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pom.xml
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pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!--
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see http://www.gnu.org/licenses/
-->
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.phenotips</groupId>
<artifactId>phenotips-parent</artifactId>
<version>1.5-SNAPSHOT</version>
<packaging>pom</packaging>
<prerequisites>
<maven>3.3</maven>
</prerequisites>
<name>PhenoTips - Parent POM</name>
<description>PhenoTips is a software tool providing an easy-to-use Web interface and standardized database back-end for collecting clinical symptoms and physical findings observed in patients with genetic disorders.</description>
<url>http://phenotips.org/</url>
<inceptionYear>2011</inceptionYear>
<licenses>
<license>
<name>AGPL 3.0</name>
<url>https://www.gnu.org/licenses/agpl-3.0.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<connection>scm:git:git://github.com/phenotips/phenotips.git</connection>
<developerConnection>scm:git:[email protected]:phenotips/phenotips.git</developerConnection>
<url>https://github.com/phenotips/phenotips.git/tree/master/</url>
<tag>HEAD</tag>
</scm>
<organization>
<name>University of Toronto, Computational Biology Lab</name>
<url>http://compbio.cs.toronto.edu/</url>
</organization>
<distributionManagement>
<site>
<id>nexus.phenotips.org</id>
<url>dav:https://nexus.phenotips.org/nexus/content/sites/site/${project.groupId}/${project.artifactId}/${project.version}</url>
</site>
<repository>
<id>nexus.phenotips.org</id>
<name>Maven2 Remote Repository for Releases</name>
<url>https://nexus.phenotips.org/nexus/content/repositories/releases</url>
</repository>
<snapshotRepository>
<id>nexus.phenotips.org</id>
<name>Maven2 Development Repository for Snapshots</name>
<url>https://nexus.phenotips.org/nexus/content/repositories/snapshots</url>
</snapshotRepository>
</distributionManagement>
<repositories>
<repository>
<id>phenotips-releases</id>
<name>PhenoTips Releases repository</name>
<url>https://nexus.phenotips.org/nexus/content/repositories/releases/</url>
<releases>
<enabled>true</enabled>
<checksumPolicy>fail</checksumPolicy>
</releases>
<snapshots>
<enabled>false</enabled>
<checksumPolicy>fail</checksumPolicy>
</snapshots>
</repository>
<repository>
<id>phenotips-snapshots</id>
<name>PhenoTips Snapshots repository</name>
<url>https://nexus.phenotips.org/nexus/content/repositories/snapshots/</url>
<releases>
<enabled>false</enabled>
<checksumPolicy>fail</checksumPolicy>
</releases>
<snapshots>
<enabled>true</enabled>
<checksumPolicy>fail</checksumPolicy>
</snapshots>
</repository>
<repository>
<id>phenotips-externals</id>
<name>PhenoTips external repositories mirror</name>
<url>https://nexus.phenotips.org/nexus/content/groups/public/</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<id>phenotips-externals</id>
<name>PhenoTips external repositories mirror</name>
<url>https://nexus.phenotips.org/nexus/content/groups/public/</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</pluginRepository>
<pluginRepository>
<id>phenotips-external-snapshots</id>
<name>PhenoTips external snapshot repositories mirror</name>
<url>https://nexus.phenotips.org/nexus/content/groups/public-snapshots/</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</pluginRepository>
</pluginRepositories>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<phenotips.version>1.5-SNAPSHOT</phenotips.version>
<project.version.previous>1.4</project.version.previous>
<xwiki.version>7.4.6</xwiki.version>
<slf4j.version>1.7.25</slf4j.version>
<poi.version>3.11</poi.version>
<selenium.version>3.14.0</selenium.version>
<jackson.codehaus.version>1.9.13</jackson.codehaus.version>
<jackson.fasterxml.version>2.9.7</jackson.fasterxml.version>
<restlet.version>2.0.15</restlet.version>
<buildtools.version>1.8</buildtools.version>
<!-- <textAnalysis.version>1.0</textAnalysis.version>-->
