Merge branch 'discvr-25.3' into 25.3_fb_newExport

hextraza · web-flow · commit c87257a2b33c · 2025-04-11T15:09:28.000-07:00
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx
@@ -2,6 +2,7 @@ import React, { useState } from 'react';
 import TextField from '@mui/material/TextField';
 import Button from '@mui/material/Button';
 import Select from '@mui/material/Select';
+import ReactSelect from 'react-select';
 import AsyncSelect from 'react-select/async';
 import MenuItem from '@mui/material/MenuItem';
 import FormControl from '@mui/material/FormControl';
@@ -109,7 +110,7 @@ const FilterForm = (props: FilterFormProps ) => {
                         updatedFilter.value = '';
                     }
 
-                    if (value === "in set" || filter.operator === "in set") {
+                    if (value === "equals one of" || filter.operator === "equals one of") {
                         updatedFilter.value = ''; 
                     }
                 }
@@ -211,25 +212,33 @@ const FilterForm = (props: FilterFormProps ) => {
                     <FormScroll>
                         {filters.map((filter, index) => (
                             <FilterRow key={index} >
-                                <FormControlMinWidth sx={ highlightedInputs[index]?.field ? highlightedSx : null }>
-                                  <InputLabel id="field-label">Field</InputLabel>
-                                  <Select
-                                        labelId="field-label"
-                                        label = 'Field'
-                                        value={filter.field}
-                                        onChange={(event) =>
-                                            handleFilterChange(index, "field", event.target.value)
+                                <FormControlMinWidth sx={highlightedInputs[index]?.field ? highlightedSx : null}>
+                                    <ReactSelect
+                                        inputId={`field-select-${index}`}
+                                        aria-labelledby={`field-label`}
+                                        placeholder="Select field..."
+                                        menuPortalTarget={document.body}
+                                        menuPosition="fixed"
+                                        styles={{
+                                            menuPortal: (base) => ({ ...base, zIndex: 9999 }),
+                                        }}
+                                        options={fieldTypeInfo.map(field => ({
+                                            value: field.name,
+                                            label: field.label ?? field.name,
+                                        }))}
+                                        onChange={(selected) =>
+                                            handleFilterChange(index, 'field', selected?.value ?? '')
                                         }
-                                    >
-                                        <MenuItem value="" style={{ display: 'none' }}>
-                                            <em>None</em>
-                                        </MenuItem>
-                                        {fieldTypeInfo.map((field) => (
-                                            <MenuItem key={field.name} value={field.name}>
-                                                {field.label ?? field.name}
-                                            </MenuItem>
-                                        ))}
-                                    </Select>
+                                        value={
+                                            filter.field
+                                                ? {
+                                                    value: filter.field,
+                                                    label: fieldTypeInfo.find(f => f.name === filter.field)?.label ?? filter.field
+                                                }
+                                                : null
+                                        }
+                                        isClearable
+                                    />
                                 </FormControlMinWidth>
 
                                 <FormControlMinWidth sx={ highlightedInputs[index]?.operator ? highlightedSx : null } >
@@ -259,7 +268,7 @@ const FilterForm = (props: FilterFormProps ) => {
                                     </Select>
                                 </FormControlMinWidth>
 
-                                {filter.operator === "in set" ? (
+                                {filter.operator === "equals one of" ? (
                                     <FormControlMinWidth sx={ highlightedInputs[index]?.value ? highlightedSx : null } >
                                         <InputLabel id="value-select-label">Value</InputLabel>
                                         <Select
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/ShareButton.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/ShareButton.tsx
@@ -0,0 +1,25 @@
+import React from 'react';
+import { Button } from '@mui/material';
+import LinkIcon from '@mui/icons-material/Link';
+
+export const ShareButton = () => {
+  return (
+      <Button
+            startIcon={<LinkIcon />}
+            size="small"
+            color="primary"
+            onClick={() => {
+                navigator.clipboard.writeText(window.location.href)
+                .then(() => {
+                    alert('URL copied to clipboard.');
+                })
+                .catch(err => {
+                    console.error('Failed to copy the URL: ', err);
+                    alert('Failed to copy the URL.');
+                });
+            }}
+        >
+        Share
+      </Button>
+  );
+};
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
@@ -39,8 +39,10 @@ import '../../jbrowse.css';
 import LoadingIndicator from './LoadingIndicator';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { lastValueFrom } from 'rxjs';
+import { ShareButton } from  './ShareButton';
 
 const VariantTableWidget = observer(props => {
+    const numberFormatter = new Intl.NumberFormat('en-US');
     const { assembly, trackId, parsedLocString, sessionId, session, pluginManager } = props;
     const { assemblyNames = [], assemblyManager } = session ?? {};
     const { view } = session ?? {};
@@ -228,25 +230,7 @@ const VariantTableWidget = observer(props => {
                     Export CSV
                 </Button>
 
