Merge pull request #1249 from alliance-genome/SCRUM-4906

Scrum 4906

Author: oblodgett

agr_api/pom.xml

@@ -25,7 +25,7 @@
 		<dependency>
 			<groupId>org.bitbucket.b_c</groupId>
 			<artifactId>jose4j</artifactId>
-			<version>0.9.3</version>
+			<version>0.9.4</version>
 		</dependency>
 
 		<dependency>

agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java

@@ -31,13 +31,12 @@
 import org.elasticsearch.client.RestHighLevelClient;
 import org.elasticsearch.common.unit.ByteSizeUnit;
 import org.elasticsearch.common.unit.ByteSizeValue;
-import org.elasticsearch.common.xcontent.XContentType;
 import org.elasticsearch.core.TimeValue;
+import org.elasticsearch.xcontent.XContentType;
 
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 
 import lombok.extern.slf4j.Slf4j;
 

agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Builder.java

@@ -2,8 +2,8 @@
 
 import java.io.IOException;
 
-import org.elasticsearch.common.xcontent.XContentBuilder;
-import org.elasticsearch.common.xcontent.XContentFactory;
+import org.elasticsearch.xcontent.XContentBuilder;
+import org.elasticsearch.xcontent.XContentFactory;
 
 public abstract class Builder {
 

agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java

@@ -2,7 +2,7 @@
 
 import java.io.IOException;
 
-import org.elasticsearch.common.xcontent.XContentBuilder;
+import org.elasticsearch.xcontent.XContentBuilder;
 
 public class Mapping extends Builder {
 

agr_java_core/src/main/java/org/alliancegenome/neo4j/repository/VariantRepository.java

@@ -62,11 +62,10 @@ 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]-(ge:Gene)--(:GenomicLocation)";
-		query += " OPTIONAL MATCH geneSpecies=(t:Transcript)-[:TRANSCRIPT]-(ge:Gene)--(:Species)";
+		query += " OPTIONAL MATCH gene=(t:Transcript)-[:TRANSCRIPT]-(ge:Gene)--(:GenomicLocation|Species)";
 		query += " OPTIONAL MATCH transcriptLocation=(t:Transcript)-[:ASSOCIATION]-(:GenomicLocation)";
 		query += " OPTIONAL MATCH exons=(:GenomicLocation)--(:Exon)-[:EXON]->(t:Transcript)";
-		query += " RETURN p1, consequence, gene, geneSpecies, exons, transcriptLocation ";
+		query += " RETURN p1, consequence, gene, exons, transcriptLocation ";
 
 		Iterable<Variant> variants = query(query, map);
 		for (Variant a : variants) {

agr_variant_indexer/src/main/java/org/alliancegenome/indexer/variant/es/managers/SourceDocumentCreation.java

@@ -26,8 +26,8 @@
 import org.elasticsearch.client.RestHighLevelClient;
 import org.elasticsearch.common.unit.ByteSizeUnit;
 import org.elasticsearch.common.unit.ByteSizeValue;
-import org.elasticsearch.common.xcontent.XContentType;
 import org.elasticsearch.core.TimeValue;
+import org.elasticsearch.xcontent.XContentType;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.MapperFeature;

agr_variant_indexer/src/main/java/org/alliancegenome/indexer/variant/scripts/TestLoadJsonFile.java

@@ -25,8 +25,8 @@
 import org.elasticsearch.client.RestHighLevelClient;
 import org.elasticsearch.common.unit.ByteSizeUnit;
 import org.elasticsearch.common.unit.ByteSizeValue;
-import org.elasticsearch.common.xcontent.XContentType;
 import org.elasticsearch.core.TimeValue;
+import org.elasticsearch.xcontent.XContentType;
 
 import lombok.extern.slf4j.Slf4j;
 

pom.xml

@@ -58,17 +58,17 @@
 			<dependency>
 				<groupId>org.elasticsearch</groupId>
 				<artifactId>elasticsearch</artifactId>
-				<version>7.14.2</version>
+				<version>7.17.14</version>
 			</dependency>
 			<dependency>
 				<groupId>org.elasticsearch</groupId>
 				<artifactId>elasticsearch-core</artifactId>
-				<version>7.14.2</version>
+				<version>7.17.14</version>
 			</dependency>
 			<dependency>
 				<groupId>org.elasticsearch.client</groupId>
 				<artifactId>elasticsearch-rest-high-level-client</artifactId>
-				<version>7.14.2</version>
+				<version>7.17.14</version>
 			</dependency>
 			<dependency>
 				<groupId>com.github.mmazi</groupId>