Revision 11aa00fb2e8f46e8ff01cc735bf754c1ccb0a91e authored by Charles Overbeck on 20 March 2019, 22:21:15 UTC, committed by GitHub on 20 March 2019, 22:21:15 UTC
#2092 Found when verifying #2092.
1 parent 09803ef
pom.xml
<!--
~ Copyright 2017 OICR
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>io.dockstore</groupId>
<artifactId>dockstore</artifactId>
<version>1.6.0-rc.0-SNAPSHOT</version>
<packaging>pom</packaging>
<name>dockstore</name>
<description>dockstore parent POM</description>
<url>https://github.com/CancerCollaboratory/dockstore</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<github.url>scm:git:git@github.com:ga4gh/dockstore.git</github.url>
<dropwizard.version>1.3.7</dropwizard.version>
<swagger-annotations-version>1.5.19</swagger-annotations-version>
<openapi-annotations-version>2.0.6</openapi-annotations-version>
<assertj.version>3.9.1</assertj.version>
<jackson.version>2.9.8</jackson.version>
<jersey-version>2.25.1</jersey-version>
<junit-version>4.12</junit-version>
<logback.version>1.2.3</logback.version>
<aws.version>1.11.313</aws.version>
<powermock.version>2.0.0-beta.5</powermock.version>
<postgresql.version>42.1.4</postgresql.version>
<mockito.version>2.22.0</mockito.version>
<cwlavro.version>2.0.4.2</cwlavro.version>
<okhttp.version>3.9.0</okhttp.version>
<slf4j.version>1.7.25</slf4j.version>
<swagger-ui.version>3.20.5</swagger-ui.version>
<maven-surefire.version>2.21.0</maven-surefire.version>
<maven-failsafe.version>2.21.0</maven-failsafe.version>
<httpcomponents.version>4.5.5</httpcomponents.version>
<httpcore.version>4.4.9</httpcore.version>
<skipTests>false</skipTests>
<skipClientITs>true</skipClientITs>
<skipITs>true</skipITs>
</properties>
<!-- deprecated, but needed by Versions Maven Plugin -->
<prerequisites>
<maven>3.3.9</maven>
</prerequisites>
<organization>
<name>Dockstore</name>
<url>https://www.dockstore.org/</url>
</organization>
<scm>
<connection>${github.url}</connection>
<developerConnection>${github.url}</developerConnection>
<url>${github.url}</url>
<tag>1.5.4</tag>
</scm>
<repositories>
<repository>
<id>artifacts.oicr.on.ca</id>
<name>artifacts.oicr.on.ca</name>
<url>https://artifacts.oicr.on.ca/artifactory/collab-release</url>
</repository>
<repository>
<id>seqware.sourceforge.net</id>
<name>SeqWare Maven Repository</name>
<url>https://seqwaremaven.oicr.on.ca/artifactory/collab-release</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>seqwaremaven.oicr.on.ca</id>
<name>seqwaremaven.oicr.on.ca-releases</name>
<url>https://seqwaremaven.oicr.on.ca/artifactory/seqware-dependencies</url>
</repository>
<repository>
<id>apache-releases</id>
<name>Apache Releases repository</name>
<url>https://repository.apache.org/content/repositories/releases/</url>
</repository>
<repository>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>jcenter</id>
<name>bintray</name>
<url>http://jcenter.bintray.com</url>
</repository>
<!-- broad -->
<repository>
<id>artifactory.broadinstitute.org</id>
<name>artifactory.broadinstitute.org</name>
<url>https://artifactory.broadinstitute.org/artifactory/libs-release</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>sagebionetworks</id>
<name>sagebionetworks-releases</name>
<url>http://sagebionetworks.artifactoryonline.com/sagebionetworks/libs-releases-local</url>
</repository>
</repositories>
<licenses>
<license>
<name>GNU General Public License (GPLv3)</name>
<url>http://www.gnu.org/licenses/gpl-3.0.html</url>
</license>
</licenses>
<distributionManagement>
<repository>
<id>central</id>
<name>artifacts.oicr.on.ca-releases</name>
<url>https://artifacts.oicr.on.ca/artifactory/collab-release</url>
</repository>
</distributionManagement>
<modules>
<module>dockstore-common</module>
<module>dockstore-file-plugin-parent</module>
<module>dockstore-webservice</module>
<module>swagger-java-client</module>
<module>openapi-java-client</module>
<module>swagger-java-quay-client</module>
<module>swagger-java-bitbucket-client</module>
<module>dockstore-client</module>
<module>swagger-java-sam-client</module>
<module>dockstore-integration-testing</module>
<module>dockstore-event-consumer</module>
<module>reports</module>
<module>openapi-java-wes-client</module>
</modules>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>com.github.stefanbirkner</groupId>
<artifactId>system-rules</artifactId>
<version>1.17.1</version>
<!-- junit:junit-dep is deprecated, and junit:junit replaces it. -->
<exclusions>
<exclusion>
