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Merge pull request #1558 from alliance-genome/SCRUM-5829
SCRUM-5829
2 parents a112c2b + 1ccca6a commit e90f950

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15 files changed

+53
-35
lines changed

15 files changed

+53
-35
lines changed

‎agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -105,12 +105,12 @@ public JsonResultResponse<ESDocument> getAllelesPerGene(String id, Integer limit
105105
Pagination pagination = new Pagination(page, limit, sortBy, asc);
106106
pagination.addFilterOption("symbol", symbol);
107107
pagination.addFilterOption("allele.alleleSynonyms.displayText", synonym);
108-
pagination.addFilterOption("variants.curatedVariantGenomicLocations.hgvs", variant);
108+
pagination.addFilterOption("variantList.curatedVariantGenomicLocations.hgvs", variant);
109109
pagination.addFilterOption("alterationType.keyword", category);
110-
pagination.addFilterOption("variants.variantType.name.keyword", variantType);
110+
pagination.addFilterOption("variantList.variantType.name.keyword", variantType);
111111
pagination.addFilterOption("hasDisease", hasDisease);
112112
pagination.addFilterOption("hasPhenotype", hasPhenotype);
113-
pagination.addFilterOption("variants.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.keyword", molecularConsequence);
113+
pagination.addFilterOption("variantList.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.keyword", molecularConsequence);
114114

115115
if (pagination.hasErrors()) {
116116
RestErrorMessage message = new RestErrorMessage();

‎agr_api/src/main/java/org/alliancegenome/api/service/AlleleESService.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -41,13 +41,13 @@ public class AlleleESService extends ESService {
4141
}};
4242

4343
LinkedHashMap<String, SortOrder> variantTypeSortMap = new LinkedHashMap<>() {{
44-
put("variants.variantType.name.sort", SortOrder.ASC);
44+
put("variantList.variantType.name.sort", SortOrder.ASC);
4545
put("symbol.sort", SortOrder.ASC);
4646
}};
4747

4848
LinkedHashMap<String, SortOrder> molecualarConsequenceSortMap = new LinkedHashMap<>() {{
49-
put("variants.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.sort", SortOrder.ASC);
50-
put("variants.variantType.name.sort", SortOrder.ASC);
49+
put("variantList.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.sort", SortOrder.ASC);
50+
put("variantList.variantType.name.sort", SortOrder.ASC);
5151
put("symbol.sort", SortOrder.ASC);
5252
}};
5353

@@ -171,8 +171,8 @@ private Map<String, Object> getAlleleSupplementalData(BoolQueryBuilder unfiltere
171171

172172
Map<String, String> aggregationFields = new HashMap<>();
173173
aggregationFields.put("alterationType.keyword", "alleleCategory");
174-
aggregationFields.put("variants.variantType.name.keyword", "variantType");
175-
aggregationFields.put("variants.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.keyword", "molecularConsequence");
174+
aggregationFields.put("variantList.variantType.name.keyword", "variantType");
175+
aggregationFields.put("variantList.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.keyword", "molecularConsequence");
176176

177177
Map<String, List<String>> distinctFieldValueMap = getAggregations(unfilteredQuery, aggregationFields, null, false, false);
178178
Map<String, Object> supplementalData = new LinkedHashMap<>();

‎agr_indexer/src/main/java/org/alliancegenome/indexer/TestSynonyms.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -37,9 +37,9 @@ public static void main(String[] args) throws Exception {
3737
System.out.println("=== Step 1: AlleleSummaryDocument from API ===");
3838
for (AlleleSummaryDocument doc : response.getResults()) {
3939
System.out.println("Allele symbol: " + (doc.getAllele() != null && doc.getAllele().getAlleleSymbol() != null ? doc.getAllele().getAlleleSymbol().getDisplayText() : "null"));
40-
System.out.println("Variants: " + (doc.getVariants() != null ? doc.getVariants().size() : "null"));
41-
if (doc.getVariants() != null) {
42-
for (Variant v : doc.getVariants()) {
40+
System.out.println("Variants: " + (doc.getVariantList() != null ? doc.getVariantList().size() : "null"));
41+
if (doc.getVariantList() != null) {
42+
for (Variant v : doc.getVariantList()) {
4343
System.out.println(" Variant type: " + (v.getVariantType() != null ? v.getVariantType().getName() : "null"));
4444
if (v.getCuratedVariantGenomicLocations() != null) {
4545
for (CuratedVariantGenomicLocationAssociation loc : v.getCuratedVariantGenomicLocations()) {

