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Batch exportCSV scoredocs #331

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Merged
hextraza merged 1 commit into from
Jun 2, 2025
Merged

Batch exportCSV scoredocs #331

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44 changes: 25 additions & 19 deletions jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java
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Original file line number Diff line number Diff line change
Expand Up @@ -380,32 +380,38 @@ private void paginateJSON(SearchConfig c, HttpServletResponse response) throws I
writer.flush();
}

private void exportCSV(SearchConfig c, HttpServletResponse response) throws IOException
{
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<>();
ScoreDoc lastDoc = null;
int batchSize = 1000;

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);
while (true) {
TopDocs topDocs = searcher.searchAfter(lastDoc, c.query, batchSize, c.sort);
ScoreDoc[] hits = topDocs.scoreDocs;

if (hits.length == 0) {
break;
}

writer.println(String.join(",", rowValues));
for (ScoreDoc scoreDoc : hits) {
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)
: "";
value = "\"" + value.replace("\"", "\"\"") + "\"";
rowValues.add(value);
}

writer.println(String.join(",", rowValues));
}
lastDoc = hits[hits.length - 1];
}

writer.flush();
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