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Upgrade curation library (#1535)
* SCRUM-5829 pickup the changes from the library * upgrade to library 0.47.9
1 parent 9b5bed9 commit 296cca5

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‎agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/TransgenicAlleleCurationIndexer.java‎

Lines changed: 15 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -1,24 +1,13 @@
11
package org.alliancegenome.indexer.indexers.curation;
22

3-
import java.util.ArrayList;
4-
import java.util.Collection;
5-
import java.util.HashMap;
6-
import java.util.HashSet;
7-
import java.util.LinkedHashMap;
8-
import java.util.List;
9-
import java.util.Map;
10-
import java.util.Set;
11-
import java.util.concurrent.LinkedBlockingDeque;
12-
3+
import com.fasterxml.jackson.databind.ObjectMapper;
4+
import lombok.extern.slf4j.Slf4j;
135
import org.alliancegenome.api.entity.GeneTransgenicAlleleSummaryDocument;
146
import org.alliancegenome.api.entity.TransgenicAlleleSummaryDocument;
157
import org.alliancegenome.core.config.ConfigHelper;
168
import org.alliancegenome.curation_api.interfaces.document.AlleleDocumentInterface;
17-
import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDTO;
18-
import org.alliancegenome.curation_api.model.entities.Allele;
19-
import org.alliancegenome.curation_api.model.entities.Construct;
20-
import org.alliancegenome.curation_api.model.entities.Gene;
21-
import org.alliancegenome.curation_api.model.entities.TransgenicAlleleConstruct;
9+
import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDocument;
10+
import org.alliancegenome.curation_api.model.entities.*;
2211
import org.alliancegenome.curation_api.model.entities.slotAnnotations.ConstructComponentSlotAnnotation;
2312
import org.alliancegenome.curation_api.model.entities.slotAnnotations.GeneSymbolSlotAnnotation;
2413
import org.alliancegenome.curation_api.response.SearchResponse;
@@ -28,12 +17,11 @@
2817
import org.alliancegenome.indexer.indexers.Indexer;
2918
import org.apache.commons.collections4.CollectionUtils;
3019
import org.apache.commons.lang3.ObjectUtils;
31-
32-
import com.fasterxml.jackson.databind.ObjectMapper;
33-
34-
import lombok.extern.slf4j.Slf4j;
3520
import si.mazi.rescu.RestProxyFactory;
3621

22+
import java.util.*;
23+
import java.util.concurrent.LinkedBlockingDeque;
24+
3725
@Slf4j
3826
public class TransgenicAlleleCurationIndexer extends Indexer {
3927

@@ -86,18 +74,22 @@ private void addGenesToMap(List<Gene> genes, Map<Gene, Set<GeneTransgenicAlleleS
8674
}
8775

8876
private List<TransgenicAlleleSummaryDocument> indexTransgenicAlleleSummary() {
89-
SearchResponse<TransgenicAlleleDTO> searchResponse = alleleApi.findDocuments(0, 0, params);
77+
SearchResponse<TransgenicAlleleDocument> searchResponse = alleleApi.findDocuments(0, 0, params);
9078
ProcessDisplayHelper display = new ProcessDisplayHelper();
9179
display.startProcess("Pulling Transgenic Alleles from curation", searchResponse.getTotalResults());
9280
Map<Allele, TransgenicAlleleSummaryDocument> documentMap = new LinkedHashMap<>();
9381
int batchSize = indexerConfig.getBufferSize();
9482
int maxPage = (int) (searchResponse.getTotalResults() / batchSize);
9583
for (int page = 0; page <= maxPage; page++) {
96-
SearchResponse<TransgenicAlleleDTO> response = alleleApi.findDocuments(page, batchSize, params);
97-
for (TransgenicAlleleDTO da : response.getResults()) {
84+
SearchResponse<TransgenicAlleleDocument> response = alleleApi.findDocuments(page, batchSize, params);
85+
for (TransgenicAlleleDocument da : response.getResults()) {
9886
if (da == null) {
9987
continue;
10088
}
89+
Species species = da.getAllele().getTaxon().getSpecies();
90+
if (species == null) {
91+
continue;
92+
}
10193
TransgenicAlleleSummaryDocument document = documentMap.computeIfAbsent(da.getAllele(), allele -> {
10294
TransgenicAlleleSummaryDocument doc = new TransgenicAlleleSummaryDocument();
10395
doc.setAllele(allele);
@@ -109,7 +101,7 @@ private List<TransgenicAlleleSummaryDocument> indexTransgenicAlleleSummary() {
109101
constructList = new ArrayList<>();
110102
document.setTransgenicAlleleConstructs(constructList);
111103
}
112-
Construct constructObj = da.getConstruct();
104+
Construct constructObj = da.getConstructList().getFirst();
113105

