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Merged
oblodgett merged 4 commits into from
Mar 26, 2026
Merged

Added better reporting for counts on all the indexers #1539

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aa4664e
Added better reporting for counts on all the indexers
oblodgett Mar 26, 2026
83bf160
Reorged the order of the indexers
oblodgett Mar 26, 2026
f0bf7fa
Update curation version
oblodgett Mar 26, 2026
f55f0ac
Removed related data as this is generated in the search helper
oblodgett Mar 26, 2026
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34 changes: 18 additions & 16 deletions agr_indexer/src/main/java/org/alliancegenome/indexer/config/IndexerConfig.java
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Expand Up @@ -28,39 +28,41 @@
public enum IndexerConfig {

// Neo Indexers
ModelIndexer("model", ModelIndexer.class, 4, 1500, 1426, 4, 1, false),
ModelIndexer("model", ModelIndexer.class, 4, 1500, 1426, 4, 1, true),

// Curation Indexers

// Run Parallelly
ParalogyIndexer("paralogy", GeneToGeneParalogyIndexer.class, 4, 5000, 5000, 8, 1, true),
GOSearchResultCurationIndexer("goSearchResult", GOSearchResultCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
HTPDatasetSearchResultCurationIndexer("htpDatasetSearchResult", HTPDatasetSearchResultCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
LiteratureIndexer("literature", LiteratureIndexer.class, 4, 5000, 5000, 1, 1, true),
GeneGeneticInteractionIndexers("geneGeneticInteraction", GeneGeneticInteractionCurationIndexer.class, 4, 1500, 1500, 2, 1, true),
AffectedGenomicModelIndexer("affectedGenomicModels", AffectedGenomicModelCurationIndexer.class, 4, 1500, 1500, 8, 1, true),
DiseaseSummaryIndexer("diseaseSummary", DiseaseSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
DiseaseSearchResultIndexer("diseaseSearchResult", DiseaseSearchResultCurationIndexer.class, 8, 50, 50, 4, 1, true),

GeneSearchResultCurationIndexer("geneSearchResult", GeneSearchResultCurationIndexer.class, 4, 1000, 1500, 4, 1, true),
GeneSummaryIndexer("geneSummary", GeneSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, true),

DiseaseSearchResultIndexer("diseaseSearchResult", DiseaseSearchResultCurationIndexer.class, 8, 50, 50, 4, 1, true),
VariantSummaryIndexer("variantSummary", VariantSummaryCurationIndexer.class, 1, 3000, 1500, 8, 1, false),
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),
GeneExpressionAnnotationIndexer("geneExpressionAnnotation", GeneExpressionAnnotationIndexer.class, 8, 125, 2000, 4, 1, true),
SiteMapAccessionCurationIndexer("sitemap", SiteMapAccessionCurationIndexer.class, 4, 1500, 1500, 8, 1, true),
DiseaseSummaryIndexer("diseaseSummary", DiseaseSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
// neo model indexer
TransgenicAlleleIndexer("transgenicAlleles", TransgenicAlleleCurationIndexer.class, 1, 3000, 1500, 8, 1, true),
GeneExpressionRibbonSummaryIndexer("geneExpressionRibbonSummary", GeneExpressionRibbonSummaryIndexer.class, 1, 1, 1, 1, 1, true),
ReleaseInfoIndexer("release", ReleaseInfoIndexer.class, 1, 1, 1, 1, 1, true),

// Run Sequentially
// Run Sequentially -- typically take a lot of RAM or do consolidation in memory
AlleleSummaryIndexer("alleleSummary", AlleleSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, false),
GeneSummaryIndexer("geneSummary", GeneSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, false),
GeneToGeneOrthologyIndexer("geneToGeneOrthology", GeneToGeneOrthologyIndexer.class, 4, 2500, 2500, 8, 1, false),

GeneExpressionAnnotationIndexer("geneExpressionAnnotation", GeneExpressionAnnotationIndexer.class, 8, 125, 2000, 4, 1, false),

PhenotypeAnnotationIndexer("phenotypeAnnotation", PhenotypeAnnotationCurationIndexer.class, 4, 1500, 1500, 2, 1, false),
TransgenicAlleleIndexer("transgenicAlleles", TransgenicAlleleCurationIndexer.class, 1, 3000, 1500, 8, 1, false),
GeneMolecularInteractionIndexers("geneMolecularInteraction", GeneMolecularInteractionCurationIndexer.class, 4, 1500, 1500, 2, 1, false),

