From a17b1c5a24bef6ab04fabed5592855943caef8e9 Mon Sep 17 00:00:00 2001 From: Olin Blodgett Date: Tue, 7 Apr 2026 08:31:03 -0400 Subject: [PATCH] SCRUM-5950 index LTP variants for search Add VariantSearchResultConverter to VariantSummaryCurationIndexer so low throughput variant HGVS names are indexed and searchable. --- .../curation/VariantSummaryCurationIndexer.java | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/VariantSummaryCurationIndexer.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/VariantSummaryCurationIndexer.java index 4941157dd..330340f6d 100644 --- a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/VariantSummaryCurationIndexer.java +++ b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/VariantSummaryCurationIndexer.java @@ -1,12 +1,15 @@ package org.alliancegenome.indexer.indexers.curation; import java.util.HashMap; +import java.util.List; import java.util.concurrent.LinkedBlockingDeque; import org.alliancegenome.core.config.ConfigHelper; +import org.alliancegenome.core.variant.converters.VariantSearchResultConverter; import org.alliancegenome.curation_api.interfaces.document.VariantDocumentInterface; import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument; import org.alliancegenome.curation_api.response.SearchResponse; +import org.alliancegenome.es.model.VariantSearchResultDocument; import org.alliancegenome.es.rest.RestConfig; import org.alliancegenome.es.util.ProcessDisplayHelper; import org.alliancegenome.exceptional.client.ExceptionCatcher; @@ -23,6 +26,8 @@ public class VariantSummaryCurationIndexer extends Indexer { private final VariantDocumentInterface variantApi = RestProxyFactory.createProxy(VariantDocumentInterface.class, ConfigHelper.getCurationApiUrl(), RestConfig.config); + private VariantSearchResultConverter variantSearchResultConverter = new VariantSearchResultConverter(); + private final HashMap params = new HashMap<>() { { put("internal", false); @@ -66,8 +71,11 @@ protected void startSingleThread(LinkedBlockingDeque queue) { String page = queue.takeFirst(); SearchResponse response = variantApi.findDocuments(Integer.valueOf(page), indexerConfig.getBufferSize(), params); - indexDocuments(response.getResults()); + + List vsrd = variantSearchResultConverter.convertToVariantSearchDocument(response.getResults()); + indexDocuments(vsrd); + } catch (Exception e) { log.error("Error while indexing...", e); ExceptionCatcher.report(e);