<groupId>junit</groupId>
<artifactId>junit-dep</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>${logback.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-access</artifactId>
<version>${logback.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>eu.timepit</groupId>
<artifactId>refined_2.11</artifactId>
<version>0.8.2</version>
</dependency>
<dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk-core</artifactId>
<version>${aws.version}</version>
</dependency>
<dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk-kms</artifactId>
<version>${aws.version}</version>
</dependency>
<dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk-s3</artifactId>
<version>${aws.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>${httpcore.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore-nio</artifactId>
<version>${httpcore.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>${httpcomponents.version}</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.10</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-joda</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.jaxrs</groupId>
<artifactId>jackson-jaxrs-json-provider</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-hibernate5</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.github.jsonld-java</groupId>
<artifactId>jsonld-java</artifactId>
<version>0.8.3</version>
<exclusions>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore-osgi</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
<version>2.9.9</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-datatype-joda</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>org.jboss.logging</groupId>
<artifactId>jboss-logging</artifactId>
<version>3.3.0.Final</version>
</dependency>
<dependency>
<groupId>com.fasterxml</groupId>
<artifactId>classmate</artifactId>
<version>1.3.1</version>
</dependency>
<!-- should not be needed, but dropwizard has a conflicting dependency within their own dependency list -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
<version>5.4.2.Final</version>
</dependency>
<!-- jersey -->
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-common</artifactId>
<version>${jersey-version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-client</artifactId>
<version>${jersey-version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-server</artifactId>
<version>${jersey-version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-multipart</artifactId>
<version>${jersey-version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-json-jackson</artifactId>
<version>2.25.1</version>
</dependency>
<dependency>
<groupId>io.swagger</groupId>
<artifactId>swagger-annotations</artifactId>
<version>${swagger-annotations-version}</version>
</dependency>
<dependency>
<groupId>io.swagger</groupId>
<artifactId>swagger-core</artifactId>
<version>${swagger-annotations-version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.swagger.core.v3/swagger-annotations -->
<dependency>
<groupId>io.swagger.core.v3</groupId>
<artifactId>swagger-annotations</artifactId>
<version>${openapi-annotations-version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.swagger.core.v3/swagger-jaxrs2-servlet-initializer -->
<dependency>
<groupId>io.swagger.core.v3</groupId>
<artifactId>swagger-jaxrs2-servlet-initializer</artifactId>
<version>${openapi-annotations-version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.swagger.core.v3/swagger-jaxrs2 -->
<dependency>
<groupId>io.swagger.core.v3</groupId>
<artifactId>swagger-jaxrs2</artifactId>
<version>${openapi-annotations-version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit-version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.7</version>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>1.9.13</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.8.2</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>24.1.1-jre</version>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.22.0-GA</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.5</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-configuration2</artifactId>
<version>2.2</version>
</dependency>
<dependency>
<groupId>org.assertj</groupId>
<artifactId>assertj-core</artifactId>
<version>${assertj.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>annotations</artifactId>
<scope>test</scope>
<version>2.0.1</version>
</dependency>
<dependency>
<groupId>javax.annotation</groupId>
<artifactId>javax.annotation-api</artifactId>