<testframework.version>1.3</testframework.version>
<solr.version>6.5.1</solr.version>
<jaxb2-fluent-api.version>3.0</jaxb2-fluent-api.version>
<maven-jaxb2-plugin.version>0.13.3</maven-jaxb2-plugin.version>
<enforcer.skip>false</enforcer.skip>
<checkstyle.skip>false</checkstyle.skip>
<!-- Clirr doesn't work well on Java 8 unfortunately... -->
<clirr.skip>true</clirr.skip>
<license.skip>false</license.skip>
<dependencyCheck.skip>false</dependencyCheck.skip>
<coverage.instructionRatio>1.00</coverage.instructionRatio>
<!-- Functional test environment -->
<xwiki.defaultSkin>PhenoTips.Skin</xwiki.defaultSkin>
<it.pattern>.*</it.pattern>
<it.patternMethod>.*</it.patternMethod>
<it.server.directory>${project.build.directory}/package/</it.server.directory>
<it.server.port>8080</it.server.port>
<it.server.stopPort>8079</it.server.stopPort>
<it.server.startCommand>sh start.sh ${it.server.port} ${it.server.stopPort}</it.server.startCommand>
<it.server.stopCommand>sh stop.sh ${it.server.stopPort}</it.server.stopCommand>
<it.server.baseURL>http://localhost</it.server.baseURL>
</properties>
<dependencyManagement>
<dependencies>
<!-- Apache Commons -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.8.1</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>4.2</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.6</version>
</dependency>
<!-- Everybody logs -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
<version>${slf4j.version}</version>
</dependency>
<!-- Logging framework -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.2.3</version>
</dependency>
<!-- Most plugins depend on the servlet API -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.0.1</version>
<!-- It should always be provided, otherwise containers will complain about it. -->
<scope>provided</scope>
</dependency>
<dependency>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
<version>2.10</version>
</dependency>
<!-- JSON serialization and deserialization -->
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20180813</version>
</dependency>
<!-- Exclude XWiki's Solr search modules -->
<dependency>
<groupId>org.xwiki.platform</groupId>
<artifactId>xwiki-platform-repository-server-api</artifactId>
<version>${xwiki.version}</version>
<exclusions>
<exclusion>
<groupId>org.xwiki.platform</groupId>
<artifactId>xwiki-platform-search-solr-query</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- HTTP libraries -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>4.4.10</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.6</version>
<exclusions>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpasyncclient</artifactId>
<version>4.1.4</version>
<exclusions>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>rome</groupId>
<artifactId>rome</artifactId>
<version>1.0</version>
<exclusions>
<exclusion>
<!-- We're using the newer org.jdom:jdom -->
<groupId>jdom</groupId>
<artifactId>jdom</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- Other commons libraries -->
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.11</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.6</version>
</dependency>
<!-- Use the latest Selenium version for browser compatibility -->
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-api</artifactId>
<version>${selenium.version}</version>
</dependency>
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-support</artifactId>
<version>${selenium.version}</version>
</dependency>
<!-- Use a more recent version of Jackson 1.x, the latest compatible with the version of restlet in use -->
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-core-asl</artifactId>
<version>${jackson.codehaus.version}</version>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>${jackson.codehaus.version}</version>
</dependency>
<!-- Use a more recent version of Jackson 2.x -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.fasterxml.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson.fasterxml.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>${jackson.fasterxml.version}</version>
