Skip to content

Commit

Permalink
WIP custom sorting fields
Browse files Browse the repository at this point in the history
  • Loading branch information
Sebastian Benjamin committed Feb 12, 2024
1 parent e170708 commit 145cd1d
Show file tree
Hide file tree
Showing 4 changed files with 78 additions and 23 deletions.
28 changes: 21 additions & 7 deletions jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,15 @@ import {
GridColumnVisibilityModel,
GridPaginationModel,
GridRenderCellParams,
GridSortDirection,
GridSortModel,
GridToolbarColumnsButton,
GridToolbarContainer,
GridToolbarDensitySelector,
GridToolbarExport
} from '@mui/x-data-grid';
import SearchIcon from '@mui/icons-material/Search';
import React, { useEffect, useState, useMemo } from 'react';
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';
import { FilterFormModal } from './FilterFormModal';
Expand Down Expand Up @@ -67,22 +69,25 @@ const VariantTableWidget = observer(props => {
session.hideWidget(widget)
}

function handleQuery(passedFilters, pushToHistory, pageQueryModel = pageSizeModel) {
function handleQuery(passedFilters, pushToHistory, pageQueryModel = pageSizeModel, sortQueryModel = sortModel) {
const { page = pageSizeModel.page, pageSize = pageSizeModel.pageSize } = pageQueryModel;
const { field = sortModel[0].field, sort = sortModel[0].sort } = sortQueryModel[0];

const encodedSearchString = createEncodedFilterString(passedFilters, false);
const currentUrl = new URL(window.location.href);
currentUrl.searchParams.set("searchString", encodedSearchString);
currentUrl.searchParams.set("page", page.toString());
currentUrl.searchParams.set("pageSize", pageSize.toString());
currentUrl.searchParams.set("sortField", field.toString());
currentUrl.searchParams.set("sortDirection", sort.toString());

if (pushToHistory) {
window.history.pushState(null, "", currentUrl.toString());
}

setFilters(passedFilters);
setDataLoaded(false)
fetchLuceneQuery(passedFilters, sessionId, trackGUID, page, pageSize, (json)=>{handleSearch(json)}, (error) => {setDataLoaded(true); setError(error)});
fetchLuceneQuery(passedFilters, sessionId, trackGUID, page, pageSize, field, sort, (json)=>{handleSearch(json)}, (error) => {setDataLoaded(true); setError(error)});
}

const TableCellWithPopover = (props: { value: any }) => {
Expand Down Expand Up @@ -234,11 +239,15 @@ const VariantTableWidget = observer(props => {
// False until initial data load or an error:
const [dataLoaded, setDataLoaded] = useState(false)

const urlParams = new URLSearchParams(window.location.search);
const page = parseInt(urlParams.get('page') || '0');
const pageSize = parseInt(urlParams.get('pageSize') || '50');
const urlParams = new URLSearchParams(window.location.search)
const page = parseInt(urlParams.get('page') || '0')
const pageSize = parseInt(urlParams.get('pageSize') || '50')
const [pageSizeModel, setPageSizeModel] = React.useState<GridPaginationModel>({ page, pageSize });

const sortField = urlParams.get('sortField') || 'genomicPosition'
const sortDirection = urlParams.get('sortDirection') || 'desc'
const [sortModel, setSortModel] = React.useState<GridSortModel>([{ field: sortField, sort: sortDirection as GridSortDirection }])

const colVisURLComponent = urlParams.get("colVisModel") || "{}"
const colVisModel = JSON.parse(decodeURIComponent(colVisURLComponent))
const [columnVisibilityModel, setColumnVisibilityModel] = useState<GridColumnVisibilityModel>(colVisModel);
Expand Down Expand Up @@ -419,6 +428,11 @@ const VariantTableWidget = observer(props => {
currentUrl.searchParams.set("colVisModel", encodeURIComponent(JSON.stringify(trueValuesModel)));
window.history.pushState(null, "", currentUrl.toString());
}}
sortingMode="server"
onSortModelChange={(newModel) => {
setSortModel(newModel)
handleQuery(filters, true, { page: 0, pageSize: pageSizeModel.pageSize }, newModel);
}}
/>
)

Expand All @@ -440,7 +454,7 @@ const VariantTableWidget = observer(props => {
fieldTypeInfo: fieldTypeInfo,
allowedGroupNames: allowedGroupNames,
promotedFilters: promotedFilters,
handleQuery: (filters) => handleQuery(filters, true)
handleQuery: (filters) => handleQuery(filters, true, { page: 0, pageSize: pageSizeModel.pageSize}, sortModel)
}}
/>
);
Expand Down
19 changes: 17 additions & 2 deletions jbrowse/src/client/JBrowse/utils.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -414,7 +414,7 @@ function generateLuceneString(field, operator, value) {
return luceneQueryString;
}

export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pageSize, successCallback, failureCallback) {
export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pageSize, sortField, sortReverseString, successCallback, failureCallback) {
if (!offset) {
offset = 0
}
Expand All @@ -434,6 +434,13 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
return
}

let sortReverse;
if(sortReverseString == "desc") {
sortReverse = false
} else {
sortReverse = true
}

return Ajax.request({
url: ActionURL.buildURL('jbrowse', 'luceneQuery.api'),
method: 'GET',
Expand All @@ -444,7 +451,15 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
failure: function(res) {
failureCallback("There was an error: " + res.status + "\n Status Body: " + res.responseText + "\n Session ID:" + sessionId)
},
params: {"searchString": createEncodedFilterString(filters, true), "sessionId": sessionId, "trackId": trackGUID, "offset": offset, "pageSize": pageSize},
params: {
"searchString": createEncodedFilterString(filters, true),
"sessionId": sessionId,
"trackId": trackGUID,
"offset": offset,
"pageSize": pageSize,
"sortField": sortField,
"sortReverse:": sortReverse
},
});
}

