From 16fc13604fd2c163eb4e691a786e52228470677b Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 7 Apr 2025 12:11:33 -0700
Subject: [PATCH 01/28] Improve data QC

---
 singlecell/resources/queries/singlecell/samples.js | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/singlecell/resources/queries/singlecell/samples.js b/singlecell/resources/queries/singlecell/samples.js
index 1a0d6d8f7..0b78206ec 100644
--- a/singlecell/resources/queries/singlecell/samples.js
+++ b/singlecell/resources/queries/singlecell/samples.js
@@ -62,4 +62,12 @@ function beforeUpsert(row, oldRow, errors){
     if (['Lung R', 'Lung Right', 'Lung-Right'].indexOf(row.tissue) !== -1){
         row.tissue = 'Lung-R';
     }
+
+    if (['Bulk', 'bulk'].indexOf(row.assaytype) !== -1){
+        row.assaytype = 'Bulk cells';
+    }
+
+    if (['Peptide Stim-BFA', 'Peptide stim-BFA'].indexOf(row.assaytype) !== -1){
+        row.assaytype = 'Peptide Stim - BFA';
+    }
 }
\ No newline at end of file

From a4f691d1c761ecc448ee3b3159b52a0518348f34 Mon Sep 17 00:00:00 2001
From: hextraza <hextraza@gmail.com>
Date: Fri, 11 Apr 2025 13:09:50 -0700
Subject: [PATCH 02/28] Misc fixes (#325)

* en localization for pagination, for commas

* React-select for autocomplete on VariantSearch

* Add share button to VariantTable

* in set -> equals one of

* Fix tests for new autocomplete input

---------

Co-authored-by: Sebastian Benjamin <sebastiancbenjamin@gmail.com>
---
 .../VariantSearch/components/FilterForm.tsx   |  49 +++++----
 .../VariantSearch/components/ShareButton.tsx  |  25 +++++
 .../components/VariantTableWidget.tsx         |  31 ++----
 .../VariantTable/components/ShareButton.tsx   |  25 +++++
 .../components/VariantTableWidget.tsx         |  35 +++++-
 jbrowse/src/client/JBrowse/utils.ts           |   4 +-
 .../external/labModules/JBrowseTest.java      | 101 +++++++++---------
 7 files changed, 173 insertions(+), 97 deletions(-)
 create mode 100644 jbrowse/src/client/JBrowse/VariantSearch/components/ShareButton.tsx
 create mode 100644 jbrowse/src/client/JBrowse/VariantTable/components/ShareButton.tsx

diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx
index 1752cabcf..f24b2e857 100644
--- 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
new file mode 100644
index 000000000..2315158be
--- /dev/null
+++ 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
index 9a186e493..c7a5ebb14 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
+++ b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
@@ -13,7 +13,6 @@ import {
     GridToolbarExport
 } from '@mui/x-data-grid';
 import SearchIcon from '@mui/icons-material/Search';
-import LinkIcon from '@mui/icons-material/Link';
 import React, { useEffect, useState } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { AppBar, Box, Button, Dialog, Paper, Popover, Toolbar, Tooltip, Typography } from '@mui/material';
@@ -37,8 +36,10 @@ 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 ?? {};
@@ -200,25 +201,7 @@ const VariantTableWidget = observer(props => {
                     delimiter: ';',
                 }} />
 
-                <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>
         );
     }
@@ -469,6 +452,14 @@ 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
new file mode 100644
index 000000000..2315158be
--- /dev/null
+++ 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
index a7b58ebc4..33f61a49d 100644
--- a/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx
+++ b/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx
@@ -3,7 +3,17 @@ 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,
@@ -11,7 +21,11 @@ import {
   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
index 1602ff088..0cbe2d0cd 100644
--- 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
index 2199ccc99..b3bb3bc57 100644
--- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
+++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
@@ -569,7 +569,6 @@ private void testFullTextSearch() throws Exception
         String sessionId = info.getKey();
         String trackId = info.getValue();
 
-
         // all
         // this should return 143 results. We can't make any other assumptions about the content
         String url = "/jbrowse/" + getProjectName() + "/luceneQuery.view?sessionId=" + sessionId + "&trackId=" + trackId + "&searchString=all&pageSize=143";
@@ -1613,20 +1612,20 @@ private void testLuceneSearchUI(String sessionId)
 
         // VariableSamples in set !TestGroup!
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "in set")).click();
+        waitForElement(Locator.tagWithText("li", "equals one of")).click();
         waitForElement(Locator.tagWithId("div", "value-select-0")).click();
         waitForElement(Locator.tagWithText("li", "!TestGroup!")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "173"));
-        clearFilterDialog("variableSamples in set !TestGroup!");
+        clearFilterDialog("variableSamples equals one of !TestGroup!");
 
         // VariableSamples variable in m000001
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "variable in")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m00001");
@@ -1637,8 +1636,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // VariableSamples not variable in m05710
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "not variable in")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m05710");
@@ -1649,8 +1648,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // VariableSamples li usage + variable in all of
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "variable in all of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
@@ -1663,8 +1662,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // VariableSamples variable in any of m00004,m00007
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "variable in any of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
@@ -1677,8 +1676,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // VariableSamples not variable in any of m00005,m00004
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "not variable in any of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
@@ -1691,8 +1690,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // VariableSamples not variable in one of m03660,m00001
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "not variable in one of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m036");
@@ -1705,8 +1704,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // samples with variant isEmpty
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "is empty")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
@@ -1715,8 +1714,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start = 2
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "=")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("2");
@@ -1726,8 +1725,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start != 2
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "!=")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("2");
@@ -1737,8 +1736,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start < 173
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "<")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("173");
@@ -1748,8 +1747,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start > 502
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", ">")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("502");
@@ -1759,8 +1758,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start <= 440
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "<=")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("440");
@@ -1770,8 +1769,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start >= 609
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", ">=")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("609");
@@ -1782,8 +1781,8 @@ private void testLuceneSearchUI(String sessionId)
         // Ref Allele equals GAAAA
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Ref Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "equals")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("GAAAA");
@@ -1794,8 +1793,8 @@ private void testLuceneSearchUI(String sessionId)
         // Impact equals HIGH
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Impact on Protein Coding")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Impact on Protein Coding"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "equals")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("HI");
@@ -1807,8 +1806,8 @@ private void testLuceneSearchUI(String sessionId)
         // Ref Allele does not equal A
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Ref Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "does not equal")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("A");
@@ -1819,8 +1818,8 @@ private void testLuceneSearchUI(String sessionId)
         // Alt Allele contains TT
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Alt Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Alt Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "contains")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("TT");
@@ -1831,8 +1830,8 @@ private void testLuceneSearchUI(String sessionId)
         // Alt Allele does not contain T
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Alt Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Alt Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "does not contain")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("T");
@@ -1843,8 +1842,8 @@ private void testLuceneSearchUI(String sessionId)
         // Ref Allele starts with GA
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Ref Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "starts with")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("GA");
@@ -1855,8 +1854,8 @@ private void testLuceneSearchUI(String sessionId)
         // Ref Allele ends with AAA
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Ref Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "ends with")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("AAA");
@@ -1866,8 +1865,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Alt Allele is empty
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Alt Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Alt Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "is empty")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
@@ -1876,8 +1875,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // IMPACT is not empty
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Impact on Protein Coding")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Impact on Protein Coding"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "is not empty")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
@@ -1886,8 +1885,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // IMPACT HIGH+MODERATE
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Impact on Protein Coding")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Impact on Protein Coding"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "equals")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("HI");

From 350d81e7836e002f4e932dfc7b7a32a052aad6a9 Mon Sep 17 00:00:00 2001
From: hextraza <hextraza@gmail.com>
Date: Fri, 11 Apr 2025 15:20:42 -0700
Subject: [PATCH 03/28] New export endpoint (#321)

* WIP

* Working export

* Remove old const

* Add CSV download test

* Simplify try/catch

---------

Co-authored-by: Sebastian Benjamin <sebastiancbenjamin@gmail.com>
---
 .../components/VariantTableWidget.tsx         | 42 +++++++-
 .../org/labkey/jbrowse/JBrowseController.java | 61 +++++++++++-
 .../labkey/jbrowse/JBrowseLuceneSearch.java   | 95 ++++++++++++++++---
 .../external/labModules/JBrowseTest.java      | 36 +++++++
 4 files changed, 215 insertions(+), 19 deletions(-)

diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
index c7a5ebb14..e3c711e78 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
+++ b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
@@ -13,6 +13,9 @@ import {
     GridToolbarExport
 } from '@mui/x-data-grid';
 import SearchIcon from '@mui/icons-material/Search';
+import LinkIcon from '@mui/icons-material/Link';
+import DownloadIcon from '@mui/icons-material/Download'
+import { ActionURL } from '@labkey/api';
 import React, { useEffect, useState } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { AppBar, Box, Button, Dialog, Paper, Popover, Toolbar, Tooltip, Typography } from '@mui/material';
@@ -92,6 +95,27 @@ const VariantTableWidget = observer(props => {
         fetchLuceneQuery(passedFilters, sessionId, trackGUID, page, pageSize, field, sort, (json)=>{handleSearch(json)}, (error) => {setDataLoaded(true); setError(error)});
     }
 
+    const handleExport = () => {
+        const currentUrl = new URL(window.location.href);
+
+        const searchString = createEncodedFilterString(filters, true);
+        const sortField = sortModel[0]?.field ?? 'genomicPosition';
+        const sortDirection = sortModel[0]?.sort ?? false;
+
+        const sortReverse = (sortDirection === 'desc');
+
+        const rawUrl = ActionURL.buildURL('jbrowse', 'luceneCSVExport.api');
+        const exportUrl = new URL(rawUrl, window.location.origin);
+
+        exportUrl.searchParams.set('sessionId', sessionId);
+        exportUrl.searchParams.set('trackId', trackGUID);
+        exportUrl.searchParams.set('searchString', searchString);
+        exportUrl.searchParams.set('sortField', sortField);
+        exportUrl.searchParams.set('sortReverse', sortReverse.toString());
+
+        window.location.href = exportUrl.toString();
+    };
+
     const TableCellWithPopover = (props: { value: any }) => {
         const { value } = props;
         const fullDisplayValue = value ? (Array.isArray(value) ? value.join(', ') : value) : ''
@@ -184,7 +208,7 @@ const VariantTableWidget = observer(props => {
         );
     }
 
-    function CustomToolbar({ setFilterModalOpen }) {
+    function CustomToolbar({ setFilterModalOpen, handleExport }) {
         return (
             <GridToolbarContainer>
                 <GridToolbarColumnsButton />
@@ -197,9 +221,14 @@ const VariantTableWidget = observer(props => {
                     Search
                 </Button>
                 <GridToolbarDensitySelector />
-                <GridToolbarExport csvOptions={{
-                    delimiter: ';',
-                }} />
+
+                <Button
+                    startIcon={<DownloadIcon />}
+                    color="primary"
+                    onClick={handleExport}
+                >
+                    Export CSV
+                </Button>
 
                 <ShareButton />
             </GridToolbarContainer>
@@ -207,7 +236,10 @@ const VariantTableWidget = observer(props => {
     }
 
     const ToolbarWithProps = () => (
-        <CustomToolbar setFilterModalOpen={setFilterModalOpen} />
+        <CustomToolbar
+            setFilterModalOpen={setFilterModalOpen}
+            handleExport={handleExport}
+        />
     );
 
     const handleOffsetChange = (newOffset: number) => {
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseController.java b/jbrowse/src/org/labkey/jbrowse/JBrowseController.java
index caaf68229..6dc297b95 100644
--- a/jbrowse/src/org/labkey/jbrowse/JBrowseController.java
+++ b/jbrowse/src/org/labkey/jbrowse/JBrowseController.java
@@ -20,6 +20,7 @@
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFFileReader;
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
@@ -78,6 +79,8 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -891,6 +894,55 @@ public void validateForm(ResolveVcfFieldsForm form, Errors errors)
         }
     }
 
+    @RequiresPermission(ReadPermission.class)
+    public static class LuceneCSVExportAction extends ReadOnlyApiAction<LuceneQueryForm>
+    {
+        @Override
+        public ApiResponse execute(LuceneQueryForm form, BindException errors)
+        {
+            try
+            {
+                JBrowseLuceneSearch searcher = JBrowseLuceneSearch.create(form.getSessionId(), form.getTrackId(), getUser());
+                DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd_HH-mm-ss");
+                String timestamp = LocalDateTime.now().format(formatter);
+                String filename = "mGAP_results_" + timestamp + ".csv";
+
+                HttpServletResponse response = getViewContext().getResponse();
+                response.setContentType("text/csv");
+                response.setHeader("Content-Disposition", "attachment; filename=\"" + filename + "\"");
+
+                searcher.doSearchCSV(
+                        getUser(),
+                        PageFlowUtil.decode(form.getSearchString()),
+                        form.getSortField(),
+                        form.getSortReverse(),
+                        response
+                );
+
+                return null;
+            }
+            catch (Exception e)
+            {
+                _log.error("Error in JBrowse lucene query", e);
+                errors.reject(ERROR_MSG, e.getMessage());
+                return null;
+            }
+        }
+
+        @Override
+        public void validateForm(LuceneQueryForm form, Errors errors)
+        {
+            if ((form.getSearchString() == null || form.getSessionId() == null || form.getTrackId() == null))
+            {
+                errors.reject(ERROR_MSG, "Must provide search string, track ID, and the JBrowse session ID");
+            }
+            else if (!isValidUUID(form.getTrackId()))
+            {
+                errors.reject(ERROR_MSG, "Invalid track ID: " + form.getTrackId());
+            }
+        }
+    }
+
     @RequiresPermission(ReadPermission.class)
     public static class LuceneQueryAction extends ReadOnlyApiAction<LuceneQueryForm>
     {
@@ -910,7 +962,14 @@ public ApiResponse execute(LuceneQueryForm form, BindException errors)
 
             try
             {
-                return new ApiSimpleResponse(searcher.doSearch(getUser(), PageFlowUtil.decode(form.getSearchString()), form.getPageSize(), form.getOffset(), form.getSortField(), form.getSortReverse()));
+                return new ApiSimpleResponse(searcher.doSearchJSON(
+                        getUser(),
+                        PageFlowUtil.decode(form.getSearchString()),
+                        form.getPageSize(),
+                        form.getOffset(),
+                        form.getSortField(),
+                        form.getSortReverse()
+                ));
             }
             catch (Exception e)
             {
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java b/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java
index f886d1c86..df0adb665 100644
--- a/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java
+++ b/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java
@@ -1,5 +1,6 @@
 package org.labkey.jbrowse;
 
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.apache.lucene.analysis.Analyzer;
@@ -20,6 +21,7 @@
 import org.apache.lucene.search.MatchAllDocsQuery;
 import org.apache.lucene.search.Query;
 import org.apache.lucene.search.QueryCachingPolicy;
+import org.apache.lucene.search.ScoreDoc;
 import org.apache.lucene.search.Sort;
 import org.apache.lucene.search.SortField;
 import org.apache.lucene.search.TopFieldDocs;
@@ -50,6 +52,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintWriter;
 import java.net.URLDecoder;
 import java.nio.charset.StandardCharsets;
 import java.text.DecimalFormat;
@@ -189,7 +192,17 @@ public String extractFieldName(String queryString)
         return parts.length > 0 ? parts[0].trim() : null;
     }
 
-    public JSONObject doSearch(User u, String searchString, final int pageSize, final int offset, String sortField, boolean sortReverse) throws IOException, ParseException
+    public JSONObject doSearchJSON(User u, String searchString, final int pageSize, final int offset, String sortField, boolean sortReverse) throws IOException, ParseException {
+        SearchConfig searchConfig = createSearchConfig(u, searchString, pageSize, offset, sortField, sortReverse);
+        return paginateJSON(searchConfig);
+    }
+
+    public void doSearchCSV(User u, String searchString, String sortField, boolean sortReverse, HttpServletResponse response) throws IOException, ParseException {
+        SearchConfig searchConfig = createSearchConfig(u, searchString, 0, 0, sortField, sortReverse);
+        exportCSV(searchConfig, response);
+    }
+
+    private SearchConfig createSearchConfig(User u, String searchString, final int pageSize, final int offset, String sortField, boolean sortReverse) throws IOException, ParseException
     {
         searchString = tryUrlDecode(searchString);
         File indexPath = _jsonFile.getExpectedLocationOfLuceneIndex(true);
@@ -199,6 +212,7 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina
         Analyzer analyzer = new StandardAnalyzer();
 
         List<String> stringQueryParserFields = new ArrayList<>();
+        List<String> fieldsList = new ArrayList<>();
         Map<String, SortField.Type> numericQueryParserFields = new HashMap<>();
         PointsConfig intPointsConfig = new PointsConfig(new DecimalFormat(), Integer.class);
         PointsConfig doublePointsConfig = new PointsConfig(new DecimalFormat(), Double.class);
@@ -208,6 +222,7 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina
         for (Map.Entry<String, JBrowseFieldDescriptor> entry : fields.entrySet())
         {
             String field = entry.getKey();
+            fieldsList.add(field);
             JBrowseFieldDescriptor descriptor = entry.getValue();
 
             switch(descriptor.getType())
@@ -267,14 +282,14 @@ else if (numericQueryParserFields.containsKey(fieldName))
                 }
                 catch (QueryNodeException e)
                 {
-                    _log.error("Unable to parse query for field " + fieldName + ": " + queryString, e);
+                    _log.error("Unable to parse query for field {}: {}", fieldName, queryString, e);
 
                     throw new IllegalArgumentException("Unable to parse query: " + queryString + " for field: " + fieldName);
                 }
             }
             else
             {
-                _log.error("No such field(s), or malformed query: " + queryString + ", field: " + fieldName);
+                _log.error("No such field(s), or malformed query: {}, field: {}", queryString, fieldName);
 
                 throw new IllegalArgumentException("No such field(s), or malformed query: " + queryString + ", field: " + fieldName);
             }
@@ -302,43 +317,79 @@ else if (numericQueryParserFields.containsKey(fieldName))
             sort = new Sort(new SortField(sortField + "_sort", fieldType, sortReverse));
         }
 
+        return new SearchConfig(cacheEntry, query, pageSize, offset, sort, fieldsList);
+    }
+
+    private JSONObject paginateJSON(SearchConfig c) throws IOException, ParseException {
         // Get chunks of size {pageSize}. Default to 1 chunk -- add to the offset to get more.
         // We then iterate over the range of documents we want based on the offset. This does grow in memory
         // linearly with the number of documents, but my understanding is that these are just score,id pairs
         // rather than full documents, so mem usage *should* still be pretty low.
         // Perform the search with sorting
-        TopFieldDocs topDocs = cacheEntry.indexSearcher.search(query, pageSize * (offset + 1), sort);
-
+        TopFieldDocs topDocs = c.cacheEntry.indexSearcher.search(c.query, c.pageSize * (c.offset + 1), c.sort);
         JSONObject results = new JSONObject();
 