‎agr_indexer/src/main/java/org/alliancegenome/indexer/config/IndexerConfig.java‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,6 @@
2121
import org.alliancegenome.indexer.indexers.curation.ReleaseInfoIndexer;
2222
import org.alliancegenome.indexer.indexers.curation.SiteMapAccessionCurationIndexer;
2323
import org.alliancegenome.indexer.indexers.curation.TransgenicAlleleCurationIndexer;
24-
import org.alliancegenome.indexer.indexers.curation.VariantSummaryCurationIndexer;
2524

2625
public enum IndexerConfig {
2726

@@ -39,7 +38,7 @@ public enum IndexerConfig {
3938
AffectedGenomicModelAnnotationIndexer("agmAnnotation", AGMAnnotationCurationIndexer.class, 4, 1500, 1500, 8, 1, true),
4039
GeneSearchResultCurationIndexer("geneSearchResult", GeneSearchResultCurationIndexer.class, 4, 1000, 1500, 4, 1, true),
4140
GeneSummaryIndexer("geneSummary", GeneSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
42-
VariantSummaryIndexer("variantSummary", VariantSummaryCurationIndexer.class, 1, 3000, 1500, 8, 1, true),
41+
//VariantSummaryIndexer("variantSummary", VariantSummaryCurationIndexer.class, 1, 3000, 1500, 8, 1, true),
4342
GeneGeneticInteractionIndexers("geneGeneticInteraction", GeneGeneticInteractionCurationIndexer.class, 4, 1500, 1500, 2, 1, true),
4443
HTPDatasetSearchResultCurationIndexer("htpDatasetSearchResult", HTPDatasetSearchResultCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
4544
LiteratureIndexer("literature", LiteratureIndexer.class, 4, 5000, 5000, 1, 1, true),

‎agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/AlleleToTdfTranslator.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -64,8 +64,8 @@ public List<AlleleDownloadRow> getAlleleDownloadRowsForGenes(List<ESDocument> an
6464

6565
private List<Variant> getVariants(AVSParentDocument doc) {
6666
return switch (doc) {
67-
case AlleleSummaryDocument asd -> asd.getVariants();
68-
case VariantSummaryDocument vsd -> vsd.getVariants();
67+
case AlleleSummaryDocument asd -> asd.getVariantList();
68+
case VariantSummaryDocument vsd -> vsd.getVariantList();
6969
default -> null;
7070
};
7171
}
@@ -252,7 +252,7 @@ public List<VariantDownloadRow> getVariantDownloadRowsForAlleles(List<VariantSum
252252

253253
private VariantDownloadRow getBaseDownloadVariantRow(VariantSummaryDocument annotation) {
254254
VariantDownloadRow row = new VariantDownloadRow();
255-
Variant rootVariant = annotation.getVariants().getFirst();
255+
Variant rootVariant = annotation.getVariantList().getFirst();
256256
CuratedVariantGenomicLocationAssociation variant = rootVariant.getCuratedVariantGenomicLocations().getFirst();
257257
if (variant == null) {
258258
return row;

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

Lines changed: 21 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -87,6 +87,13 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
8787
searchDoc.setModCrossRefCompleteUrl(doc.getCrossReference().getReferencedCurie());
8888
}
8989

90+
Set<String> crossRefs = new HashSet<>();
91+
crossRefs.add(allele.getPrimaryExternalId());
92+
if (doc.getAlleleOfGene() != null && doc.getAlleleOfGene().getPrimaryExternalId() != null) {
93+
crossRefs.add(doc.getAlleleOfGene().getPrimaryExternalId());
94+
}
95+
searchDoc.setCrossReferences(crossRefs);
96+
9097
if (allele.getPopularity() != null) {
9198
searchDoc.setPopularity(allele.getPopularity());
9299
} else {
@@ -103,6 +110,10 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
103110
searchDoc.setDiseasesWithParents(new ArrayList<>(doc.getDiseasesWithParents()));
104111
}
105112

113+
if (doc.getPhenotypeStatements() != null && !doc.getPhenotypeStatements().isEmpty()) {
114+
searchDoc.setPhenotypeStatements(new ArrayList<>(doc.getPhenotypeStatements()));
115+
}
116+
106117
if (doc.getConstructExpressedComponents() != null && !doc.getConstructExpressedComponents().isEmpty()) {
107118
searchDoc.setConstructExpressedComponent(doc.getConstructExpressedComponents());
108119
}
@@ -115,8 +126,8 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
115126
searchDoc.setConstructKnockdownComponent(doc.getConstructKnockdownComponents());
116127
}
117128

