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Merged
cmpich merged 2 commits into from
Mar 25, 2026
Merged

Upgrade curation library #1535

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532817c
SCRUM-5829 pickup the changes from the library
cmpich Mar 24, 2026
5dbb9b5
upgrade to library 0.47.9
cmpich Mar 25, 2026
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38 changes: 15 additions & 23 deletions ...in/java/org/alliancegenome/indexer/indexers/curation/TransgenicAlleleCurationIndexer.java
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Original file line number Diff line number Diff line change
@@ -1,24 +1,13 @@
package org.alliancegenome.indexer.indexers.curation;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.LinkedBlockingDeque;

import com.fasterxml.jackson.databind.ObjectMapper;
import lombok.extern.slf4j.Slf4j;
import org.alliancegenome.api.entity.GeneTransgenicAlleleSummaryDocument;
import org.alliancegenome.api.entity.TransgenicAlleleSummaryDocument;
import org.alliancegenome.core.config.ConfigHelper;
import org.alliancegenome.curation_api.interfaces.document.AlleleDocumentInterface;
import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDTO;
import org.alliancegenome.curation_api.model.entities.Allele;
import org.alliancegenome.curation_api.model.entities.Construct;
import org.alliancegenome.curation_api.model.entities.Gene;
import org.alliancegenome.curation_api.model.entities.TransgenicAlleleConstruct;
import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDocument;
import org.alliancegenome.curation_api.model.entities.*;
import org.alliancegenome.curation_api.model.entities.slotAnnotations.ConstructComponentSlotAnnotation;
import org.alliancegenome.curation_api.model.entities.slotAnnotations.GeneSymbolSlotAnnotation;
import org.alliancegenome.curation_api.response.SearchResponse;
Expand All @@ -28,12 +17,11 @@
import org.alliancegenome.indexer.indexers.Indexer;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.ObjectUtils;

import com.fasterxml.jackson.databind.ObjectMapper;

import lombok.extern.slf4j.Slf4j;
import si.mazi.rescu.RestProxyFactory;

import java.util.*;
import java.util.concurrent.LinkedBlockingDeque;

@Slf4j
public class TransgenicAlleleCurationIndexer extends Indexer {

Expand Down Expand Up @@ -86,18 +74,22 @@ private void addGenesToMap(List<Gene> genes, Map<Gene, Set<GeneTransgenicAlleleS
}

private List<TransgenicAlleleSummaryDocument> indexTransgenicAlleleSummary() {
SearchResponse<TransgenicAlleleDTO> searchResponse = alleleApi.findDocuments(0, 0, params);
SearchResponse<TransgenicAlleleDocument> searchResponse = alleleApi.findDocuments(0, 0, params);
ProcessDisplayHelper display = new ProcessDisplayHelper();
display.startProcess("Pulling Transgenic Alleles from curation", searchResponse.getTotalResults());
Map<Allele, TransgenicAlleleSummaryDocument> documentMap = new LinkedHashMap<>();
int batchSize = indexerConfig.getBufferSize();
int maxPage = (int) (searchResponse.getTotalResults() / batchSize);
for (int page = 0; page <= maxPage; page++) {
SearchResponse<TransgenicAlleleDTO> response = alleleApi.findDocuments(page, batchSize, params);
for (TransgenicAlleleDTO da : response.getResults()) {
SearchResponse<TransgenicAlleleDocument> response = alleleApi.findDocuments(page, batchSize, params);
for (TransgenicAlleleDocument da : response.getResults()) {
if (da == null) {
continue;
}
Species species = da.getAllele().getTaxon().getSpecies();
if (species == null) {
continue;
}
TransgenicAlleleSummaryDocument document = documentMap.computeIfAbsent(da.getAllele(), allele -> {
TransgenicAlleleSummaryDocument doc = new TransgenicAlleleSummaryDocument();
doc.setAllele(allele);
Expand All @@ -109,7 +101,7 @@ private List<TransgenicAlleleSummaryDocument> indexTransgenicAlleleSummary() {
constructList = new ArrayList<>();
document.setTransgenicAlleleConstructs(constructList);
}
Construct constructObj = da.getConstruct();
Construct constructObj = da.getConstructList().getFirst();

TransgenicAlleleConstruct construct = new TransgenicAlleleConstruct();
// MGI special handling
Expand Down
22 changes: 16 additions & 6 deletions ...src/main/java/org/alliancegenome/core/variant/converters/AlleleSearchResultConverter.java
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Expand Up @@ -3,15 +3,13 @@
import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
import org.alliancegenome.curation_api.model.entities.Allele;
import org.alliancegenome.curation_api.model.entities.ontology.NCBITaxonTerm;
import org.alliancegenome.curation_api.model.entities.slotAnnotations.NameSlotAnnotation;
import org.alliancegenome.es.model.AlleleSearchResultDocument;
import org.alliancegenome.es.model.search.Category;
import org.alliancegenome.es.model.search.RelatedDataLink;
import org.apache.commons.collections.CollectionUtils;

import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.*;
import java.util.stream.Collectors;

public class AlleleSearchResultConverter {
Expand Down Expand Up @@ -51,8 +49,8 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle

if (CollectionUtils.isNotEmpty(allele.getAlleleSynonyms())) {
List<String> synonyms = allele.getAlleleSynonyms().stream()
.map(syn -> syn.getDisplayText())
.filter(s -> s != null)
.map(NameSlotAnnotation::getDisplayText)
.filter(Objects::nonNull)
.collect(Collectors.toList());
if (!synonyms.isEmpty()) {
searchDoc.setSynonyms(synonyms);
Expand Down Expand Up @@ -105,6 +103,18 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
searchDoc.setDiseasesAgrSlim(new ArrayList<>(doc.getDiseasesAgrSlim()));
}

if (doc.getConstructExpressedComponents() != null && !doc.getConstructExpressedComponents().isEmpty()) {
searchDoc.setConstructExpressedComponent(doc.getConstructExpressedComponents());
}

if (doc.getConstructRegulatoryRegions() != null && !doc.getConstructRegulatoryRegions().isEmpty()) {
searchDoc.setConstructRegulatoryRegion(doc.getConstructRegulatoryRegions());
}

if (doc.getConstructKnockdownComponents() != null && !doc.getConstructKnockdownComponents().isEmpty()) {
searchDoc.setConstructKnockdownComponent(doc.getConstructKnockdownComponents());
}

if (CollectionUtils.isNotEmpty(doc.getVariants())) {
List<String> variantTypes = doc.getVariants().stream()
.filter(v -> v.getVariantType() != null && v.getVariantType().getName() != null)
Expand Down
3 changes: 3 additions & 0 deletions agr_java_core/src/main/java/org/alliancegenome/es/model/AlleleSearchResultDocument.java
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Expand Up @@ -31,6 +31,9 @@ public AlleleSearchResultDocument() {
private String alterationType;
private List<String> variantTypes;
private Set<String> molecularConsequences;
private Set<String> constructExpressedComponent;
private Set<String> constructRegulatoryRegion;
private Set<String> constructKnockdownComponent;
private List<String> synonyms;
private List<String> secondaryIds;
private List<String> genes;
Expand Down
2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -23,7 +23,7 @@
<maven-checkstyle-plugin.version>3.3.1</maven-checkstyle-plugin.version>
<checkstyle.version>10.17.0</checkstyle.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<curation.version>v0.47.6</curation.version>
<curation.version>v0.47.9</curation.version>
</properties>
<dependencyManagement>
<dependencies>
Expand Down
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