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Merge pull request #1175 from alliance-genome/SCRUM-3872
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SCRUM-3872 Bump curation library to v0.31.0
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@oblodgett
oblodgett authored Apr 1, 2024
2 parents fadb0db + 36238f3 commit 8daac6a
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Showing 4 changed files with 35 additions and 35 deletions.
22 changes: 11 additions & 11 deletions ...rc/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
import org.alliancegenome.core.translators.tdf.DownloadHeader;
import org.alliancegenome.curation_api.model.entities.ExperimentalCondition;
import org.alliancegenome.curation_api.model.entities.*;
import org.alliancegenome.curation_api.model.entities.base.CurieAuditedObject;
import org.alliancegenome.curation_api.model.entities.base.SubmittedObject;
import org.alliancegenome.neo4j.entity.DiseaseAnnotation;
import org.alliancegenome.neo4j.entity.PrimaryAnnotatedEntity;
import org.alliancegenome.neo4j.entity.node.CrossReference;
Expand Down Expand Up @@ -193,13 +193,13 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance
row.setMainEntitySymbol(subjectSymbol);
// needs better generics or have subject attribute on the parent class (DiseaseAnnotation)
if (primaryAnnotation instanceof AGMDiseaseAnnotation pAnnotation) {
row.setGeneticEntityID(pAnnotation.getSubject().getCurie());
row.setGeneticEntityName(pAnnotation.getSubject().getName());
row.setGeneticEntityType(pAnnotation.getSubject().getSubtype().getName());
row.setGeneticEntityID(pAnnotation.getDiseaseAnnotationSubject().getIdentifier());
row.setGeneticEntityName(pAnnotation.getDiseaseAnnotationSubject().getName());
row.setGeneticEntityType(pAnnotation.getDiseaseAnnotationSubject().getSubtype().getName());
List<org.alliancegenome.curation_api.model.entities.Gene> assertedGenes = pAnnotation.getAssertedGenes();
if (CollectionUtils.isNotEmpty(assertedGenes)) {
row.setAssertedGeneID(assertedGenes.stream().filter(gene -> !gene.getCurie().equals(subjectCurie))
.map(CurieAuditedObject::getCurie).collect(Collectors.joining("|")));
.map(SubmittedObject::getIdentifier).collect(Collectors.joining("|")));
row.setAssertedGeneName(assertedGenes.stream().filter(gene -> !gene.getCurie().equals(subjectCurie))
.map(gene -> gene.getGeneSymbol().getDisplayText()).collect(Collectors.joining("|")));
}
Expand All @@ -211,17 +211,17 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance
row.setGeneticEntityType("gene");
} else {
if (primaryAnnotation instanceof GeneDiseaseAnnotation pAnnotation) {
row.setGeneticEntityID(pAnnotation.getSubject().getCurie());
row.setGeneticEntityName(pAnnotation.getSubject().getGeneSymbol().getDisplayText());
row.setGeneticEntityID(pAnnotation.getDiseaseAnnotationSubject().getIdentifier());
row.setGeneticEntityName(pAnnotation.getDiseaseAnnotationSubject().getGeneSymbol().getDisplayText());
if (pAnnotation.getSgdStrainBackground() != null) {
row.setStrainBackgroundID(pAnnotation.getSgdStrainBackground().getCurie());
row.setStrainBackgroundName(pAnnotation.getSgdStrainBackground().getName());
}
row.setGeneticEntityType("gene");
}
if (primaryAnnotation instanceof AlleleDiseaseAnnotation pAnnotation) {
row.setGeneticEntityID(pAnnotation.getSubject().getCurie());
row.setGeneticEntityName(pAnnotation.getSubject().getAlleleSymbol().getDisplayText());
row.setGeneticEntityID(pAnnotation.getDiseaseAnnotationSubject().getIdentifier());
row.setGeneticEntityName(pAnnotation.getDiseaseAnnotationSubject().getAlleleSymbol().getDisplayText());
row.setGeneticEntityType("Allele");
}
}
Expand All @@ -245,7 +245,7 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance
row.setDateAssigned(primaryAnnotation.getDateCreated().toString());
}
if (CollectionUtils.isNotEmpty(primaryAnnotation.getWith())) {
row.setBasedOnID(primaryAnnotation.getWith().stream().map(CurieAuditedObject::getCurie).collect(Collectors.joining("|")));
row.setBasedOnID(primaryAnnotation.getWith().stream().map(SubmittedObject::getIdentifier).collect(Collectors.joining("|")));
row.setBasedOnName(primaryAnnotation.getWith().stream().map(gene -> gene.getGeneSymbol().getDisplayText()).collect(Collectors.joining("|")));
}
if (primaryAnnotation.getGeneticSex() != null) {
Expand All @@ -272,7 +272,7 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance
}
List<BiologicalEntity> diseaseGeneticModifiers = primaryAnnotation.getDiseaseGeneticModifiers();
if (CollectionUtils.isNotEmpty(diseaseGeneticModifiers)) {
row.setDiseaseGeneticModifierID(diseaseGeneticModifiers.stream().map(CurieAuditedObject::getCurie).collect(Collectors.joining("|")));
row.setDiseaseGeneticModifierID(diseaseGeneticModifiers.stream().map(SubmittedObject::getIdentifier).collect(Collectors.joining("|")));
StringJoiner joiner = new StringJoiner("|");
diseaseGeneticModifiers.forEach(entity -> {
if (entity instanceof org.alliancegenome.curation_api.model.entities.Gene gene) {
Expand Down
36 changes: 18 additions & 18 deletions ...n/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
import org.alliancegenome.api.entity.AlleleDiseaseAnnotationDocument;
import org.alliancegenome.api.entity.GeneDiseaseAnnotationDocument;
import org.alliancegenome.curation_api.model.entities.*;
import org.alliancegenome.curation_api.model.entities.base.CurieAuditedObject;
import org.alliancegenome.curation_api.model.entities.base.SubmittedObject;
import org.alliancegenome.curation_api.model.entities.ontology.DOTerm;
import org.alliancegenome.curation_api.model.entities.ontology.ECOTerm;
import org.alliancegenome.curation_api.model.entities.ontology.OntologyTerm;
Expand Down Expand Up @@ -120,7 +120,7 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationViaOrthol
// Group By:
// Disease, association type, Disease qualifiers, BasedOn Gene List (names),
Map<DOTerm, Map<VocabularyTerm, Map<String, Map<String, List<DiseaseAnnotation>>>>> groupedByAnnotations = diseaseAnnotations.stream()
.collect(groupingBy(DiseaseAnnotation::getObject,
.collect(groupingBy(DiseaseAnnotation::getDiseaseAnnotationObject,
groupingBy(DiseaseAnnotation::getRelation,
groupingBy(diseaseAnnotation -> {
List<VocabularyTerm> terms = diseaseAnnotation.getDiseaseQualifiers();
Expand Down Expand Up @@ -148,7 +148,7 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationViaOrthol
String generatedRelationString = getGeneratedRelationString(gdad.getRelation().getName(), diseaseAnnotation.getNegated());
gdad.setGeneratedRelationString(generatedRelationString);
gdad.setObject(diseaseTerm);
gdad.setParentSlimIDs(closureMap.get(diseaseAnnotation.getObject().getCurie()));
gdad.setParentSlimIDs(closureMap.get(diseaseAnnotation.getDiseaseAnnotationObject().getCurie()));

