<commit_before><?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>
  <parent>
    <groupId>org.phenomecentral</groupId>
    <artifactId>phenomecentral-parent</artifactId>
    <version>1.1-SNAPSHOT</version>
  </parent>
  <artifactId>phenomecentral-war</artifactId>
  <name>PhenomeCentral - War package</name>
  <packaging>war</packaging>
  <properties>
    <!-- By default we don't include Legacy modules and thus we don't need to exclude the non legacy JARs -->
    <xwiki.war.legacy.excludes />

    <!-- The default UI associated to this WAR -->
    <xwiki.extension.distribution.ui>org.phenomecentral:phenomecentral-ui</xwiki.extension.distribution.ui>
  </properties>
  <dependencies>
    <!-- Extend the base war -->
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-base-war</artifactId>
      <version>${phenotips.version}</version>
      <type>war</type>
    </dependency>

    <!-- XWiki dependencies -->
    <!-- Make sure to include the proper version of antlr for hibernate-core -->
    <dependency>
      <groupId>antlr</groupId>
      <artifactId>antlr</artifactId>
    </dependency>

    <!-- The new version of HTMLCleaner is required for PDFs to work properly -->
    <dependency>
      <groupId>net.sourceforge.htmlcleaner</groupId>
      <artifactId>htmlcleaner</artifactId>
    </dependency>

    <!-- The Big Old Core -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-oldcore</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
      <exclusions>
        <exclusion>
          <groupId>org.codehaus.groovy</groupId>
          <artifactId>groovy-all</artifactId>
        </exclusion>
      </exclusions>
    </dependency>

    <!-- Components Modules -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-component-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- REST module -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rest-server</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- ClassLoader -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-classloader-xwiki</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Container -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-container-servlet</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Extension Manager -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-extension-handler-jar</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-extension-handler-xar</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-extension-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-extension-repository-maven</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-extension-repository-xwiki</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-extension-cluster</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-extension-distribution</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>

    <!-- Default Rendering Macros we want available by default in XE.
         Please keep them in alphabetical order -->
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-box</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-comment</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-html</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-id</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-message</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-toc</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-content</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-wikimacro-store</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-dashboard-macro</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-code</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-container</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-gallery</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-include</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-display-macro</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-useravatar</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-velocity</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- XWiki Rendering Syntax Parsers -->
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-doxia</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
      <!-- Incompatible with the version of plexus used by Extension Manager aether module -->
      <exclusions>
        <exclusion>
          <artifactId>plexus-container-default</artifactId>
          <groupId>org.codehaus.plexus</groupId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-xwiki20</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-xwiki21</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-xhtml</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-html5</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-html</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-plain</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Captcha component -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-captcha</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Crypto Module -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-crypto-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-crypto-store-filesystem</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-crypto-store-wiki</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- CSRF protection -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-csrf</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- XML Script Service -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-xml-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Filesystem attachment storage -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-store-filesystem-attachments</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- User Interface extensions -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-uiextension-api</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Security Script Services -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-security-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Skin Extension -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-skin-skinx</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- ZIP Explorer -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-zipexplorer</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Mailsender -->
    <!-- New Mail Sender API -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-mail-send-storage</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Old Mail Sender Plugin -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-mailsender</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- JODA Time -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-jodatime</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Diff Script Services -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-diff-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Blame Script Services -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-blame-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Logging Dependencies. Ensures all logging goes through SLF4J and Logback. -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-logging-logback</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-logging-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>jcl-over-slf4j</artifactId>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>log4j-over-slf4j</artifactId>
      <scope>runtime</scope>
    </dependency>
    <!-- Configuration -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-configuration-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Security -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-security-bridge</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Localization -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-localization-source-legacy</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-localization-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-localization-macro</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- URL -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-url-scheme-standard</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Filter -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-filter-stream-xml</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-filter-instance-oldcore</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-filter-instance-extension</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-filter-instance-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-filter-stream-xar</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Wiki Module -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-template-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-template-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-user-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-user-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- LESS CSS Module -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-lesscss-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- LDAP -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-ldap-authenticator</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <!-- jQuery -->
    <dependency>
      <groupId>org.webjars</groupId>
      <artifactId>jquery</artifactId>
      <version>1.11.1</version>
    </dependency>
    <!-- Servlets for Resource API -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-resource-servlet</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <!-- PhenoTips components -->
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>component-registry</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>solr-access-service-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>gene-panels-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>gene-panels-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabularies-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabularies-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-hpo-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-hpo-annotations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-hpo-translation-spanish</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-chebi-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-omim-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-hgnc-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-ethnicity-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-ordo-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-contacts</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-default-impl</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-indexing</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-data-export-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-authorization</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-security-bridge</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-crypto-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-crypto-xproperty</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-access-rules-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-access-rules-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-access-rules-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-measurements-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-measurements-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>users-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-studies-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>xwiki-platform-users-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>xwiki-platform-users-wiki</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>application-configuration-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>application-configuration-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-tools</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>ncbieutils-services-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>obo2solr</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-sharing-push-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-sharing-receiver-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>specificity-meter-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-navigation-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-pedigree-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-skin-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-widgets-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>jodatime-service</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>storage-migrators-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>storage-migrators-attachments-migrator</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>storage-migrators-attachments-database</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>storage-migrators-attachments-filesystem</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>diagnosis-suggestion-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-proxy-authentication</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>pingback-common</artifactId>
      <version>1.1</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>pingback-client-api</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>family-studies-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>family-studies-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>family-studies-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>

