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pom: Added develop dependencies to review #TASK-2095
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@juanfeSanahuja
juanfeSanahuja committed Oct 19, 2023
1 parent fa4e8a5 commit d4bbc30
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Showing 14 changed files with 283 additions and 86 deletions.
46 changes: 8 additions & 38 deletions opencga-analysis/pom.xml
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Expand Up @@ -52,10 +52,6 @@
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
Expand All @@ -73,11 +69,6 @@
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<!-- Need dependency for running hadoop tests. -->
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>${opencga-storage-hadoop-deps.artifactId}</artifactId>
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<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-mongodb</artifactId>
Expand Down Expand Up @@ -242,21 +229,17 @@
<artifactId>hamcrest-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>
<!-- RGA test dependencies -->
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-test-framework</artifactId>
</dependency>
<!-- /RGA -->

<!-- TODO Review -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

<build>
Expand Down Expand Up @@ -292,20 +275,7 @@
</ignoredUsedUndeclaredDependency>
</ignoredUsedUndeclaredDependencies>
<ignoredUnusedDeclaredDependencies>
<ignoredUnusedDeclaredDependency>
com.google.code.findbugs:annotations:jar:${findbugs-annotations.version}
</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>
javax.servlet:javax.servlet-api*
</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>
org.opencb.opencga:opencga-storage-hadoop-deps-*
</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>
org.apache.solr:*
</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>org.opencb.opencga:opencga-clinical*
</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
</ignoredUnusedDeclaredDependencies>
</configuration>
</execution>
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40 changes: 30 additions & 10 deletions opencga-app/pom.xml
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Expand Up @@ -42,10 +42,6 @@
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-catalog</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-analysis</artifactId>
Expand All @@ -64,10 +60,6 @@
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-client</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-app</artifactId>
Expand All @@ -94,6 +86,14 @@
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-mongodb</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-catalog</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-solr</artifactId>
Expand Down Expand Up @@ -227,6 +227,27 @@
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>

<!-- TODO Review -->
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-catalog</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.jline</groupId>
<artifactId>jline-terminal-jna</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>


</dependencies>

<build>
Expand Down Expand Up @@ -581,8 +602,7 @@
<configuration>
<failOnWarning>true</failOnWarning>
<ignoredUnusedDeclaredDependencies>
<ignoredUnusedDeclaredDependency>org.opencb.opencga:opencga-storage-hadoop-*</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>jakarta.ws.rs:jakarta.ws.rs-api:jar:2.1.6</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
</ignoredUnusedDeclaredDependencies>
</configuration>
</execution>
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36 changes: 29 additions & 7 deletions opencga-catalog/pom.xml
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Expand Up @@ -168,10 +168,6 @@
<groupId>org.mongodb</groupId>
<artifactId>bson</artifactId>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure-client-runtime</artifactId>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure-client-authentication</artifactId>
Expand Down Expand Up @@ -211,6 +207,34 @@
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>

<!-- TODO Review -->
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure-client-runtime</artifactId>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure</artifactId>
</dependency>
<dependency>
<groupId>io.fabric8</groupId>
<artifactId>kubernetes-client</artifactId>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure-batch</artifactId>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-jackson</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-test-framework</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

<build>
Expand Down Expand Up @@ -274,9 +298,7 @@
</ignoredUsedUndeclaredDependency>
</ignoredUsedUndeclaredDependencies>
<ignoredUnusedDeclaredDependencies>
<ignoredUnusedDeclaredDependency>
com.google.code.findbugs:annotations:jar:${findbugs-annotations.version}
</ignoredUnusedDeclaredDependency>
<ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
</ignoredUnusedDeclaredDependencies>
</configuration>
</execution>
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22 changes: 22 additions & 0 deletions opencga-client/pom.xml
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Expand Up @@ -138,6 +138,28 @@
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>

<!-- TODO Review -->
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-impl</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.inject</groupId>
<artifactId>jersey-hk2</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-jackson</artifactId>
<scope>runtime</scope>
</dependency>

</dependencies>

<build>
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48 changes: 48 additions & 0 deletions opencga-clinical/pom.xml
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Expand Up @@ -12,6 +12,54 @@

<artifactId>opencga-clinical</artifactId>
<packaging>jar</packaging>

<dependencies>
<!-- TODO Review -->
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-test-framework</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-catalog</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-catalog</artifactId>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-solrj</artifactId>
</dependency>

</dependencies>
<build>
<resources>
<resource>
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15 changes: 11 additions & 4 deletions opencga-core/pom.xml
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Expand Up @@ -54,10 +54,6 @@
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase-client</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.oskar</groupId>
<artifactId>oskar-analysis</artifactId>
Expand Down Expand Up @@ -130,6 +126,17 @@
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>

<!-- TODO Review -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>

</dependencies>

<build>
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11 changes: 11 additions & 0 deletions opencga-master/pom.xml
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Expand Up @@ -157,6 +157,17 @@
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>

<!-- TODO Review -->
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-json-jackson</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
</dependency>

</dependencies>

<build>
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27 changes: 27 additions & 0 deletions opencga-server/pom.xml
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Expand Up @@ -215,6 +215,33 @@
<artifactId>junit</artifactId>
</dependency>


<!-- TODO Review -->
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-json-jackson</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>${opencga-storage-hadoop-deps.artifactId}</artifactId>
<classifier>shaded</classifier>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-hadoop-core</artifactId>
</dependency>
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-all</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.inject</groupId>
<artifactId>jersey-hk2</artifactId>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet</artifactId>
</dependency>
</dependencies>

<build>
Expand Down
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