         // Iterate over the doc list, (either to the total end or until the page ends) grab the requested docs,
         // and add to returned results
         List<JSONObject> data = new ArrayList<>();
-        for (int i = pageSize * offset; i < Math.min(pageSize * (offset + 1), topDocs.scoreDocs.length); i++)
+        for (int i = c.pageSize * c.offset; i < Math.min(c.pageSize * (c.offset + 1), topDocs.scoreDocs.length); i++)
         {
             JSONObject elem = new JSONObject();
-            Document doc = cacheEntry.indexSearcher.storedFields().document(topDocs.scoreDocs[i].doc);
+            Document doc = c.cacheEntry.indexSearcher.storedFields().document(topDocs.scoreDocs[i].doc);
 
-            for (IndexableField field : doc.getFields()) {
+            for (IndexableField field : doc.getFields())
+            {
                 String fieldName = field.name();
                 String[] fieldValues = doc.getValues(fieldName);
-                if (fieldValues.length > 1) {
+                if (fieldValues.length > 1)
+                {
                     elem.put(fieldName, fieldValues);
-                } else {
+                }
+                else
+                {
                     elem.put(fieldName, fieldValues[0]);
                 }
             }
-
             data.add(elem);
         }
 
         results.put("data", data);
         results.put("totalHits", topDocs.totalHits.value);
 
-        //TODO: we should probably stream this
         return results;
     }
 
+    private void exportCSV(SearchConfig c, HttpServletResponse response) throws IOException
+    {
+        PrintWriter writer = response.getWriter();
+        IndexSearcher searcher = c.cacheEntry.indexSearcher;
+        TopFieldDocs topDocs = searcher.search(c.query, Integer.MAX_VALUE, c.sort);
+
+        writer.println(String.join(",", c.fields));
+
+        for (ScoreDoc scoreDoc : topDocs.scoreDocs)
+        {
+            Document doc = searcher.storedFields().document(scoreDoc.doc);
+            List<String> rowValues = new ArrayList<>();
+
+            for (String fieldName : c.fields)
+            {
+                String[] values = doc.getValues(fieldName);
+                String value = values.length > 0
+                        ? String.join(",", values)
+                        : "";
+
+                // Escape strings
+                value = "\"" + value.replace("\"", "\"\"") + "\"";
+                rowValues.add(value);
+            }
+
+            writer.println(String.join(",", rowValues));
+        }
+
+        writer.flush();
+    }
+
     public static class DefaultJBrowseFieldCustomizer extends AbstractJBrowseFieldCustomizer
     {
         public DefaultJBrowseFieldCustomizer()
@@ -583,7 +634,7 @@ public void cacheDefaultQuery()
         try
         {
             JBrowseLuceneSearch.clearCache(_jsonFile.getObjectId());
-            doSearch(_user, ALL_DOCS, 100, 0, GENOMIC_POSITION, false);
+            doSearchJSON(_user, ALL_DOCS, 100, 0, GENOMIC_POSITION, false);
         }
         catch (ParseException | IOException e)
         {
@@ -641,4 +692,22 @@ public void shutdownStarted()
             JBrowseLuceneSearch.emptyCache();
         }
     }
+
+    private class SearchConfig {
+        CacheEntry cacheEntry;
+        Query query;
+        int pageSize;
+        int offset;
+        Sort sort;
+        List<String> fields;
+
+        public SearchConfig(CacheEntry cacheEntry, Query query, int pageSize, int offset, Sort sort, List<String> fields) {
+            this.cacheEntry = cacheEntry;
+            this.query = query;
+            this.pageSize = pageSize;
+            this.offset = offset;
+            this.sort = sort;
+            this.fields = fields;
+        }
+    }
 }
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
index b3bb3bc57..8ef002a10 100644
--- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
+++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
@@ -15,6 +15,7 @@
  */
 package org.labkey.test.tests.external.labModules;
 
+import au.com.bytecode.opencsv.CSVReader;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.json.JSONArray;
@@ -50,6 +51,7 @@
 import org.openqa.selenium.support.Color;
 
 import java.io.File;
+import java.io.FileReader;
 import java.io.IOException;
 import java.util.List;
 import java.util.Map;
@@ -1896,6 +1898,40 @@ private void testLuceneSearchUI(String sessionId)
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "0.029"));
 
+        // Test the CSV export on this discrete case prior to clearing -- there should be 2 rows
+        File downloadCSV = doAndWaitForDownload(() -> clickButton("Export CSV", 0));
+        try (FileReader fileReader = new FileReader(downloadCSV))
+        {
+            CSVReader csvReader = new CSVReader(fileReader);
+            String[] line = csvReader.readNext();
+            Assert.assertArrayEquals(new String[] {
+                    "contig", "start", "end", "ref", "alt", "genomicPosition",
+                    "nCalled", "fractionHet", "variableSamples", "homozygousVarSamples",
+                    "nHomVar", "nHet", "AF", "AC", "CADD_PH", "CLN_ALLELE", "OMIMD", "IMPACT"
+            }, line);
+            line = csvReader.readNext();
+            Assert.assertArrayEquals(new String[] {
+                    "1", "2", "2", "A", "T", "2", "1523", "0.9268293",
+                    "m00004,m00013,m00029,m00101,m00391,m00435,m00458,m00598,m00610,m00789,m00801,m00816,m00969,m02168," +
+                            "m02169,m02179,m02225,m02230,m02280,m02324,m02344,m02369,m02391,m03592,m03655,m03667,m03669," +
+                            "m03684,m03694,m05192,m05264,m05270,m05273,m05550,m05551,m05557,m05622,m05640,m05658,m05659," +
+                            "m05660,m05662,m05666,m05668,m05669,m05671,m05672,m05673,m05675,m05795,m05812,m05834,m05855," +
+                            "m05861,m05895,m06088,m06969,m06970,m06985,m06986,m06988,m06993,m07003,m07006,m07007,m07025," +
+                            "m07034,m07037,m07045,m07409,m07418,m07426,m07438,m07446,m07458,m07489,m07495,m07513,m07863," +
+                            "m07929,m07951,m07952",
+                    "m03694,m05671,m05672,m06970,m06993,m07951",
+                    "6", "76", "0.029", "88", "7.292", "", "", "HIGH"
+            }, line);
+            line = csvReader.readNext();
+            Assert.assertArrayEquals(new String[] {
+                    "1","5336","5336","A","G","5336","1524","1.0","m05373","","0","1","3.281E-4","1","2.868","","","MODERATE"
+            }, line);
+        }
+        catch (Exception e)
+        {
+            Assert.fail();
+        }
+
         clearFilterDialog("IMPACT equals HIGH,MODERATE");
 
         testLuceneColumnSerialization(sessionId);

From 175d28d25a6a3c43cfd3dd40e3a1702ecdce581c Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Sat, 12 Apr 2025 07:04:33 -0700
Subject: [PATCH 04/28] Support scatter/gather for liftover

---
 .../panel/VariantScatterGatherPanel.js              |  1 +
 .../web/SequenceAnalysis/window/LiftoverWindow.js   | 13 +++++++++----
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantScatterGatherPanel.js b/SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantScatterGatherPanel.js
index 5b0204a11..3b8daa105 100644
--- a/SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantScatterGatherPanel.js
+++ b/SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantScatterGatherPanel.js
@@ -3,6 +3,7 @@ Ext4.define('SequenceAnalysis.panel.VariantScatterGatherPanel', {
     alias: 'widget.sequenceanalysis-variantscattergatherpanel',
 
     defaultFieldWidth: null,
+    labelWidth: null,
 
     initComponent: function (){
         Ext4.apply(this, {
diff --git a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
index 8398fc47a..e6f7565ce 100644
--- a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
+++ b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
@@ -56,7 +56,7 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
                                         containerPath: containerPath,
                                         dataRegionName: dataRegionName,
                                         outputFileIds: checked,
-                                        libraryId: distinctGenomes.length == 1 ? distinctGenomes[0] : null,
+                                        libraryId: distinctGenomes.length === 1 ? distinctGenomes[0] : null,
                                         toolParameters: results.toolParameters
                                     }).show();
                                 }
@@ -71,7 +71,7 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
     initComponent: function(){
         Ext4.apply(this, {
             bodyStyle: 'padding: 5px;',
-            width: 500,
+            width: 600,
             modal: true,
             title: 'Liftover File(s) To Alternate Genome',
             items: [{
@@ -117,12 +117,17 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
                 itemId: 'useBcfTools',
                 checked: true,
                 fieldLabel: 'Use bcftools'
-            },{
+            }, {
                 xtype: 'checkbox',
                 itemId: 'doNotRetainUnmapped',
                 checked: false,
                 fieldLabel: 'Do Not Retain Unmapped'
-            }].concat(SequenceAnalysis.window.OutputHandlerWindow.getCfgForToolParameters(this.toolParameters)),
+            }].concat(SequenceAnalysis.window.OutputHandlerWindow.getCfgForToolParameters(this.toolParameters)).concat([{
+                xtype: 'sequenceanalysis-variantscattergatherpanel',
+                defaultFieldWidth: 500,
+                labelWidth: 200,
+                bodyStyle: ''
+            }]),
             buttons: [{
                 text: 'Submit',
                 handler: this.onSubmit,

From 3da91fac8b4b0e88f2fcffde4670482acc34b65d Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 14 Apr 2025 10:23:17 -0700
Subject: [PATCH 05/28] Support scatter/gather for liftover

---
 .../web/SequenceAnalysis/window/LiftoverWindow.js    |  4 ++++
 .../resources/views/singleCellDataManagement.html    | 12 ++++++++++++
 2 files changed, 16 insertions(+)

diff --git a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
index e6f7565ce..c0333f803 100644
--- a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
+++ b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
@@ -175,6 +175,10 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
             params.doNotRetainUnmapped = this.down('#doNotRetainUnmapped').getValue();
         }
 
+        Ext4.Array.forEach(this.down('sequenceanalysis-variantscattergatherpanel').query('field'), function(field){
+            params[field.name] = field.getValue();
+        }, this);
+
         Ext4.Msg.wait('Saving...');
         LABKEY.Ajax.request({
             url: LABKEY.ActionURL.buildURL('sequenceanalysis', 'runSequenceHandler', this.containerPath),
diff --git a/singlecell/resources/views/singleCellDataManagement.html b/singlecell/resources/views/singleCellDataManagement.html
index cfda8679e..0c0393de9 100644
--- a/singlecell/resources/views/singleCellDataManagement.html
+++ b/singlecell/resources/views/singleCellDataManagement.html
@@ -48,6 +48,18 @@
                     },{
                         name: 'cDNA Libraries with Hashing and Single HTO/Lane',
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'singlecell', queryName: 'cdna_libraries', 'query.uniqueHtos~in': '0;1', 'query.hashingReadsetId/name~isnonblank': null, 'query.hashingReadsetId/totalFiles~eq': 0})
+                    },{
+                        name: 'GEX Readsets Missing Nimble (Measured using MHC)',
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
+                            schemaName: 'sequenceanalysis',
+                            queryName: 'sequence_readsets',
+                            'query.distinctOutputGenomes~contains': 'Mmul_10',
+                            'query.status~isblank': null,
+                            'query.totalForwardReads~isnonblank': null,
+                            'query.sort': 'rowid',
+                            'query.librarytype~eq': '10x 5\' GEX',
+                            'query.distinctOutputGenomes~doesnotcontain': 'Rhesus Macaque MHC v2'
+                        })
                     },{
                         name: 'Analyses In Novogene-Related Workbook',
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_analyses', 'query.container/title~containsoneof': 'Novogene;shipment'})

From d114fd1f7c9953cb663dd78f4ddd2b6960508f56 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 14 Apr 2025 13:45:39 -0700
Subject: [PATCH 06/28] Bugfix for liftover scatter/gather

---
 .../web/SequenceAnalysis/window/LiftoverWindow.js         | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
index c0333f803..3c979cb7b 100644
--- a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
+++ b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
@@ -179,9 +179,15 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
             params[field.name] = field.getValue();
         }, this);
 
+        var actionName = 'runSequenceHandler';
+        if (params.scatterGatherMethod && params.scatterGatherMethod !== 'none') {
+            params.scatterGather = true;
+            actionName = 'runVariantProcessing';
+        }
+
         Ext4.Msg.wait('Saving...');
         LABKEY.Ajax.request({
-            url: LABKEY.ActionURL.buildURL('sequenceanalysis', 'runSequenceHandler', this.containerPath),
+            url: LABKEY.ActionURL.buildURL('sequenceanalysis', actionName, this.containerPath),
             jsonData: {
                 handlerClass: 'org.labkey.sequenceanalysis.analysis.LiftoverHandler',
                 outputFileIds: this.outputFileIds,

From f1d5379c8aed42be4f6a13b4090bf747abdb1262 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 16 Apr 2025 13:09:22 -0700
Subject: [PATCH 07/28] Bugfix for liftover scatter/gather

---
 .../analysis/LiftoverHandler.java             | 21 ++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
index 93189cde9..2135c7e44 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -44,6 +44,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.text.NumberFormat;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.LinkedHashSet;
@@ -175,6 +176,8 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             PipelineJob job = ctx.getJob();
             JSONObject params = ctx.getParams();
 
+            List<Interval> intervals = ProcessVariantsHandler.getIntervals(ctx);
+
             boolean dropGenotypes = params.optBoolean("dropGenotypes", false);
             boolean useBcfTools = params.optBoolean("useBcfTools", false);
             boolean doNotRetainUnmapped = params.optBoolean("doNotRetainUnmapped", false);
@@ -233,7 +236,7 @@ else if (_vcfFileType.isType(f.getFile()))
                     {
                         ReferenceGenome targetGenome = ctx.getSequenceSupport().getCachedGenome(targetGenomeId);
                         ReferenceGenome sourceGenome = ctx.getSequenceSupport().getCachedGenome(f.getLibrary_id());
-                        liftOverVcf(ctx, targetGenome, sourceGenome, chainFile, f.getFile(), lifted, unmappedOutput, job, pct, dropGenotypes, useBcfTools);
+                        liftOverVcf(ctx, targetGenome, sourceGenome, chainFile, f.getFile(), lifted, unmappedOutput, job, pct, dropGenotypes, useBcfTools, intervals);
                     }
                 }
                 catch (Exception e)
@@ -313,7 +316,7 @@ else if (!SequenceUtil.hasLineCount(unmappedOutput))
         }
     }
 
-    public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceGenome sourceGenome, File chain, File input, File output, @Nullable File unmappedOutput, PipelineJob job, double pct, boolean dropGenotypes, boolean useBcfTools) throws IOException, PipelineJobException
+    public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceGenome sourceGenome, File chain, File input, File output, @Nullable File unmappedOutput, PipelineJob job, double pct, boolean dropGenotypes, boolean useBcfTools, @Nullable List<Interval> intervals) throws IOException, PipelineJobException
     {
         File currentVCF = input;
         if (dropGenotypes)
@@ -326,8 +329,20 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
             }
             else
             {
+                List<String> extraArgs = new ArrayList<>();
+                extraArgs.add("--sites-only-vcf-output");
+                if (intervals != null)
+                {
+                    intervals.forEach(interval -> {
+                        extraArgs.add("-L");
+                        extraArgs.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
+                    });
+
+                    extraArgs.add("--ignore-variants-starting-outside-interval");
+                }
+
                 SelectVariantsWrapper wrapper = new SelectVariantsWrapper(job.getLogger());
-                wrapper.execute(sourceGenome.getWorkingFastaFile(), currentVCF, outputFile, List.of("--sites-only-vcf-output"));
+                wrapper.execute(sourceGenome.getWorkingFastaFile(), currentVCF, outputFile, extraArgs);
             }
             currentVCF = outputFile;
 

From e295d10e9ed5773dce9094091ca50d2c362085ae Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 16 Apr 2025 13:10:47 -0700
Subject: [PATCH 08/28] More robust logic for liftover and intervals

---
 .../sequenceanalysis/analysis/LiftoverHandler.java     | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
index 2135c7e44..acdba05a0 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -319,9 +319,9 @@ else if (!SequenceUtil.hasLineCount(unmappedOutput))
     public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceGenome sourceGenome, File chain, File input, File output, @Nullable File unmappedOutput, PipelineJob job, double pct, boolean dropGenotypes, boolean useBcfTools, @Nullable List<Interval> intervals) throws IOException, PipelineJobException
     {
         File currentVCF = input;
-        if (dropGenotypes)
+        if (dropGenotypes || intervals != null)
         {
-            ctx.getLogger().info("creating VCF wihtout genotypes");
+            ctx.getLogger().info("subsetting VCF");
             File outputFile = new File(output.getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(currentVCF.getName()) + ".noGenotypes.vcf.gz");
             if (new File(outputFile.getPath() + ".tbi").exists())
             {
@@ -330,7 +330,11 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
             else
             {
                 List<String> extraArgs = new ArrayList<>();
-                extraArgs.add("--sites-only-vcf-output");
+                if (dropGenotypes)
+                {
+                    extraArgs.add("--sites-only-vcf-output");
+                }
+
                 if (intervals != null)
                 {
                     intervals.forEach(interval -> {

From 8007471f77004d7921e7b6f9f0bbc47581158ae6 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 16 Apr 2025 15:05:49 -0700
Subject: [PATCH 09/28] Switch to GATK's --variant-output-filtering

---
 .../labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java | 4 +++-
 .../org/labkey/sequenceanalysis/analysis/LiftoverHandler.java | 3 ++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java
index 1968a55d8..82d19d3dd 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java
@@ -717,7 +717,9 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
                         toolParams.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
                     });
                 }
-                toolParams.add("--only-output-calls-starting-in-intervals");
+
+                toolParams.add("--variant-output-filtering");
+                toolParams.add("STARTS_IN");
             }
 
             if (ctx.getParams().optBoolean("variantCalling.GenotypeGVCFs.disableFileLocking", false))
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
index acdba05a0..f1ff60cfb 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -342,7 +342,8 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
                         extraArgs.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
                     });
 
-                    extraArgs.add("--ignore-variants-starting-outside-interval");
+                    extraArgs.add("--variant-output-filtering");
+                    extraArgs.add("STARTS_IN");
                 }
 
                 SelectVariantsWrapper wrapper = new SelectVariantsWrapper(job.getLogger());

From 4e5cb4396db99642f1502f911e170475d978415a Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 16 Apr 2025 15:07:50 -0700
Subject: [PATCH 10/28] Update liftover default

---
 .../resources/web/SequenceAnalysis/window/LiftoverWindow.js     | 2 +-
 .../org/labkey/sequenceanalysis/analysis/LiftoverHandler.java   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
index 3c979cb7b..7b4165ee9 100644
--- a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
+++ b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
@@ -120,7 +120,7 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
             }, {
                 xtype: 'checkbox',
                 itemId: 'doNotRetainUnmapped',
-                checked: false,
+                checked: true,
                 fieldLabel: 'Do Not Retain Unmapped'
             }].concat(SequenceAnalysis.window.OutputHandlerWindow.getCfgForToolParameters(this.toolParameters)).concat([{
                 xtype: 'sequenceanalysis-variantscattergatherpanel',
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
index f1ff60cfb..5ac7bf744 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -180,7 +180,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
 
             boolean dropGenotypes = params.optBoolean("dropGenotypes", false);
             boolean useBcfTools = params.optBoolean("useBcfTools", false);
-            boolean doNotRetainUnmapped = params.optBoolean("doNotRetainUnmapped", false);
+            boolean doNotRetainUnmapped = params.optBoolean("doNotRetainUnmapped", true);
             if (!doNotRetainUnmapped && !useBcfTools)
             {
                 ctx.getLogger().debug("Picard LiftoverVcf requires an output file for rejected sites, so setting doNotRetainUnmapped to true");