</dependency>
<!-- REST -->
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>jsr311-api</artifactId>
<version>1.0</version>
</dependency>
<dependency>
<groupId>org.restlet.jse</groupId>
<artifactId>org.restlet</artifactId>
<version>${restlet.version}</version>
</dependency>
<dependency>
<groupId>org.restlet.jse</groupId>
<artifactId>org.restlet.ext.jackson</artifactId>
<version>${restlet.version}</version>
</dependency>
<dependency>
<groupId>org.restlet.jse</groupId>
<artifactId>org.restlet.ext.jaxrs</artifactId>
<version>${restlet.version}</version>
<exclusions>
<exclusion>
<groupId>org.restlet.jse</groupId>
<artifactId>org.restlet.lib.org.json</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- TEST -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>1.10.19</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>3.6.9.Final</version>
</dependency>
<!-- Security -->
<dependency>
<groupId>org.jasypt</groupId>
<artifactId>jasypt</artifactId>
<version>1.9.2</version>
</dependency>
<!-- Database connectors for MySQL and HSQLDB, the most commonly used ones. -->
<dependency>
<groupId>org.hsqldb</groupId>
<artifactId>hsqldb</artifactId>
<version>2.4.1</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.47</version>
</dependency>
<!-- XWiki dependencies -->
<!-- Make sure to include the proper version of antlr for hibernate-core -->
<dependency>
<groupId>antlr</groupId>
<artifactId>antlr</artifactId>
<version>2.7.6</version>
</dependency>
<!-- The new version of HTMLCleaner is required for PDFs to work properly -->
<dependency>
<groupId>net.sourceforge.htmlcleaner</groupId>
<artifactId>htmlcleaner</artifactId>
<version>2.22</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>26.0-jre</version>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.2</version>
</dependency>
<dependency>
<groupId>net.jcip</groupId>
<artifactId>jcip-annotations</artifactId>
<version>1.0</version>
</dependency>
<dependency>
<groupId>de.charite.compbio</groupId>
<artifactId>ontologizer-core</artifactId>
<version>2.1.2</version>
</dependency>
<dependency>
<groupId>de.charite.compbio</groupId>
<artifactId>ontologizer-benchmark</artifactId>
<version>2.1.2</version>
</dependency>
<!-- Batik 1.10 is used, but css4j pulls in a few 1.7 modules; force 1.10 throughout -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-util</artifactId>
<version>1.10</version>
</dependency>
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-css</artifactId>
<version>1.10</version>
</dependency>
</dependencies>
</dependencyManagement>
<build>
<defaultGoal>install</defaultGoal>
<extensions>
<extension>
<groupId>org.apache.maven.wagon</groupId>
<artifactId>wagon-webdav-jackrabbit</artifactId>
<version>3.2.0</version>
</extension>
<!-- Adds support for the "functional-tests" packaging -->
<extension>
<groupId>org.phenotips</groupId>
<artifactId>phenotips-functional-tests-lifecycle</artifactId>
<version>${testframework.version}</version>
</extension>
<!-- Adds support for the "xar" packaging -->
<extension>
<groupId>org.xwiki.commons</groupId>
<artifactId>xwiki-commons-tool-xar-handlers</artifactId>
<version>${xwiki.version}</version>
</extension>
</extensions>
<plugins>
<!-- Show compiler warnings -->
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<compilerArgument>-Xlint:all</compilerArgument>
<showWarnings>true</showWarnings>
<showDeprecation>true</showDeprecation>
</configuration>
</plugin>
<plugin>
<!-- Run Checkstyle -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
</plugin>
<plugin>
<!-- Check license headers -->
<groupId>com.mycila</groupId>
<artifactId>license-maven-plugin</artifactId>
</plugin>
<plugin>
<!-- API backwards compatibility check -->
<groupId>org.codehaus.mojo</groupId>
<artifactId>clirr-maven-plugin</artifactId>
<configuration>
<comparisonVersion>${project.version.previous}</comparisonVersion>
<!-- List of specific CLIRR excludes.