    <!-- PhenomeCentral specific -->
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-similarity-data-api</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-similarity-data-impl</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-network-access-rules</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-similarity-search</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>anonymous-communication</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>matching-notification-api</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>matching-notification-resources</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>remote-matching-core-server</artifactId>
      <version>${remoteMatching.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>remote-matching-core-client</artifactId>
      <version>${remoteMatching.version}</version>
    </dependency>

    <!-- Add dependencies on the XAR distributions so that we transitively include all JAR dependencies in the generated WAR -->
    <dependency>
      <groupId>${project.groupId}</groupId>
      <artifactId>phenomecentral-ui</artifactId>
      <version>${project.version}</version>
      <type>xar</type>
    </dependency>
  </dependencies>
  <build>
    <plugins>
      <!-- Inject XWiki's configuration (only xwiki.cfg, not hibernate.cfg.xml) -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-remote-resources-plugin</artifactId>
        <executions>
          <execution>
            <id>xwiki-configuration-resources</id>
          </execution>
          <execution>
            <id>xwiki-platform-tool-configuration-resources</id>
            <goals>
              <goal>process</goal>
            </goals>
            <configuration>
              <resourceBundles>
                <resourceBundle>org.xwiki.platform:xwiki-platform-tool-configuration-resources:${xwiki.version}</resourceBundle>
              </resourceBundles>
              <properties>
                <xwikiDbConnectionUrl>jdbc:hsqldb:file:${environment.permanentDirectory}/database/xwiki_db;shutdown=true;hsqldb.cache_size=50000;hsqldb.script_format=3;hsqldb.nio_max_size=512;hsqldb.lob_file_scale=16;hsqldb.default_table_type=cached;hsqldb.tx=mvcc</xwikiDbConnectionUrl>
                <xwikiDbConnectionUsername>sa</xwikiDbConnectionUsername>
                <xwikiDbConnectionPassword />
                <xwikiDbConnectionDriverClass>org.hsqldb.jdbcDriver</xwikiDbConnectionDriverClass>
                <xwikiDbDialect>org.hibernate.dialect.HSQLDialect</xwikiDbDialect>
                <xwikiDbHbmXwiki>xwiki.hbm.xml</xwikiDbHbmXwiki>
                <xwikiDbHbmFeeds>feeds.hbm.xml</xwikiDbHbmFeeds>
                <xwikiDbHbmCommonExtraMappings>instance.hbm.xml,mailsender.hbm.xml</xwikiDbHbmCommonExtraMappings>
                <xwikiCfgPlugins>\
  com.xpn.xwiki.monitor.api.MonitorPlugin,\
  com.xpn.xwiki.plugin.skinx.JsSkinExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.JsSkinFileExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.JsResourceSkinExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.CssSkinExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.CssSkinFileExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.CssResourceSkinExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.LinkExtensionPlugin,\
  com.xpn.xwiki.plugin.mail.MailPlugin,\
  com.xpn.xwiki.plugin.packaging.PackagePlugin,\
  com.xpn.xwiki.plugin.svg.SVGPlugin,\
  com.xpn.xwiki.plugin.fileupload.FileUploadPlugin,\
  com.xpn.xwiki.plugin.image.ImagePlugin,\
  com.xpn.xwiki.plugin.zipexplorer.ZipExplorerPlugin,\
  com.xpn.xwiki.plugin.diff.DiffPlugin,\
  com.xpn.xwiki.plugin.rightsmanager.RightsManagerPlugin,\
  com.xpn.xwiki.plugin.jodatime.JodaTimePlugin,\
  com.xpn.xwiki.plugin.mailsender.MailSenderPlugin</xwikiCfgPlugins>
                <xwikiCfgVirtual>0</xwikiCfgVirtual>
                <xwikiCfgVirtualUsepath>0</xwikiCfgVirtualUsepath>
                <xwikiCfgEditCommentMandatory>0</xwikiCfgEditCommentMandatory>
                <xwikiCfgDefaultSkin>phenotips</xwikiCfgDefaultSkin>
                <xwikiCfgDefaultBaseSkin>colibri</xwikiCfgDefaultBaseSkin>
                <xwikiCfgEncoding>UTF-8</xwikiCfgEncoding>
                <xwikiCfgAdditionalProperties>
xwiki.plugin.watchlist.automaticwatch=none
xwiki.authentication.group.allgroupimplicit=1
xwiki.authentication.rightsclass=org.phenotips.security.authorization.ModularRightServiceImpl
xwiki.section.edit=0
xwiki.backlinks=0
xwiki.showviewaction=0
xwiki.defaultweb=data
xwiki.usedefaultweb=1
xwiki.usedefaultaction=0
xwiki.monitor=0
xwiki.authentication.loginpage=/PhenomeCentral/login
xwiki.authentication.loginsubmitpage=/loginsubmit/PhenomeCentral/login
xwiki.store.attachment.hint=file