<version>1.2</version>
</dependency>
<!-- mocking dependencies -->
<dependency>
<groupId>org.powermock</groupId>
<artifactId>powermock-core</artifactId>
<version>${powermock.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.powermock</groupId>
<artifactId>powermock-module-junit4</artifactId>
<version>${powermock.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.powermock</groupId>
<artifactId>powermock-api-mockito2</artifactId>
<version>${powermock.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.powermock</groupId>
<artifactId>powermock-api-support</artifactId>
<version>${powermock.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.powermock</groupId>
<artifactId>powermock-api-easymock</artifactId>
<version>${powermock.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.powermock</groupId>
<artifactId>powermock-api-mockito-common</artifactId>
<!-- <version>${powermock.version}</version> seems to have gone out of sync with 2.0.0 -->
<version>1.7.4</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.objenesis</groupId>
<artifactId>objenesis</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.bytebuddy</groupId>
<artifactId>byte-buddy-agent</artifactId>
<version>1.8.21</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.bytebuddy</groupId>
<artifactId>byte-buddy</artifactId>
<version>1.8.21</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.easymock</groupId>
<artifactId>easymock</artifactId>
<version>3.6</version>
<exclusions>
<exclusion>
<groupId>org.objenesis</groupId>
<artifactId>objenesis</artifactId>
</exclusion>
</exclusions>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
<version>1.3</version>
</dependency>
<!-- slf4j -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${slf4j.version}</version>
</dependency>
<!-- broad component management -->
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>findbugs</artifactId>
<version>3.0.1</version>
<exclusions>
<exclusion>
<groupId>org.ow2.asm</groupId>
<artifactId>asm-debug-all</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.objenesis</groupId>
<artifactId>objenesis</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client</artifactId>
<version>1.22.0</version>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-core-asl</artifactId>
<version>1.9.13</version>
</dependency>
<dependency>
<groupId>com.google.apis</groupId>
<artifactId>google-api-services-storage</artifactId>
<version>v1-rev35-1.20.0</version>
</dependency>
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-xml_2.11</artifactId>
<version>1.0.6</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-reflect</artifactId>
<version>2.11.11</version>
</dependency>
<dependency>
<groupId>org.scalacheck</groupId>
<artifactId>scalacheck_2.11</artifactId>
<version>1.12.5</version>
</dependency>
<dependency>
<groupId>org.typelevel</groupId>
<artifactId>macro-compat_2.11</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>org.jvnet.mimepull</groupId>
<artifactId>mimepull</artifactId>
<version>1.9.6</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.11.12</version>
</dependency>
<dependency>
<groupId>io.spray</groupId>
<artifactId>spray-json_2.11</artifactId>
<version>1.3.5</version>
</dependency>
<dependency>
<groupId>com.google.api-client</groupId>
<artifactId>google-api-client</artifactId>
<version>1.22.0</version>
</dependency>
<dependency>
<groupId>org.yaml</groupId>
<artifactId>snakeyaml</artifactId>
<version>1.23</version>
</dependency>
<dependency>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
<version>3.3</version>
</dependency>
<!-- cwl management -->
<dependency>
<groupId>io.cwl</groupId>
<artifactId>cwlavro-tools</artifactId>
<version>${cwlavro.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient-osgi</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore-osgi</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>io.cwl</groupId>
<artifactId>cwlavro-generated</artifactId>
<version>${cwlavro.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient-osgi</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore-osgi</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>${okhttp.version}</version>
</dependency>
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp-urlconnection</artifactId>
<version>${okhttp.version}</version>
</dependency>
<dependency>
<groupId>commons-dbutils</groupId>
<artifactId>commons-dbutils</artifactId>
<version>1.7</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.google.oauth-client/google-oauth-client -->
