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TASK-4437 - Update general dependencies from dependabot (security alerts) #681

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merged 3 commits into from
Jan 23, 2024
Merged

TASK-4437 - Update general dependencies from dependabot (security alerts) #681

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15b3d59
pom: Some security version updates #TASK-4437
juanfeSanahuja Dec 11, 2023
9f1f78e
Merge branch 'develop' into TASK-4437
juanfeSanahuja Jan 12, 2024
68a3c83
pom: Restore htsjdk version #TASK-4437
juanfeSanahuja Jan 15, 2024
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4 changes: 2 additions & 2 deletions cellbase-lib/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -137,10 +137,10 @@
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</dependency>
<dependency>
<!-- <dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
</dependency>
</dependency>-->
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-api</artifactId>
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3 changes: 2 additions & 1 deletion cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/MetaMongoDBAdaptor.java
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Expand Up @@ -16,14 +16,15 @@

package org.opencb.cellbase.lib.impl.core;


import com.fasterxml.jackson.databind.ObjectMapper;
import com.mongodb.ReadPreference;
import com.mongodb.WriteConcern;
import com.mongodb.client.model.Filters;
import com.mongodb.client.model.Updates;
import org.bson.BsonDocument;
import org.bson.Document;
import org.bson.conversions.Bson;
import org.codehaus.jackson.map.ObjectMapper;
import org.opencb.cellbase.core.api.key.ApiKeyStats;
import org.opencb.cellbase.core.api.query.AbstractQuery;
import org.opencb.cellbase.core.api.query.ProjectionQueryOptions;
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15 changes: 8 additions & 7 deletions pom.xml
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Expand Up @@ -26,15 +26,17 @@
<java-common-libs.version>4.13.0-SNAPSHOT</java-common-libs.version>
<biodata.version>2.13.0-SNAPSHOT</biodata.version>
<bionetdb.version>0.1.0</bionetdb.version>
<jackson.version>2.11.4</jackson.version>
<jackson-asl.version>1.9.13</jackson-asl.version>
<jetty.version>9.4.51.v20230217</jetty.version>

<jackson.version>2.14.3</jackson.version>
<commons-lang3.version>3.14.0</commons-lang3.version>
<slf4j.version>1.7.36</slf4j.version>

<jersey.version>2.30.1</jersey.version>
<slf4j.version>1.7.32</slf4j.version>
<log4j.version>2.17.2</log4j.version>
<junit.platform.version>1.5.2</junit.platform.version>
<junit.jupiter.version>5.5.2</junit.jupiter.version>
<jacoco.version>0.8.8</jacoco.version>
<jetty.version>9.4.17.v20190418</jetty.version>
<jjwt.version>0.11.5</jjwt.version>
<swagger-annotations.version>1.6.5</swagger-annotations.version>
<javax.servlet-api.version>3.1.0</javax.servlet-api.version>
Expand All @@ -50,7 +52,6 @@
<grpc.version>1.48.0</grpc.version>
<commons-lang.version>2.4</commons-lang.version>
<commons-io.version>2.4</commons-io.version>
<commons-lang3.version>3.12.0</commons-lang3.version>
<jakarta.ws.rs-api.version>2.1.6</jakarta.ws.rs-api.version>
<commons-collections4.version>4.4</commons-collections4.version>
<jcommander.version>1.69</jcommander.version>
Expand Down Expand Up @@ -412,11 +413,11 @@
<artifactId>swagger-annotations</artifactId>
<version>${swagger-annotations.version}</version>
</dependency>
<dependency>
<!-- <dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>${jackson-asl.version}</version>
</dependency>
</dependency>-->
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-jackson</artifactId>
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