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client: generate clients after merging develop, #TASK-4158
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@jtarraga
jtarraga committed Nov 16, 2023
2 parents 4a54bc0 + d210409 commit 7757fab
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Showing 92 changed files with 2,509 additions and 609 deletions.
177 changes: 163 additions & 14 deletions opencga-analysis/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,18 +42,19 @@
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
</dependency>

<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-catalog</artifactId>
<version>${project.parent.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
<version>${project.parent.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
Expand All @@ -68,18 +69,9 @@
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<!-- Need dependency for running hadoop tests. -->
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.1.0</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>${opencga-storage-hadoop-deps.artifactId}</artifactId>
<version>${project.parent.version}</version>
<classifier>shaded</classifier>
<scope>test</scope>
</dependency>
Expand All @@ -106,16 +98,148 @@
<version>${project.parent.version}</version>
<scope>compile</scope>
</dependency>
<!-- RGA test dependencies -->
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-mongodb</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-solr</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-models</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-tools</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase-core</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase-client</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.oskar</groupId>
<artifactId>oskar-analysis</artifactId>
</dependency>
<dependency>
<groupId>org.opencb.ga4gh</groupId>
<artifactId>ga4gh</artifactId>
<exclusions>
<exclusion>
<groupId>arg.apache.avro</groupId>
<artifactId>avro-ipc</artifactId>
</exclusion>
</exclusions>
</dependency>

<!-- Added dependencies -->
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</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>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</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-databind</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-solrj</artifactId>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>mongodb-driver-core</artifactId>
</dependency>
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-api</artifactId>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>annotations</artifactId>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
<scope>test</scope>
</dependency>
<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 All @@ -132,6 +256,31 @@
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.6.0</version>
<executions>
<execution>
<id>analyze</id>
<goals>
<goal>analyze-only</goal>
</goals>
<configuration>
<failOnWarning>true</failOnWarning>
<!-- This plugin is having a weird issue with biodata libraries. It fails if biodata is declared before. -->
<ignoredUsedUndeclaredDependencies>
<ignoredUsedUndeclaredDependency>
com.google.code.findbugs:jsr305:jar:3.0.2
</ignoredUsedUndeclaredDependency>
</ignoredUsedUndeclaredDependencies>
<ignoredUnusedDeclaredDependencies>
<ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
</ignoredUnusedDeclaredDependencies>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

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