-                <Button
-                    startIcon={<LinkIcon />}
-                    size="small"
-                    color="primary"
-                    onClick={() => {
-                        navigator.clipboard.writeText(window.location.href)
-                        .then(() => {
-                            // Popup message for successful copy
-                            alert('URL copied to clipboard.');
-                        })
-                        .catch(err => {
-                            // Error handling
-                            console.error('Failed to copy the URL: ', err);
-                            alert('Failed to copy the URL.');
-                        });
-                    }}
-                >
-                Share
-                </Button>
+                <ShareButton />
             </GridToolbarContainer>
         );
     }
@@ -500,6 +484,14 @@ const VariantTableWidget = observer(props => {
                 setSortModel(newModel)
                 handleQuery(filters, true, { page: 0, pageSize: pageSizeModel.pageSize }, newModel);
             }}
+            localeText={{
+                MuiTablePagination: {
+                    labelDisplayedRows: ({ from, to, count }) =>
+                        `${numberFormatter.format(from)}–${numberFormatter.format(to)} of ${
+                            count !== -1 ? numberFormatter.format(count) : 'more than ' + numberFormatter.format(to)
+                        }`,
+                    },
+                }}
         />
     )
 
diff --git a/jbrowse/src/client/JBrowse/VariantTable/components/ShareButton.tsx b/jbrowse/src/client/JBrowse/VariantTable/components/ShareButton.tsx
@@ -0,0 +1,25 @@
+import React from 'react';
+import { Button } from '@mui/material';
+import LinkIcon from '@mui/icons-material/Link';
+
+export const ShareButton = () => {
+  return (
+      <Button
+            startIcon={<LinkIcon />}
+            size="small"
+            color="primary"
+            onClick={() => {
+                navigator.clipboard.writeText(window.location.href)
+                .then(() => {
+                    alert('URL copied to clipboard.');
+                })
+                .catch(err => {
+                    console.error('Failed to copy the URL: ', err);
+                    alert('Failed to copy the URL.');
+                });
+            }}
+        >
+        Share
+      </Button>
+  );
+};
diff --git a/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx
@@ -3,15 +3,29 @@ import React, { useEffect, useState } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { ParsedLocString, parseLocString } from '@jbrowse/core/util';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { AppBar, Box, Button, Dialog, Grid, MenuItem, Paper, Toolbar, Typography } from '@mui/material';
+import {
+    AppBar,
+    Box,
+    Button,
+    Dialog,
+    Grid,
+    MenuItem,
+    Paper,
+    Toolbar,
+    Typography,
+} from '@mui/material';
 import ScopedCssBaseline from '@mui/material/ScopedCssBaseline';
 import {
   DataGrid,
   GridColDef,
   GridColumnVisibilityModel, GridFilterPanel,
   GridPaginationModel,
   GridRenderCellParams,
-  GridToolbar
+  GridToolbar,
+  GridToolbarColumnsButton,
+  GridToolbarFilterButton,
+  GridToolbarDensitySelector,
+  GridToolbarExport
 } from '@mui/x-data-grid';
 import MenuButton from './MenuButton';
 import '../../jbrowse.css';
@@ -27,6 +41,7 @@ import {
   passesSampleFilters
 } from '../../utils';
 import LoadingIndicator from './LoadingIndicator';
+import { ShareButton } from './ShareButton';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import StandaloneSearchComponent from '../../Search/components/StandaloneSearchComponent';
 import { VcfFeature } from '@jbrowse/plugin-variants';
@@ -352,12 +367,24 @@ const VariantTableWidget = observer(props => {
     }
   }
 
+  const CustomToolbar = () => (
+    <Box sx={{ display: 'flex', justifyContent: 'space-between', p: 1 }}>
+      <Box>
+        <GridToolbarColumnsButton />
+        <GridToolbarFilterButton />
+        <GridToolbarDensitySelector />
+        <GridToolbarExport />
+        <ShareButton />
+      </Box>
+    </Box>
+  );
+
   const gridElement = (
     // NOTE: the filterPanel/sx override is added to fix an issue where the grid column filter value input doesn't align with the field and operator inputs
     <DataGrid
         columns={[...gridColumns, actionsCol]}
         rows={features.map((rawFeature, id) => rawFeatureToRow(rawFeature, id, gridColumns, trackId))}
-        slots={{ toolbar: GridToolbar, filterPanel: GridFilterPanel }}
+        slots={{ toolbar: CustomToolbar, filterPanel: GridFilterPanel }}
         slotProps={{
           filterPanel: {
             filterFormProps: {
@@ -444,7 +471,7 @@ const VariantTableWidget = observer(props => {
           </Grid>
 
           {supportsLuceneIndex ? <Grid key='luceneViewButton' item xs="auto">
-            <Button hidden={!supportsLuceneIndex} style={{ marginTop:"8px"}} color="primary" variant="contained" onClick={() => handleMenu("luceneRedirect")}>Switch to Free-text Search</Button>
+            <Button hidden={!supportsLuceneIndex} style={{ marginTop:"8px"}} color="primary" variant="contained" onClick={() => handleMenu("luceneRedirect")}>Switch to Full-text Search</Button>
           </Grid> : null}
         </Grid>
       </div>
diff --git a/jbrowse/src/client/JBrowse/utils.ts b/jbrowse/src/client/JBrowse/utils.ts
@@ -330,7 +330,7 @@ export function serializeLocationToLuceneQuery(contig, start, end) {
 function generateLuceneString(field, operator, value) {
   let luceneQueryString = '';
 
-  if (field === 'variableSamples' && operator == "in set") {
+  if (field === 'variableSamples' && operator == "equals one of") {
     return `variableSamples:~${value}~`;
   }
   let intValue = parseInt(value);
@@ -656,7 +656,7 @@ export function searchStringToInitialFilters(knownFieldNames: string[]) : Filter
 
 export function getOperatorsForField(fieldObj: FieldModel): string[] {
     const stringOperators = ["equals", "does not equal", "contains", "does not contain", "starts with", "ends with", "is empty", "is not empty"];
-    const variableSamplesType = ["in set", "variable in", "not variable in", "variable in all of", "variable in any of", "not variable in any of", "not variable in one of", "is empty", "is not empty"];
+    const variableSamplesType = ["equals one of", "variable in", "not variable in", "variable in all of", "variable in any of", "not variable in any of", "not variable in one of", "is empty", "is not empty"];
     const numericOperators = ["=", "!=", ">", ">=", "<", "<="];
     const noneOperators = [];
 
diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