PhenotypeAnnotationIndexer("phenotypeAnnotation", PhenotypeAnnotationCurationIndexer.class, 4, 1500, 1500, 2, 1, false),
DiseaseAnnotationIndexer("diseaseAnnotation", DiseaseAnnotationCurationIndexer.class, 1, 1500, 1500, 2, 1, false),
VariantSummaryIndexer("variantSummary", VariantSummaryCurationIndexer.class, 1, 3000, 1500, 8, 1, false),

GeneSearchResultCurationIndexer("geneSearchResult", GeneSearchResultCurationIndexer.class, 4, 1000, 1500, 4, 1, false),



;


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3 changes: 2 additions & 1 deletion agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/DatasetIndexer.java
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Expand Up @@ -6,6 +6,7 @@
import org.alliancegenome.core.translators.document.HTPDatasetTranslator;
import org.alliancegenome.es.index.site.cache.DatasetDocumentCache;
import org.alliancegenome.es.index.site.document.SearchableItemDocument;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.neo4j.entity.node.HTPDataset;
Expand All @@ -24,7 +25,7 @@ public DatasetIndexer(IndexerConfig config) {
}

@Override
public void index() {
public void index(ProcessDisplayHelper display) {
try {
repo = new DatasetIndexerRepository();
cache = repo.getCache();
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3 changes: 2 additions & 1 deletion agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/DiseaseIndexer.java
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Expand Up @@ -7,6 +7,7 @@
import org.alliancegenome.core.translators.document.DiseaseTranslator;
import org.alliancegenome.es.index.site.cache.DiseaseDocumentCache;
import org.alliancegenome.es.index.site.document.SearchableItemDocument;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.neo4j.entity.node.DOTerm;
Expand All @@ -25,7 +26,7 @@ public DiseaseIndexer(IndexerConfig config) {
}

@Override
public void index() {
public void index(ProcessDisplayHelper display) {
try {
DiseaseIndexerRepository diseaseIndexerRepository = new DiseaseIndexerRepository();
diseaseDocumentCache = diseaseIndexerRepository.getDiseaseDocumentCache();
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3 changes: 2 additions & 1 deletion agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/GeneIndexer.java
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Expand Up @@ -8,6 +8,7 @@
import org.alliancegenome.core.translators.document.GeneTranslator;
import org.alliancegenome.es.index.site.cache.GeneDocumentCache;
import org.alliancegenome.es.index.site.document.SearchableItemDocument;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.neo4j.entity.node.Gene;
Expand All @@ -25,7 +26,7 @@ public GeneIndexer(IndexerConfig config) {
}

@Override
public void index() {
public void index(ProcessDisplayHelper display) {

try {
LinkedBlockingDeque<String> queue = new LinkedBlockingDeque<>();
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3 changes: 2 additions & 1 deletion agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/GoIndexer.java
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Expand Up @@ -4,6 +4,7 @@

import org.alliancegenome.core.translators.document.GoTranslator;
import org.alliancegenome.es.index.site.document.SearchableItemDocument;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.neo4j.entity.node.GOTerm;
import org.alliancegenome.neo4j.repository.GoRepository;
Expand All @@ -21,7 +22,7 @@ public GoIndexer(IndexerConfig config) {
}

@Override
public void index() {
public void index(ProcessDisplayHelper display) {

goRepo = new GoRepository();
goTrans = new GoTranslator();
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6 changes: 3 additions & 3 deletions agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java
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Expand Up @@ -104,7 +104,7 @@ public void runIndex() {
try {
Instant start = Instant.now();
display.startProcess(getClass().getSimpleName());
index();
index(display);
log.info("Waiting for bulkProcessor to finish");
bulkProcessor.flush();
bulkProcessor.awaitClose(30L, TimeUnit.DAYS);
Expand All @@ -126,7 +126,7 @@ public void run() {
try {
Instant start = Instant.now();
display.startProcess(getClass().getSimpleName());
index();
index(display);
log.info("Waiting for bulkProcessor to finish");
bulkProcessor.flush();
bulkProcessor.awaitClose(30L, TimeUnit.DAYS);
Expand Down Expand Up @@ -213,7 +213,7 @@ protected <T> List<List<T>> partition(List<T> list, int size) {
return parts;
}

protected abstract void index();
protected abstract void index(ProcessDisplayHelper display);

protected abstract void startSingleThread(LinkedBlockingDeque<String> queue);

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3 changes: 2 additions & 1 deletion agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/LiteratureIndexer.java
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Expand Up @@ -7,6 +7,7 @@

import org.alliancegenome.api.entity.LiteratureSummaryDocument;
import org.alliancegenome.core.config.ConfigHelper;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.indexer.indexers.curation.interfaces.ElasticSearchInterface;
Expand All @@ -27,7 +28,7 @@ public LiteratureIndexer(IndexerConfig indexerConfig) {