See http://www.mojohaus.org/clirr-maven-plugin/examples/ignored-differences.html
-->
<ignored>
<!-- Remove the following ignores after we release 1.4 -->
<difference>
<className>org/phenotips/vocabulary/SolrVocabularyResourceManager</className>
<differenceType>7012</differenceType>
<method>void createReplacementCore(java.lang.String)</method>
<justification>New methods for safe vocabulary reindexing.</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/SolrVocabularyResourceManager</className>
<differenceType>7012</differenceType>
<method>void replaceCore(java.lang.String)</method>
<justification>New methods for safe vocabulary reindexing.</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/SolrVocabularyResourceManager</className>
<differenceType>7012</differenceType>
<method>org.apache.solr.client.solrj.SolrClient getReplacementSolrConnection(java.lang.String)</method>
<justification>New methods for safe vocabulary reindexing.</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/SolrVocabularyResourceManager</className>
<differenceType>7012</differenceType>
<method>void discardReplacementCore(java.lang.String)</method>
<justification>New methods for safe vocabulary reindexing.</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/VocabularyManager</className>
<differenceType>7012</differenceType>
<method>java.util.List search(java.lang.String, java.lang.String, int)</method>
<justification>Adding support for searches in vocabulary category</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/VocabularyManager</className>
<differenceType>7012</differenceType>
<method>java.util.List search(java.lang.String, java.lang.String, int, java.lang.String, java.lang.String)</method>
<justification>Adding support for searches in vocabulary category</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/VocabularyManager</className>
<differenceType>7012</differenceType>
<method>java.util.List getAvailableCategories()</method>
<justification>New method to get a list of all available vocabulary categories.</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/VocabularyManager</className>
<differenceType>7012</differenceType>
<method>java.util.Set getVocabularies(java.lang.String)</method>
<justification>New method to get a list of all vocabularies that fall under some category.</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/VocabularyManager</className>
<differenceType>7012</differenceType>
<method>boolean hasCategory(java.lang.String)</method>
<justification>New method that returns true iff a category name is valid.</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/VocabularyManager</className>
<differenceType>7012</differenceType>
<method>boolean hasVocabulary(java.lang.String)</method>
<justification>New method that returns true iff a vocabulary id is valid.</justification>
</difference>
<difference>
<className>org/phenotips/data/permissions/script/PermissionsManagerScriptService</className>
<differenceType>7005</differenceType>
<method>org.phenotips.data.permissions.PatientAccess getPatientAccess(org.phenotips.data.Patient)</method>
<to>org.phenotips.data.permissions.PatientAccess getPatientAccess(java.lang.String)</to>
<justification>after SecurePatient update this service now needs to get its own non-read-only copy of a patient</justification>
</difference>
<difference>
<className>org/phenotips/configuration/Record*</className>
<differenceType>7012</differenceType>
<method>void set*(*)</method>
<justification>New API methods needed for making the configuration more extensible.</justification>
</difference>
<difference>
<className>org/phenotips/configuration/RecordConfigurationManager</className>
<differenceType>7012</differenceType>
<method>org.phenotips.configuration.RecordConfiguration getConfiguration(java.lang.String)</method>
<justification>New API methods needed for making the configuration more extensible.</justification>
<className>org/phenotips/vocabulary/Vocabulary</className>
<differenceType>7012</differenceType>
<method>java.util.Collection getSupportedCategories()</method>
<justification>Adding support for vocabulary categories</justification>
</difference>
<difference>
<className>org/phenotips/vocabulary/Vocabulary</className>
<differenceType>7012</differenceType>
<method>java.util.List search(java.lang.String, java.lang.String, int, java.lang.String, java.lang.String)</method>
<justification>Adding support for vocabulary categories</justification>
</difference>
<difference>
<className>org/phenotips/groups/GroupManager</className>
<differenceType>7012</differenceType>
<method>java.util.List getAllMembersForGroup(java.lang.String)</method>
<justification>Adding new method to get all members of the group</justification>
</difference>
<difference>
<className>org/phenotips/data/permissions/internal</className>
<differenceType>7012</differenceType>
<method>com.xpn.xwiki.api.Document getDocument(org.xwiki.model.reference.EntityReference)</method>
