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Merge pull request #671 from opencb/TASK-2095
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TASK-2095 - Duplicated libraries at opencga/build/libs
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@juanfeSanahuja
juanfeSanahuja authored Nov 15, 2023
2 parents baa3631 + 35e2c3e commit a5ce842
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Showing 6 changed files with 675 additions and 114 deletions.
118 changes: 114 additions & 4 deletions cellbase-app/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,25 +28,135 @@
<artifactId>cellbase-server</artifactId>
<version>${project.parent.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-tools</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-models</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase-lib</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-mongodb</artifactId>
<exclusions>
<exclusion>
<artifactId>slf4j-simple</artifactId>
<groupId>org.slf4j</groupId>
</exclusion>
</exclusions>
</dependency>

<!-- General dependencies -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-api</artifactId>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>jakarta.ws.rs</groupId>
<artifactId>jakarta.ws.rs-api</artifactId>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</dependency>
<dependency>
<groupId>org.rocksdb</groupId>
<artifactId>rocksdbjni</artifactId>
</dependency>
<dependency>
<groupId>com.beust</groupId>
<artifactId>jcommander</artifactId>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>bson</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util-ajax</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</dependency>

<!-- Test dependencies -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<scope>test</scope>
</dependency>

<!--TODO Review -->
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-engine</artifactId>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-engine</artifactId>
<scope>test</scope>
</dependency>


</dependencies>

<build>
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86 changes: 75 additions & 11 deletions cellbase-client/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,17 +19,26 @@
<artifactId>cellbase-core</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-client</artifactId>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-models</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.inject</groupId>
<artifactId>jersey-hk2</artifactId>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet</artifactId>
<scope>test</scope>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
</dependency>

<!-- General dependencies -->
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-client</artifactId>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
Expand All @@ -42,8 +51,49 @@
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-engine</artifactId>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>jakarta.ws.rs</groupId>
<artifactId>jakarta.ws.rs-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
</dependency>

<!-- Test dependencies -->
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
<scope>test</scope>
</dependency>

<!--TODO Review -->
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<scope>test</scope>
</dependency>
<dependency>
Expand All @@ -52,9 +102,23 @@
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<groupId>org.glassfish.jersey.inject</groupId>
<artifactId>jersey-hk2</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-engine</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</dependency>
</dependencies>
</project>

73 changes: 62 additions & 11 deletions cellbase-core/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,24 @@
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-tools</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-models</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>

<!-- General dependencies -->
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
Expand All @@ -30,30 +47,56 @@
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-api</artifactId>
<version>${jwt.version}</version>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-impl</artifactId>
<version>${jwt.version}</version>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-jackson</artifactId>
<version>${jwt.version}</version>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
</dependency>

<!-- Test dependencies -->
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<scope>test</scope>
</dependency>

<!--TODO Review -->
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-engine</artifactId>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<scope>test</scope>
</dependency>
<dependency>
Expand All @@ -62,10 +105,18 @@
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</dependency>
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-engine</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-jackson</artifactId>
</dependency>
</dependencies>

<build>
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