// with multiple thread
@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
log.info("IndexName: " + indexName);
Map<String, Object> countObject = literatureESApi.count(indexName);
try {
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5 changes: 3 additions & 2 deletions agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/ModelIndexer.java
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Expand Up @@ -6,6 +6,7 @@
import org.alliancegenome.core.translators.document.ModelTranslator;
import org.alliancegenome.es.index.site.cache.ModelDocumentCache;
import org.alliancegenome.es.index.site.document.SearchableItemDocument;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.neo4j.entity.node.AffectedGenomicModel;
Expand All @@ -24,13 +25,13 @@ public ModelIndexer(IndexerConfig config) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
try {
repo = new ModelIndexerRepository();
cache = repo.getModelDocumentCache();

LinkedBlockingDeque<String> queue = new LinkedBlockingDeque<>(cache.getModelMap().keySet());

display.startProcess(queue.size());
initiateThreading(queue);
repo.close();
} catch (Exception e) {
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3 changes: 2 additions & 1 deletion agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/VariantIndexer.java
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Expand Up @@ -7,6 +7,7 @@
import org.alliancegenome.core.translators.document.VariantTranslator;
import org.alliancegenome.es.index.site.cache.IndexerCache;
import org.alliancegenome.es.index.site.document.SearchableItemDocument;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.neo4j.entity.node.Variant;
Expand All @@ -25,7 +26,7 @@ public VariantIndexer(IndexerConfig config) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {

// for now, variants only get indexed if an additional flag is set
if (!ConfigHelper.getIndexVariants()) {
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5 changes: 3 additions & 2 deletions ...ava/org/alliancegenome/indexer/indexers/curation/AffectedGenomicModelCurationIndexer.java
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Expand Up @@ -8,6 +8,7 @@
import org.alliancegenome.curation_api.model.document.es.AffectedGenomicModelDocument;
import org.alliancegenome.curation_api.response.SearchResponse;
import org.alliancegenome.es.rest.RestConfig;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.indexer.indexers.Indexer;
Expand All @@ -30,13 +31,13 @@ public AffectedGenomicModelCurationIndexer(IndexerConfig config) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
try {
log.info("Fetching all AGM IDs...");
SearchResponse<Long> idsResponse = modelApi.getAllIds();
List<Long> allIds = idsResponse.getResults();
log.info("Fetched {} AGM IDs", allIds.size());

display.startProcess(allIds.size());
idBatches = partition(allIds, indexerConfig.getBufferSize());
log.info("Partitioned into {} batches of up to {}", idBatches.size(), indexerConfig.getBufferSize());

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5 changes: 3 additions & 2 deletions .../main/java/org/alliancegenome/indexer/indexers/curation/AlleleSummaryCurationIndexer.java
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Expand Up @@ -13,6 +13,7 @@
import org.alliancegenome.curation_api.response.SearchResponse;
import org.alliancegenome.curation_api.view.CurationView;
import org.alliancegenome.es.rest.RestConfig;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.indexer.indexers.Indexer;
Expand All @@ -37,13 +38,13 @@ public AlleleSummaryCurationIndexer(IndexerConfig indexerConfig) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
try {
log.info("Fetching all allele IDs...");
SearchResponse<Long> idsResponse = alleleApi.getAllIds();
List<Long> allIds = idsResponse.getResults();
log.info("Fetched {} allele IDs", allIds.size());

display.startProcess(allIds.size());
idBatches = partition(allIds, indexerConfig.getBufferSize());
log.info("Partitioned into {} batches of up to {}", idBatches.size(), indexerConfig.getBufferSize());

Expand Down
2 changes: 1 addition & 1 deletion ...n/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java
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Expand Up @@ -96,7 +96,7 @@ protected void startSingleThread(LinkedBlockingDeque<String> queue) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
geneService = new GeneDiseaseAnnotationService();
alleleService = new AlleleDiseaseAnnotationService();
agmService = new AGMDiseaseAnnotationService();
Expand Down
5 changes: 3 additions & 2 deletions ...java/org/alliancegenome/indexer/indexers/curation/DiseaseSearchResultCurationIndexer.java
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Expand Up @@ -7,6 +7,7 @@
import org.alliancegenome.curation_api.model.document.es.DiseaseSearchResultDocument;
import org.alliancegenome.curation_api.response.SearchResponse;
import org.alliancegenome.es.rest.RestConfig;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.indexer.indexers.Indexer;
Expand All @@ -26,12 +27,12 @@ public DiseaseSearchResultCurationIndexer(IndexerConfig indexerConfig) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
try {
log.info("Fetching all disease search result documents...");
SearchResponse<DiseaseSearchResultDocument> response = diseaseApi.findAll();
log.info("Fetched {} disease search result documents", response.getResults().size());