<justification>Adding new method to get Document of user or group reference</justification>
</difference>
</ignored>
<excludes>
<exclude>**/internal/**</exclude>
<exclude>**/test/**</exclude>
<!-- Remove the following excludes after we release the current version as final -->
</excludes>
</configuration>
</plugin>
<!-- We want to force packaging the license resources in the produced XWiki artifacts -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-remote-resources-plugin</artifactId>
<executions>
<execution>
<id>license-resources</id>
<goals>
<goal>process</goal>
</goals>
<configuration>
<resourceBundles>
<resourceBundle>org.phenotips:phenotips-license-resources:${buildtools.version}</resourceBundle>
</resourceBundles>
</configuration>
</execution>
</executions>
</plugin>
<!-- Check that declared dependencies match what's actually used -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>check-dependencies</id>
<goals>
<goal>analyze-only</goal>
</goals>
<configuration>
<failOnWarning>true</failOnWarning>
<ignoreNonCompile>true</ignoreNonCompile>
<skip>${dependencyCheck.skip}</skip>
</configuration>
</execution>
</executions>
</plugin>
<!-- Fail the build if the test coverage is below a given value. -->
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.1</version>
<executions>
<execution>
<id>jacoco-prepare</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>jacoco-check</id>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
<configuration>
<rules>
<rule>
<limits>
<limit>
<counter>INSTRUCTION</counter>
<minimum>${coverage.instructionRatio}</minimum>
</limit>
</limits>
</rule>
</rules>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<dependencies>
<dependency>
<groupId>org.xwiki.commons</groupId>
<artifactId>xwiki-commons-tool-enforcer-dependencies</artifactId>
<version>${xwiki.version}</version>
</dependency>
</dependencies>
<executions>
<!-- Check that all Maven plugins have versions defined -->
<execution>
<id>enforce-plugins</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requirePluginVersions>
<message>Best Practice is to always define plugin versions!</message>
<banLatest>false</banLatest>
<banRelease>false</banRelease>
<banSnapshots>false</banSnapshots>
</requirePluginVersions>
</rules>
</configuration>
</execution>
<!-- Check that we're using commons-lang3 and not commons-lang -->
<execution>
<id>enforce-commons-lang3</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<bannedDependencies>
<searchTransitive>false</searchTransitive>
<message>
Best practice is to use Commons Lang 3.x
</message>
<excludes>
<exclude>commons-lang:commons-lang</exclude>
</excludes>
</bannedDependencies>
</rules>
</configuration>
</execution>
<execution>
<id>enforce-no-legacy-dependencies</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<xwikiBannedDependencies implementation="org.xwiki.tool.enforcer.XWikiBannedDependencies">
<searchTransitive>true</searchTransitive>
<message>Don't depend on a XWiki Legacy module!</message>
<excludes>
<exclude>.*xwiki.*:.*-legacy-.*</exclude>
</excludes>
</xwikiBannedDependencies>
</rules>
</configuration>
</execution>
</executions>
<configuration>
<skip>${enforcer.skip}</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<executions>
<execution>
<id>generate-javadocs</id>
<goals>
<goal>javadoc</goal>
</goals>
<phase>prepare-package</phase>
</execution>
</executions>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>1.4.1</version>
</plugin>
<!-- Apply checkstyle rules and fail the build in case of errors. The checkstyle config
files are taken from the build-tools JAR module.-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>2.17</version>
<dependencies>
<dependency>
<groupId>com.puppycrawl.tools</groupId>
<artifactId>checkstyle</artifactId>
<version>8.12</version>
</dependency>
<dependency>
<groupId>org.phenotips</groupId>
<artifactId>phenotips-checkstyle-configuration</artifactId>
<version>${buildtools.version}</version>
</dependency>
</dependencies>
<configuration>
<consoleOutput>true</consoleOutput>
<skip>${checkstyle.skip}</skip>
<configLocation>checkstyle.xml</configLocation>
</configuration>
<executions>
<execution>
<id>source-checkstyle</id>
<goals>
<goal>check</goal>
</goals>
</execution>
<execution>
<id>test-checkstyle</id>
<goals>
<goal>check</goal>
</goals>
<configuration>
<configLocation>test-checkstyle.xml</configLocation>
<includeTestSourceDirectory>true</includeTestSourceDirectory>
<sourceDirectory>src/test/java/</sourceDirectory>
</configuration>
</execution>
</executions>
</plugin>
<!-- Check license headers and fail the build if they're missing or not matching the defined format -->
<plugin>
<groupId>com.mycila</groupId>
<artifactId>license-maven-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>3.0</version>
<configuration>
<skip>${license.skip}</skip>
<header>license.txt</header>
<strictCheck>true</strictCheck>
<headerDefinitions>
<!-- Our style for XML headers isn't standard so we need to define it in a custom manner.
