diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/config/IndexerConfig.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/config/IndexerConfig.java index 8505b7be7..bc0e6e7e2 100644 --- a/agr_indexer/src/main/java/org/alliancegenome/indexer/config/IndexerConfig.java +++ b/agr_indexer/src/main/java/org/alliancegenome/indexer/config/IndexerConfig.java @@ -21,7 +21,6 @@ import org.alliancegenome.indexer.indexers.curation.ReleaseInfoIndexer; import org.alliancegenome.indexer.indexers.curation.SiteMapAccessionCurationIndexer; import org.alliancegenome.indexer.indexers.curation.TransgenicAlleleCurationIndexer; -import org.alliancegenome.indexer.indexers.curation.VariantSummaryCurationIndexer; public enum IndexerConfig { @@ -39,7 +38,7 @@ public enum IndexerConfig { AffectedGenomicModelAnnotationIndexer("agmAnnotation", AGMAnnotationCurationIndexer.class, 4, 1500, 1500, 8, 1, true), GeneSearchResultCurationIndexer("geneSearchResult", GeneSearchResultCurationIndexer.class, 4, 1000, 1500, 4, 1, true), GeneSummaryIndexer("geneSummary", GeneSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, true), - VariantSummaryIndexer("variantSummary", VariantSummaryCurationIndexer.class, 1, 3000, 1500, 8, 1, true), + //VariantSummaryIndexer("variantSummary", VariantSummaryCurationIndexer.class, 1, 3000, 1500, 8, 1, true), GeneGeneticInteractionIndexers("geneGeneticInteraction", GeneGeneticInteractionCurationIndexer.class, 4, 1500, 1500, 2, 1, true), HTPDatasetSearchResultCurationIndexer("htpDatasetSearchResult", HTPDatasetSearchResultCurationIndexer.class, 4, 1500, 1500, 4, 1, true), LiteratureIndexer("literature", LiteratureIndexer.class, 4, 5000, 5000, 1, 1, true), 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);