From 974067857fead3a04770f7a47684f405ac79d792 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 18 Apr 2025 09:58:20 -0700
Subject: [PATCH 11/28] Improve liftover behavior for scatter/gather

---
 .../SequenceAnalysis/window/LiftoverWindow.js |  20 +-
 .../analysis/LiftoverHandler.java             | 266 ++++++++++--------
 2 files changed, 153 insertions(+), 133 deletions(-)

diff --git a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
index 7b4165ee9..8b30bf513 100644
--- a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
+++ b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
@@ -119,9 +119,9 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
                 fieldLabel: 'Use bcftools'
             }, {
                 xtype: 'checkbox',
-                itemId: 'doNotRetainUnmapped',
-                checked: true,
-                fieldLabel: 'Do Not Retain Unmapped'
+                itemId: 'retainUnmapped',
+                checked: false,
+                fieldLabel: 'Retain Unmapped Variants'
             }].concat(SequenceAnalysis.window.OutputHandlerWindow.getCfgForToolParameters(this.toolParameters)).concat([{
                 xtype: 'sequenceanalysis-variantscattergatherpanel',
                 defaultFieldWidth: 500,
@@ -163,17 +163,9 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
             params.pct = this.down('#pctField').getValue();
         }
 
-        if (this.down('#dropGenotypes').getValue()){
-            params.dropGenotypes = this.down('#dropGenotypes').getValue();
-        }
-
-        if (this.down('#useBcfTools').getValue()){
-            params.useBcfTools = this.down('#useBcfTools').getValue();
-        }
-
-        if (this.down('#doNotRetainUnmapped').getValue()){
-            params.doNotRetainUnmapped = this.down('#doNotRetainUnmapped').getValue();
-        }
+        params.dropGenotypes = !!this.down('#dropGenotypes').getValue();
+        params.useBcfTools = !!this.down('#useBcfTools').getValue();
+        params.retainUnmapped = !!this.down('#retainUnmapped').getValue();
 
         Ext4.Array.forEach(this.down('sequenceanalysis-variantscattergatherpanel').query('field'), function(field){
             params[field.name] = field.getValue();
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
index 5ac7bf744..a4ff03c55 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -30,14 +30,14 @@
 import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep;
+import org.labkey.api.sequenceanalysis.run.LiftoverBcfToolsWrapper;
 import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper;
 import org.labkey.api.util.FileType;
-import org.labkey.api.util.FileUtil;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.SequenceAnalysisModule;
 import org.labkey.sequenceanalysis.pipeline.ProcessVariantsHandler;
-import org.labkey.api.sequenceanalysis.run.LiftoverBcfToolsWrapper;
+import org.labkey.sequenceanalysis.pipeline.SequenceOutputHandlerJob;
 import org.labkey.sequenceanalysis.run.util.LiftoverVcfWrapper;
 import org.labkey.sequenceanalysis.util.SequenceUtil;
 
@@ -53,11 +53,10 @@
 /**
  * Created by bimber on 8/26/2014.
  */
-public class LiftoverHandler implements SequenceOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>, VariantProcessingStep.SupportsScatterGather
+public class LiftoverHandler implements SequenceOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>, VariantProcessingStep.SupportsScatterGather, SequenceOutputHandler.TracksVCF
 {
-    private final FileType _bedFileType = new FileType(".bed", false);
-    //private FileType _gffFileType = new FileType("gff", false);
-    private final FileType _vcfFileType = new FileType(Arrays.asList(".vcf", ".bcf"), ".vcf", false, FileType.gzSupportLevel.SUPPORT_GZ);
+    private static final FileType _bedFileType = new FileType(".bed", false);
+    private static final FileType _vcfFileType = new FileType(Arrays.asList(".vcf", ".bcf"), ".vcf", false, FileType.gzSupportLevel.SUPPORT_GZ);
 
     public LiftoverHandler()
     {
@@ -132,6 +131,30 @@ public boolean canProcess(SequenceOutputFile f)
                 _vcfFileType.isType(f.getFile()));
     }
 
+    private static File getUnmappedOutputFile(File liftedVcfFile)
+    {
+        return new File(liftedVcfFile.getParentFile(), liftedVcfFile.getName().replaceAll(".lifted-", ".unmapped-"));
+    }
+
+    private static String getOutputExtension(File inputFile)
+    {
+        String ext = null;
+        if (_bedFileType.isType(inputFile))
+        {
+            ext = ".bed";
+        }
+        else if (_vcfFileType.isType(inputFile))
+        {
+            ext = ".vcf.gz";
+        }
+        else
+        {
+            throw new UnsupportedOperationException("Unsupported file type: " + inputFile.getName());
+        }
+
+        return ext;
+    }
+
     @Override
     public SequenceOutputProcessor getProcessor()
     {
@@ -141,7 +164,7 @@ public SequenceOutputProcessor getProcessor()
     @Override
     public boolean doSplitJobs()
     {
-        return false;
+        return true;
     }
 
     public class Processor implements SequenceOutputProcessor
@@ -180,139 +203,110 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
 
             boolean dropGenotypes = params.optBoolean("dropGenotypes", false);
             boolean useBcfTools = params.optBoolean("useBcfTools", false);
-            boolean doNotRetainUnmapped = params.optBoolean("doNotRetainUnmapped", true);
-            if (!doNotRetainUnmapped && !useBcfTools)
-            {
-                ctx.getLogger().debug("Picard LiftoverVcf requires an output file for rejected sites, so setting doNotRetainUnmapped to true");
-                doNotRetainUnmapped = true;
-            }
+            boolean retainUnmapped = params.optBoolean("retainUnmapped", false);
 
             int chainFileId = params.getInt("chainFileId");
             File chainFile = ctx.getSequenceSupport().getCachedData(chainFileId);
             int targetGenomeId = params.getInt("targetGenomeId");
 
-            for (SequenceOutputFile f : inputFiles)
+            if (inputFiles.size() > 1)
             {
-                job.getLogger().info("processing output: " + f.getFile().getName());
+                throw new PipelineJobException("Expected single input file");
+            }
+
+            SequenceOutputFile f = inputFiles.get(0);
+            job.getLogger().info("processing output: " + f.getFile().getName());
 
-                RecordedAction action = new RecordedAction(getName());
-                action.setStartTime(new Date());
+            RecordedAction action = new RecordedAction(getName());
+            action.setStartTime(new Date());
 
-                boolean isGzip = f.getFile().getPath().toLowerCase().endsWith("gz");
-                int dots = isGzip ? 2 : 1;
-                String baseName = FileUtil.getBaseName(f.getFile(), dots);
+            double pct = params.has("pct") ? params.getDouble("pct") : 0.95;
+            job.getLogger().info("using minimum percent match: " + pct);
 
-                double pct = params.has("pct") ? params.getDouble("pct") : 0.95;
-                job.getLogger().info("using minimum percent match: " + pct);
+            action.addInput(f.getFile(), "Input File");
+            action.addInput(chainFile, "Chain File");
 
-                action.addInput(f.getFile(), "Input File");
-                action.addInput(chainFile, "Chain File");
+            File outDir = ((FileAnalysisJobSupport) job).getAnalysisDirectory();
+            String baseName = SequenceAnalysisService.get().getUnzippedBaseName(f.getFile().getName());
+            File lifted = new File(outDir, baseName + ".lifted-" + targetGenomeId + getOutputExtension(f.getFile()));
+            File unmappedOutput = retainUnmapped ? getUnmappedOutputFile(lifted) : null;
 
-                File outDir = ((FileAnalysisJobSupport) job).getAnalysisDirectory();
-                String ext = null;
+            try
+            {
                 if (_bedFileType.isType(f.getFile()))
                 {
-                    ext = ".bed";
+                    liftOverBed(chainFile, f.getFile(), lifted, unmappedOutput, job, pct);
                 }
                 else if (_vcfFileType.isType(f.getFile()))
                 {
-                    ext = ".vcf.gz";
-                }
-                else
-                {
-                    throw new UnsupportedOperationException("Unsupported file type: " + f.getFile().getName());
+                    ReferenceGenome targetGenome = ctx.getSequenceSupport().getCachedGenome(targetGenomeId);
+                    ReferenceGenome sourceGenome = ctx.getSequenceSupport().getCachedGenome(f.getLibrary_id());
+                    liftOverVcf(ctx, targetGenome, sourceGenome, chainFile, f.getFile(), lifted, unmappedOutput, job, pct, dropGenotypes, useBcfTools, intervals);
                 }
+            }
+            catch (Exception e)
+            {
+                throw new PipelineJobException(e);
+            }
 
-                File lifted = new File(outDir, baseName + ".lifted-" + targetGenomeId + ext);
-                File unmappedOutput = doNotRetainUnmapped ? null : new File(outDir, baseName + ".unmapped-" + targetGenomeId + ext);
+            job.getLogger().info("adding outputs");
+            action.addOutput(lifted, "Lifted Features", lifted.exists(), true);
+            if (lifted.exists())
+            {
+                job.getLogger().info("adding lifted features: " + lifted.getName());
+
+                SequenceOutputFile so1 = new SequenceOutputFile();
+                so1.setName(f.getName() + " (lifted)");
+                so1.setDescription("Contains features from " + f.getName() + " after liftover");
+                so1.setFile(lifted);
+                so1.setLibrary_id(targetGenomeId);
+                so1.setReadset(f.getReadset());
+                so1.setAnalysis_id(f.getAnalysis_id());
+                so1.setCategory(f.getCategory());
+                so1.setContainer(job.getContainerId());
+                so1.setCreated(new Date());
+                so1.setModified(new Date());
+
+                ctx.addSequenceOutput(so1);
+            }
 
-                try
-                {
-                    if (_bedFileType.isType(f.getFile()))
-                    {
-                        liftOverBed(chainFile, f.getFile(), lifted, unmappedOutput, job, pct);
-                    }
-                    else if (_vcfFileType.isType(f.getFile()))
-                    {
-                        ReferenceGenome targetGenome = ctx.getSequenceSupport().getCachedGenome(targetGenomeId);
-                        ReferenceGenome sourceGenome = ctx.getSequenceSupport().getCachedGenome(f.getLibrary_id());
-                        liftOverVcf(ctx, targetGenome, sourceGenome, chainFile, f.getFile(), lifted, unmappedOutput, job, pct, dropGenotypes, useBcfTools, intervals);
-                    }
-                }
-                catch (Exception e)
-                {
-                    throw new PipelineJobException(e);
-                }
+            if (unmappedOutput == null)
+            {
+                // skip
+            }
+            else if (!unmappedOutput.exists())
+            {
+                job.getLogger().info("no unmapped intervals");
+            }
+            else if (!SequenceUtil.hasLineCount(unmappedOutput))
+            {
+                job.getLogger().info("no unmapped intervals");
+                unmappedOutput.delete();
+            }
+            else
+            {
+                job.getLogger().info("adding unmapped features: " + unmappedOutput.getName());
 
-                job.getLogger().info("adding outputs");
-                action.addOutput(lifted, "Lifted Features", lifted.exists(), true);
-                if (lifted.exists())
-                {
-                    job.getLogger().info("adding lifted features: " + lifted.getName());
-
-                    SequenceOutputFile so1 = new SequenceOutputFile();
-                    so1.setName(f.getName() + " (lifted)");
-                    so1.setDescription("Contains features from " + f.getName() + " after liftover");
-                    //ExpData liftedData = ExperimentService.get().createData(job.getContainer(), new DataType("Liftover Output"));
-                    //liftedData.setDataFileURI(lifted.toURI());
-                    //liftedData.setName(lifted.getName());
-                    //liftedData.save(job.getUser());
-                    //so1.setDataId(liftedData.getRowId());
-                    so1.setFile(lifted);
-                    so1.setLibrary_id(targetGenomeId);
-                    so1.setReadset(f.getReadset());
-                    so1.setAnalysis_id(f.getAnalysis_id());
-                    so1.setCategory(f.getCategory());
-                    so1.setContainer(job.getContainerId());
-                    so1.setCreated(new Date());
-                    so1.setModified(new Date());
-
-                    ctx.addSequenceOutput(so1);
-                }
+                action.addOutput(unmappedOutput, "Unmapped features", false, true);
 
-                if (unmappedOutput == null)
-                {
-                    // skip
-                }
-                else if (!unmappedOutput.exists())
-                {
-                    job.getLogger().info("no unmapped intervals");
-                }
-                else if (!SequenceUtil.hasLineCount(unmappedOutput))
-                {
-                    job.getLogger().info("no unmapped intervals");
-                    unmappedOutput.delete();
-                }
-                else
-                {
-                    job.getLogger().info("adding unmapped features: " + unmappedOutput.getName());
-
-                    action.addOutput(unmappedOutput, "Unmapped features", false, true);
-
-                    SequenceOutputFile so2 = new SequenceOutputFile();
-                    so2.setName(f.getName() + " (lifted/unmapped)");
-                    so2.setDescription("Contains the unmapped features after attempted liftover of " + f.getName());
-
-                    //ExpData unmappedData = ExperimentService.get().createData(job.getContainer(), new DataType("Liftover Output"));
-                    //unmappedData.setName(unmappedOutput.getName());
-                    //unmappedData.setDataFileURI(unmappedOutput.toURI());
-                    //unmappedData.save(job.getUser());
-                    //so2.setDataId(unmappedData.getRowId());
-                    so2.setFile(unmappedOutput);
-                    so2.setLibrary_id(f.getLibrary_id());
-                    so2.setReadset(f.getReadset());
-                    so2.setAnalysis_id(f.getAnalysis_id());
-                    so2.setCategory(f.getCategory());
-                    so2.setContainer(job.getContainerId());
-                    so2.setCreated(new Date());
-                    so2.setModified(new Date());
-
-                    ctx.addSequenceOutput(so2);
-                }
+                SequenceOutputFile so2 = new SequenceOutputFile();
+                so2.setName(f.getName() + " (lifted/unmapped)");
+                so2.setDescription("Contains the unmapped features after attempted liftover of " + f.getName());
+
+                so2.setFile(unmappedOutput);
+                so2.setLibrary_id(f.getLibrary_id());
+                so2.setReadset(f.getReadset());
+                so2.setAnalysis_id(f.getAnalysis_id());
+                so2.setCategory(f.getCategory());
+                so2.setContainer(job.getContainerId());
+                so2.setCreated(new Date());
+                so2.setModified(new Date());
 
-                action.setEndTime(new Date());
-                ctx.addActions(action);
+                ctx.addSequenceOutput(so2);
             }
+
+            action.setEndTime(new Date());
+            ctx.addActions(action);
         }
     }
 
@@ -364,8 +358,21 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
         }
         else
         {
+            File unmappedOutputFile = unmappedOutput;
+            if (unmappedOutputFile == null)
+            {
+                unmappedOutputFile = new File(currentVCF.getParentFile(), "liftoverRejects.vcf.gz");
+            }
+
             LiftoverVcfWrapper wrapper = new LiftoverVcfWrapper(job.getLogger());
             wrapper.doLiftover(currentVCF, chain, targetGenome.getWorkingFastaFile(), unmappedOutput, output, pct);
+
+            if (unmappedOutput == null)
+            {
+                ctx.getLogger().debug("Deleting liftover rejects VCF");
+                new File(unmappedOutputFile.getPath() + ".tbi").delete();
+                unmappedOutputFile.delete();
+            }
         }
 
         Long mapped = null;
@@ -378,7 +385,7 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
             SequenceAnalysisService.get().ensureVcfIndex(output, job.getLogger());
         }
 
-        Long unmapped = 0L;
+        long unmapped = 0L;
         if (unmappedOutput != null && unmappedOutput.exists())
         {
             String unmappedStr = ProcessVariantsHandler.getVCFLineCount(unmappedOutput, job.getLogger(), false, true);
@@ -390,11 +397,32 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
 
         if (mapped != null)
         {
-            Double fraction = (double)mapped / (mapped + unmapped);
+            double fraction = (double)mapped / (mapped + unmapped);
             job.getLogger().info("fraction mapped of total: " + fraction);
         }
     }
 
+    @Override
+    public File getScatterJobOutput(JobContext ctx) throws PipelineJobException
+    {
+        if (ctx.getJob() instanceof SequenceOutputHandlerJob sj)
+        {
+            SequenceOutputFile so = sj.getFiles().get(0);
+
+            return ProcessVariantsHandler.getScatterOutputByCategory(ctx, so.getCategory());
+        }
+        else
+        {
+            throw new IllegalStateException("Expected job to be instanceof SequenceOutputHandlerJob , was " + ctx.getJob().getClass().getName());
+        }
+    }
+
+    @Override
+    public SequenceOutputFile createFinalSequenceOutput(PipelineJob job, File processed, List<SequenceOutputFile> inputFiles) throws PipelineJobException
+    {
+        return ProcessVariantsHandler.createSequenceOutput(job, processed, inputFiles, inputFiles.get(0).getCategory());
+    }
+
     public void liftOverBed(File chain, File input, File output, @Nullable File unmappedOutput, PipelineJob job, double pct) throws IOException, PipelineJobException
     {
         LiftOver lo = new LiftOver(chain);

From 1db76632af4b25cd21c264079bad110cb69ef3c3 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 18 Apr 2025 10:02:26 -0700
Subject: [PATCH 12/28] Improve liftover behavior for scatter/gather

---
 .../analysis/LiftoverHandler.java             | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
index a4ff03c55..67df9f2d6 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -468,4 +468,50 @@ public void liftOverBed(File chain, File input, File output, @Nullable File unma
         //sort resulting file
         SequenceUtil.sortROD(output, job.getLogger(), 2);
     }
+
+    @Override
+    public void performAdditionalMergeTasks(JobContext ctx, PipelineJob job, ReferenceGenome genome, List<File> orderedScatterOutputs, List<String> orderedJobDirs) throws PipelineJobException
+    {
+        boolean retainUnmapped = ctx.getParams().optBoolean("retainUnmapped", true);
+        if (retainUnmapped)
+        {
+            job.getLogger().info("Merging liftOver reject VCFs");
+            List<File> toConcat = orderedScatterOutputs.stream().map(vcfFile -> {
+                File f = getUnmappedOutputFile(vcfFile);
+                if (!f.exists())
+                {
+                    throw new IllegalStateException("Missing file: " + f.getPath());
+                }
+
+                ctx.getFileManager().addIntermediateFile(f);
+                ctx.getFileManager().addIntermediateFile(new File(f.getPath() + ".tbi"));
+
+                return f;
+            }).toList();
+
+            job.getLogger().debug("Total VCFs to merge: " + toConcat.size());
+            if (toConcat.isEmpty())
+            {
+                throw new PipelineJobException("No unmapped VCF found");
+            }
+
+            File combined = getUnmappedOutputFile(orderedScatterOutputs.get(0));
+            File combinedIdx = new File(combined.getPath() + ".tbi");
+            if (combinedIdx.exists())
+            {
+                job.getLogger().info("VCF exists, will not recreate: " + combined.getPath());
+            }
+            else
+            {
+                combined = SequenceAnalysisService.get().combineVcfs(toConcat, combined, genome, job.getLogger(), true, null);
+            }
+
+            SequenceOutputFile so = new SequenceOutputFile();
+            so.setName(orderedScatterOutputs.get(0).getName() + ": Lifted/Unmapped");
+            so.setFile(combined);
+            so.setCategory("VCF File");
+            so.setLibrary_id(genome.getGenomeId());
+            ctx.getFileManager().addSequenceOutput(so);
+        }
+    }
 }