118-
if (CollectionUtils.isNotEmpty(doc.getVariants())) {
119-
List<String> variantTypes = doc.getVariants().stream()
129+
if (CollectionUtils.isNotEmpty(doc.getVariantList())) {
130+
List<String> variantTypes = doc.getVariantList().stream()
120131
.filter(v -> v.getVariantType() != null && v.getVariantType().getName() != null)
121132
.map(v -> v.getVariantType().getName())
122133
.distinct()
@@ -126,11 +137,15 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
126137
}
127138

128139
Set<String> consequences = new HashSet<>();
129-
for (var variant : doc.getVariants()) {
140+
Set<String> variantHgvs = new HashSet<>();
141+
for (var variant : doc.getVariantList()) {
130142
if (variant.getCuratedVariantGenomicLocations() == null) {
131143
continue;
132144
}
133145
for (var location : variant.getCuratedVariantGenomicLocations()) {
146+
if (location.getHgvs() != null) {
147+
variantHgvs.add(location.getHgvs());
148+
}
134149
if (location.getPredictedVariantConsequences() == null) {
135150
continue;
136151
}
@@ -149,6 +164,9 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
149164
if (!consequences.isEmpty()) {
150165
searchDoc.setMolecularConsequence(consequences);
151166
}
167+
if (!variantHgvs.isEmpty()) {
168+
searchDoc.setVariants(variantHgvs);
169+
}
152170
}
153171

154172
result.add(searchDoc);

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ public List<SequenceSummaryDocument> convert(List<AlleleSummaryDocument> alleleD
1717
List<SequenceSummaryDocument> result = new ArrayList<>();
1818

1919
for (AlleleSummaryDocument doc : alleleDocs) {
20-
if (CollectionUtils.isEmpty(doc.getVariants())) {
20+
if (CollectionUtils.isEmpty(doc.getVariantList())) {
2121
continue;
2222
}
2323

@@ -26,7 +26,7 @@ public List<SequenceSummaryDocument> convert(List<AlleleSummaryDocument> alleleD
2626
geneIds.add(doc.getAlleleOfGene().getPrimaryExternalId());
2727
}
2828

29-
for (Variant variant : doc.getVariants()) {
29+
for (Variant variant : doc.getVariantList()) {
3030
if (CollectionUtils.isEmpty(variant.getCuratedVariantGenomicLocations())) {
3131
continue;
3232
}

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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ public List<SequenceSummaryDocument> convertToSequenceSummary(List<VariantSummar
2121
List<SequenceSummaryDocument> result = new ArrayList<>();
2222

2323
for (VariantSummaryDocument doc : docs) {
24-
CuratedVariantGenomicLocationAssociation variantLocation = doc.getVariants().get(0).getCuratedVariantGenomicLocations().get(0);
24+
CuratedVariantGenomicLocationAssociation variantLocation = doc.getVariantList().getFirst().getCuratedVariantGenomicLocations().get(0);
2525
if (variantLocation == null || variantLocation.getPredictedVariantConsequences() == null) {
2626
continue;
2727
}
@@ -31,7 +31,7 @@ public List<SequenceSummaryDocument> convertToSequenceSummary(List<VariantSummar
3131
SequenceSummaryDocument ssd = new SequenceSummaryDocument();
3232
ssd.setAllele(doc.getAllele());
3333
ssd.setSymbol(doc.getSymbol());
34-
ssd.setVariant(doc.getVariants().get(0));
34+
ssd.setVariant(doc.getVariantList().getFirst());
3535
ssd.setConsequence(consequence);
3636
ssd.setAlterationType("variant");
3737
ssd.setAlterationTypeSortOrder(4);

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ public List<VariantSearchResultDocument> convertToVariantSearchDocument(List<Var
1818
List<VariantSearchResultDocument> result = new ArrayList<>();
1919

2020
for (VariantSummaryDocument doc : variantSummaryDocuments) {
21-
CuratedVariantGenomicLocationAssociation variantLocation = doc.getVariants().get(0).getCuratedVariantGenomicLocations().get(0);
21+
CuratedVariantGenomicLocationAssociation variantLocation = doc.getVariantList().get(0).getCuratedVariantGenomicLocations().get(0);
2222
if (variantLocation == null) {
2323
continue;
2424
}

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -275,7 +275,7 @@ public List<VariantSummaryDocument> convertContextToDocument(VariantContext ctx,
275275
variantWrapper.setTaxon(taxon);
276276
variantWrapper.setCuratedVariantGenomicLocations(List.of(cvgla));
277277
variantWrapper.setCrossReferences(variant.getCrossReferences());
278-
doc.setVariants(List.of(variantWrapper));
278+
doc.setVariantList(List.of(variantWrapper));
279279
doc.setGeneIds(resultPair.getRight());
280280
returnDocuments.add(doc);
281281
}

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