See xwiki-commons-tool-validation-resources module -->
<headerDefinition>license-xml-definition.xml</headerDefinition>
<headerDefinition>license-script-definition.xml</headerDefinition>
<headerDefinition>license-batch-definition.xml</headerDefinition>
</headerDefinitions>
<!-- Our Java and XML styles aren't the default so we need to change the mapping -->
<mapping>
<java>SLASHSTAR_STYLE</java>
<aj>SLASHSTAR_STYLE</aj>
</mapping>
<!-- We're only interested in checking our sources and our POMs -->
<!-- At the moment, only check the license headers in Java, XML and shell script files -->
<!-- FIXME: fix other types of files as well -->
<includes>
<include>src/**/*.java</include>
<include>src/**/*.xml</include>
<include>src/**/*.bat</include>
<include>src/**/*.sh</include>
<include>pom.xml</include>
</includes>
<excludes>
<!-- At the moment we don't have a comment syntax for components.txt files so we need to exclude them
from the check -->
<exclude>**/components.txt</exclude>
<exclude>**/component-overrides.txt</exclude>
<!-- Since there's no comment syntax for Maven IT tests's goal.txt file we need to exclude it -->
<exclude>**/it/**/goals.txt</exclude>
<exclude>**/goal.txt</exclude>
<!-- Exclude sample patient records -->
<exclude>**/P0*.xml</exclude>
<exclude>**/F0*.xml</exclude>
</excludes>
<useDefaultExcludes>false</useDefaultExcludes>
</configuration>
<!-- Add a dependency since this is where the maven-license-plugin plugin will find the license.txt file -->
<dependencies>
<dependency>
<groupId>org.phenotips</groupId>
<artifactId>phenotips-license-verification-resources</artifactId>
<version>${buildtools.version}</version>
</dependency>
</dependencies>
<executions>
<execution>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>3.1.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-remote-resources-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>1.5</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>2.5.3</version>
<configuration>
<arguments>-Pquick</arguments>
<!-- Avoid site generation during the release:perform to speed up release process -->
<goals>deploy</goals>
<mavenExecutorId>forked-path</mavenExecutorId>
<autoVersionSubmodules>true</autoVersionSubmodules>
<localCheckout>true</localCheckout>
<pushChanges>false</pushChanges>
<tagNameFormat>phenotips-@{project.version}</tagNameFormat>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>3.1.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>3.0.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-plugin-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>3.5.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>2.5.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>3.8.0</version>
<!-- Java 1.8 is required -->
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<!-- Lock down plugin version for build reproducibility -->
<version>2.22.0</version>
<!-- Rule is to put tests in *Test classes -->
<configuration>
<includes>
<include>**/*Test.class</include>
</includes>
<parallel>classesAndMethods</parallel>
<threadCount>2</threadCount>
<systemProperties>
<property>
<name>pattern</name>
<value>${it.pattern}</value>
</property>
<property>
<name>patternMethod</name>
<value>${it.patternMethod}</value>
</property>
<property>
<name>xwiki.test.baseURL</name>
<value>${it.server.baseURL}</value>
</property>
<property>
<name>xwiki.test.skipStart</name>
<value>${it.skipStart}</value>
</property>
<property>
<name>xwikiPort</name>
<value>${it.server.port}</value>
</property>
<property>
<name>xwikiStopPort</name>
<value>${it.server.stopPort}</value>
</property>
<property>
<name>xwikiExecutionDirectory</name>
<value>${it.server.directory}</value>
</property>
<property>
<name>screenshotDirectory</name>
<value>${basedir}/target/screenshots</value>
</property>
<property>
<name>xwikiExecutionStartCommand</name>
<value>${it.server.startCommand}</value>
</property>
<property>