From 163934047ce516f2c73d1953fd13844330790ace Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 18 Apr 2025 11:38:47 -0700
Subject: [PATCH 13/28] Add intermediate file for cleanup

---
 .../org/labkey/sequenceanalysis/analysis/LiftoverHandler.java  | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
index 67df9f2d6..5b1cda83b 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -342,6 +342,9 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
 
                 SelectVariantsWrapper wrapper = new SelectVariantsWrapper(job.getLogger());
                 wrapper.execute(sourceGenome.getWorkingFastaFile(), currentVCF, outputFile, extraArgs);
+
+                ctx.getFileManager().addIntermediateFile(outputFile);
+                ctx.getFileManager().addIntermediateFile(new File(outputFile.getPath() + ".tbi"));
             }
             currentVCF = outputFile;
 

From 1323530177f33732dbc2e9ecebc7601c43f06ae6 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Thu, 24 Apr 2025 06:13:45 -0700
Subject: [PATCH 14/28] Add TCR info to prototype description

---
 .../analysis/AbstractSingleCellHandler.java   | 72 +++++++++++++++++++
 1 file changed, 72 insertions(+)

diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
index 5c63eed6f..a42533b9e 100644
--- a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
+++ b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
@@ -1015,6 +1015,17 @@ public static String getOutputDescription(JobContext ctx, File seuratObj, @Nulla
                 int hashingIdx = -1;
                 int saturationIdx = -1;
                 boolean hashingUsed = true;
+                int riraIdx = -1;
+                int traIdx = -1;
+                int trbIdx = -1;
+                int trdIdx = -1;
+                int trgIdx = -1;
+
+                int totalTNK = 0;
+                int cellsWithTRA = 0;
+                int cellsWithTRB = 0;
+                int cellsWithTRD = 0;
+                int cellsWithTRG = 0;
                 while ((line = reader.readNext()) != null)
                 {
                     // This will test whether this is the first line or not
@@ -1029,6 +1040,11 @@ public static String getOutputDescription(JobContext ctx, File seuratObj, @Nulla
                         }
 
                         saturationIdx = Arrays.asList(line).indexOf("Saturation.RNA");
+                        traIdx = Arrays.asList(line).indexOf("TRA");
+                        trbIdx = Arrays.asList(line).indexOf("TRB");
+                        trdIdx = Arrays.asList(line).indexOf("TRD");
+                        trgIdx = Arrays.asList(line).indexOf("TRG");
+                        riraIdx = Arrays.asList(line).indexOf("RIRA_Immune_v2.cellclass");
                     }
                     else
                     {
@@ -1063,6 +1079,49 @@ else if ("NotUsed".equals(val))
                             double saturation = Double.parseDouble(line[saturationIdx]);
                             totalSaturation += saturation;
                         }
+
+                        if (riraIdx >= 0)
+                        {
+                            if ("T_NK".equals(line[riraIdx]))
+                            {
+                                totalTNK++;
+                                if (traIdx >= 0)
+                                {
+                                    String tra = StringUtils.trimToNull(line[traIdx]);
+                                    if (tra != null)
+                                    {
+                                        cellsWithTRA++;
+                                    }
+                                }
+
+                                if (trbIdx >= 0)
+                                {
+                                    String trb = StringUtils.trimToNull(line[trbIdx]);
+                                    if (trb != null)
+                                    {
+                                        cellsWithTRB++;
+                                    }
+                                }
+
+                                if (trdIdx >= 0)
+                                {
+                                    String trd = StringUtils.trimToNull(line[trdIdx]);
+                                    if (trd != null)
+                                    {
+                                        cellsWithTRD++;
+                                    }
+                                }
+
+                                if (trgIdx >= 0)
+                                {
+                                    String trg = StringUtils.trimToNull(line[trgIdx]);
+                                    if (trg != null)
+                                    {
+                                        cellsWithTRG++;
+                                    }
+                                }
+                            }
+                        }
                     }
                 }
 
@@ -1090,6 +1149,19 @@ else if ("NotUsed".equals(val))
                 {
                     descriptions.add("Mean RNA Saturation: " + (totalSaturation / (double) totalCells));
                 }
+
+                if (totalTNK > 0)
+                {
+                    descriptions.add("Total T/NK Cells: " + totalTNK);
+                    descriptions.add("Fraction T/NK Cells with TRA: " + (cellsWithTRA / (double)totalTNK));
+                    descriptions.add("Fraction T/NK Cells with TRB: " + (cellsWithTRB / (double)totalTNK));
+                    descriptions.add("Fraction T/NK Cells with TRD: " + (cellsWithTRD / (double)totalTNK));
+                    descriptions.add("Fraction T/NK Cells with TRG: " + (cellsWithTRG / (double)totalTNK));
+                }
+                else if (riraIdx == -1 || traIdx == -1)
+                {
+                    descriptions.add("TCR information not present");
+                }
             }
             catch (IOException e)
             {

From 78a9da3269a82455b8da83d97843b39ab4d14dae Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Thu, 24 Apr 2025 10:27:28 -0700
Subject: [PATCH 15/28] Remove false positives from OrphanFilePipelineJob
 warnings

---
 .../labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java
index 026177561..e6a657190 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java
@@ -534,7 +534,7 @@ private void getOrphanFilesForDirectory(Set<Integer> knownExpDatas, Map<URI, Set
                         getJob().getLogger().warn("WARNING: Extremely large log file: " + f.getPath() + ", " + FileUtils.byteCountToDisplaySize(f.length()));
                     }
 
-                    if (f.getName().endsWith(".rds"))
+                    if (f.getName().endsWith(".rds") && !f.getName().endsWith("hashing.rawCounts.rds"))
                     {
                         if (!dataMap.containsKey(f.toURI()))
                         {

From 8c7dea6960f1caab55cada7fd20a59f427b5129e Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 25 Apr 2025 12:40:08 -0700
Subject: [PATCH 16/28] Add action to update description field on existing
 seurat prototypes

---
 .../singlecell/SingleCellController.java      | 98 +++++++++++++++++++
 .../analysis/AbstractSingleCellHandler.java   | 20 ++--
 .../pipeline/singlecell/SeuratPrototype.java  |  2 +-
 3 files changed, 109 insertions(+), 11 deletions(-)

diff --git a/singlecell/src/org/labkey/singlecell/SingleCellController.java b/singlecell/src/org/labkey/singlecell/SingleCellController.java
index 5252fe424..5b86e08c6 100644
--- a/singlecell/src/org/labkey/singlecell/SingleCellController.java
+++ b/singlecell/src/org/labkey/singlecell/SingleCellController.java
@@ -21,10 +21,13 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.NotNull;
 import org.json.JSONArray;
+import org.json.JSONObject;
 import org.labkey.api.action.ApiResponse;
 import org.labkey.api.action.ApiSimpleResponse;
 import org.labkey.api.action.ApiUsageException;
+import org.labkey.api.action.ConfirmAction;
 import org.labkey.api.action.ExportAction;
 import org.labkey.api.action.MutatingApiAction;
 import org.labkey.api.action.ReadOnlyApiAction;
@@ -45,6 +48,7 @@
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleHtmlView;
 import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryService;
@@ -58,14 +62,18 @@
 import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.JsonUtil;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Path;
 import org.labkey.api.util.URLHelper;
+import org.labkey.api.view.HtmlView;
 import org.labkey.api.view.NavTree;
 import org.labkey.api.view.template.ClientDependency;
+import org.labkey.singlecell.analysis.AbstractSingleCellHandler;
 import org.labkey.singlecell.run.CellRangerWrapper;
 import org.springframework.validation.BindException;
+import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
 import java.io.File;
@@ -558,4 +566,94 @@ public void setCombineHashingCite(boolean combineHashingCite)
             _combineHashingCite = combineHashingCite;
         }
     }
+
+    @RequiresPermission(AdminPermission.class)
+    public static class UpdatePrototypeDescriptionsAction extends ConfirmAction<Object>
+    {
+        @Override
+        public void validateCommand(Object form, Errors errors)
+        {
+
+        }
+
+        @Override
+        public @NotNull URLHelper getSuccessURL(Object form)
+        {
+            return getContainer().getStartURL(getUser());
+        }
+
+        @Override
+        public ModelAndView getConfirmView(Object form, BindException errors) throws Exception
+        {
+            return new HtmlView(HtmlString.unsafe("This will update the description field for all seurat prototypes. Do you want to continue?"));
+        }
+
+        @Override
+        public boolean handlePost(Object form, BindException errors) throws Exception
+        {
+            UserSchema sa = QueryService.get().getUserSchema(getUser(), getContainer(), SingleCellSchema.SEQUENCE_SCHEMA_NAME);
+            new TableSelector(sa.getTable("outputfiles"), PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("category"), "Seurat Object Prototype"), null).forEach(Integer.class, rowId -> {
+                SequenceOutputFile so = SequenceOutputFile.getForId(rowId);
+                if (so == null)
+                {
+                    throw new IllegalStateException("Unable to create SequenceOutputFile for: " + rowId);
+                }
+
+                try
+                {
+                    JSONObject params = new JSONObject();
+
+                    String oldDescription = so.getDescription();
+                    if (oldDescription.contains("SoupX: true"))
+                    {
+                        params.put("singleCellRawData.PrepareRawCounts.useSoupX", true);
+                    }
+
+                    if (oldDescription.contains("Hashing: "))
+                    {
+                        List<String> matching = Arrays.stream(oldDescription.split("\n")).filter(x -> x.contains("Hashing: ")).toList();
+                        if (!matching.isEmpty())
+                        {
+                            if (matching.size() == 1)
+                            {
+                                params.put("singleCell.RunCellHashing.consensusMethods", matching.get(0).replaceFirst("Hashing: ", ""));
+                            }
+                            else
+                            {
+                                _log.error("Expected single match for Hashing on rowId: "+ rowId);
+                            }
+                        }
+                    }
+
+                    if (oldDescription.contains("Cite-seq Normalization: "))
+                    {
+                        List<String> matching = Arrays.stream(oldDescription.split("\n")).filter(x -> x.contains("Cite-seq Normalization: ")).toList();
+                        if (!matching.isEmpty())
+                        {
+                            if (matching.size() == 1)
+                            {
+                                params.put("singleCell.AppendCiteSeq.normalizeMethod", matching.get(0).replaceFirst("Cite-seq Normalization: ", ""));
+                            }
+                            else
+                            {
+                                _log.error("Expected single match for Cite-seq Normalization on rowId: "+ rowId);
+                            }
+                        }
+                    }
+
+                    String description = AbstractSingleCellHandler.getOutputDescription(params, _log, so.getFile(), null);
+                    so.setDescription(description);
+
+                    _log.info(rowId);
+                    _log.info(description);
+                }
+                catch (PipelineJobException e)
+                {
+                    _log.error("Error generating description for: " + rowId, e);
+                }
+            });
+
+            return true;
+        }
+    }
 }
diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
index a42533b9e..f93e75677 100644
--- a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
+++ b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
@@ -616,7 +616,7 @@ else if (step.createsSeuratObjects())
                 so.setName(output.getDatasetName() == null ? output.getDatasetId() : output.getDatasetName());
                 so.setCategory("Seurat Object");
                 so.setFile(output.getFile());
-                String description = getOutputDescription(ctx, output.getFile(), List.of("Steps: " + steps.stream().map(x -> x.getProvider().getName()).collect(Collectors.joining("; "))));
+                String description = getOutputDescription(ctx.getParams(), ctx.getLogger(), output.getFile(), List.of("Steps: " + steps.stream().map(x -> x.getProvider().getName()).collect(Collectors.joining("; "))));
                 if (jobDescription != null)
                 {
                     description = jobDescription + "\n" + description;
@@ -986,7 +986,7 @@ public void serializeTest() throws Exception
         }
     }
 
-    public static String getOutputDescription(JobContext ctx, File seuratObj, @Nullable List<String> descriptions) throws PipelineJobException
+    public static String getOutputDescription(JSONObject jsonParams, Logger log, File seuratObj, @Nullable List<String> descriptions) throws PipelineJobException
     {
         if (descriptions == null)
         {
@@ -1034,7 +1034,7 @@ public static String getOutputDescription(JobContext ctx, File seuratObj, @Nulla
                         hashingIdx = Arrays.asList(line).indexOf("HTO.Classification");
                         if (hashingIdx == -1)
                         {
-                            ctx.getLogger().debug("HTO.Classification field not present, skipping");
+                            log.debug("HTO.Classification field not present, skipping");
                             hashingUsed = false;
                             hashingIdx = -2;
                         }
@@ -1088,7 +1088,7 @@ else if ("NotUsed".equals(val))
                                 if (traIdx >= 0)
                                 {
                                     String tra = StringUtils.trimToNull(line[traIdx]);
-                                    if (tra != null)
+                                    if (tra != null && !"NA".equals(tra))
                                     {
                                         cellsWithTRA++;
                                     }
@@ -1097,7 +1097,7 @@ else if ("NotUsed".equals(val))
                                 if (trbIdx >= 0)
                                 {
                                     String trb = StringUtils.trimToNull(line[trbIdx]);
-                                    if (trb != null)
+                                    if (trb != null && !"NA".equals(trb))
                                     {
                                         cellsWithTRB++;
                                     }
@@ -1106,7 +1106,7 @@ else if ("NotUsed".equals(val))
                                 if (trdIdx >= 0)
                                 {
                                     String trd = StringUtils.trimToNull(line[trdIdx]);
-                                    if (trd != null)
+                                    if (trd != null && !"NA".equals(trd))
                                     {
                                         cellsWithTRD++;
                                     }
@@ -1115,7 +1115,7 @@ else if ("NotUsed".equals(val))
                                 if (trgIdx >= 0)
                                 {
                                     String trg = StringUtils.trimToNull(line[trgIdx]);
-                                    if (trg != null)
+                                    if (trg != null && !"NA".equals(trg))
                                     {
                                         cellsWithTRG++;
                                     }
@@ -1169,18 +1169,18 @@ else if (riraIdx == -1 || traIdx == -1)
             }
         }
 
-        if (ctx.getParams().optBoolean("singleCellRawData.PrepareRawCounts.useSoupX", false))
+        if (jsonParams.optBoolean("singleCellRawData.PrepareRawCounts.useSoupX", false))
         {
             descriptions.add("SoupX: true");
         }
 
-        String hashingMethods = ctx.getParams().optString("singleCell.RunCellHashing.consensusMethods");
+        String hashingMethods = jsonParams.optString("singleCell.RunCellHashing.consensusMethods");
         if (StringUtils.trimToNull(hashingMethods) != null)
         {
             descriptions.add("Hashing: " + hashingMethods);
         }
 
-        String citeNormalize = ctx.getParams().optString("singleCell.AppendCiteSeq.normalizeMethod");
+        String citeNormalize = jsonParams.optString("singleCell.AppendCiteSeq.normalizeMethod");
         if (StringUtils.trimToNull(citeNormalize) != null)
         {
             descriptions.add("Cite-seq Normalization: " + citeNormalize);
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SeuratPrototype.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SeuratPrototype.java
index 02c00c9d5..c7f1ccddf 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SeuratPrototype.java
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SeuratPrototype.java
@@ -145,7 +145,7 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
             String readsetName = ctx.getSequenceSupport().getCachedReadset(wrapper.getReadsetId()).getName();
             so.setReadset(wrapper.getReadsetId());
             so.setName(readsetName + ": Prototype Seurat Object");
-            so.setDescription(AbstractSingleCellHandler.getOutputDescription(ctx, so.getFile(), null));
+            so.setDescription(AbstractSingleCellHandler.getOutputDescription(ctx.getParams(), ctx.getLogger(), so.getFile(), null));
 
             ctx.getFileManager().addSequenceOutput(so);
         }

From e6fb9d94195a606d9259c37c5853ca9a3a834e91 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 25 Apr 2025 12:47:22 -0700
Subject: [PATCH 17/28] Improve add comma/percent formatting

---
 .../singlecell/analysis/AbstractSingleCellHandler.java | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
index f93e75677..025879352 100644
--- a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
+++ b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
@@ -1152,11 +1152,11 @@ else if ("NotUsed".equals(val))
 
                 if (totalTNK > 0)
                 {
-                    descriptions.add("Total T/NK Cells: " + totalTNK);
-                    descriptions.add("Fraction T/NK Cells with TRA: " + (cellsWithTRA / (double)totalTNK));
-                    descriptions.add("Fraction T/NK Cells with TRB: " + (cellsWithTRB / (double)totalTNK));
-                    descriptions.add("Fraction T/NK Cells with TRD: " + (cellsWithTRD / (double)totalTNK));
-                    descriptions.add("Fraction T/NK Cells with TRG: " + (cellsWithTRG / (double)totalTNK));
+                    descriptions.add("Total T/NK Cells: " + decimal.format(totalTNK));
+                    descriptions.add("% T/NK Cells with TRA: " + pf.format(cellsWithTRA / (double)totalTNK));
+                    descriptions.add("% T/NK Cells with TRB: " + pf.format(cellsWithTRB / (double)totalTNK));
+                    descriptions.add("% T/NK Cells with TRD: " + pf.format(cellsWithTRD / (double)totalTNK));
+                    descriptions.add("% T/NK Cells with TRG: " + pf.format(cellsWithTRG / (double)totalTNK));
                 }
                 else if (riraIdx == -1 || traIdx == -1)
                 {

From 842ead883c78289698d0b017d2133bcf904757df Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 28 Apr 2025 15:12:29 -0700
Subject: [PATCH 18/28] Augment seurat prototype description field

---
 .../singlecell/SingleCellController.java      | 27 ++++++++++++++++---
 .../analysis/AbstractSingleCellHandler.java   | 12 +++++++++
 2 files changed, 35 insertions(+), 4 deletions(-)

diff --git a/singlecell/src/org/labkey/singlecell/SingleCellController.java b/singlecell/src/org/labkey/singlecell/SingleCellController.java
index 5b86e08c6..d113cf993 100644
--- a/singlecell/src/org/labkey/singlecell/SingleCellController.java
+++ b/singlecell/src/org/labkey/singlecell/SingleCellController.java
@@ -79,6 +79,7 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -592,6 +593,7 @@ public ModelAndView getConfirmView(Object form, BindException errors) throws Exc
         public boolean handlePost(Object form, BindException errors) throws Exception
         {
             UserSchema sa = QueryService.get().getUserSchema(getUser(), getContainer(), SingleCellSchema.SEQUENCE_SCHEMA_NAME);
+            List<Map<String, Object>> toUpdate = new ArrayList<>();
             new TableSelector(sa.getTable("outputfiles"), PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("category"), "Seurat Object Prototype"), null).forEach(Integer.class, rowId -> {
                 SequenceOutputFile so = SequenceOutputFile.getForId(rowId);
                 if (so == null)
@@ -642,10 +644,7 @@ public boolean handlePost(Object form, BindException errors) throws Exception
                     }
 