<dependency>
<groupId>com.google.oauth-client</groupId>
<artifactId>google-oauth-client</artifactId>
<version>1.22.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.google.http-client/google-http-client-jackson -->
<dependency>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client-jackson</artifactId>
<version>1.22.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/commons-beanutils/commons-beanutils -->
<dependency>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
<version>1.9.3</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-exec</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
<version>1.8.1</version>
</dependency>
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20180130</version>
</dependency>
<dependency>
<groupId>org.broadinstitute</groupId>
<artifactId>wdl4s-wom_2.11</artifactId>
<version>0.15</version>
</dependency>
<dependency>
<groupId>ro.fortsoft.pf4j</groupId>
<artifactId>pf4j</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>1.18</version>
</dependency>
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>javax.ws.rs-api</artifactId>
<version>2.0.1</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>zenodo-client-generated</artifactId>
<version>0.1</version>
</dependency>
<dependency>
<groupId>org.ow2.asm</groupId>
<artifactId>asm</artifactId>
<version>5.0.3</version>
</dependency>
<dependency>
<groupId>org.ow2.asm</groupId>
<artifactId>asm-tree</artifactId>
<version>5.0.3</version>
</dependency>
<dependency>
<groupId>org.codehaus.groovy</groupId>
<artifactId>groovy</artifactId>
<version>2.5.5</version>
</dependency>
<dependency>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
<version>1.1.6</version>
</dependency>
<dependency>
<groupId>org.ow2.asm</groupId>
<artifactId>asm-commons</artifactId>
<version>5.0.3</version>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.2.8</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<version>2.2.8</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.2.8</version>
</dependency>
<!-- CVE-2018-1000180 -->
<dependency>
<groupId>org.bouncycastle</groupId>
<artifactId>bcprov-jdk15on</artifactId>
<version>1.60</version>
</dependency>
</dependencies>
</dependencyManagement>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.1</version>
</plugin>
<plugin>
<groupId>com.googlecode.maven-download-plugin</groupId>
<artifactId>download-maven-plugin</artifactId>
<version>1.4.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-scm-publish-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<showDeprecation>true</showDeprecation>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
</archive>
<!-- exclude logback.xml -->
<excludes>
<exclude>**/logback.xml</exclude>
</excludes>
</configuration>
</plugin>
<!-- version fixed at 2.17 due to https://sourceforge.net/p/eclipse-cs/discussion/274376/thread/ba316e08/?limit=25 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>2.17</version>
<dependencies>
<dependency>
<groupId>com.puppycrawl.tools</groupId>
<artifactId>checkstyle</artifactId>
<version>8.9</version>
</dependency>
</dependencies>
<configuration>
<configLocation>checkstyle.xml</configLocation>
<suppressionsLocation>checkstyle-suppressions.xml</suppressionsLocation>
</configuration>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.1</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<filesets>
<fileset>
<directory>datastore</directory>
</fileset>
<fileset>
<directory>cromwell-executions</directory>
</fileset>
<fileset>
<directory>cromwell-input</directory>
</fileset>
<fileset>
<directory>cromwell-workflow-logs</directory>
</fileset>
<fileset>
<directory>.</directory>
<includes>
<include>Cromwell.stderr.txt</include>
<include>Cromwell.stdout.txt</include>
</includes>
</fileset>
</filesets>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.7</version>
</plugin>
<!-- fix at 2.7 until a solution to symbolic links not being copied is ready -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.7</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire.version}</version>
<configuration>
<excludedGroups>${excludeGroups}</excludedGroups>
<skipTests>${skipTests}</skipTests>
<!-- enforce that tests should be independent -->
<runOrder>random</runOrder>
<!-- re-run flaky tests once -->
<rerunFailingTestsCount>1</rerunFailingTestsCount>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>${maven-failsafe.version}</version>
<configuration>
