Merge branch 'stage' into add_checkstyle

alliance-genome · Jul 11, 2024 · 21a4b47 · 21a4b47
2 parents 970b35e + 5198e53
commit 21a4b47
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Showing 4 changed files with 17 additions and 9 deletions.
diff --git a/...ava/org/alliancegenome/indexer/indexers/curation/service/AGMDiseaseAnnotationService.java b/...ava/org/alliancegenome/indexer/indexers/curation/service/AGMDiseaseAnnotationService.java
@@ -43,7 +43,7 @@ public List<AGMDiseaseAnnotation> getFiltered() {
 			SearchResponse<AGMDiseaseAnnotation> response = agmApi.findForPublic(page, batchSize, params);
 
 			for (AGMDiseaseAnnotation da: response.getResults()) {
-				if (isValidEntity(allModelIDs, da.getDiseaseAnnotationSubject().getIdentifier()) || hasNoObsoletedOrInternalEntities(da)) {
+				if (isValidEntity(allModelIDs, da.getDiseaseAnnotationSubject().getIdentifier()) && hasNoObsoletedOrInternalEntities(da)) {
 					if (hasValidEntities(da, allGeneIDs, allAlleleIds, allModelIDs)) {
 						if (da.getInferredGene() != null && da.getInferredGene().getConstructGenomicEntityAssociations() != null) {
 							da.getInferredGene().getConstructGenomicEntityAssociations().clear();

diff --git a/.../org/alliancegenome/indexer/indexers/curation/service/AlleleDiseaseAnnotationService.java b/.../org/alliancegenome/indexer/indexers/curation/service/AlleleDiseaseAnnotationService.java
@@ -35,13 +35,13 @@ public List<AlleleDiseaseAnnotation> getFiltered() {
 		HashMap<String, Object> params = new HashMap<>();
 		params.put("internal", false);
 		params.put("obsolete", false);
-		// params.put("diseaseAnnotationSubject.modEntityId", "RGD:5144089");
+		//params.put("diseaseAnnotationSubject.modEntityId", "WB:WBVar00266693");
 
 		do {
 			SearchResponse<AlleleDiseaseAnnotation> response = alleleApi.findForPublic(page, batchSize, params);
 
 			for (AlleleDiseaseAnnotation da: response.getResults()) {
-				if (isValidEntity(allAlleleIds, da.getDiseaseAnnotationSubject().getIdentifier()) || hasNoObsoletedOrInternalEntities(da)) {
+				if (isValidEntity(allAlleleIds, da.getDiseaseAnnotationSubject().getIdentifier()) && hasNoObsoletedOrInternalEntities(da)) {
 					if (hasValidEntities(da, allGeneIDs, allAlleleIds, allModelIDs)) {
 						if (da.getInferredGene() != null && da.getInferredGene().getConstructGenomicEntityAssociations() != null) {
 							da.getInferredGene().getConstructGenomicEntityAssociations().clear();

diff --git a/...va/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java b/...va/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java
@@ -63,7 +63,7 @@ public List<GeneDiseaseAnnotation> getFiltered() {
 		do {
 			SearchResponse<GeneDiseaseAnnotation> response = geneApi.findForPublic(page, batchSize, params);
 			for (GeneDiseaseAnnotation da : response.getResults()) {
-				if (isValidEntity(allGeneIDs, da.getDiseaseAnnotationSubject().getIdentifier()) || hasNoObsoletedOrInternalEntities(da)) {
+				if (isValidEntity(allGeneIDs, da.getDiseaseAnnotationSubject().getIdentifier()) && hasNoObsoletedOrInternalEntities(da)) {
 					if (hasValidGeneticModifiers(da, allGeneIDs, allAlleleIds, allModelIDs)) {
 						ret.add(da);
 					}

diff --git a/agr_java_core/src/main/java/org/alliancegenome/neo4j/repository/VariantRepository.java b/agr_java_core/src/main/java/org/alliancegenome/neo4j/repository/VariantRepository.java
@@ -9,7 +9,9 @@
 import java.util.stream.StreamSupport;
 
 import org.alliancegenome.neo4j.entity.node.Allele;
+import org.alliancegenome.neo4j.entity.node.Transcript;
 import org.alliancegenome.neo4j.entity.node.Variant;
+import org.apache.commons.collections4.CollectionUtils;
 import org.neo4j.ogm.model.Result;
 
 public class VariantRepository extends Neo4jRepository<Variant> {
@@ -44,7 +46,7 @@ public List<Variant> getVariantsOfAllele(String id) {
 		query += " OPTIONAL MATCH p2=(variant:Variant)<-[:COMPUTED_GENE]-(:Gene)-[:ASSOCIATION]->(:GenomicLocation)";
 		query += " WITH p1, collect(p2) AS p2, locs, consequences, synonyms, transcripts, transcriptConsequences, notes, crossRefs, pubs";
 		query += " RETURN p1, p2, locs, consequences, synonyms, transcripts, transcriptConsequences, notes, crossRefs, pubs ";
-		
+
 		Iterable<Variant> alleles = query(query, map);
 		return StreamSupport.stream(alleles.spliterator(), false)
 				.collect(Collectors.toList());
@@ -60,20 +62,26 @@ public Variant getVariant(String variantID) {
 		query += " WHERE variant.primaryKey = $" + paramName;
 		query += " OPTIONAL MATCH consequence=(:GenomicLocation)--(variant:Variant)-[:ASSOCIATION]->(:TranscriptLevelConsequence)"
 				+ "<-[:ASSOCIATION]-(t:Transcript)<-[:TRANSCRIPT_TYPE]-(:SOTerm)";
-		query += " OPTIONAL MATCH gene=(t:Transcript)-[:TRANSCRIPT]-(:Gene)--(:GenomicLocation)";
+		query += " OPTIONAL MATCH gene=(t:Transcript)-[:TRANSCRIPT]-(ge:Gene)--(:GenomicLocation)";
+		query += " OPTIONAL MATCH geneSpecies=(ge:Gene)--(:Species)";
 		query += " OPTIONAL MATCH transcriptLocation=(t:Transcript)-[:ASSOCIATION]-(:GenomicLocation)";
 		query += " OPTIONAL MATCH exons=(:GenomicLocation)--(:Exon)-[:EXON]->(t:Transcript)";
-		query += " RETURN p1, consequence, gene, exons, transcriptLocation ";
+		query += " RETURN p1, consequence, gene, geneSpecies, exons, transcriptLocation ";
 
 		Iterable<Variant> variants = query(query, map);
 		for (Variant a : variants) {
 			if (a.getPrimaryKey().equals(variantID)) {
+				List<Transcript> list = a.getTranscriptList();
+				if (CollectionUtils.isNotEmpty(list)) {
+					a.setSpecies(list.get(0).getGene().getSpecies());
+					a.setGene(list.get(0).getGene());
+				}
 				return a;
 			}
 		}
 		return null;
 	}
-	
+
 	public List<String> getAllVariantKeys() {
 		String query = "MATCH (v:Variant)-[:VARIATION]-(a:Allele)-[:FROM_SPECIES]-(q:Species) RETURN v.primaryKey";
 
@@ -88,7 +96,7 @@ public List<String> getAllVariantKeys() {
 		}
 		return list;
 	}
-	
+
 	public List<Allele> getAllelesOfVariant(String variantID) {
 		String query = "";
 		query += " MATCH p1=(a:Allele)<-[:VARIATION]-(variant:Variant)--(soTerm:SOTerm) ";