xwiki.store.attachment.versioning.hint=file
xwiki.store.attachment.recyclebin.hint=file
                </xwikiCfgAdditionalProperties>
                <xwikiPropertiesEnvironmentPermanentDirectory>/var/lib/phenotips/</xwikiPropertiesEnvironmentPermanentDirectory>
                <xwikiPropertiesAdditionalProperties>
model.reference.default.space=data
extension.repositories=maven-central:maven:https://nexus.phenotips.org/nexus/content/groups/public/
extension.repositories=maven-phenotips:maven:https://nexus.phenotips.org/nexus/content/repositories/releases/
extension.repositories=phenotips.org:xwiki:https://phenotips.org/rest/
rendering.transformations=macro
activeinstalls.pingURL=https://stats.phenotips.org
activeinstalls.ipFetchURL=https://phenotips.org/get/Stats/Id
                </xwikiPropertiesAdditionalProperties>
              </properties>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-war-plugin</artifactId>
        <configuration>
          <webResources>
            <!-- Include License resources -->
            <resource>
              <directory>${project.build.directory}/maven-shared-archive-resources/META-INF</directory>
              <targetPath>META-INF</targetPath>
            </resource>
            <resource>
              <directory>${project.build.directory}/maven-shared-archive-resources</directory>
              <targetPath>WEB-INF</targetPath>
              <includes>
                <include>xwiki.cfg</include>
                <include>xwiki.properties</include>
                <include>hibernate.cfg.xml</include>
              </includes>
            </resource>
          </webResources>
          <!-- - Exclude JCL and LOG4J since we want all logging to go through SLF4J. Note that we're excluding
                 log4j-<version>.jar but keeping log4j-over-slf4j-<version>.jar
               - Exclude legacy modules if the legacy profile is not enabled so that we don't have both aspectified JAR
                 and non aspectified ones
               - Exclude batik-js to prevent conflict with the patched version of Rhino used by yuicompressor used for
                 JSX. See http://jira.xwiki.org/jira/browse/XWIKI-6151 for more details.
               - Exclude JavaBeans Activation Framework (activation-*.jar) since it's included in Java SE 6.
          -->
          <packagingExcludes>
            WEB-INF/lib/activation-*.jar,
            WEB-INF/lib/batik-js-*.jar,
            WEB-INF/lib/commons-logging-*.jar,
            resources/js/xwiki/wysiwyg/**
          </packagingExcludes>
          <overlays>
            <overlay>
              <groupId>org.phenotips</groupId>
              <artifactId>phenotips-base-war</artifactId>
              <type>war</type>
              <targetPath>/</targetPath>
            </overlay>
             <overlay>
              <groupId>org.phenotips</groupId>
              <artifactId>matching-notification-resources</artifactId>
              <type>jar</type>
              <targetPath></targetPath>
            </overlay>
          </overlays>
        </configuration>
      </plugin>
      <!-- Ensure that some modules are not added as dependencies. -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-enforcer-plugin</artifactId>
        <executions>
          <execution>
            <id>enforce-banned-dependencies</id>
            <goals>
              <goal>enforce</goal>
            </goals>
            <configuration>
              <rules>
                <bannedDependencies>
                  <excludes>
                    <exclude>org.jmock:*</exclude>
                    <exclude>junit:*</exclude>
                    <exclude>javax.servlet:servlet-api:*:*:compile</exclude>
                    <exclude>javax.servlet:javax.servlet-api:*:*:compile</exclude>
                  </excludes>
                  <includes>
                    <!-- Allow only JUnit and JMock with scope test because -->
                    <include>org.jmock:*:*:*:test</include>
                    <include>junit:*:*:*:test</include>
                  </includes>
                </bannedDependencies>
              </rules>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>
</project>
<commit_msg>[misc] Reverted a change that broke the build<commit_after><?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>
  <parent>
    <groupId>org.phenomecentral</groupId>
    <artifactId>phenomecentral-parent</artifactId>
    <version>1.1-SNAPSHOT</version>
  </parent>
  <artifactId>phenomecentral-war</artifactId>
  <name>PhenomeCentral - War package</name>
  <packaging>war</packaging>
  <properties>
    <!-- By default we don't include Legacy modules and thus we don't need to exclude the non legacy JARs -->
    <xwiki.war.legacy.excludes />

