "55px"}}>
                                             <Button
                                                 title="Add option set."
                                                 className="btn btn-primary"