                     String description = AbstractSingleCellHandler.getOutputDescription(params, _log, so.getFile(), null);
-                    so.setDescription(description);
-
-                    _log.info(rowId);
-                    _log.info(description);
+                    toUpdate.add(new CaseInsensitiveHashMap<>(Map.of("rowid", so.getRowid(), "description", description)));
                 }
                 catch (PipelineJobException e)
                 {
@@ -653,6 +652,26 @@ public boolean handlePost(Object form, BindException errors) throws Exception
                 }
             });
 
+            if (!toUpdate.isEmpty())
+            {
+                try
+                {
+                    BatchValidationException bve = new BatchValidationException();
+                    List<Map<String, Object>> oldKeys = toUpdate.stream().map(row -> Map.of("rowid", row.get("rowid"))).toList();
+                    sa.getTable("outputfiles").getUpdateService().updateRows(getUser(), getContainer(), toUpdate, oldKeys, bve, null, null);
+
+                    if (bve.hasErrors())
+                    {
+                        throw bve;
+                    }
+                }
+                catch (SQLException | BatchValidationException e)
+                {
+                    _log.error("Unable to update outputfiles", e);
+                    return false;
+                }
+            }
+
             return true;
         }
     }
diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
index 025879352..6e9c2fb0d 100644
--- a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
+++ b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
@@ -1026,6 +1026,7 @@ public static String getOutputDescription(JSONObject jsonParams, Logger log, Fil
                 int cellsWithTRB = 0;
                 int cellsWithTRD = 0;
                 int cellsWithTRG = 0;
+                int cellsLackingCDR3 = 0;
                 while ((line = reader.readNext()) != null)
                 {
                     // This will test whether this is the first line or not
@@ -1084,6 +1085,7 @@ else if ("NotUsed".equals(val))
                         {
                             if ("T_NK".equals(line[riraIdx]))
                             {
+                                boolean hasCDR3 = false;
                                 totalTNK++;
                                 if (traIdx >= 0)
                                 {
@@ -1091,6 +1093,7 @@ else if ("NotUsed".equals(val))
                                     if (tra != null && !"NA".equals(tra))
                                     {
                                         cellsWithTRA++;
+                                        hasCDR3 = true;
                                     }
                                 }
 
@@ -1100,6 +1103,7 @@ else if ("NotUsed".equals(val))
                                     if (trb != null && !"NA".equals(trb))
                                     {
                                         cellsWithTRB++;
+                                        hasCDR3 = true;
                                     }
                                 }
 
@@ -1109,6 +1113,7 @@ else if ("NotUsed".equals(val))
                                     if (trd != null && !"NA".equals(trd))
                                     {
                                         cellsWithTRD++;
+                                        hasCDR3 = true;
                                     }
                                 }
 
@@ -1118,8 +1123,14 @@ else if ("NotUsed".equals(val))
                                     if (trg != null && !"NA".equals(trg))
                                     {
                                         cellsWithTRG++;
+                                        hasCDR3 = true;
                                     }
                                 }
+
+                                if (!hasCDR3)
+                                {
+                                    cellsLackingCDR3++;
+                                }
                             }
                         }
                     }
@@ -1157,6 +1168,7 @@ else if ("NotUsed".equals(val))
                     descriptions.add("% T/NK Cells with TRB: " + pf.format(cellsWithTRB / (double)totalTNK));
                     descriptions.add("% T/NK Cells with TRD: " + pf.format(cellsWithTRD / (double)totalTNK));
                     descriptions.add("% T/NK Cells with TRG: " + pf.format(cellsWithTRG / (double)totalTNK));
+                    descriptions.add("% T/NK Cells without TCR: " + pf.format(cellsLackingCDR3 / (double)totalTNK));
                 }
                 else if (riraIdx == -1 || traIdx == -1)
                 {

From cbe8bd68c9dc56c3a5e09b2ee62c292fb3ea7a62 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Tue, 29 Apr 2025 06:23:07 -0700
Subject: [PATCH 19/28] npm dependency updates

---
 jbrowse/package-lock.json | 2540 +++++++++++++++++++------------------
 1 file changed, 1309 insertions(+), 1231 deletions(-)

diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json
index a272bd98a..3938e1886 100644
--- a/jbrowse/package-lock.json
+++ b/jbrowse/package-lock.json
@@ -92,22 +92,21 @@
       }
     },
     "node_modules/@babel/core": {
-      "version": "7.26.8",
-      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.26.8.tgz",
-      "integrity": "sha512-l+lkXCHS6tQEc5oUpK28xBOZ6+HwaH7YwoYQbLFiYb4nS2/l1tKnZEtEWkD0GuiYdvArf9qBS0XlQGXzPMsNqQ==",
+      "version": "7.26.10",
+      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.26.10.tgz",
+      "integrity": "sha512-vMqyb7XCDMPvJFFOaT9kxtiRh42GwlZEg1/uIgtZshS5a/8OaduUfCi7kynKgc3Tw/6Uo2D+db9qBttghhmxwQ==",
       "dev": true,
       "dependencies": {
         "@ampproject/remapping": "^2.2.0",
         "@babel/code-frame": "^7.26.2",
-        "@babel/generator": "^7.26.8",
+        "@babel/generator": "^7.26.10",
         "@babel/helper-compilation-targets": "^7.26.5",
         "@babel/helper-module-transforms": "^7.26.0",
-        "@babel/helpers": "^7.26.7",
-        "@babel/parser": "^7.26.8",
-        "@babel/template": "^7.26.8",
-        "@babel/traverse": "^7.26.8",
-        "@babel/types": "^7.26.8",
-        "@types/gensync": "^1.0.0",
+        "@babel/helpers": "^7.26.10",
+        "@babel/parser": "^7.26.10",
+        "@babel/template": "^7.26.9",
+        "@babel/traverse": "^7.26.10",
+        "@babel/types": "^7.26.10",
         "convert-source-map": "^2.0.0",
         "debug": "^4.1.0",
         "gensync": "^1.0.0-beta.2",
@@ -129,12 +128,12 @@
       "dev": true
     },
     "node_modules/@babel/generator": {
-      "version": "7.26.8",
-      "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.26.8.tgz",
-      "integrity": "sha512-ef383X5++iZHWAXX0SXQR6ZyQhw/0KtTkrTz61WXRhFM6dhpHulO/RJz79L8S6ugZHJkOOkUrUdxgdF2YiPFnA==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.27.0.tgz",
+      "integrity": "sha512-VybsKvpiN1gU1sdMZIp7FcqphVVKEwcuj02x73uvcHE0PTihx1nlBcowYWhDwjpoAXRv43+gDzyggGnn1XZhVw==",
       "dependencies": {
-        "@babel/parser": "^7.26.8",
-        "@babel/types": "^7.26.8",
+        "@babel/parser": "^7.27.0",
+        "@babel/types": "^7.27.0",
         "@jridgewell/gen-mapping": "^0.3.5",
         "@jridgewell/trace-mapping": "^0.3.25",
         "jsesc": "^3.0.2"
@@ -167,12 +166,12 @@
       }
     },
     "node_modules/@babel/helper-compilation-targets": {
-      "version": "7.26.5",
-      "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.26.5.tgz",
-      "integrity": "sha512-IXuyn5EkouFJscIDuFF5EsiSolseme1s0CZB+QxVugqJLYmKdxI1VfIBOst0SUu4rnk2Z7kqTwmoO1lp3HIfnA==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.27.0.tgz",
+      "integrity": "sha512-LVk7fbXml0H2xH34dFzKQ7TDZ2G4/rVTOrq9V+icbbadjbVxxeFeDsNHv2SrZeWoA+6ZiTyWYWtScEIW07EAcA==",
       "dev": true,
       "dependencies": {
-        "@babel/compat-data": "^7.26.5",
+        "@babel/compat-data": "^7.26.8",
         "@babel/helper-validator-option": "^7.25.9",
         "browserslist": "^4.24.0",
         "lru-cache": "^5.1.1",
@@ -183,17 +182,17 @@
       }
     },
     "node_modules/@babel/helper-create-class-features-plugin": {
-      "version": "7.25.9",
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+      "version": "4.17.0",
+      "resolved": "https://registry.npmjs.org/memfs/-/memfs-4.17.0.tgz",
+      "integrity": "sha512-4eirfZ7thblFmqFjywlTmuWVSvccHAJbn1r8qQLzmTO11qcqpohOjmY2mFce6x7x7WtskzRqApPD0hv+Oa74jg==",
       "dev": true,
-      "license": "Apache-2.0",
       "dependencies": {
         "@jsonjoy.com/json-pack": "^1.0.3",
         "@jsonjoy.com/util": "^1.3.0",
@@ -12089,14 +12156,15 @@
       }
     },
     "node_modules/webpack-dev-server": {
-      "version": "5.1.0",
-      "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.1.0.tgz",
-      "integrity": "sha512-aQpaN81X6tXie1FoOB7xlMfCsN19pSvRAeYUHOdFWOlhpQ/LlbfTqYwwmEDFV0h8GGuqmCmKmT+pxcUV/Nt2gQ==",
+      "version": "5.2.1",
+      "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.2.1.tgz",
+      "integrity": "sha512-ml/0HIj9NLpVKOMq+SuBPLHcmbG+TGIjXRHsYfZwocUBIqEvws8NnS/V9AFQ5FKP+tgn5adwVwRrTEpGL33QFQ==",
       "dev": true,
       "dependencies": {
         "@types/bonjour": "^3.5.13",
         "@types/connect-history-api-fallback": "^1.5.4",
         "@types/express": "^4.17.21",
+        "@types/express-serve-static-core": "^4.17.21",
         "@types/serve-index": "^1.9.4",
         "@types/serve-static": "^1.15.5",
         "@types/sockjs": "^0.3.36",
@@ -12107,10 +12175,9 @@
         "colorette": "^2.0.10",
         "compression": "^1.7.4",
         "connect-history-api-fallback": "^2.0.0",
-        "express": "^4.19.2",
+        "express": "^4.21.2",
         "graceful-fs": "^4.2.6",
-        "html-entities": "^2.4.0",
-        "http-proxy-middleware": "^2.0.3",
+        "http-proxy-middleware": "^2.0.7",
         "ipaddr.js": "^2.1.0",
         "launch-editor": "^2.6.1",
         "open": "^10.0.3",
@@ -12145,71 +12212,80 @@
         }
       }
     },
-    "node_modules/webpack-merge": {
-      "version": "5.10.0",
+    "node_modules/webpack-dev-server/node_modules/chokidar": {
+      "version": "3.6.0",
+      "resolved": "https://registry.npmjs.org/chokidar/-/chokidar-3.6.0.tgz",
+      "integrity": "sha512-7VT13fmjotKpGipCW9JEQAusEPE+Ei8nl6/g4FBAmIm0GOOLMua9NDDo/DWp0ZAxCr3cPq5ZpBqmPAQgDda2Pw==",
       "dev": true,
-      "license": "MIT",
       "dependencies": {
-        "clone-deep": "^4.0.1",
-        "flat": "^5.0.2",
-        "wildcard": "^2.0.0"
+        "anymatch": "~3.1.2",
+        "braces": "~3.0.2",
+        "glob-parent": "~5.1.2",
+        "is-binary-path": "~2.1.0",
+        "is-glob": "~4.0.1",
+        "normalize-path": "~3.0.0",
+        "readdirp": "~3.6.0"
       },
       "engines": {
-        "node": ">=10.0.0"
+        "node": ">= 8.10.0"
+      },
+      "funding": {
+        "url": "https://paulmillr.com/funding/"
+      },
+      "optionalDependencies": {
+        "fsevents": "~2.3.2"
       }
     },
-    "node_modules/webpack-sources": {
-      "version": "3.2.3",
-      "license": "MIT",
+    "node_modules/webpack-dev-server/node_modules/glob-parent": {
+      "version": "5.1.2",
+      "resolved": "https://registry.npmjs.org/glob-parent/-/glob-parent-5.1.2.tgz",
+      "integrity": "sha512-AOIgSQCepiJYwP3ARnGx+5VnTu2HBYdzbGP45eLw1vr3zB3vZLeyed1sC9hnbcOc9/SrMyM5RPQrkGz4aS9Zow==",
+      "dev": true,
+      "dependencies": {
+        "is-glob": "^4.0.1"
+      },
       "engines": {
-        "node": ">=10.13.0"
+        "node": ">= 6"
       }
     },
-    "node_modules/webpack/node_modules/ajv": {
-      "version": "6.12.6",
-      "license": "MIT",
+    "node_modules/webpack-dev-server/node_modules/readdirp": {
+      "version": "3.6.0",
+      "resolved": "https://registry.npmjs.org/readdirp/-/readdirp-3.6.0.tgz",
+      "integrity": "sha512-hOS089on8RduqdbhvQ5Z37A0ESjsqz6qnRcffsMU3495FuTdqSm+7bhJ29JvIOsBDEEnan5DPu9t3To9VRlMzA==",
+      "dev": true,
       "dependencies": {
-        "fast-deep-equal": "^3.1.1",
-        "fast-json-stable-stringify": "^2.0.0",
-        "json-schema-traverse": "^0.4.1",
-        "uri-js": "^4.2.2"
+        "picomatch": "^2.2.1"
       },
-      "funding": {
-        "type": "github",
-        "url": "https://github.com/sponsors/epoberezkin"
+      "engines": {
+        "node": ">=8.10.0"
       }
     },
-    "node_modules/webpack/node_modules/ajv-keywords": {
-      "version": "3.5.2",
-      "license": "MIT",
-      "peerDependencies": {
-        "ajv": "^6.9.1"
+    "node_modules/webpack-merge": {
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-6.0.1.tgz",
+      "integrity": "sha512-hXXvrjtx2PLYx4qruKl+kyRSLc52V+cCvMxRjmKwoA+CBbbF5GfIBtR6kCvl0fYGqTUPKB+1ktVmTHqMOzgCBg==",
+      "dev": true,
+      "dependencies": {
+        "clone-deep": "^4.0.1",
+        "flat": "^5.0.2",
+        "wildcard": "^2.0.1"
+      },
+      "engines": {
+        "node": ">=18.0.0"
       }
     },
-    "node_modules/webpack/node_modules/json-schema-traverse": {
-      "version": "0.4.1",
-      "license": "MIT"
-    },
-    "node_modules/webpack/node_modules/schema-utils": {
-      "version": "3.3.0",
+    "node_modules/webpack-sources": {
+      "version": "3.2.3",
       "license": "MIT",
-      "dependencies": {
-        "@types/json-schema": "^7.0.8",
-        "ajv": "^6.12.5",
-        "ajv-keywords": "^3.5.2"
-      },
       "engines": {
-        "node": ">= 10.13.0"
-      },
-      "funding": {
-        "type": "opencollective",
-        "url": "https://opencollective.com/webpack"
+        "node": ">=10.13.0"
       }
     },
     "node_modules/websocket-driver": {
       "version": "0.7.4",
+      "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.7.4.tgz",
+      "integrity": "sha512-b17KeDIQVjvb0ssuSDF2cYXSg2iztliJ4B9WdsuB6J952qCPKmnVq4DyW5motImXHDC1cBT/1UezrJVsKw5zjg==",
       "dev": true,
-      "license": "Apache-2.0",
       "dependencies": {
         "http-parser-js": ">=0.5.1",
         "safe-buffer": ">=5.1.0",
@@ -12221,8 +12297,9 @@
     },
     "node_modules/websocket-extensions": {
       "version": "0.1.4",
+      "resolved": "https://registry.npmjs.org/websocket-extensions/-/websocket-extensions-0.1.4.tgz",
+      "integrity": "sha512-OqedPIGOfsDlo31UNwYbCFMSaO9m9G/0faIHj5/dZFDMFqPTcx6UwqyOy3COEaEOg/9VsGIpdqn62W5KhoKSpg==",
       "dev": true,
-      "license": "Apache-2.0",
       "engines": {
         "node": ">=0.8.0"
       }
@@ -12268,8 +12345,9 @@
     },
     "node_modules/wildcard": {
       "version": "2.0.1",
-      "dev": true,
-      "license": "MIT"
+      "resolved": "https://registry.npmjs.org/wildcard/-/wildcard-2.0.1.tgz",
+      "integrity": "sha512-CC1bOL87PIWSBhDcTrdeLo6eGT7mCFtrg0uIJtqJUFyK+eJnzl8A1niH56uu7KMa5XFrtiV+AQuHO3n7DsHnLQ==",
+      "dev": true
     },
     "node_modules/wrap-ansi": {
       "version": "7.0.0",
@@ -12308,9 +12386,10 @@
       "license": "ISC"
     },
     "node_modules/ws": {
-      "version": "8.18.0",
+      "version": "8.18.1",
+      "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.1.tgz",
+      "integrity": "sha512-RKW2aJZMXeMxVpnZ6bck+RswznaxmzdULiBr6KY7XkTnW8uvt0iT9H5DkHUChXrc+uurzwa0rVI16n/Xzjdz1w==",
       "dev": true,
-      "license": "MIT",
       "engines": {
         "node": ">=10.0.0"
       },
@@ -12390,12 +12469,11 @@
       }
     },
     "node_modules/yocto-queue": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-1.1.1.tgz",
-      "integrity": "sha512-b4JR1PFR10y1mKjhHY9LaGo6tmrgjit7hxVIeAmyMw3jegXR4dhYqLaQF5zMXZxY7tLpMyJeLjr1C4rLmkVe8g==",
-      "dev": true,
+      "version": "0.1.0",
+      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
+      "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
       "engines": {
-        "node": ">=12.20"
+        "node": ">=10"
       },
       "funding": {
         "url": "https://github.com/sponsors/sindresorhus"

From a66fb92d404735aabbf008673f3ec52b661f2d44 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Tue, 29 Apr 2025 15:17:11 -0700
Subject: [PATCH 20/28] Bugfix to seurat prototype update action

---
 .../singlecell/SingleCellController.java      | 51 ++++++++++++-------
 1 file changed, 34 insertions(+), 17 deletions(-)

diff --git a/singlecell/src/org/labkey/singlecell/SingleCellController.java b/singlecell/src/org/labkey/singlecell/SingleCellController.java
index d113cf993..f88c17dbf 100644
--- a/singlecell/src/org/labkey/singlecell/SingleCellController.java
+++ b/singlecell/src/org/labkey/singlecell/SingleCellController.java
@@ -51,7 +51,9 @@
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.InvalidKeyException;
 import org.labkey.api.query.QueryService;
+import org.labkey.api.query.QueryUpdateServiceException;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.User;
@@ -594,7 +596,7 @@ public boolean handlePost(Object form, BindException errors) throws Exception
         {
             UserSchema sa = QueryService.get().getUserSchema(getUser(), getContainer(), SingleCellSchema.SEQUENCE_SCHEMA_NAME);
             List<Map<String, Object>> toUpdate = new ArrayList<>();
-            new TableSelector(sa.getTable("outputfiles"), PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("category"), "Seurat Object Prototype"), null).forEach(Integer.class, rowId -> {
+            new TableSelector(sa.getTable("outputfiles"), PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("category"), "Seurat Object Prototype").addCondition(FieldKey.fromString("modified"), "2025-04-29", CompareType.DATE_LT), null).forEach(Integer.class, rowId -> {
                 SequenceOutputFile so = SequenceOutputFile.getForId(rowId);
                 if (so == null)
                 {
@@ -645,6 +647,12 @@ public boolean handlePost(Object form, BindException errors) throws Exception
 