    <!-- The default UI associated to this WAR -->
    <xwiki.extension.distribution.ui>org.phenomecentral:phenomecentral-ui</xwiki.extension.distribution.ui>
  </properties>
  <dependencies>
    <!-- Extend the base war -->
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-base-war</artifactId>
      <version>${phenotips.version}</version>
      <type>war</type>
    </dependency>

    <!-- XWiki dependencies -->
    <!-- Make sure to include the proper version of antlr for hibernate-core -->
    <dependency>
      <groupId>antlr</groupId>
      <artifactId>antlr</artifactId>
    </dependency>

    <!-- The new version of HTMLCleaner is required for PDFs to work properly -->
    <dependency>
      <groupId>net.sourceforge.htmlcleaner</groupId>
      <artifactId>htmlcleaner</artifactId>
    </dependency>

    <!-- The Big Old Core -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-oldcore</artifactId>
      <version>${xwiki.version}</version>
      <exclusions>
        <exclusion>
          <groupId>org.codehaus.groovy</groupId>
          <artifactId>groovy-all</artifactId>
        </exclusion>
      </exclusions>
    </dependency>

    <!-- Components Modules -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-component-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- REST module -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rest-server</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- ClassLoader -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-classloader-xwiki</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Container -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-container-servlet</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Extension Manager -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-extension-handler-jar</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-extension-handler-xar</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-extension-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-extension-repository-maven</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-extension-repository-xwiki</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-extension-cluster</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-extension-distribution</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>