display.startProcess(response.getResults().size());
indexDocuments(response.getResults());
} catch (Exception e) {
log.error("Error while indexing...", e);
Expand Down
4 changes: 3 additions & 1 deletion ...main/java/org/alliancegenome/indexer/indexers/curation/DiseaseSummaryCurationIndexer.java
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Expand Up @@ -8,6 +8,7 @@
import org.alliancegenome.curation_api.model.document.es.DiseaseSummaryDocument;
import org.alliancegenome.curation_api.response.SearchResponse;
import org.alliancegenome.es.rest.RestConfig;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.indexer.indexers.Indexer;
Expand All @@ -33,9 +34,10 @@ public DiseaseSummaryCurationIndexer(IndexerConfig indexerConfig) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
try {
SearchResponse<DiseaseSummaryDocument> diseaseSummaryResponse = diseaseApi.findSummary(0, 0, params);
display.startProcess(diseaseSummaryResponse.getTotalResults());
int totalPages = (int) (diseaseSummaryResponse.getTotalResults() / indexerConfig.getBufferSize());
LinkedBlockingDeque<String> queue = new LinkedBlockingDeque<>();
for (int i = 0; i <= totalPages; i++) {
Expand Down
5 changes: 3 additions & 2 deletions ...main/java/org/alliancegenome/indexer/indexers/curation/GOSearchResultCurationIndexer.java
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Expand Up @@ -8,6 +8,7 @@
import org.alliancegenome.curation_api.model.document.es.GOSearchResultDocument;
import org.alliancegenome.curation_api.response.SearchResponse;
import org.alliancegenome.es.rest.RestConfig;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.indexer.indexers.Indexer;
Expand All @@ -30,13 +31,13 @@ public GOSearchResultCurationIndexer(IndexerConfig indexerConfig) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
try {
log.info("Fetching all GO search result IDs...");
SearchResponse<Long> idsResponse = goApi.getAllIds();
List<Long> allIds = idsResponse.getResults();
log.info("Fetched {} GO search result IDs", allIds.size());

display.startProcess(allIds.size());
idBatches = partition(allIds, indexerConfig.getBufferSize());
log.info("Partitioned into {} batches of up to {}", idBatches.size(), indexerConfig.getBufferSize());

Expand Down
5 changes: 3 additions & 2 deletions ...in/java/org/alliancegenome/indexer/indexers/curation/GeneExpressionAnnotationIndexer.java
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Expand Up @@ -11,6 +11,7 @@
import org.alliancegenome.curation_api.model.entities.Species;
import org.alliancegenome.curation_api.response.SearchResponse;
import org.alliancegenome.es.rest.RestConfig;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.indexer.indexers.Indexer;
Expand Down Expand Up @@ -38,7 +39,7 @@ public GeneExpressionAnnotationIndexer(IndexerConfig indexerConfig) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
try {
speciesOrderLookup = new HashMap<>();
List<Species> allSpecies = speciesApi.findForPublic(0, 100, "FieldsOnly", new HashMap<>()).getResults();
Expand All @@ -55,7 +56,7 @@ protected void index() {

List<String> primaryExternalIds = idsResponse.getResults();
log.info("Fetched {} gene IDs", primaryExternalIds.size());

display.startProcess(primaryExternalIds.size());
idBatches = partition(primaryExternalIds, indexerConfig.getBufferSize());
log.info("Partitioned into {} batches of up to {}", idBatches.size(), indexerConfig.getBufferSize());

Expand Down
3 changes: 2 additions & 1 deletion ...java/org/alliancegenome/indexer/indexers/curation/GeneExpressionRibbonSummaryIndexer.java
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Expand Up @@ -6,6 +6,7 @@
import org.alliancegenome.curation_api.interfaces.document.GeneExpressionRibbonDocumentInterface;
import org.alliancegenome.curation_api.model.document.es.GeneExpressionRibbonSummaryDocument;
import org.alliancegenome.es.rest.RestConfig;
import org.alliancegenome.es.util.ProcessDisplayHelper;
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.indexer.indexers.Indexer;
Expand All @@ -24,7 +25,7 @@ public GeneExpressionRibbonSummaryIndexer(IndexerConfig indexerConfig) {
}

@Override
protected void index() {
protected void index(ProcessDisplayHelper display) {
try {
GeneExpressionRibbonSummaryDocument response = api.findDocument();
if (response == null) {
Expand Down
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