                     String description = AbstractSingleCellHandler.getOutputDescription(params, _log, so.getFile(), null);
                     toUpdate.add(new CaseInsensitiveHashMap<>(Map.of("rowid", so.getRowid(), "description", description)));
+
+                    if (toUpdate.size() % 250 == 0)
+                    {
+                        doUpdate(toUpdate, getUser(), getContainer());
+                        toUpdate.clear();
+                    }
                 }
                 catch (PipelineJobException e)
                 {
@@ -654,25 +662,34 @@ public boolean handlePost(Object form, BindException errors) throws Exception
 
             if (!toUpdate.isEmpty())
             {
-                try
-                {
-                    BatchValidationException bve = new BatchValidationException();
-                    List<Map<String, Object>> oldKeys = toUpdate.stream().map(row -> Map.of("rowid", row.get("rowid"))).toList();
-                    sa.getTable("outputfiles").getUpdateService().updateRows(getUser(), getContainer(), toUpdate, oldKeys, bve, null, null);
-
-                    if (bve.hasErrors())
-                    {
-                        throw bve;
-                    }
-                }
-                catch (SQLException | BatchValidationException e)
-                {
-                    _log.error("Unable to update outputfiles", e);
-                    return false;
-                }
+                doUpdate(toUpdate, getUser(), getContainer());
+                toUpdate.clear();
             }
 
             return true;
         }
     }
+
+    private static void doUpdate(List<Map<String, Object>> toUpdate, User u, Container c)
+    {
+        try
+        {
+            _log.info("Total prototype updates: " + toUpdate.size());
+
+            BatchValidationException bve = new BatchValidationException();
+            List<Map<String, Object>> oldKeys = toUpdate.stream().map(row -> Map.of("rowid", row.get("rowid"))).toList();
+
+            UserSchema sa = QueryService.get().getUserSchema(u, c, SingleCellSchema.SEQUENCE_SCHEMA_NAME);
+            sa.getTable("outputfiles").getUpdateService().updateRows(u, c, toUpdate, oldKeys, bve, null, null);
+
+            if (bve.hasErrors())
+            {
+                throw bve;
+            }
+        }
+        catch (SQLException | InvalidKeyException | QueryUpdateServiceException | BatchValidationException e)
+        {
+            _log.error("Unable to update outputfiles", e);
+        }
+    }
 }

From c819cb3f3c45c0b151412de80113fb81206a591d Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 30 Apr 2025 08:18:04 -0700
Subject: [PATCH 21/28] Bugfixes to prototype update action

---
 .../src/org/labkey/singlecell/SingleCellController.java       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/singlecell/src/org/labkey/singlecell/SingleCellController.java b/singlecell/src/org/labkey/singlecell/SingleCellController.java
index f88c17dbf..3ad268982 100644
--- a/singlecell/src/org/labkey/singlecell/SingleCellController.java
+++ b/singlecell/src/org/labkey/singlecell/SingleCellController.java
@@ -646,9 +646,9 @@ public boolean handlePost(Object form, BindException errors) throws Exception
                     }
 
                     String description = AbstractSingleCellHandler.getOutputDescription(params, _log, so.getFile(), null);
-                    toUpdate.add(new CaseInsensitiveHashMap<>(Map.of("rowid", so.getRowid(), "description", description)));
+                    toUpdate.add(new CaseInsensitiveHashMap<>(Map.of("rowid", so.getRowid(), "container", so.getContainer(), "description", description)));
 
-                    if (toUpdate.size() % 250 == 0)
+                    if (toUpdate.size() % 200 == 0)
                     {
                         doUpdate(toUpdate, getUser(), getContainer());
                         toUpdate.clear();

From beef45c1af2540d4dae66146577e8d273e4e13bf Mon Sep 17 00:00:00 2001
From: hextraza <hextraza@gmail.com>
Date: Wed, 30 Apr 2025 11:26:40 -0700
Subject: [PATCH 22/28] Typed filters (#326)

* Filter refactor

* Fix FilterForm bugs, rename filters, add defaultOperator

* Fix URL encoding behavior and tests

* Fix ranges on > and < operators

---------

Co-authored-by: Sebastian Benjamin <sebastiancbenjamin@gmail.com>
---
 .../VariantSearch/components/FilterForm.tsx   | 203 +++++++-----
 .../components/VariantTableWidget.tsx         |  12 +-
 .../client/JBrowse/VariantSearch/operators.ts | 185 +++++++++++
 jbrowse/src/client/JBrowse/utils.ts           | 302 +++++++-----------
 .../external/labModules/JBrowseTest.java      |  48 +--
 5 files changed, 443 insertions(+), 307 deletions(-)
 create mode 100644 jbrowse/src/client/JBrowse/VariantSearch/operators.ts

diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx
index f24b2e857..6a8346ea0 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx
+++ b/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx
@@ -9,7 +9,8 @@ import FormControl from '@mui/material/FormControl';
 import InputLabel from '@mui/material/InputLabel';
 import CardActions from '@mui/material/CardActions';
 import Card from '@mui/material/Card';
-import { FieldModel, Filter, getOperatorsForField, searchStringToInitialFilters } from '../../utils';
+import { FieldModel, Filter, searchStringToInitialFilters } from '../../utils';
+import { OperatorKey, OperatorRegistry } from '../operators';
 import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
 import { Box, Menu } from '@mui/material';
 import { styled } from '@mui/material/styles';
@@ -77,19 +78,22 @@ const SubmitAndExternal = styled('div')(({ theme }) => ({
 
 const FilterForm = (props: FilterFormProps ) => {
     const { handleQuery, setFilters, handleClose, fieldTypeInfo, allowedGroupNames, promotedFilters } = props
-    const [filters, localSetFilters] = useState<Filter[]>(searchStringToInitialFilters(fieldTypeInfo.map((x) => x.name)));
+    const initial = searchStringToInitialFilters(fieldTypeInfo.map(x => x.name))
+    const [filters, localSetFilters] = useState<Filter[]>(
+        initial.length ? initial : [ new Filter('', OperatorKey.None, '') ]
+    )
     const [highlightedInputs, setHighlightedInputs] = useState<{ [index: number]: { field: boolean, operator: boolean, value: boolean } }>({});
     const [commonFilterMenuOpen, setCommonFilterMenuOpen] = useState<boolean>(false)
     const buttonRef = React.useRef(null);
 
     const handleAddFilter = () => {
-        localSetFilters([...filters, new Filter()]);
+        localSetFilters([...filters, new Filter('', OperatorKey.None, '')]);
     };
 
     const handleRemoveFilter = (index) => {
         // If it's the last filter, just reset its values to default empty values
         if (filters.length === 1) {
-            localSetFilters([new Filter()]);
+            localSetFilters([new Filter('', OperatorKey.None, '')]);
         } else {
             // Otherwise, remove the filter normally
             localSetFilters(
@@ -100,64 +104,81 @@ const FilterForm = (props: FilterFormProps ) => {
         }
     };
 
-    const handleFilterChange = (index, key, value) => {
-        const newFilters = filters.map((filter, i) => {
-            if (i === index) {
-                const updatedFilter = Object.assign(new Filter(), { ...filter, [key]: value });
-
-                if (key === "operator") {
-                    if (value === "is empty" || value === "is not empty") {
-                        updatedFilter.value = '';
-                    }
-
-                    if (value === "equals one of" || filter.operator === "equals one of") {
-                        updatedFilter.value = ''; 
-                    }
-                }
+    const handleFilterChange = (
+      index: number,
+      key: 'field' | 'operator' | 'value',
+      value: any
+    ) => {
+      const newFilters = filters.map((filter, i) => {
+        if (i !== index) return filter;
+
+        const updatedFilter = Object.assign(
+          new Filter('', OperatorKey.None, ''),
+          { ...filter, [key]: value }
+        );
+
+        if (key === 'field') {
+          const fieldInfo = fieldTypeInfo.find(f => f.name === value);
+          const defaultOp = fieldInfo?.getDefaultOperator() ?? OperatorRegistry[OperatorKey.None];
+          updatedFilter.operator = defaultOp;
+          updatedFilter.value = '';
+        }
+        else if (key === 'operator') {
+          updatedFilter.operator = OperatorRegistry[value as OperatorKey];
+          updatedFilter.value = '';
+        }
 
-                return updatedFilter;
-            }
-            return filter;
-        });
+        return updatedFilter;
+      });
 
-        localSetFilters(newFilters);
+      localSetFilters(newFilters);
     };
 
+
     const handleSubmit = (event) => {
-        event.preventDefault();
-        const highlightedInputs = {};
-
-        filters.forEach((filter, index) => {
-            highlightedInputs[index] = { field: false, operator: false, value: false };
-
-            filter.field = filter.field ?? '';
-            filter.operator = filter.operator ?? '';
-            filter.value = filter.value ?? '';
-
-            if (filter.field === '') {
-                highlightedInputs[index].field = true;
-            }
-
-            if (filter.operator === '') {
-                highlightedInputs[index].operator = true;
-            }
-
-            if (filter.operator === 'is empty' || filter.operator === 'is not empty') {
-                filter.value = '';
-            } else if (filter.value === '') {
-                highlightedInputs[index].value = true;
-            }
-        });
-
-        const isSingleEmptyFilter = filters.length === 1 && !filters[0].field && !filters[0].operator && !filters[0].value;
-
-        setHighlightedInputs(highlightedInputs);
-        if (isSingleEmptyFilter || !Object.values(highlightedInputs).some(v => (v as any).field || (v as any).operator || (v as any).value)) {
-            handleQuery(filters);
-            setFilters(filters);
-            handleClose();
+      event.preventDefault()
+      const highlighted: Record<number, { field: boolean; operator: boolean; value: boolean }> = {}
+
+      filters.forEach((filter, i) => {
+        highlighted[i] = { field: false, operator: false, value: false }
+
+        filter.field = filter.field ?? ''
+        filter.value = filter.value ?? ''
+
+        if (!filter.field) {
+          highlighted[i].field = true
         }
-    };
+
+        if (!filter.operator.key) {
+          highlighted[i].operator = true
+        }
+
+        if (
+          filter.operator.key === OperatorKey.IsEmpty ||
+          filter.operator.key === OperatorKey.IsNotEmpty
+        ) {
+          filter.value = ''
+        } else if (!filter.value) {
+          highlighted[i].value = true
+        }
+      })
+
+      const isSingleEmpty =
+        filters.length === 1 &&
+        !filters[0].field &&
+        !filters[0].operator.key &&
+        !filters[0].value
+
+      setHighlightedInputs(highlighted)
+      if (
+        isSingleEmpty ||
+        !Object.values(highlighted).some(v => v.field || v.operator || v.value)
+      ) {
+        handleQuery(filters)
+        setFilters(filters)
+        handleClose?.()
+      }
+    }
 
     const handleMenuClose = () => {
         setCommonFilterMenuOpen(false)
@@ -241,34 +262,33 @@ const FilterForm = (props: FilterFormProps ) => {
                                     />
                                 </FormControlMinWidth>
 
-                                <FormControlMinWidth sx={ highlightedInputs[index]?.operator ? highlightedSx : null } >
-                                    <InputLabel id="operator-label">Operator</InputLabel>
-                                    <Select
-                                        labelId="operator-label"
-                                        label="Operator"
-                                        value={filter.operator}
-                                        onChange={(event) =>
-                                            handleFilterChange(index, "operator", event.target.value)
-                                        }
-                                    >
-                                        <MenuItem value="None" style={{ display: 'none' }}>
-                                            <em>None</em>
-                                        </MenuItem>
-
-                                        {getOperatorsForField(fieldTypeInfo.find(obj => obj.name === filter.field)) ? (
-                                            getOperatorsForField(fieldTypeInfo.find(obj => obj.name === filter.field)).map((operator) => (
-                                                <MenuItem key={operator} value={operator}>
-                                                    {operator}
-                                                </MenuItem>
-                                            ))
-                                        ) : (
-                                            <MenuItem></MenuItem>
-                                        )}
-
-                                    </Select>
+                                <FormControlMinWidth sx={highlightedInputs[index]?.operator ? highlightedSx : null}>
+                                  <InputLabel id="operator-label">Operator</InputLabel>
+                                  <Select
+                                    labelId="operator-label"
+                                    label="Operator"
+                                    value={filter.operator.key}
+                                    onChange={event =>
+                                      handleFilterChange(index, "operator", event.target.value as OperatorKey)
+                                    }
+                                  >
+                                    <MenuItem value={OperatorKey.None}>
+                                      <em>None</em>
+                                    </MenuItem>
+                                    {(() => {
+                                      const ops = fieldTypeInfo.find(f => f.name === filter.field)?.getOperators() ?? [];
+                                      return ops.length > 0
+                                        ? ops.map(op => (
+                                            <MenuItem key={op.key} value={op.key}>
+                                              {op.label}
+                                            </MenuItem>
+                                          ))
+                                        : <MenuItem />;
+                                    })()}
+                                  </Select>
                                 </FormControlMinWidth>
 
-                                {filter.operator === "equals one of" ? (
+                                {filter.operator.key === OperatorKey.EqualsOneOf ? (
                                     <FormControlMinWidth sx={ highlightedInputs[index]?.value ? highlightedSx : null } >
                                         <InputLabel id="value-select-label">Value</InputLabel>
                                         <Select
@@ -288,13 +308,14 @@ const FilterForm = (props: FilterFormProps ) => {
                                 ) : fieldTypeInfo.find(obj => obj.name === filter.field)?.allowableValues?.length > 1 ? (
                                     <FormControlMinWidth sx={ highlightedInputs[index]?.value ? highlightedSx : null } >
                                         <AsyncSelect
+                                            key={`async-${index}-${filter.operator.key}`}
                                             id={`value-select-${index}`}
                                             inputId={`value-select-${index}`}
                                             aria-labelledby={`value-select-${index}`}
                                             noOptionsMessage={() => 'Type to search...'}
                                             menuPortalTarget={document.body}
                                             menuPosition={'fixed'}
-                                            isDisabled={filter.operator === "is empty" || filter.operator === "is not empty"}
+                                            isDisabled={filter.operator.key === OperatorKey.IsEmpty || filter.operator.key === OperatorKey.IsNotEmpty}
                                             menuShouldBlockScroll={true}
                                             // See here: https://stackoverflow.com/questions/77625507/my-react-project-with-react-18-2-0-version-and-react-select-5-4-0-v
                                             styles={{ menuPortal: (base: any) => ({ ...base, zIndex: 9999 }) }}
@@ -309,8 +330,16 @@ const FilterForm = (props: FilterFormProps ) => {
                                                     .map(value => ({label: value, value}))
                                                 );
                                             }}
-                                            onChange={(selected) => handleFilterChange(index, "value", selected?.length > 0 ? selected.map(s => s.value).join(',') : undefined)}
-                                            value={filter.value ? filter.value.split(',').map(value => ({label: value, value})) : undefined}
+                                            onChange={(selected) => {
+                                                const arr = Array.isArray(selected) ? selected : [selected].filter(Boolean)
+                                                const val = arr.map(s => s.value).join(',')
+                                                handleFilterChange(index, 'value', val)
+                                            }}
+                                            value={
+                                                filter.value
+                                                  ? (filter.value as string).split(',').map(v => ({ label: v, value: v }))
+                                                  : null
+                                              }
                                         />
                                     </FormControlMinWidth>
                                 ) : fieldTypeInfo.find(obj => obj.name === filter.field)?.allowableValues?.length > 0 ? (
@@ -321,7 +350,7 @@ const FilterForm = (props: FilterFormProps ) => {
                                             label="Value"
                                             id={`value-select-${index}`}
                                             value={filter.value}
-                                            disabled={filter.operator === "is empty" || filter.operator === "is not empty"}
+                                            disabled={filter.operator.key === OperatorKey.IsEmpty || filter.operator.key === OperatorKey.IsNotEmpty}
                                             onChange={(event) =>
                                                 handleFilterChange(index, "value", event.target.value)
                                             }
@@ -340,7 +369,7 @@ const FilterForm = (props: FilterFormProps ) => {
                                         sx={ highlightedInputs[index]?.value ? highlightedSx : null }
                                         variant="outlined"
                                         value={filter.value}
-                                        disabled={filter.operator === "is empty" || filter.operator === "is not empty"}
+                                        disabled={filter.operator.key === OperatorKey.IsEmpty || filter.operator.key === OperatorKey.IsNotEmpty}
                                         onChange={(event) =>
                                             handleFilterChange(index, 'value', event.target.value)
                                         }
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
index e3c711e78..8b5b799b4 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
+++ b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
@@ -13,6 +13,7 @@ import {
     GridToolbarExport
 } from '@mui/x-data-grid';
 import SearchIcon from '@mui/icons-material/Search';
+import { OperatorKey } from '../operators'
 import LinkIcon from '@mui/icons-material/Link';
 import DownloadIcon from '@mui/icons-material/Download'
 import { ActionURL } from '@labkey/api';
@@ -25,6 +26,7 @@ import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { toArray } from 'rxjs/operators';
 import {
     createEncodedFilterString,
+    buildLuceneQuery,
     fetchFieldTypeInfo,
     fetchLuceneQuery,
     FieldModel,
@@ -78,7 +80,7 @@ const VariantTableWidget = observer(props => {
         const { page = pageSizeModel.page, pageSize = pageSizeModel.pageSize } = pageQueryModel;
         const { field = "genomicPosition", sort = false } = sortQueryModel[0] ?? {};
 
-        const encodedSearchString = createEncodedFilterString(passedFilters, false);
+        const encodedSearchString = createEncodedFilterString(passedFilters);
         const currentUrl = new URL(window.location.href);
         currentUrl.searchParams.set("searchString", encodedSearchString);
         currentUrl.searchParams.set("page", page.toString());
@@ -98,7 +100,7 @@ const VariantTableWidget = observer(props => {
     const handleExport = () => {
         const currentUrl = new URL(window.location.href);
 
-        const searchString = createEncodedFilterString(filters, true);
+        const searchString = encodeURIComponent(buildLuceneQuery(filters));
         const sortField = sortModel[0]?.field ?? 'genomicPosition';
         const sortDirection = sortModel[0]?.sort ?? false;
 