    <!-- Default Rendering Macros we want available by default in XE.
         Please keep them in alphabetical order -->
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-box</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-comment</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-html</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-id</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-message</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-toc</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-macro-content</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-wikimacro-store</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-dashboard-macro</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-code</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-container</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-gallery</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-include</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-display-macro</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-useravatar</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-rendering-macro-velocity</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- XWiki Rendering Syntax Parsers -->
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-doxia</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
      <!-- Incompatible with the version of plexus used by Extension Manager aether module -->
      <exclusions>
        <exclusion>
          <artifactId>plexus-container-default</artifactId>
          <groupId>org.codehaus.plexus</groupId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-xwiki20</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-xwiki21</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-xhtml</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-html5</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-html</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.rendering</groupId>
      <artifactId>xwiki-rendering-syntax-plain</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Captcha component -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-captcha</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Crypto Module -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-crypto-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-crypto-store-filesystem</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-crypto-store-wiki</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- CSRF protection -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-csrf</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- XML Script Service -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-xml-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Filesystem attachment storage -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-store-filesystem-attachments</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- User Interface extensions -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-uiextension-api</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Security Script Services -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-security-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Skin Extension -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-skin-skinx</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- ZIP Explorer -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-zipexplorer</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Mailsender -->
    <!-- New Mail Sender API -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-mail-send-storage</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Old Mail Sender Plugin -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-mailsender</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- JODA Time -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-jodatime</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Diff Script Services -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-diff-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Blame Script Services -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-blame-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Logging Dependencies. Ensures all logging goes through SLF4J and Logback. -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-logging-logback</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-logging-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>jcl-over-slf4j</artifactId>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>log4j-over-slf4j</artifactId>
      <scope>runtime</scope>
    </dependency>
    <!-- Configuration -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-configuration-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Security -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-security-bridge</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Localization -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-localization-source-legacy</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-localization-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-localization-macro</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- URL -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-url-scheme-standard</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Filter -->
    <dependency>
      <groupId>org.xwiki.commons</groupId>
      <artifactId>xwiki-commons-filter-stream-xml</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-filter-instance-oldcore</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-filter-instance-extension</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-filter-instance-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-filter-stream-xar</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- Wiki Module -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-template-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-template-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-user-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-wiki-user-script</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- LESS CSS Module -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-lesscss-default</artifactId>
      <version>${xwiki.version}</version>
      <scope>runtime</scope>
    </dependency>
    <!-- LDAP -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-ldap-authenticator</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <!-- jQuery -->
    <dependency>
      <groupId>org.webjars</groupId>
      <artifactId>jquery</artifactId>
      <version>1.11.1</version>
    </dependency>
    <!-- Servlets for Resource API -->
    <dependency>
      <groupId>org.xwiki.platform</groupId>
      <artifactId>xwiki-platform-resource-servlet</artifactId>
      <version>${xwiki.version}</version>
    </dependency>
    <!-- PhenoTips components -->
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>component-registry</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>solr-access-service-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>gene-panels-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>gene-panels-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabularies-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabularies-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-hpo-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-hpo-annotations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-hpo-translation-spanish</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-chebi-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-omim-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-hgnc-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-ethnicity-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>vocabulary-ordo-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-contacts</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-default-impl</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-indexing</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-data-export-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-authorization</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-security-bridge</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-crypto-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-crypto-xproperty</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-access-rules-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-access-rules-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-access-rules-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-measurements-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-measurements-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>users-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-studies-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>xwiki-platform-users-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>xwiki-platform-users-wiki</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>application-configuration-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>application-configuration-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-tools</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>ncbieutils-services-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>obo2solr</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-sharing-push-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-data-sharing-receiver-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>specificity-meter-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-navigation-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-pedigree-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-skin-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-widgets-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>jodatime-service</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>storage-migrators-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>storage-migrators-attachments-migrator</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>storage-migrators-attachments-database</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>storage-migrators-attachments-filesystem</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>diagnosis-suggestion-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>phenotips-proxy-authentication</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>pingback-common</artifactId>
      <version>1.1</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>pingback-client-api</artifactId>
      <version>1.0</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>family-studies-api</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>family-studies-migrations</artifactId>
      <version>${phenotips.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>family-studies-rest</artifactId>
      <version>${phenotips.version}</version>
    </dependency>

    <!-- PhenomeCentral specific -->
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-similarity-data-api</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-similarity-data-impl</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-network-access-rules</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>patient-similarity-search</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>anonymous-communication</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>matching-notification-api</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>matching-notification-resources</artifactId>
      <version>${patientNetwork.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>remote-matching-core-server</artifactId>
      <version>${remoteMatching.version}</version>
    </dependency>
    <dependency>
      <groupId>org.phenotips</groupId>
      <artifactId>remote-matching-core-client</artifactId>
      <version>${remoteMatching.version}</version>
    </dependency>