Expand Down
14 changes: 13 additions & 1 deletion jbrowse/src/org/labkey/jbrowse/JBrowseController.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -910,7 +910,7 @@ public ApiResponse execute(LuceneQueryForm form, BindException errors)

try
{
return new ApiSimpleResponse(searcher.doSearch(getUser(), PageFlowUtil.decode(form.getSearchString()), form.getPageSize(), form.getOffset()));
return new ApiSimpleResponse(searcher.doSearch(getUser(), PageFlowUtil.decode(form.getSearchString()), form.getPageSize(), form.getOffset(), form.getSortField(), form.getSortReverse()));
}
catch (Exception e)
{
Expand Down Expand Up @@ -947,6 +947,10 @@ public static class LuceneQueryForm

private int _offset = 0;

private String _sortField = "genomicPosition";

private boolean _sortReverse = false;

public String getSearchString()
{
return _searchString;
Expand Down Expand Up @@ -987,6 +991,14 @@ public void setOffset(int offset)
_offset = offset;
}

public String getSortField() { return _sortField; }

public void setSortField(String sortField) { _sortField = sortField; }

public boolean getSortReverse() { return _sortReverse; }

public void setSortReverse(boolean sortReverse) { _sortReverse = sortReverse; }

public String getTrackId()
{
return _trackId;
Expand Down
40 changes: 27 additions & 13 deletions jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,8 @@ public class JBrowseLuceneSearch
private final JsonFile _jsonFile;
private final User _user;
private final String[] specialStartPatterns = {"*:* -", "+", "-"};
private static final String ALL_DOCS = "all";
private static final String GENOMIC_POSITION = "genomicPosition";

private JBrowseLuceneSearch(final JBrowseSession session, final JsonFile jsonFile, User u)
{
Expand Down Expand Up @@ -130,7 +132,7 @@ 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) throws IOException, ParseException
public JSONObject doSearch(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);
Expand All @@ -146,7 +148,7 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina
IndexSearcher indexSearcher = new IndexSearcher(indexReader);

List<String> stringQueryParserFields = new ArrayList<>();
List<String> numericQueryParserFields = 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);
Map<String, PointsConfig> pointsConfigMap = new HashMap<>();
Expand All @@ -161,11 +163,11 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina
{
case Flag, String, Character -> stringQueryParserFields.add(field);
case Float -> {
numericQueryParserFields.add(field);
numericQueryParserFields.put(field, SortField.Type.FLOAT);
pointsConfigMap.put(field, doublePointsConfig);
}
case Integer -> {
numericQueryParserFields.add(field);
numericQueryParserFields.put(field, SortField.Type.INT);
pointsConfigMap.put(field, intPointsConfig);
}
}
Expand All @@ -182,14 +184,14 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina

BooleanQuery.Builder booleanQueryBuilder = new BooleanQuery.Builder();

if (searchString.equals("all")) {
if (searchString.equals(ALL_DOCS)) {
booleanQueryBuilder.add(new MatchAllDocsQuery(), BooleanClause.Occur.MUST);
}

// Split input into tokens, 1 token per query separated by &
StringTokenizer tokenizer = new StringTokenizer(searchString, "&");

while (tokenizer.hasMoreTokens() && !searchString.equals("all"))
while (tokenizer.hasMoreTokens() && !searchString.equals(ALL_DOCS))
{
String queryString = tokenizer.nextToken();
Query query = null;
Expand All @@ -205,7 +207,7 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina
{
query = queryParser.parse(queryString);
}
else if (numericQueryParserFields.contains(fieldName))
else if (numericQueryParserFields.containsKey(fieldName))
{
try
{
Expand All @@ -226,16 +228,28 @@ else if (numericQueryParserFields.contains(fieldName))

BooleanQuery query = booleanQueryBuilder.build();

// By default, sort in INDEXORDER, which is by genomicPosition
Sort sort = Sort.INDEXORDER;

// If the sort field is not genomicPosition and/or we need to sort in reverse, we construct a new sort
if (!sortField.equals(GENOMIC_POSITION) || sortReverse) {
SortField.Type fieldType;

if (stringQueryParserFields.contains(sortField)) {
fieldType = SortField.Type.STRING;
} else if (numericQueryParserFields.containsKey(sortField)) {
fieldType = numericQueryParserFields.get(sortField);
} else {
throw new IllegalArgumentException("Could not find type for sort field: " + sortField);
}

sort = new Sort(new SortField(sortField, fieldType, sortReverse));
}

// 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.
//TopDocs topDocs = indexSearcher.search(query, pageSize * (offset + 1));

// Define sort field
SortField sortField = new SortField("pos", SortField.Type.INT, false);
Sort sort = new Sort(sortField);

// Perform the search with sorting
TopFieldDocs topDocs = indexSearcher.search(query, pageSize * (offset + 1), sort);

Expand Down

0 comments on commit 145cd1d

Please sign in to comment.