From eb701fb7e0533ef566f3260d57cc27680c415490 Mon Sep 17 00:00:00 2001 From: Olin Blodgett Date: Mon, 3 Mar 2025 15:36:00 -0500 Subject: [PATCH 1/3] Updated query to get gene --- .../alliancegenome/neo4j/repository/VariantRepository.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) 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 index 2e5f770ad..621af28f8 100644 --- 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 @@ -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 variants = query(query, map); for (Variant a : variants) { From 2abe3eef33968cf0b0c48aa79bc7c58564a16a01 Mon Sep 17 00:00:00 2001 From: Olin Blodgett Date: Mon, 3 Mar 2025 15:37:35 -0500 Subject: [PATCH 2/3] Updated jose --- agr_api/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/agr_api/pom.xml b/agr_api/pom.xml index afdc66ced..a1898e832 100644 --- a/agr_api/pom.xml +++ b/agr_api/pom.xml @@ -25,7 +25,7 @@ org.bitbucket.b_c jose4j - 0.9.3 + 0.9.4 From 7dcc2f29986ba9bc02d706aa12fb8cb88738e7b5 Mon Sep 17 00:00:00 2001 From: Olin Blodgett Date: Mon, 3 Mar 2025 15:43:03 -0500 Subject: [PATCH 3/3] Upgrade elastic search --- .../java/org/alliancegenome/indexer/indexers/Indexer.java | 3 +-- .../org/alliancegenome/es/index/site/schema/Builder.java | 4 ++-- .../org/alliancegenome/es/index/site/schema/Mapping.java | 2 +- .../indexer/variant/es/managers/SourceDocumentCreation.java | 2 +- .../indexer/variant/scripts/TestLoadJsonFile.java | 2 +- pom.xml | 6 +++--- 6 files changed, 9 insertions(+), 10 deletions(-) diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java index a1e2561d7..bd7098a77 100644 --- a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java +++ b/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; diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Builder.java b/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Builder.java index f9ba707a5..17ca083c1 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Builder.java +++ b/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 { diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java b/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java index 553e8b9ca..0f2af72cd 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java +++ b/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 { diff --git a/agr_variant_indexer/src/main/java/org/alliancegenome/indexer/variant/es/managers/SourceDocumentCreation.java b/agr_variant_indexer/src/main/java/org/alliancegenome/indexer/variant/es/managers/SourceDocumentCreation.java index b258d6d55..c278dec27 100644 --- a/agr_variant_indexer/src/main/java/org/alliancegenome/indexer/variant/es/managers/SourceDocumentCreation.java +++ b/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; diff --git a/agr_variant_indexer/src/main/java/org/alliancegenome/indexer/variant/scripts/TestLoadJsonFile.java b/agr_variant_indexer/src/main/java/org/alliancegenome/indexer/variant/scripts/TestLoadJsonFile.java index 2cc7f3b77..94e735e90 100644 --- a/agr_variant_indexer/src/main/java/org/alliancegenome/indexer/variant/scripts/TestLoadJsonFile.java +++ b/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; diff --git a/pom.xml b/pom.xml index 9b33c6629..7df6b67b9 100644 --- a/pom.xml +++ b/pom.xml @@ -58,17 +58,17 @@ org.elasticsearch elasticsearch - 7.14.2 + 7.17.14 org.elasticsearch elasticsearch-core - 7.14.2 + 7.17.14 org.elasticsearch.client elasticsearch-rest-high-level-client - 7.14.2 + 7.17.14 com.github.mmazi