    <!-- Add dependencies on the XAR distributions so that we transitively include all JAR dependencies in the generated WAR -->
    <dependency>
      <groupId>${project.groupId}</groupId>
      <artifactId>phenomecentral-ui</artifactId>
      <version>${project.version}</version>
      <type>xar</type>
    </dependency>
  </dependencies>
  <build>
    <plugins>
      <!-- Inject XWiki's configuration (only xwiki.cfg, not hibernate.cfg.xml) -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-remote-resources-plugin</artifactId>
        <executions>
          <execution>
            <id>xwiki-configuration-resources</id>
          </execution>
          <execution>
            <id>xwiki-platform-tool-configuration-resources</id>
            <goals>
              <goal>process</goal>
            </goals>
            <configuration>
              <resourceBundles>
                <resourceBundle>org.xwiki.platform:xwiki-platform-tool-configuration-resources:${xwiki.version}</resourceBundle>
              </resourceBundles>
              <properties>
                <xwikiDbConnectionUrl>jdbc:hsqldb:file:${environment.permanentDirectory}/database/xwiki_db;shutdown=true;hsqldb.cache_size=50000;hsqldb.script_format=3;hsqldb.nio_max_size=512;hsqldb.lob_file_scale=16;hsqldb.default_table_type=cached;hsqldb.tx=mvcc</xwikiDbConnectionUrl>
                <xwikiDbConnectionUsername>sa</xwikiDbConnectionUsername>
                <xwikiDbConnectionPassword />
                <xwikiDbConnectionDriverClass>org.hsqldb.jdbcDriver</xwikiDbConnectionDriverClass>
                <xwikiDbDialect>org.hibernate.dialect.HSQLDialect</xwikiDbDialect>
                <xwikiDbHbmXwiki>xwiki.hbm.xml</xwikiDbHbmXwiki>
                <xwikiDbHbmFeeds>feeds.hbm.xml</xwikiDbHbmFeeds>
                <xwikiDbHbmCommonExtraMappings>instance.hbm.xml,mailsender.hbm.xml</xwikiDbHbmCommonExtraMappings>
                <xwikiCfgPlugins>\
  com.xpn.xwiki.monitor.api.MonitorPlugin,\
  com.xpn.xwiki.plugin.skinx.JsSkinExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.JsSkinFileExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.JsResourceSkinExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.CssSkinExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.CssSkinFileExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.CssResourceSkinExtensionPlugin,\
  com.xpn.xwiki.plugin.skinx.LinkExtensionPlugin,\
  com.xpn.xwiki.plugin.mail.MailPlugin,\
  com.xpn.xwiki.plugin.packaging.PackagePlugin,\
  com.xpn.xwiki.plugin.svg.SVGPlugin,\
  com.xpn.xwiki.plugin.fileupload.FileUploadPlugin,\
  com.xpn.xwiki.plugin.image.ImagePlugin,\
  com.xpn.xwiki.plugin.zipexplorer.ZipExplorerPlugin,\
  com.xpn.xwiki.plugin.diff.DiffPlugin,\
  com.xpn.xwiki.plugin.rightsmanager.RightsManagerPlugin,\
  com.xpn.xwiki.plugin.jodatime.JodaTimePlugin,\
  com.xpn.xwiki.plugin.mailsender.MailSenderPlugin</xwikiCfgPlugins>
                <xwikiCfgVirtual>0</xwikiCfgVirtual>
                <xwikiCfgVirtualUsepath>0</xwikiCfgVirtualUsepath>
                <xwikiCfgEditCommentMandatory>0</xwikiCfgEditCommentMandatory>
                <xwikiCfgDefaultSkin>phenotips</xwikiCfgDefaultSkin>
                <xwikiCfgDefaultBaseSkin>colibri</xwikiCfgDefaultBaseSkin>
                <xwikiCfgEncoding>UTF-8</xwikiCfgEncoding>
                <xwikiCfgAdditionalProperties>
xwiki.plugin.watchlist.automaticwatch=none
xwiki.authentication.group.allgroupimplicit=1
xwiki.authentication.rightsclass=org.phenotips.security.authorization.ModularRightServiceImpl
xwiki.section.edit=0
xwiki.backlinks=0
xwiki.showviewaction=0
xwiki.defaultweb=data
xwiki.usedefaultweb=1
xwiki.usedefaultaction=0
xwiki.monitor=0
xwiki.authentication.loginpage=/PhenomeCentral/login
xwiki.authentication.loginsubmitpage=/loginsubmit/PhenomeCentral/login
xwiki.store.attachment.hint=file
xwiki.store.attachment.versioning.hint=file
xwiki.store.attachment.recyclebin.hint=file
                </xwikiCfgAdditionalProperties>
                <xwikiPropertiesEnvironmentPermanentDirectory>/var/lib/phenotips/</xwikiPropertiesEnvironmentPermanentDirectory>
                <xwikiPropertiesAdditionalProperties>
model.reference.default.space=data
