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TASK-6789 - Variant query fails with large skip values #2498

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Aug 30, 2024
Merged

TASK-6789 - Variant query fails with large skip values #2498

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4 changes: 4 additions & 0 deletions .../java/org/opencb/opencga/storage/core/variant/search/SearchIndexVariantQueryExecutor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -262,6 +262,10 @@ public boolean doIntersectWithSearch(Query query, QueryOptions options) {
intersect = true;
} else {
if (options.getBoolean(QueryOptions.COUNT)) {
// The SearchIndex is better than anyone in terms of counting
intersect = true;
} else if (options.getInt(QueryOptions.SKIP, 0) > 500) {
// Large "skip" queries should use SearchIndex when possible
intersect = true;
} else {
// TODO: Improve this heuristic
Expand Down
36 changes: 35 additions & 1 deletion ...va/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryUsingSearchIndexTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,22 @@

import com.google.common.base.Throwables;
import org.junit.ClassRule;
import org.junit.Test;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.commons.datastore.core.DataResult;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.opencga.storage.core.variant.query.VariantQueryResult;
import org.opencb.opencga.storage.core.variant.VariantStorageEngine;
import org.opencb.opencga.storage.core.variant.adaptors.iterators.VariantDBIterator;
import org.opencb.opencga.storage.core.variant.query.VariantQueryResult;
import org.opencb.opencga.storage.core.variant.search.solr.VariantSearchManager;
import org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource;

import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.CoreMatchers.not;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.opencb.opencga.storage.core.variant.search.solr.VariantSearchManager.SEARCH_ENGINE_ID;

/**
* Created on 22/12/17.
*
Expand Down Expand Up @@ -87,4 +93,32 @@ public DataResult rank(int limit, Query query, String field, boolean asc) {
throw Throwables.propagate(e);
}
}

@Test
public void testQueryExecutor() {
assertThat(variantStorageEngine.get(new VariantQuery(), new QueryOptions()
.append(QueryOptions.LIMIT, 10)
.append(QueryOptions.COUNT, false)
.append(QueryOptions.SKIP, 0)).getSource(),
not(containsString(SEARCH_ENGINE_ID)));

assertThat(variantStorageEngine.get(new VariantQuery(), new QueryOptions()
.append(QueryOptions.LIMIT, 10)
.append(QueryOptions.COUNT, true)
.append(QueryOptions.SKIP, 0)).getSource(),
containsString(SEARCH_ENGINE_ID));

assertThat(variantStorageEngine.get(new VariantQuery(), new QueryOptions()
.append(QueryOptions.LIMIT, 10)
.append(QueryOptions.COUNT, false)
.append(QueryOptions.SKIP, 100)).getSource(),
not(containsString(SEARCH_ENGINE_ID)));

assertThat(variantStorageEngine.get(new VariantQuery(), new QueryOptions()
.append(QueryOptions.LIMIT, 10)
.append(QueryOptions.COUNT, false)
.append(QueryOptions.SKIP, 1000)).getSource(),
containsString(SEARCH_ENGINE_ID));

}
}
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