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Merged
oblodgett merged 3 commits into from
Mar 3, 2025
Merged

Scrum 4906 #1249

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eb701fb
Updated query to get gene
oblodgett Mar 3, 2025
2abe3ee
Updated jose
oblodgett Mar 3, 2025
7dcc2f2
Upgrade elastic search
oblodgett Mar 3, 2025
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2 changes: 1 addition & 1 deletion agr_api/pom.xml
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Expand Up @@ -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>
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3 changes: 1 addition & 2 deletions agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java
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Expand Up @@ -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;

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4 changes: 2 additions & 2 deletions agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Builder.java
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Expand Up @@ -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 {

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2 changes: 1 addition & 1 deletion agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java
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Expand Up @@ -2,7 +2,7 @@

import java.io.IOException;

import org.elasticsearch.common.xcontent.XContentBuilder;
import org.elasticsearch.xcontent.XContentBuilder;

public class Mapping extends Builder {

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5 changes: 2 additions & 3 deletions agr_java_core/src/main/java/org/alliancegenome/neo4j/repository/VariantRepository.java
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Expand Up @@ -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) {
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2 changes: 1 addition & 1 deletion .../src/main/java/org/alliancegenome/indexer/variant/es/managers/SourceDocumentCreation.java
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Expand Up @@ -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;
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2 changes: 1 addition & 1 deletion ...nt_indexer/src/main/java/org/alliancegenome/indexer/variant/scripts/TestLoadJsonFile.java
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Expand Up @@ -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;

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6 changes: 3 additions & 3 deletions pom.xml
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Expand Up @@ -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>
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