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Pom: several fixes and improvements
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@imedina
imedina committed Oct 27, 2020
1 parent 2e15ceb commit 94469ad
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Showing 4 changed files with 66 additions and 77 deletions.
14 changes: 5 additions & 9 deletions bionetdb-app/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,22 +25,18 @@
<groupId>org.opencb.bionetdb</groupId>
<artifactId>bionetdb-lib</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.bionetdb</groupId>
<artifactId>bionetdb-server</artifactId>
<version>${bionetdb.version}</version>
<scope>provided</scope>
<type>war</type>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
</dependency>
<!--<dependency>-->
<!--<groupId>org.sbml.libsbml</groupId>-->
<!--<artifactId>libsbml</artifactId>-->
<!--<systemPath>${basedir}/app/ext-libs/libsbmlj.jar</systemPath>-->
<!--</dependency>-->


<dependency>
<groupId>com.beust</groupId>
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32 changes: 8 additions & 24 deletions bionetdb-core/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,15 +16,6 @@
<packaging>jar</packaging>

<dependencies>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-tools</artifactId>
<version>${biodata.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
Expand All @@ -33,6 +24,14 @@
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
</dependency>
<!-- <dependency>-->
<!-- <groupId>org.opencb.biodata</groupId>-->
<!-- <artifactId>biodata-tools</artifactId>-->
<!-- </dependency>-->

<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
Expand All @@ -42,25 +41,10 @@
<groupId>org.biopax.paxtools</groupId>
<artifactId>paxtools-core</artifactId>
</dependency>
<!--<dependency>-->
<!--<groupId>org.sbml.libsbml</groupId>-->
<!--<artifactId>libsbml</artifactId>-->
<!--<systemPath>${basedir}/../bionetdb-app/app/ext-libs/libsbmlj.jar</systemPath>-->
<!--</dependency>-->
<!--
<dependency>
<groupId>psidev.psi.mi</groupId>
<artifactId>psimitab</artifactId>
</dependency>
-->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
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27 changes: 11 additions & 16 deletions bionetdb-lib/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,15 +20,6 @@
<groupId>org.opencb.bionetdb</groupId>
<artifactId>bionetdb-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-tools</artifactId>
<version>${biodata.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
Expand All @@ -37,21 +28,29 @@
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-tools</artifactId>
</dependency>

<dependency>
<groupId>org.neo4j</groupId>
<artifactId>neo4j</artifactId>
<version>4.1.3</version>
<version>${neo4j.version}</version>
</dependency>
<dependency>
<groupId>org.neo4j</groupId>
<artifactId>neo4j-kernel</artifactId>
<version>4.1.3</version>
<version>${neo4j.version}</version>
</dependency>
<dependency>
<groupId>org.neo4j.driver</groupId>
<artifactId>neo4j-java-driver</artifactId>
<version>4.1.1</version>
<version>${neo4j-driver.version}</version>
</dependency>
<dependency>
<groupId>org.biopax.paxtools</groupId>
Expand All @@ -65,10 +64,6 @@
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
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70 changes: 42 additions & 28 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,12 @@
<properties>
<bionetdb.version>0.2.0-SNAPSHOT</bionetdb.version>
<java.version>1.8</java.version>
<neo4j.version>4.1.3</neo4j.version>
<neo4j-driver.version>4.1.1</neo4j-driver.version>
<java-common-libs.version>4.0.4-SNAPSHOT</java-common-libs.version>
<biodata.version>2.1.0-SNAPSHOT</biodata.version>
<slf4j.version>1.7.25</slf4j.version>
<log4j2.version>2.13.3</log4j2.version>
<jackson.version>2.10.1</jackson.version>
<jersey.version>2.29.1</jersey.version>
<junit.jupiter.version>5.5.2</junit.jupiter.version>
Expand Down Expand Up @@ -85,6 +89,16 @@
<artifactId>bionetdb-lib</artifactId>
<version>${bionetdb.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
Expand All @@ -99,43 +113,48 @@
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-lite</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
</exclusion>
<exclusion>
<groupId>org.mortbay.jetty</groupId>
<artifactId>servlet-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
<version>${java-common-libs.version}</version>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-tools</artifactId>
<version>${biodata.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.avro</groupId>
<artifactId>avro-ipc</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
</exclusion>
</exclusions>
</dependency>

<!-- General dependencies -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.biopax.paxtools</groupId>
<artifactId>paxtools-core</artifactId>
<version>4.3.1</version>
</dependency>
<!--<dependency>-->
<!--<groupId>org.sbml.libsbml</groupId>-->
<!--<artifactId>libsbml</artifactId>-->
<!--<version>5.11.4</version>-->
<!--<scope>system</scope>-->
<!--<systemPath>${basedir}/bionetdb-app/app/ext-libs/libsbmlj.jar</systemPath>-->
<!--</dependency>-->
<!--
<dependency>
<groupId>psidev.psi.mi</groupId>
<artifactId>psimitab</artifactId>
<version>1.8.5</version>
</dependency>
-->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
Expand Down Expand Up @@ -166,11 +185,6 @@
<artifactId>jersey-hk2</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.5</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
Expand Down Expand Up @@ -206,7 +220,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.6.0</version>
<version>3.8.1</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
Expand Down

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