// create distinct and sorted list of ECOTerm objects
Set<ECOTerm> ecoTerms = diseaseAnnotations1.stream().map(DiseaseAnnotation::getEvidenceCodes).flatMap(Collection::stream).collect(Collectors.toSet());
Expand All @@ -163,7 +163,7 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationViaOrthol

// create distinct list of basedOn Genes
Set<Gene> basedOnGenes = diseaseAnnotations1.stream().map(DiseaseAnnotation::getWith).flatMap(Collection::stream).collect(Collectors.toSet());
List<String> ids = basedOnGenes.stream().map(CurieAuditedObject::getCurie).toList();
List<String> ids = basedOnGenes.stream().map(SubmittedObject::getIdentifier).toList();
gdad.setBasedOnGenes(new ArrayList<>(basedOnGenes));

gdad.addReference(diseaseAnnotation.getSingleReference());
Expand Down Expand Up @@ -207,7 +207,7 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationDocuments
addCreatedDiseaseAnnotationsImplicatedToMap(generatedAnnotation, gene);
}

String key = relation.getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
String key = relation.getName() + "_" + da.getDiseaseAnnotationObject().getName() + "_" + da.getNegated();

if (da.getDiseaseQualifiers() != null) {
key += "_" + da.getDiseaseQualifiers().stream().map(VocabularyTerm::getName).sorted().collect(Collectors.joining("_"));
Expand All @@ -227,8 +227,8 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationDocuments
gdad.setRelation(relation);
String generatedRelationString = getGeneratedRelationString(gdad.getRelation().getName(), da.getNegated());
gdad.setGeneratedRelationString(generatedRelationString);
gdad.setObject(da.getObject());
gdad.setParentSlimIDs(closureMap.get(da.getObject().getCurie()));
gdad.setObject(da.getDiseaseAnnotationObject());
gdad.setParentSlimIDs(closureMap.get(da.getDiseaseAnnotationObject().getCurie()));
lookup.put(key, gdad);
}

