ivy.xml

<?xml version="1.0" encoding="UTF-8"?>
<ivy-module version="2.0"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://ant.apache.org/ivy/schemas/ivy.xsd">
  <info organisation="nibiohn" module="panomicon" />

<configurations>
  <conf name="compile"  description="Required to compile application"/>
  <conf name="runtime"  description="Additional run-time dependencies" extends="compile"/>
  <conf name="test"     description="Required for test only" extends="runtime"/>
  <conf name="provided" description="Needed for compile, but will be present on the target platform."/>
</configurations>

<!-- Dependencies go into the 'compile' configuration by default. -->
<dependencies defaultconf="compile->default">

  <!-- ===== OTGTool/backend dependencies ===== -->

  <dependency org="org.apache.commons" name="commons-math3" rev="latest.integration"/>

  <!--    <dependency org="com.sksamuel.scapegoat" name="scalac-scapegoat-plugin_2.12" rev="1.3.9"/> -->

  <!-- 3.7.4 is the latest version that supports Java 8. -->
  <dependency org="org.eclipse.rdf4j" name="rdf4j-repository-sparql" rev="3.7.4"/>

  <dependency org="org.eclipse.rdf4j" name="rdf4j-rio-turtle" rev="3.7.4"/>

  <dependency org="com.fizzed" name="jne" rev="latest.integration"/>

  <!-- for javax.annotation.Nullable -->
  <dependency org="com.google.code.findbugs" name="jsr305" rev="latest.integration"/>

  <dependency org="org.intermine" name="intermine-ws-java" rev="latest.integration">
    <!-- This pulls in a lot of dependencies that we probably do not need for our uses of the intermine ws client -->
    <exclude module="intermine-webapp" />
    <!-- We use the JCL to SLF4J bridge instead of commons-logging directly -->
    <exclude module="commons-logging" /> 
  </dependency>

  <!-- For intermine -->
  <dependency org="antlr" name="antlr" rev="2.7.6" />

  <!-- Various logging APIs are included indirectly, e.g. the JCL to SLF4J bridge. 
    (The 'ant ivyreport' task may be used to inspect the dependency graph.) 
    SLF4J is our preferred logging framework. -->
    <!-- <dependency org="org.slf4j" name="log4j-over-slf4j" rev="latest.integration" /> -->

      <dependency org="org.apache.logging.log4j" name="log4j-slf4j-impl" rev="latest.integration" /> 
      <dependency org="org.apache.logging.log4j" name="log4j-api" rev="latest.integration" />
      <dependency org="org.apache.logging.log4j" name="log4j-web" rev="latest.integration" />


  <!-- mapping maven scope'default' into the ivy configuration 'test' pulls in all 
  the dependencies, not just the top level module. -->
  <dependency org="org.scalatest" name="scalatest_2.12" rev="3.0.4" conf="test->default">
    <exclude module="scala-library" />
    <exclude module="scala-reflect" />
  </dependency>

  <dependency org="junit" name="junit" rev="4.12" conf="test->default" />

  <!-- ===== Panomicon/Toxygates/frontend dependencies ===== -->

  <dependency org="commons-fileupload" name="commons-fileupload" rev="latest.integration" />

  <dependency org="javax.mail" name="mail" rev="latest.integration"/>

  <!-- for R -->
  <dependency org="org.rosuda.REngine" name="Rserve" rev="latest.integration"/>

  <!-- ===== Scalatra server related dependencies ===== -->

  <dependency org="com.lihaoyi" name="upickle_2.12" rev ="latest.integration" />

  <!-- required for upickle -->
  <dependency org="org.scala-lang.modules" name="scala-collection-compat_2.12" rev="latest.integration" />

  <dependency org="org.scalatra" name="scalatra_2.12" rev="2.7.0" />


  <dependency org="io.fusionauth" name="fusionauth-java-client" rev="1.42.0" />

</dependencies>
</ivy-module>