@@ -552,14 +554,14 @@ const VariantTableWidget = observer(props => {
             <div style={{ marginBottom: "10px", display: "flex", alignItems: "center" }}>
                 <div style={{ flex: 1 }}>
                     {filters.map((filter, index) => {
-                        if ((filter as any).field && ((filter as any).operator === "is empty" || (filter as any).operator === "is not empty") && !(filter as any).value) {
+                        if ((filter as any).field && ((filter as any).operator.key === OperatorKey.IsEmpty || (filter as any).operator.key === OperatorKey.IsNotEmpty) && !(filter as any).value) {
                             return (
                                 <Button
                                     key={index}
                                     onClick={() => setFilterModalOpen(true)}
                                     style={{ border: "1px solid gray", margin: "5px" }}
                                 >
-                                    {`${(filter as any).field} ${(filter as any).operator}`}
+                                    {`${(filter as any).field} ${(filter as any).operator.key}`}
                                 </Button>
                             );
                         }
@@ -577,7 +579,7 @@ const VariantTableWidget = observer(props => {
                                 key={index}
                                 onClick={() => setFilterModalOpen(true)}
                                 style={{ border: "1px solid gray", margin: "5px" }}                            >
-                                {`${(filter as any).field} ${(filter as any).operator} ${(filter as any).value}`}
+                                {`${(filter as any).field} ${(filter as any).operator.key} ${(filter as any).value}`}
                             </Button>
                         );
                     })}
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/operators.ts b/jbrowse/src/client/JBrowse/VariantSearch/operators.ts
new file mode 100644
index 000000000..928f502de
--- /dev/null
+++ b/jbrowse/src/client/JBrowse/VariantSearch/operators.ts
@@ -0,0 +1,185 @@
+export enum OperatorKey {
+  Equals             = 'equals',
+  NotEquals          = 'does not equal',
+  Contains           = 'contains',
+  NotContains        = 'does not contain',
+  StartsWith         = 'starts with',
+  EndsWith           = 'ends with',
+  IsEmpty            = 'is empty',
+  IsNotEmpty         = 'is not empty',
+  NumericEq          = '=',
+  NumericNeq         = '!=',
+  NumericGt          = '>',
+  NumericGte         = '>=',
+  NumericLt          = '<',
+  NumericLte         = '<=',
+  IsIn             = 'is in',
+  IsNotIn          = 'is not in',
+  IsInAllOf        = 'is in all of',
+  IsInAnyOf        = 'is in any of',
+  IsNotInAnyOf     = 'is not in any of',
+  IsNotInOneOf     = 'is not in one of',
+  EqualsOneOf        = 'equals one of',
+  None              = ''
+}
+
+export type Value = string | number
+
+export interface Operator<T extends Value = Value> {
+  key: OperatorKey
+  label: string
+  generateLucene(field: string, value: T): string
+}
+
+function fuzzyNumRange(field: string, raw: string | number) {
+  const floatValue = parseFloat(String(raw))
+  const intValue   = parseInt(String(raw), 10)
+
+  if (floatValue === intValue) {
+    return `[${intValue} TO ${intValue}]`
+  }
+
+  return `[${floatValue - 0.000001} TO ${floatValue + 0.000001}]`
+}
+
+function fuzzyGtRange(f: string, raw: string | number) {
+  const floatValue = parseFloat(String(raw))
+  const intValue   = parseInt(String(raw), 10)
+  if (floatValue !== intValue) {
+    return `${f}:[${floatValue + 0.000001} TO *]`
+  }
+  return `${f}:{${intValue} TO *]`
+}
+
+function fuzzyLtRange(f: string, raw: string | number) {
+  const floatValue = parseFloat(String(raw))
+  const intValue   = parseInt(String(raw), 10)
+  if (floatValue !== intValue) {
+    return `${f}:[* TO ${floatValue - 0.000001}]`
+  }
+  return `${f}:[* TO ${intValue}}`
+}
+
+export const OperatorRegistry: Record<OperatorKey, Operator> = {
+  [OperatorKey.Equals]: {
+    key: OperatorKey.Equals,
+    label: 'Equals',
+    generateLucene: (f, v: string) => `${f}:${v}`,
+  },
+  [OperatorKey.NotEquals]: {
+    key: OperatorKey.NotEquals,
+    label: 'Does Not Equal',
+    generateLucene: (f, v: string) => `*:* -${f}:${v}`,
+  },
+  [OperatorKey.Contains]: {
+    key: OperatorKey.Contains,
+    label: 'Contains',
+    generateLucene: (f, v: string) => `${f}:*${v}*`,
+  },
+  [OperatorKey.NotContains]: {
+    key: OperatorKey.NotContains,
+    label: 'Does Not Contain',
+    generateLucene: (f, v: string) => `*:* -${f}:*${v}*`,
+  },
+  [OperatorKey.StartsWith]: {
+    key: OperatorKey.StartsWith,
+    label: 'Starts With',
+    generateLucene: (f, v: string) => `${f}:${v}*`,
+  },
+  [OperatorKey.EndsWith]: {
+    key: OperatorKey.EndsWith,
+    label: 'Ends With',
+    generateLucene: (f, v: string) => `${f}:*${v}`,
+  },
+  [OperatorKey.IsEmpty]: {
+    key: OperatorKey.IsEmpty,
+    label: 'Is Empty',
+    generateLucene: (f) => `*:* -${f}:*`,
+  },
+  [OperatorKey.IsNotEmpty]: {
+    key: OperatorKey.IsNotEmpty,
+    label: 'Is Not Empty',
+    generateLucene: (f) => `${f}:*`,
+  },
+  [OperatorKey.NumericEq]: {
+    key: OperatorKey.NumericEq,
+    label: '=',
+    generateLucene: (f, v: number) =>
+      Number.isInteger(v) ? `${f}:[${v} TO ${v}]` : `${f}:${fuzzyNumRange(f, v)}`,
+  },
+  [OperatorKey.NumericNeq]: {
+    key: OperatorKey.NumericNeq,
+    label: '!=',
+    generateLucene: (f, v: number) => {
+      if (Number.isInteger(v)) {
+        return `*:* -${f}:[${v} TO ${v}]`
+      }
+      const range = fuzzyNumRange(f, v)
+      return `*:* -${f}:${range}`
+    },
+  },
+  [OperatorKey.NumericGt]: {
+    key: OperatorKey.NumericGt,
+    label: '>',
+    generateLucene: fuzzyGtRange,
+  },
+  [OperatorKey.NumericGte]: {
+    key: OperatorKey.NumericGte,
+    label: '>=',
+    generateLucene: (f, v: number) => `${f}:[${v} TO *]`,
+  },
+  [OperatorKey.NumericLt]: {
+    key: OperatorKey.NumericLt,
+    label: '<',
+    generateLucene: fuzzyLtRange,
+  },
+  [OperatorKey.NumericLte]: {
+    key: OperatorKey.NumericLte,
+    label: '<=',
+    generateLucene: (f, v: number) => `${f}:[* TO ${v}]`,
+  },
+  [OperatorKey.EqualsOneOf]: {
+    key: OperatorKey.EqualsOneOf,
+    label: 'Equals One Of',
+    generateLucene: (f, v: string) => `${f}:~${v}~`,
+  },
+ [OperatorKey.IsIn]: {
+    key: OperatorKey.IsIn,
+    label: 'Is In',
+    generateLucene: (f, v: string) => `${f}:${v}`,
+  },
+  [OperatorKey.IsNotIn]: {
+    key: OperatorKey.IsNotIn,
+    label: 'Is Not In',
+    generateLucene: (f, v: string) => `*:* -${f}:${v}`,
+  },
+  [OperatorKey.IsInAllOf]: {
+    key: OperatorKey.IsInAllOf,
+    label: 'Is In All Of',
+    generateLucene: (f, v: string) =>
+      v.split(',').map(val => `+${f}:${val}`).join(' '),
+  },
+  [OperatorKey.IsInAnyOf]: {
+    key: OperatorKey.IsInAnyOf,
+    label: 'Is In Any Of',
+    generateLucene: (f, v: string) =>
+      v.split(',').map(val => `${f}:${val}`).join(' OR '),
+  },
+  [OperatorKey.IsNotInAnyOf]: {
+    key: OperatorKey.IsNotInAnyOf,
+    label: 'Is Not In Any Of',
+    generateLucene: (f, v: string) =>
+      v.split(',').map(val => `*:* -${f}:${val}`).join(' AND '),
+  },
+  [OperatorKey.IsNotInOneOf]: {
+    key: OperatorKey.IsNotInOneOf,
+    label: 'Is Not In One Of',
+    generateLucene: (f, v: string) =>
+      v.split(',').map(val => `*:* -${f}:${val}`).join(' OR '),
+  },
+  [OperatorKey.None]: {
+    key: OperatorKey.None,
+    label: '',
+    generateLucene: () => ''
+  }
+}
\ No newline at end of file
diff --git a/jbrowse/src/client/JBrowse/utils.ts b/jbrowse/src/client/JBrowse/utils.ts
index 0cbe2d0cd..75fa6a195 100644
--- a/jbrowse/src/client/JBrowse/utils.ts
+++ b/jbrowse/src/client/JBrowse/utils.ts
@@ -12,6 +12,7 @@ import {
 } from '@mui/x-data-grid';
 import { ParsedLocString, parseLocString } from '@jbrowse/core/util';
 import { VcfFeature } from '@jbrowse/plugin-variants';
+import { Operator, OperatorKey, OperatorRegistry, Value } from './VariantSearch/operators'
 
 export function arrayMax(array) {
     return Array.isArray(array) ? Math.max(...array) : array
@@ -239,7 +240,7 @@ export function navigateToSearch(sessionId, locString, trackId, isValidRefNameFo
         const start = parsedLocString.start;
         const end = parsedLocString.end;
 
-        searchString = serializeLocationToLuceneQuery(contig, start, end)
+        searchString = serializeLocationToEncodedSearchString(contig, start, end)
     }
 
     window.location.href = ActionURL.buildURL("jbrowse", "variantSearch.view", null, {session: sessionId, location: locString, trackId: trackId, activeTracks: trackId, sampleFilters: sampleFilterURL, infoFilters: infoFilterURL, searchString: searchString})
@@ -317,106 +318,14 @@ export function getGenotypeURL(trackId, contig, start, end) {
     return ActionURL.buildURL("jbrowse", "genotypeTable.view", null, {trackId: trackId, chr: contig, start: start, stop: end})
 }
 
-export function serializeLocationToLuceneQuery(contig, start, end) {
+export function serializeLocationToEncodedSearchString(contig, start, end) {
     const filters = [
-        {field: "contig", operator: "equals", value: contig.toString()},
-        {field: "start", operator: ">=", value: start.toString()},
-        {field: "end", operator: "<=", value: end.toString()}
+        new Filter("contig", OperatorKey.Equals, contig.toString()),
+        new Filter("start", OperatorKey.NumericGte, start.toString()),
+        new Filter("end", OperatorKey.NumericLte, end.toString())
     ]
 
-    return createEncodedFilterString(filters, false)
-}
-
-function generateLuceneString(field, operator, value) {
-  let luceneQueryString = '';
-
-  if (field === 'variableSamples' && operator == "equals one of") {
-    return `variableSamples:~${value}~`;
-  }
-  let intValue = parseInt(value);
-  let floatValue = parseFloat(value);
-
-  // Generate Lucene query string based on operator and type of value
-  switch (operator) {
-    case '=': // Exact match for numeric fields
-        luceneQueryString = floatValue !== intValue 
-            ? `${field}:[${Number(value) - 0.000001} TO ${Number(value) + 0.000001}]`
-            : `${field}:[${value} TO ${value}]`;
-        break;
-    case '!=': // Not equal to, for numeric fields
-        luceneQueryString = floatValue !== intValue 
-            ? `${field}:[* TO ${Number(value) - 0.000001}] OR ${field}:[${Number(value) + 0.000001} TO *]` 
-            : `${field}:[* TO ${value}} OR ${field}:{${value} TO *]`;
-        break;
-    case '>': // Greater than for numeric fields
-        luceneQueryString = floatValue !== intValue 
-            ? `${field}:[${Number(value) + 0.000001} TO *]`
-            : `${field}:{${value} TO *]`;
-        break;
-    case '>=': // Greater than or equal to for numeric fields
-        luceneQueryString = `${field}:[${value} TO *]`;
-        break;
-    case '<': // Less than for numeric fields
-        luceneQueryString = floatValue !== intValue 
-            ? `${field}:[* TO ${Number(value) - 0.000001}]`
-            : `${field}:[* TO ${value}}`;
-        break;
-    case '<=': // Less than or equal to for numeric fields
-        luceneQueryString = `${field}:[* TO ${value}]`;
-        break;
-    case 'equals': // Exact match for string fields
-        luceneQueryString = `${field}:${value}`;
-        break;
-    case 'contains': // Substring search for string fields
-        luceneQueryString = `${field}:*${value}*`;
-        break;
-    case 'does not equal': // Not equal to for string fields
-        luceneQueryString = `*:* -${field}:${value}`;
-        break;
-    case 'does not contain': // Does not contain for string fields
-        luceneQueryString = `*:* -${field}:*${value}*`;
-        break;
-    case 'starts with': // Starts with for string fields
-        luceneQueryString = `${field}:${value}*`;
-        break;
-    case 'ends with': // Ends with for string fields
-        luceneQueryString = `${field}:*${value}`;
-        break;
-    case 'is empty': // Field is empty
-        luceneQueryString = `*:* -${field}:*`;
-        break;
-    case 'is not empty': // Field is not empty
-        luceneQueryString = `${field}:*`;
-        break;
-    case 'variable in': // Variable in for multi-valued fields
-        luceneQueryString = `${field}:${value}`;
-        break;
-    case 'not variable in': // Not variable in for multi-valued fields
-        luceneQueryString = `*:* -${field}:${value}`;
-        break;
-    default:
-        // Operators that require multiple values
-        const values = value.split(',');
-
-        switch (operator) {
-        case 'variable in all of': // Variable in all of the provided values
-            luceneQueryString = values.map(v => `+${field}:${v}`).join(' ');
-            break;
-        case 'variable in any of': // Variable in any of the provided values
-            luceneQueryString = values.map(v => `${field}:${v}`).join(' OR ');
-            break;
-        case 'not variable in any of': // Not variable in any of the provided values
-            luceneQueryString = values.map(v => `*:* -${field}:${v}`).join(' AND ');
-            break;
-        case 'not variable in one of': // Not variable in one of the provided values
-            luceneQueryString = values.map(v => `*:* -${field}:${v}`).join(' OR ');
-            break;
-        default:
-            throw new Error(`Invalid operator: ${operator}`);
-        }
-    }
-
-  return luceneQueryString;
+    return createEncodedFilterString(filters)
 }
 
 export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pageSize, sortField, sortReverseString, successCallback, failureCallback) {
@@ -439,6 +348,9 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
         return
     }
 
+    const lucene = buildLuceneQuery(filters)
+    const encoded = encodeURIComponent(lucene)
+
     let sortReverse;
     if(sortReverseString == "asc") {
         sortReverse = true
@@ -457,7 +369,7 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
             failureCallback("There was an error: " + res.status + "\n Status Body: " + res.responseText + "\n Session ID:" + sessionId)
         },
         params: {
-            "searchString": createEncodedFilterString(filters, true),
+            "searchString": encoded,
             "sessionId": sessionId,
             "trackId": trackGUID,
             "offset": offset,
@@ -468,23 +380,6 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
     });
 }
 
-export function createEncodedFilterString(filters: Array<{field: string; operator: string; value: string}>, lucenify: boolean) {
-    let ret: any = []
-
-    if(!filters || filters.length == 0 || (filters.length == 1 && filters[0].field == "" && filters[0].operator == "" && filters[0].value == "")) {
-        return "all"
-    }
-
-    if(lucenify) {
-        ret = filters.map(val => generateLuceneString(val.field, val.operator, val.value));
-    } else {
-        ret = filters.map(val => val.field + "," + val.operator + "," + val.value)
-    }
-    const concatenatedString = ret.join('&');
-
-    return encodeURIComponent(concatenatedString.replace(/\+/g, "%2B"));
-}
-
 export class FieldModel {
     name: string
     label: string
@@ -501,6 +396,7 @@ export class FieldModel {
     url: string
     flex: number
     supportsFilter: boolean = true
+    defaultOperator: string
 
     getLabel(): string {
         return this.label ?? this.name
@@ -525,6 +421,58 @@ export class FieldModel {
         return muiFieldType
     }
 
+    getOperators(): Operator[] {
+        if (this.name === 'variableSamples') {
+          return [
+            OperatorKey.EqualsOneOf,
+            OperatorKey.IsIn,
+            OperatorKey.IsNotIn,
+            OperatorKey.IsInAllOf,
+            OperatorKey.IsInAnyOf,
+            OperatorKey.IsNotInAnyOf,
+            OperatorKey.IsNotInOneOf,
+            OperatorKey.IsEmpty,
+            OperatorKey.IsNotEmpty,
+          ].map(k => OperatorRegistry[k])
+        }
+
+        switch (this.type) {
+          case 'String':
+          case 'Flag':
+          case 'Character':
+          case 'Impact':
+            return [
+              OperatorKey.Equals,
+              OperatorKey.NotEquals,
+              OperatorKey.Contains,
+              OperatorKey.NotContains,
+              OperatorKey.StartsWith,
+              OperatorKey.EndsWith,
+              OperatorKey.IsEmpty,
+              OperatorKey.IsNotEmpty,
+            ].map(k => OperatorRegistry[k])
+
+          case 'Float':
+          case 'Integer':
+            return [
+              OperatorKey.NumericEq,
+              OperatorKey.NumericNeq,
+              OperatorKey.NumericGt,
+              OperatorKey.NumericGte,
+              OperatorKey.NumericLt,
+              OperatorKey.NumericLte,
+            ].map(k => OperatorRegistry[k])
+
+          default:
+            return []
+        }
+    }
+
+    getDefaultOperator(): Operator | undefined {
+        if (this.defaultOperator && this.defaultOperator != "") return OperatorRegistry[this.defaultOperator]
+        return this.getOperators()[0]
+    }
+
     toGridColDef(): GridColDef {
         let gridCol: GridColDef = {
             field: this.name,
@@ -562,6 +510,19 @@ export class FieldModel {
     }
 }
 
+export function createEncodedFilterString(filters: Filter[]): string {
+    if (!filters.length || filters.every(f => f.isEmpty())) return 'all'
+    return encodeURIComponent(filters.map(f => f.encode()).join('&'))
+}
+
+export function buildLuceneQuery(filters: Filter[]): string {
+  if (!filters.length || filters.every(f => f.isEmpty())) return 'all'
+  return filters
+      .filter(f => !f.isEmpty())
+      .map(f => f.toLucene())
+      .join('&')
+}
+
 export async function fetchFieldTypeInfo(sessionId: string, trackId: string, successCallback: (fields: FieldModel[], groups: string[], promotedFilters: Map<string, Filter[]>) => void, failureCallback) {
     if (!sessionId || !trackId) {
         console.error("Cannot fetch field type info: sessionId or trackId not provided")
@@ -601,46 +562,45 @@ export function truncateToValidGUID(str: string) {
     return str;
 }
 
-export declare type FilterType = {
-    field: string,
-    value: any,
-    operator: string
-}
+export class Filter {
+  field: string
+  operator: Operator
+  value: Value
 
-export class Filter implements FilterType {
-    field: string = ""
-    value: any = ""
-    operator: string = ""
-
-    encode(): string {
-        return [this.field, this.operator, this.value].join(',')
-    }
+  constructor(field: string, operatorKey: OperatorKey, value: Value) {
+    this.field = field
+    this.operator = OperatorRegistry[operatorKey]
+    this.value = value
+  }
 
-    isEmpty(): boolean {
-        return !!this.field
-    }
+  encode(): string {
+    return [this.field, this.operator.key, this.value].join(',')
+  }
 
-    static fromString(str: string): Filter[] {
-        const decodedSearchString = decodeURIComponent(str)
-        const searchStringsArray = decodedSearchString.split("&").filter((x) => x !== "all")
+  toLucene(): string {
+    return this.operator.generateLucene(this.field, this.value as any)
+  }
 