Expand Down Expand Up @@ -273,15 +273,15 @@ private DiseaseAnnotation createImplicatedDA(DiseaseAnnotation da) {
DiseaseAnnotation implicatedDA = null;
if (da instanceof AGMDiseaseAnnotation agmAnnotation) {
AGMDiseaseAnnotation agmAnno = new AGMDiseaseAnnotation();
agmAnno.setSubject(agmAnnotation.getSubject());
agmAnno.setDiseaseAnnotationSubject(agmAnnotation.getDiseaseAnnotationSubject());
implicatedDA = agmAnno;
} else if (da instanceof AlleleDiseaseAnnotation alleleAnno) {
AlleleDiseaseAnnotation alleleDA = new AlleleDiseaseAnnotation();
alleleDA.setSubject(alleleAnno.getSubject());
alleleDA.setDiseaseAnnotationSubject(alleleAnno.getDiseaseAnnotationSubject());
implicatedDA = alleleDA;
}
implicatedDA.setRelation(da.getRelation());
implicatedDA.setObject(da.getObject());
implicatedDA.setDiseaseAnnotationObject(da.getDiseaseAnnotationObject());
implicatedDA.setDiseaseQualifiers(da.getDiseaseQualifiers());
implicatedDA.setDiseaseQualifiers(da.getDiseaseQualifiers());
implicatedDA.setSingleReference(da.getSingleReference());
Expand Down Expand Up @@ -327,7 +327,7 @@ private List<AlleleDiseaseAnnotationDocument> createAlleleDiseaseAnnotationDocum
relation = da.getRelation();
}

String key = relation.getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
String key = relation.getName() + "_" + da.getDiseaseAnnotationObject().getName() + "_" + da.getNegated();
AlleleDiseaseAnnotationDocument adad = lookup.get(key);

if (adad == null) {
Expand All @@ -338,15 +338,15 @@ private List<AlleleDiseaseAnnotationDocument> createAlleleDiseaseAnnotationDocum
adad.setRelation(relation);
String generatedRelationString = getGeneratedRelationString(relation.getName(), da.getNegated());
adad.setGeneratedRelationString(generatedRelationString);
adad.setObject(da.getObject());
adad.setObject(da.getDiseaseAnnotationObject());
lookup.put(key, adad);
}
adad.setEvidenceCodes(da.getEvidenceCodes());
if (CollectionUtils.isNotEmpty(da.getDiseaseQualifiers())) {
Set<String> diseaseQualifiers = da.getDiseaseQualifiers().stream().map(term -> term.getName().replace("_", " ")).collect(Collectors.toSet());
adad.setDiseaseQualifiers(diseaseQualifiers);
}
adad.setParentSlimIDs(closureMap.get(da.getObject().getCurie()));
adad.setParentSlimIDs(closureMap.get(da.getDiseaseAnnotationObject().getCurie()));

// gdad.setDataProvider(da.getDataProvider());
adad.addReference(da.getSingleReference());
Expand Down Expand Up @@ -375,7 +375,7 @@ private List<AGMDiseaseAnnotationDocument> createAGMDiseaseAnnotationDocuments()
HashMap<String, AGMDiseaseAnnotationDocument> lookup = new HashMap<>();

for (DiseaseAnnotation da : entry.getValue().getRight()) {
String key = da.getRelation().getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
String key = da.getRelation().getName() + "_" + da.getDiseaseAnnotationObject().getName() + "_" + da.getNegated();
AGMDiseaseAnnotationDocument adad = lookup.get(key);

if (adad == null) {
Expand All @@ -384,7 +384,7 @@ private List<AGMDiseaseAnnotationDocument> createAGMDiseaseAnnotationDocuments()
adad.setSpeciesOrder(order);
adad.setSubject(entry.getValue().getLeft());
adad.setRelation(da.getRelation());
adad.setObject(da.getObject());
adad.setObject(da.getDiseaseAnnotationObject());
lookup.put(key, adad);
}
adad.setEvidenceCodes(da.getEvidenceCodes());
Expand All @@ -407,7 +407,7 @@ private void indexGenes() {
private void addDiseaseAnnotationsToLGlobalMap(List<GeneDiseaseAnnotation> geneDiseaseAnnotations) {
log.info("Filtered Genes: " + geneDiseaseAnnotations.size());
for (GeneDiseaseAnnotation da : geneDiseaseAnnotations) {
Gene gene = da.getSubject();
Gene gene = da.getDiseaseAnnotationSubject();
Pair<Gene, ArrayList<DiseaseAnnotation>> pair = geneMap.computeIfAbsent(gene.getCurie(), geneCurie -> Pair.of(gene, new ArrayList<>()));
pair.getRight().add(da);
}
Expand All @@ -423,7 +423,7 @@ private void indexAlleles() {
List<AlleleDiseaseAnnotation> alleleDiseaseAnnotations = alleleService.getFiltered();
log.info("Filtered Alleles: " + alleleDiseaseAnnotations.size());
for (AlleleDiseaseAnnotation da : alleleDiseaseAnnotations) {
Allele allele = da.getSubject();
Allele allele = da.getDiseaseAnnotationSubject();
Pair<Allele, ArrayList<DiseaseAnnotation>> allelePair = alleleMap.computeIfAbsent(allele.getCurie(), alleleCurie -> Pair.of(allele, new ArrayList<>()));
allelePair.getRight().add(da);