extension.repositories=maven-central:maven:https://nexus.phenotips.org/nexus/content/groups/public/
extension.repositories=maven-phenotips:maven:https://nexus.phenotips.org/nexus/content/repositories/releases/
extension.repositories=phenotips.org:xwiki:https://phenotips.org/rest/
rendering.transformations=macro
activeinstalls.pingURL=https://stats.phenotips.org
activeinstalls.ipFetchURL=https://phenotips.org/get/Stats/Id
                </xwikiPropertiesAdditionalProperties>
              </properties>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-war-plugin</artifactId>
        <configuration>
          <webResources>
            <!-- Include License resources -->
            <resource>
              <directory>${project.build.directory}/maven-shared-archive-resources/META-INF</directory>
              <targetPath>META-INF</targetPath>
            </resource>
            <resource>
              <directory>${project.build.directory}/maven-shared-archive-resources</directory>
              <targetPath>WEB-INF</targetPath>
              <includes>
                <include>xwiki.cfg</include>
                <include>xwiki.properties</include>
                <include>hibernate.cfg.xml</include>
              </includes>
            </resource>
          </webResources>
          <!-- - Exclude JCL and LOG4J since we want all logging to go through SLF4J. Note that we're excluding
                 log4j-<version>.jar but keeping log4j-over-slf4j-<version>.jar
               - Exclude legacy modules if the legacy profile is not enabled so that we don't have both aspectified JAR
                 and non aspectified ones
               - Exclude batik-js to prevent conflict with the patched version of Rhino used by yuicompressor used for
                 JSX. See http://jira.xwiki.org/jira/browse/XWIKI-6151 for more details.
               - Exclude JavaBeans Activation Framework (activation-*.jar) since it's included in Java SE 6.
          -->
          <packagingExcludes>
            WEB-INF/lib/activation-*.jar,
            WEB-INF/lib/batik-js-*.jar,
            WEB-INF/lib/commons-logging-*.jar,
            resources/js/xwiki/wysiwyg/**
          </packagingExcludes>
          <overlays>
            <overlay>
              <groupId>org.phenotips</groupId>
              <artifactId>phenotips-base-war</artifactId>
              <type>war</type>
              <targetPath>/</targetPath>
            </overlay>
             <overlay>
              <groupId>org.phenotips</groupId>
              <artifactId>matching-notification-resources</artifactId>
              <type>jar</type>
              <targetPath></targetPath>
            </overlay>
          </overlays>
        </configuration>
      </plugin>
      <!-- Ensure that some modules are not added as dependencies. -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-enforcer-plugin</artifactId>
        <executions>
          <execution>
            <id>enforce-banned-dependencies</id>
            <goals>
              <goal>enforce</goal>
            </goals>
            <configuration>
              <rules>
                <bannedDependencies>
                  <excludes>
                    <exclude>org.jmock:*</exclude>
                    <exclude>junit:*</exclude>
                    <exclude>javax.servlet:servlet-api:*:*:compile</exclude>
                    <exclude>javax.servlet:javax.servlet-api:*:*:compile</exclude>
                  </excludes>
                  <includes>
                    <!-- Allow only JUnit and JMock with scope test because -->
                    <include>org.jmock:*:*:*:test</include>
                    <include>junit:*:*:*:test</include>
                  </includes>
                </bannedDependencies>
              </rules>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>
</project>

{'fraction_non_alphanumeric': 0.14774650535949352, 'fraction_numerical': 0.0018805240393656366, 'mean_word_length': 3.044518811479566, 'pattern_counts': {'":': 0, '<': 3127, '<?xml version=': 2, '>': 3127, 'https://': 10, 'lorem ipsum': 0, 'www.': 4, 'xml': 22}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3159909', 'n_tokens_mistral': 26581, 'n_tokens_neox': 23373, 'n_words': 2806}