-        return searchStringsArray.map((item) => {
-            const parts = item.split(",");
-            const field = parts[0];
-            const operator = parts[1];
-            const value = parts.slice(2).join(",");
-            return Object.assign(new Filter(), { field: field, operator: operator, value: value })
-        })
-    }
+  isEmpty(): boolean {
+    return this.field === ''
+  }
 
-    static deduplicate(filters: Filter[]): Filter[] {
-        const filterMap = {}
-        filters.forEach((f) => {
-            filterMap[f.encode()] = f
-        })
+  static fromString(str: string): Filter[] {
+    const decoded = decodeURIComponent(str)
+    return decoded
+      .split('&')
+      .filter(x => x !== 'all')
+      .map(item => {
+        const [field, opKey, ...valParts] = item.split(',')
+        const value = valParts.join(',')
+        return new Filter(field, opKey as OperatorKey, isNaN(Number(value)) ? value : Number(value))
+      })
+  }
 
-        return Object.keys(filterMap).map((key) => filterMap[key])
-    }
+  static deduplicate(filters: Filter[]): Filter[] {
+    const map = new Map(filters.map(f => [f.encode(), f]))
+    return Array.from(map.values())
+  }
 }
 
 export function searchStringToInitialFilters(knownFieldNames: string[]) : Filter[] {
@@ -651,49 +611,9 @@ export function searchStringToInitialFilters(knownFieldNames: string[]) : Filter
         return Filter.fromString(searchString).filter(({ field }) => knownFieldNames.includes(field))
     }
 
-    return [new Filter()]
+    return []
 }
 
-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 = ["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 = [];
-
-    // This can occur for the blank placeholder field:
-    if (!fieldObj) {
-        return[]
-    }
-
-    const field = fieldObj.name;
-    const type = fieldObj.type;
-
-    let allowedOperators;
-    switch (type) {
-        case 'Flag':
-        case 'String':
-        case 'Character':
-            allowedOperators = stringOperators;
-            break;
-        case 'Float':
-        case 'Integer':
-            allowedOperators = numericOperators;
-            break;
-        case 'Impact':
-            allowedOperators = stringOperators;
-            break;
-        case 'None':
-        default:
-            allowedOperators = noneOperators;
-            break;
-    }
-
-    if (field === "variableSamples") {
-        return variableSamplesType
-    }
-
-    return allowedOperators
-}
 
 export const multiValueComparator: GridComparatorFn = (v1, v2) => {
     return arrayMax(parseCellValue(v1)) - arrayMax(parseCellValue(v2))
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
index 8ef002a10..9ee4094ac 100644
--- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
+++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
@@ -1617,7 +1617,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "equals one of")).click();
+        waitForElement(Locator.tagWithText("li", "Equals One Of")).click();
         waitForElement(Locator.tagWithId("div", "value-select-0")).click();
         waitForElement(Locator.tagWithText("li", "!TestGroup!")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
@@ -1629,87 +1629,87 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "variable in")).click();
+        waitForElement(Locator.tagWithText("li", "Is In")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m00001");
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys(Keys.ENTER);
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "0.553"));
-        clearFilterDialog("variableSamples variable in m00001");
+        clearFilterDialog("variableSamples is in m00001");
 
         // VariableSamples not variable in m05710
         waitAndClick(Locator.tagWithText("button", "Search"));
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "not variable in")).click();
+        waitForElement(Locator.tagWithText("li", "Is Not In")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m05710");
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys(Keys.ENTER);
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "3.277E-4"));
-        clearFilterDialog("variableSamples not variable in m05710");
+        clearFilterDialog("variableSamples is not in m05710");
 
         // VariableSamples li usage + variable in all of
         waitAndClick(Locator.tagWithText("button", "Search"));
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "variable in all of")).click();
+        waitForElement(Locator.tagWithText("li", "Is In All Of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00005")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00004")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "0.3"));
-        clearFilterDialog("variableSamples variable in all of m00005,m00004");
+        clearFilterDialog("variableSamples is in all of m00005,m00004");
 
         // VariableSamples variable in any of m00004,m00007
         waitAndClick(Locator.tagWithText("button", "Search"));
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "variable in any of")).click();
+        waitForElement(Locator.tagWithText("li", "Is In Any Of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00004")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00007")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "2"));
-        clearFilterDialog("variableSamples variable in any of m00004,m00007");
+        clearFilterDialog("variableSamples is in any of m00004,m00007");
 
         // VariableSamples not variable in any of m00005,m00004
         waitAndClick(Locator.tagWithText("button", "Search"));
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "not variable in any of")).click();
+        waitForElement(Locator.tagWithText("li", "Is Not In Any Of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00005")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00004")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "2"));
-        clearFilterDialog("variableSamples not variable in any of m00005,m00004");
+        clearFilterDialog("variableSamples is not in any of m00005,m00004");
 
         // VariableSamples not variable in one of m03660,m00001
         waitAndClick(Locator.tagWithText("button", "Search"));
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "not variable in one of")).click();
+        waitForElement(Locator.tagWithText("li", "Is Not In One Of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m036");
         waitForElement(Locator.tagWithText("div", "m03660")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00001")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "609"));
-        clearFilterDialog("variableSamples not variable in one of m03660,m00001");
+        clearFilterDialog("variableSamples is not in one of m03660,m00001");
 
         // samples with variant isEmpty
         waitAndClick(Locator.tagWithText("button", "Search"));
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "is empty")).click();
+        waitForElement(Locator.tagWithText("li", "Is Empty")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "2"));
         clearFilterDialog("variableSamples is empty");
@@ -1786,7 +1786,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "equals")).click();
+        waitForElement(Locator.tagWithText("li", "Equals")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("GAAAA");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "4506"));
@@ -1798,7 +1798,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Impact on Protein Coding"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "equals")).click();
+        waitForElement(Locator.tagWithText("li", "Equals")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("HI");
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys(Keys.ENTER);
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
@@ -1811,7 +1811,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "does not equal")).click();
+        waitForElement(Locator.tagWithText("li", "Does Not Equal")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("A");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "711"));
@@ -1823,7 +1823,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Alt Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "contains")).click();
+        waitForElement(Locator.tagWithText("li", "Contains")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("TT");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "22559"));
@@ -1835,7 +1835,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Alt Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "does not contain")).click();
+        waitForElement(Locator.tagWithText("li", "Does Not Contain")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("T");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "2"));
@@ -1847,7 +1847,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "starts with")).click();
+        waitForElement(Locator.tagWithText("li", "Starts With")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("GA");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "14716"));
@@ -1859,7 +1859,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "ends with")).click();
+        waitForElement(Locator.tagWithText("li", "Ends With")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("AAA");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "4506"));
@@ -1870,7 +1870,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Alt Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "is empty")).click();
+        waitForElement(Locator.tagWithText("li", "Is Empty")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "18235"));
         clearFilterDialog("alt is empty");
@@ -1880,7 +1880,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Impact on Protein Coding"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "is not empty")).click();
+        waitForElement(Locator.tagWithText("li", "Is Not Empty")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "914"));
         clearFilterDialog("IMPACT is not empty");
@@ -1890,7 +1890,7 @@ private void testLuceneSearchUI(String sessionId)
         waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
         waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Impact on Protein Coding"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "equals")).click();
+        waitForElement(Locator.tagWithText("li", "Equals")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("HI");
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys(Keys.ENTER);
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("MO");

From 825648d3476fdd19ff9f1e7d50bbf9399fe55c90 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Thu, 1 May 2025 14:25:12 -0700
Subject: [PATCH 23/28] Smarter resume with nimble

---
 singlecell/src/org/labkey/singlecell/run/NimbleHelper.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
index c33ed37c4..5dd635db4 100644
--- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
+++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -538,7 +538,7 @@ public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineSt
         reportArgs.add("-o");
         reportArgs.add(reportResultsGz.getPath());
 
-        runUsingDocker(reportArgs, output, null, ctx);
+        runUsingDocker(reportArgs, output, "nimble.report." + genomeId, ctx);
 
         if (!reportResultsGz.exists())
         {
@@ -566,7 +566,7 @@ public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineSt
             plotArgs.add("--output_file");
             plotArgs.add(plotResultsHtml.getPath());
 
-            runUsingDocker(plotArgs, output, null, ctx);
+            runUsingDocker(plotArgs, output, "nimble.plot." + genomeId, ctx);
 
             if (!plotResultsHtml.exists())
             {

From e6c038e029bd559823c3b806bd0e67fd2cf056fc Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 2 May 2025 16:54:26 -0700
Subject: [PATCH 24/28] Support tricycle

---
 singlecell/resources/chunks/RunTricycle.R     | 12 ++++++
 .../labkey/singlecell/SingleCellModule.java   |  2 +
 .../pipeline/singlecell/RunTricycle.java      | 39 +++++++++++++++++++
 3 files changed, 53 insertions(+)
 create mode 100644 singlecell/resources/chunks/RunTricycle.R
 create mode 100644 singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java

diff --git a/singlecell/resources/chunks/RunTricycle.R b/singlecell/resources/chunks/RunTricycle.R
new file mode 100644
index 000000000..b04162f1d
--- /dev/null
+++ b/singlecell/resources/chunks/RunTricycle.R
@@ -0,0 +1,12 @@
+ for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- CellMembrane::RunTricycle(seuratObj)
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}
\ No newline at end of file
diff --git a/singlecell/src/org/labkey/singlecell/SingleCellModule.java b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
index 28d08146f..5559f897f 100644
--- a/singlecell/src/org/labkey/singlecell/SingleCellModule.java
+++ b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
@@ -94,6 +94,7 @@
 import org.labkey.singlecell.pipeline.singlecell.RunScGate;
 import org.labkey.singlecell.pipeline.singlecell.RunScGateBuiltin;
 import org.labkey.singlecell.pipeline.singlecell.RunSingleR;
+import org.labkey.singlecell.pipeline.singlecell.RunTricycle;
 import org.labkey.singlecell.pipeline.singlecell.RunVision;
 import org.labkey.singlecell.pipeline.singlecell.ScoreCellCycle;
 import org.labkey.singlecell.pipeline.singlecell.SeuratPrototype;
@@ -297,6 +298,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new RunDecoupler.Provider());
         SequencePipelineService.get().registerPipelineStep(new PerformDefaultNimbleAppend.Provider());
         SequencePipelineService.get().registerPipelineStep(new PerformMhcDimRedux.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunTricycle.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java
new file mode 100644
index 000000000..5e059a782
--- /dev/null
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java
@@ -0,0 +1,39 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.json.JSONObject;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+
+public class RunTricycle extends AbstractCellMembraneStep
+{
+    public RunTricycle(PipelineContext ctx, RunTricycle.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunTricycle", "Run Tricycle", "CellMembrane/Tricycle", "This will run tricycle on the input object(s) to score cell cycle, and save the results in metadata.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public RunTricycle create(PipelineContext ctx)
+        {
+            return new RunTricycle(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "tricycle";
+    }
+}

From 1ac0d6c124eac7899c9d978cc604eb72410a62f0 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 2 May 2025 17:04:26 -0700
Subject: [PATCH 25/28] Bugfix to JBrowse popup

---
 .../ExtendedVariantWidget/ExtendedVariantWidget.tsx            | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
index 1fe878691..c6035b856 100644
--- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
+++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
@@ -348,6 +348,7 @@ export default jbrowse => {
         const infoKeys = Object.keys(feat.INFO)
         let isApiSubscribed = true
         useEffect(() => {
+            console.log('called!')
             Ajax.request({
                 url: ActionURL.buildURL('jbrowse', 'resolveVcfFields.api'),
                 method: 'POST',
@@ -366,7 +367,7 @@ export default jbrowse => {
             return () => {
                 isApiSubscribed = false;
             };
-        }, [infoKeys])
+        }, [])
 
         let annTable;
         if (feat["INFO"]["ANN"]){

From 776546992b42a09e15462e482dd33a89206b11fb Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 2 May 2025 17:04:51 -0700
Subject: [PATCH 26/28] Remove accidental logging

---
 .../ExtendedVariantWidget/ExtendedVariantWidget.tsx              | 1 -
 1 file changed, 1 deletion(-)

diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
index c6035b856..107a19976 100644
--- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
+++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
@@ -348,7 +348,6 @@ export default jbrowse => {
         const infoKeys = Object.keys(feat.INFO)
         let isApiSubscribed = true
         useEffect(() => {
-            console.log('called!')
             Ajax.request({
                 url: ActionURL.buildURL('jbrowse', 'resolveVcfFields.api'),
                 method: 'POST',

From c7cde2c81d9db8857221681dd0b788f899aee02e Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Sun, 4 May 2025 12:41:27 -0700
Subject: [PATCH 27/28] No need to save UCell correlation results

---
 singlecell/resources/chunks/CustomUCell.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/singlecell/resources/chunks/CustomUCell.R b/singlecell/resources/chunks/CustomUCell.R
index d1a958669..c5c9b0a02 100644
--- a/singlecell/resources/chunks/CustomUCell.R
+++ b/singlecell/resources/chunks/CustomUCell.R
@@ -25,7 +25,6 @@ for (datasetId in names(seuratObjects)) {
 
   seuratObj <- UCell::AddModuleScore_UCell(seuratObj, features = toCalculate, storeRanks = storeRanks, assay = assayName)
   corData <- RIRA::PlotUcellCorrelation(seuratObj, toCalculate)
-  saveRDS(corData, file = paste0(datasetId, '.ucellcorr.rds'))
 
   for (n in names(toCalculate)) {
     print(Seurat::FeaturePlot(seuratObj, features = paste0(n, '_UCell'), min.cutoff = 'q02', max.cutoff = 'q98'))

From d06a478ee7af55cbf89c0bcc9210ba2259ec04e4 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 5 May 2025 07:44:52 -0700
Subject: [PATCH 28/28] Allow resume for vireo/cellsnp

---
 .../pipeline/singlecell/VireoHandler.java     | 127 ++++++++++--------
 1 file changed, 74 insertions(+), 53 deletions(-)

diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java
index c3e432cf8..eb7ae055d 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java
@@ -160,81 +160,102 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             }
             ctx.getFileManager().addIntermediateFile(barcodes);
 
-            List<String> cellsnp = new ArrayList<>();
-            cellsnp.add("cellsnp-lite");
-            cellsnp.add("-s");
-            cellsnp.add(bam.getPath());
-            cellsnp.add("-b");
-            cellsnp.add(barcodes.getPath());
-            cellsnp.add("--genotype");
+            Integer maxThreads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
+            ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenome(inputFiles.get(0).getLibrary_id());
 
             File cellsnpDir = new File(ctx.getWorkingDirectory(), "cellsnp");
-            if (cellsnpDir.exists())
+            File cellsnpVcf = new File(cellsnpDir, "cellSNP.base.vcf.gz");
+            File cellsnpVcfIdx = new File(cellsnpVcf.getPath() + ".tbi");
+            if (cellsnpVcfIdx.exists())
             {
-                try
+                ctx.getLogger().info("cellsnp has already run, resuming");
+            }
+            else
+            {
+                List<String> cellsnp = new ArrayList<>();
+                cellsnp.add("cellsnp-lite");
+                cellsnp.add("-s");
+                cellsnp.add(bam.getPath());
+                cellsnp.add("-b");
+                cellsnp.add(barcodes.getPath());
+                cellsnp.add("--genotype");
+
+                if (cellsnpDir.exists())
                 {
-                    FileUtils.deleteDirectory(cellsnpDir);
+                    try
+                    {
+                        FileUtils.deleteDirectory(cellsnpDir);
+                    }
+                    catch (IOException e)
+                    {
+                        throw new PipelineJobException(e);
+                    }
                 }
-                catch (IOException e)
+
+                cellsnp.add("-O");
+                cellsnp.add(cellsnpDir.getPath());
+
+                if (maxThreads != null)
                 {
-                    throw new PipelineJobException(e);
+                    cellsnp.add("-p");
+                    cellsnp.add(maxThreads.toString());
                 }
-            }
 
-            cellsnp.add("-O");
-            cellsnp.add(cellsnpDir.getPath());
+                cellsnp.add("--minMAF");
+                cellsnp.add("0.1");
 
-            Integer maxThreads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
-            if (maxThreads != null)
-            {
-                cellsnp.add("-p");
-                cellsnp.add(maxThreads.toString());
-            }
+                cellsnp.add("--minCOUNT");
+                cellsnp.add("100");
 
-            cellsnp.add("--minMAF");
-            cellsnp.add("0.1");
+                String maxDepth = StringUtils.trimToNull(ctx.getParams().optString("maxDepth"));
+                if (maxDepth != null)
+                {
+                    cellsnp.add("--maxDEPTH");
+                    cellsnp.add(maxDepth);
+                }
 
-            cellsnp.add("--minCOUNT");
-            cellsnp.add("100");
+                cellsnp.add("--gzip");
 
-            String maxDepth = StringUtils.trimToNull(ctx.getParams().optString("maxDepth"));
-            if (maxDepth != null)
-            {
-                cellsnp.add("--maxDEPTH");
-                cellsnp.add(maxDepth);
-            }
+                cellsnp.add("--refseq");
+                cellsnp.add(genome.getWorkingFastaFile().getPath());
 
-            cellsnp.add("--gzip");
+                int vcfFile = ctx.getParams().optInt(REF_VCF, -1);
+                if (vcfFile > -1)
+                {
+                    File vcf = ctx.getSequenceSupport().getCachedData(vcfFile);
+                    if (vcf == null || !vcf.exists())
+                    {
+                        throw new PipelineJobException("Unable to find file with ID: " + vcfFile);
+                    }
 
-            ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenome(inputFiles.get(0).getLibrary_id());
+                    cellsnp.add("-R");
+                    cellsnp.add(vcf.getPath());
+                }
+                else
+                {
+                    String contigs = ctx.getParams().optString("contigs", "");
+                    if (!StringUtils.isEmpty(contigs))
+                    {
+                        cellsnp.add("--chrom");
+                        cellsnp.add(contigs);
+                    }
+                }
 
-            cellsnp.add("--refseq");
-            cellsnp.add(genome.getWorkingFastaFile().getPath());
+                new SimpleScriptWrapper(ctx.getLogger()).execute(cellsnp);
 
-            int vcfFile = ctx.getParams().optInt(REF_VCF, -1);
-            if (vcfFile > -1)
-            {
-                File vcf = ctx.getSequenceSupport().getCachedData(vcfFile);
-                if (vcf == null || ! vcf.exists())
+                try
                 {
-                    throw new PipelineJobException("Unable to find file with ID: " + vcfFile);
-                }
+                    SequenceAnalysisService.get().ensureVcfIndex(cellsnpVcf, ctx.getLogger());
 
-                cellsnp.add("-R");
-                cellsnp.add(vcf.getPath());
-            }
-            else
-            {
-                String contigs = ctx.getParams().optString("contigs", "");
-                if (!StringUtils.isEmpty(contigs))
+                    File cellsVcf = new File(cellsnpDir, "cellSNP.cells.vcf.gz");
+                    SequenceAnalysisService.get().ensureVcfIndex(cellsVcf, ctx.getLogger());
+                }
+                catch (IOException e)
                 {
-                    cellsnp.add("--chrom");
-                    cellsnp.add(contigs);
+                    throw new PipelineJobException(e);
                 }
             }
 
-            new SimpleScriptWrapper(ctx.getLogger()).execute(cellsnp);
-
             List<String> vireo = new ArrayList<>();
             vireo.add("vireo");
             vireo.add("-c");