114106
TransgenicAlleleConstruct construct = new TransgenicAlleleConstruct();
115107
// MGI special handling

‎agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/AlleleSearchResultConverter.java‎

Lines changed: 16 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -3,15 +3,13 @@
33
import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
44
import org.alliancegenome.curation_api.model.entities.Allele;
55
import org.alliancegenome.curation_api.model.entities.ontology.NCBITaxonTerm;
6+
import org.alliancegenome.curation_api.model.entities.slotAnnotations.NameSlotAnnotation;
67
import org.alliancegenome.es.model.AlleleSearchResultDocument;
78
import org.alliancegenome.es.model.search.Category;
89
import org.alliancegenome.es.model.search.RelatedDataLink;
910
import org.apache.commons.collections.CollectionUtils;
1011

11-
import java.util.ArrayList;
12-
import java.util.HashSet;
13-
import java.util.List;
14-
import java.util.Set;
12+
import java.util.*;
1513
import java.util.stream.Collectors;
1614

1715
public class AlleleSearchResultConverter {
@@ -51,8 +49,8 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
5149

5250
if (CollectionUtils.isNotEmpty(allele.getAlleleSynonyms())) {
5351
List<String> synonyms = allele.getAlleleSynonyms().stream()
54-
.map(syn -> syn.getDisplayText())
55-
.filter(s -> s != null)
52+
.map(NameSlotAnnotation::getDisplayText)
53+
.filter(Objects::nonNull)
5654
.collect(Collectors.toList());
5755
if (!synonyms.isEmpty()) {
5856
searchDoc.setSynonyms(synonyms);
@@ -105,6 +103,18 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
105103
searchDoc.setDiseasesAgrSlim(new ArrayList<>(doc.getDiseasesAgrSlim()));
106104
}
107105

106+
if (doc.getConstructExpressedComponents() != null && !doc.getConstructExpressedComponents().isEmpty()) {
107+
searchDoc.setConstructExpressedComponent(doc.getConstructExpressedComponents());
108+
}
109+
110+
if (doc.getConstructRegulatoryRegions() != null && !doc.getConstructRegulatoryRegions().isEmpty()) {
111+
searchDoc.setConstructRegulatoryRegion(doc.getConstructRegulatoryRegions());
112+
}
113+
114+
if (doc.getConstructKnockdownComponents() != null && !doc.getConstructKnockdownComponents().isEmpty()) {
115+
searchDoc.setConstructKnockdownComponent(doc.getConstructKnockdownComponents());
116+
}
117+
108118
if (CollectionUtils.isNotEmpty(doc.getVariants())) {
109119
List<String> variantTypes = doc.getVariants().stream()
110120
.filter(v -> v.getVariantType() != null && v.getVariantType().getName() != null)

‎agr_java_core/src/main/java/org/alliancegenome/es/model/AlleleSearchResultDocument.java‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,9 @@ public AlleleSearchResultDocument() {
3131
private String alterationType;
3232
private List<String> variantTypes;
3333
private Set<String> molecularConsequences;
34+
private Set<String> constructExpressedComponent;
35+
private Set<String> constructRegulatoryRegion;
36+
private Set<String> constructKnockdownComponent;
3437
private List<String> synonyms;
3538
private List<String> secondaryIds;
3639
private List<String> genes;

‎pom.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@
2323
<maven-checkstyle-plugin.version>3.3.1</maven-checkstyle-plugin.version>
2424
<checkstyle.version>10.17.0</checkstyle.version>
2525
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
26-
<curation.version>v0.47.6</curation.version>
26+
<curation.version>v0.47.9</curation.version>
2727
</properties>
2828
<dependencyManagement>
2929
<dependencies>

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