Expand Down Expand Up @@ -458,7 +458,7 @@ private void indexAGMs() {
log.info("Filtered AGMs: " + agmDiseaseAnnotations.size());

for (AGMDiseaseAnnotation da : agmDiseaseAnnotations) {
AffectedGenomicModel genomicModel = da.getSubject();
AffectedGenomicModel genomicModel = da.getDiseaseAnnotationSubject();
Pair<AffectedGenomicModel, ArrayList<DiseaseAnnotation>> allelePair = agmMap.computeIfAbsent(genomicModel.getCurie(), agmCurie -> Pair.of(genomicModel, new ArrayList<>()));
allelePair.getRight().add(da);

Expand Down
10 changes: 5 additions & 5 deletions ...va/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -110,17 +110,17 @@ public Map<Gene, List<DiseaseAnnotation>> getOrthologousGeneDiseaseAnnotations(M
DiseaseAnnotation gda = null;
if (focusDiseaseAnnotation instanceof AGMDiseaseAnnotation agmda) {
AGMDiseaseAnnotation da = new AGMDiseaseAnnotation();
da.setSubject(agmda.getSubject());
da.setDiseaseAnnotationSubject(agmda.getDiseaseAnnotationSubject());
gda = da;
}
if (focusDiseaseAnnotation instanceof AlleleDiseaseAnnotation ada) {
AlleleDiseaseAnnotation da = new AlleleDiseaseAnnotation();
da.setSubject(ada.getSubject());
da.setDiseaseAnnotationSubject(ada.getDiseaseAnnotationSubject());
gda = da;
}
if (focusDiseaseAnnotation instanceof GeneDiseaseAnnotation gdann) {
GeneDiseaseAnnotation da = new GeneDiseaseAnnotation();
da.setSubject(gdann.getSubject());
da.setDiseaseAnnotationSubject(gdann.getDiseaseAnnotationSubject());
gda = da;
}

Expand All @@ -136,7 +136,7 @@ public Map<Gene, List<DiseaseAnnotation>> getOrthologousGeneDiseaseAnnotations(M
gda.setDataProvider(dataProvider);
gda.setWith(List.of(geneGeneOrthology.getSubjectGene()));
gda.setSingleReference(allianceReference);
gda.setObject(focusDiseaseAnnotation.getObject());
gda.setDiseaseAnnotationObject(focusDiseaseAnnotation.getDiseaseAnnotationObject());
gda.setEvidenceCodes(List.of(ecoTermIEA));
gda.setDiseaseQualifiers(focusDiseaseAnnotation.getDiseaseQualifiers());
List<DiseaseAnnotation> geneAnnotations = newDAMap.computeIfAbsent(orthologousGene, k -> new ArrayList<>());
Expand All @@ -149,7 +149,7 @@ public Map<Gene, List<DiseaseAnnotation>> getOrthologousGeneDiseaseAnnotations(M
// consolidating DAs:
// by: disease, relation and disease qualifier
newDAMap.forEach((gene, diseaseAnnotations) -> {
Map<String, Map<String, Map<String, List<DiseaseAnnotation>>>> groupedDAs = diseaseAnnotations.stream().collect(groupingBy(da1 -> da1.getObject().getCurie(),
Map<String, Map<String, Map<String, List<DiseaseAnnotation>>>> groupedDAs = diseaseAnnotations.stream().collect(groupingBy(da1 -> da1.getDiseaseAnnotationObject().getCurie(),
groupingBy(da -> da.getRelation().getName(), groupingBy(da -> {
List<VocabularyTerm> diseaseQualifiers = da.getDiseaseQualifiers();
// allow for grouping by missing based-on genes
Expand Down
2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
<quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
<quarkus.platform.group-id>io.quarkus.platform</quarkus.platform.group-id>
<quarkus.platform.version>${quarkus.version}</quarkus.platform.version>
<curation.version>v0.30.0</curation.version>
<curation.version>v0.31.0</curation.version>
<!-- <curation.version>0.0.0-SNAPSHOT</curation.version> -->
</properties>
<dependencyManagement>
Expand Down

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