<excludedGroups>${excludeGroups}</excludedGroups>
<!-- enforce that tests should be independent -->
<runOrder>random</runOrder>
<!-- re-run flaky tests once -->
<rerunFailingTestsCount>1</rerunFailingTestsCount>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5.3</version>
<configuration>
<autoVersionSubmodules>true</autoVersionSubmodules>
</configuration>
</plugin>
<plugin>
<groupId>com.github.spotbugs</groupId>
<artifactId>spotbugs-maven-plugin</artifactId>
<version>3.1.3</version>
<dependencies>
<!-- overwrite dependency on spotbugs if you want to specify the version of spotbugs -->
<dependency>
<groupId>com.github.spotbugs</groupId>
<artifactId>spotbugs</artifactId>
<version>3.1.3</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.1.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<!-- Akka used by Cromwell expects a consistant reference.conf file. Also order matters, so keep it first in the list of transformers -->
<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>reference.conf</resource>
</transformer>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.eluder.coveralls</groupId>
<artifactId>coveralls-maven-plugin</artifactId>
<version>4.3.0</version>
<dependencies>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.2.8</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>1.4.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<!-- https://mvnrepository.com/artifact/org.scala-tools/maven-scala-plugin -->
<plugin>
<groupId>org.scala-tools</groupId>
<artifactId>maven-scala-plugin</artifactId>
<version>2.15.2</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>io.swagger</groupId>
<artifactId>swagger-codegen-maven-plugin</artifactId>
<version>2.3.1</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.6.0</version>
</plugin>
<!-- https://mvnrepository.com/artifact/org.codehaus.mojo/versions-maven-plugin -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.5</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<executions>
<execution>
<id>enforce</id>
<configuration>
<rules>
<DependencyConvergence />
<requirePluginVersions>
<message>Best Practice is to always define plugin versions!</message>
</requirePluginVersions>
<requireReleaseDeps>
<message>No Snapshots Allowed!</message>
<failWhenParentIsSnapshot>false</failWhenParentIsSnapshot>
<excludes>
<exclude>io.dockstore:*</exclude>
</excludes>
</requireReleaseDeps>
<requireUpperBoundDeps />
<requireMavenVersion>
<version>3.3.9</version>
</requireMavenVersion>
<requireJavaVersion>
<version>1.8.0</version>
</requireJavaVersion>
<banDuplicatePomDependencyVersions />
<bannedDependencies>
<!-- currently, some of these dependencies are brought in transitively -->
<searchTransitive>false</searchTransitive>
<excludes>
<!-- superceded by org.apache.commons:commons-lang3 for direct dependencies-->
<exclude>commons-lang:commons-lang</exclude>
<!-- superceded by org.apache.commons:commons-configuration2 for direct dependencies-->
<exclude>commons-configuration:commons-configuration</exclude>
<!-- superceded by org.apache.httpcomponents:httpclient -->
<exclude>commons-httpclient:commons-httpclient</exclude>
</excludes>
</bannedDependencies>
</rules>
</configuration>
<goals>
<goal>enforce</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>analyze</id>
<goals>
<goal>analyze-only</goal>
</goals>
<configuration>
<failOnWarning>true</failOnWarning>
<outputXML>true</outputXML>
<ignoreNonCompile>true</ignoreNonCompile>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<inherited>false</inherited>
<executions>
<execution>
<inherited>false</inherited>
<phase>site-deploy</phase>
<goals>
<goal>aggregate</goal>
<goal>test-aggregate</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<configuration>
<enableFilesSummary>true</enableFilesSummary>
<enableRulesSummary>true</enableRulesSummary>
</configuration>
<executions>
<execution>
<phase>
compile
</phase>
<goals>
<goal>check</goal>
</goals>
<configuration>
<consoleOutput>true</consoleOutput>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.github.spotbugs</groupId>
<artifactId>spotbugs-maven-plugin</artifactId>
<version>3.1.3</version>
<executions>
<execution>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
<configuration>
<threshold>High</threshold>
<excludeFilterFile>
${project.basedir}/findbugs-exclude.xml
</excludeFilterFile>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<executions>
<execution>
<id>integration-test</id>
<goals>
<goal>integration-test</goal>
