Merge branch 'main' into deletion-dates

bmds_ui/analysis/apps.py

@@ -3,6 +3,3 @@
 
 class Config(AppConfig):
     name = "bmds_ui.analysis"
-
-    def ready(self):
-        from .signals import init_command  # noqa: F401

bmds_ui/desktop/sqlite3/base.py

@@ -0,0 +1,31 @@
+from sqlite3 import dbapi2 as Database
+
+from django.db.backends.sqlite3 import base
+from django.db.backends.sqlite3._functions import register as register_functions
+from django.utils.asyncio import async_unsafe
+
+
+class DatabaseWrapper(base.DatabaseWrapper):
+    # TODO - remove w/ django 5.1 release
+    # adapted from https://blog.pecar.me/sqlite-django-config
+    # https://gcollazo.com/optimal-sqlite-settings-for-django/
+    def _start_transaction_under_autocommit(self):
+        # Acquire a write lock immediately for transactions
+        self.cursor().execute("BEGIN IMMEDIATE")
+
+    @async_unsafe
+    def get_new_connection(self, conn_params):
+        conn = Database.connect(**conn_params)
+        register_functions(conn)
+
+        conn.execute("PRAGMA foreign_keys=ON")
+        conn.execute("PRAGMA legacy_alter_table = OFF")
+        conn.execute("PRAGMA journal_mode = WAL")
+        conn.execute("PRAGMA synchronous = NORMAL")
+        conn.execute("PRAGMA busy_timeout = 5000")
+        conn.execute("PRAGMA temp_store = MEMORY")
+        conn.execute("PRAGMA mmap_size = 134217728")
+        conn.execute("PRAGMA journal_size_limit = 67108864")
+        conn.execute("PRAGMA cache_size = 2000")
+
+        return conn

bmds_ui/main/settings/desktop.py

@@ -32,9 +32,8 @@
 
 DATABASES = {
     "default": {
-        "ENGINE": "django.db.backends.sqlite3",
-        "NAME": os.getenv("BMDS_DB", APP_HOME / "pybmds.sqlite3"),
-        "STARTUP_OPTIONS": {"init_command": "PRAGMA journal_mode=wal;"},
+        "ENGINE": "bmds_ui.desktop.sqlite3",
+        "NAME": os.getenv("BMDS_DB", APP_HOME / "bmds-desktop.db"),
     }
 }
 

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),

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;

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} />;
     }

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} />;

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>

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>

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>

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,

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;