</goals>
</execution>
<execution>
<id>verify</id>
<goals>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.eluder.coveralls</groupId>
<artifactId>coveralls-maven-plugin</artifactId>
<configuration>
<jacocoReports>
<param>${project.basedir}/reports/target/site/jacoco-aggregate/jacoco.xml</param>
</jacocoReports>
</configuration>
</plugin>
<!-- identify and fail if we use problematic Java dependencies for Java 9 -->
<plugin>
<groupId>org.codefx.mvn</groupId>
<artifactId>jdeps-maven-plugin</artifactId>
<version>0.2</version>
<configuration>
<defaultSeverity>FAIL</defaultSeverity>
</configuration>
<executions>
<execution>
<goals>
<goal>jdkinternals</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
</plugin>
<plugin>
<groupId>net.revelc.code</groupId>
<artifactId>impsort-maven-plugin</artifactId>
<version>1.2.0</version>
<configuration>
<groups>java.,javax.,*</groups>
<staticAfter>true</staticAfter>
</configuration>
<executions>
<execution>
<id>sort-imports</id>
<goals>
<goal>sort</goal><!-- runs at process-sources phase by default -->
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<profiles>
<profile>
<id>default</id>
<!-- run only non-confidential, relatively fast tests -->
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<properties>
<excludeGroups>io.dockstore.common.RegressionTest, io.dockstore.common.ConfidentialTest,io.dockstore.common.SlowTest,
io.dockstore.common.BenchmarkTest,io.dockstore.common.ToilOnlyTest
</excludeGroups>
</properties>
</profile>
<profile>
<id>toil-integration-tests</id>
<!-- run only tests that are relevant for toil (tests that use cwltool, cwlrunner, toil -->
<properties>
<skipTests>true</skipTests>
<skipITs>false</skipITs>
<groups>io.dockstore.common.ToilCompatibleTest,io.dockstore.common.ToilOnlyTest</groups>
</properties>
</profile>
<profile>
<id>regression-integration-tests</id>
<!-- run only regression tests-->
<properties>
<skipTests>true</skipTests>
<skipITs>false</skipITs>
<skipClientITs>true</skipClientITs>
<groups>io.dockstore.common.RegressionTest</groups>
</properties>
</profile>
<profile>
<id>workflow-integration-tests</id>
<!-- Only run integration tests for workflows -->
<properties>
<skipTests>true</skipTests>
<skipITs>false</skipITs>
<groups>io.dockstore.common.WorkflowTest</groups>
<excludeGroups>io.dockstore.common.SlowTest,io.dockstore.common.RegressionTest, io.dockstore.common.ToilOnlyTest</excludeGroups>
</properties>
</profile>
<profile>
<id>tool-integration-tests</id>
<!-- Only run integration tests for tools -->
<properties>
<skipTests>true</skipTests>
<skipITs>false</skipITs>
<groups>io.dockstore.common.ToolTest</groups>
<excludeGroups>io.dockstore.common.SlowTest,io.dockstore.common.RegressionTest, io.dockstore.common.ToilOnlyTest</excludeGroups>
</properties>
</profile>
<profile>
<id>other-integration-tests</id>
<!-- Only run integration tests not related to only tools or workflows. This is a catch all. -->
<properties>
<skipTests>true</skipTests>
<skipITs>false</skipITs>
<excludeGroups>io.dockstore.common.ToolTest,io.dockstore.common.WorkflowTest,io.dockstore.common.SlowTest,io.dockstore.common.RegressionTest, io.dockstore.common.ToilOnlyTest</excludeGroups>
</properties>
</profile>
<profile>
<id>unit-tests</id>
<!-- run all non-integration tests -->
<properties>
<skipTests>false</skipTests>
<skipITs>true</skipITs>
<skipClientITs>true</skipClientITs>
</properties>
</profile>
<profile>
<id>integration-tests</id>
<!-- run all integration tests -->
<properties>
<skipTests>true</skipTests>
<skipITs>false</skipITs>
<skipClientITs>false</skipClientITs>
<excludeGroups>io.dockstore.common.SlowTest,io.dockstore.common.RegressionTest, io.dockstore.common.ToilOnlyTest</excludeGroups>
</properties>
</profile>
<profile>
<id>coverage</id>
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<append>true</append>
<excludes>
<exclude>io/dockstore/webservice/resources/Description.*</exclude>
<exclude>io/dockstore/common/Bridge.*</exclude>
<!-- exclude client classes, but not the server classes to help guide tests -->
<exclude>io/swagger/client/**/*</exclude>
<exclude>io/swagger/client/*</exclude>
<exclude>**/*$*</exclude>
</excludes>
</configuration>
<executions>
<execution>
<id>prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>prepare-agent-integration</id>
<phase>package</phase>
<goals>
<goal>prepare-agent-integration</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>
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