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Gradle - FAQs

Gradle is InterMine’s build tool. In InterMine 2.0 Gradle replaced ant.

Please see Upgrade instructions for details on how to migrate your system to use Gradle and Gradle Quick Start for common Gradle commands.

I got an error: “Caused by: java.security.InvalidKeyException: EC parameters error”

InterMine 2.0 only works with Java 8+. Please update your Java version and that will fix this error.

I got an error: “Caused by: java.security.NoSuchProviderException: no such provider: SunEC”

InterMine 2.0 only works with Java 8+. Please update your Java version and that will fix this error.

I got an out of memory error! Help!

Gradle gets its properties differently from ant. Instead of ANT_OPTS, set GRADLE_OPTS. Use the same values but also append -Dorg.gradle.daemon=false to prevent the use of Gradle daemons.

I set GRADLE_OPTS properly and I still am getting an “out of memory” error message

Append -Dorg.gradle.daemon=false to prevent the use of Gradle daemons.

I got ANOTHER error: “java.lang.ClassCastException: org.apache.xerces.parsers.XIncludeAwareParserConfiguration cannot be cast to org.apache.xerces.xni.parser.XMLParserConfiguration “

Update your GRADLE_OPTS to disable deamons.

export GRADLE_OPTS=”-Dorg.gradle.daemon=false”

Error in log file when I deploy my webapp: “Caused by: java.io.IOException: Error writing request body to server”

Try ./gradlew cargoRedeployRemote instead of ./gradlew cargoDeployRemote

I tried to install my data source, but I got an exception saying it can’t find a class. I know this class IS in my data model though!

Update your source’s additions file to include this class.

Previously, all additions files listed in your project XML were merged into a single genomic_model.xml that was placed on your classpath. Now, instead, only the core data model and your additions file are merged into genomic_model.xml and placed in the JAR of the data source.

Alternatively, you can set the globalAdditionsFile parameter to specify a single file that will be merged into each of your data sources. Look for this configuration in your mine’s bio sources build.gradle file.

Where is InterMine code on my server?

The InterMine JARs are here on your machine:

# gradle - remote repos
~/.gradle/caches/modules-2/files-2.1/org.intermine/
# maven - local installs
~/.m2

You normally will be pulling the JARs down from the remote repository, unless you have installed the JARs locally yourself.

Which JAR am I using? I have JARs in both of those directories.

Here is an excerpt from the mine’s build.gradle file the determines which JAR is being used:

repositories {
    mavenLocal()
    jcenter()
    maven {
        url "https://oss.jfrog.org/artifactory/oss-snapshot-local"
    }
}

Gradle will go through each of these repositories and use the best version it finds.

Maven Local

Gradle first looks in mavenLocal() which is your ~/.m2/repository directory. These are JARs you have installed locally.

Remote Repositiories (JCenter and JFrog)

Gradle then looks in the remote repositories (JCenter and Jfrog).

JCenter is where our InterMine JARs are stored remotely.

JFrog is where our InterMine SNAPSHOT JARs are currently.

Gradle will use the JAR with the latest version. This is because we use the 2.0+ notation.

The versions for the JARs are set in each project:

intermine/build.gradle
plugin/build.gradle
bio/build.gradle
bio/sources/build.gradle
bio/postprocess/build.gradle

Currently this version is 2.1.1

Which dependency versions to use is set in the gradle.properties file for each project:

intermine/gradle.properties
plugin/gradle.properties
bio/gradle.properties
bio/sources/gradle.properties
bio/postprocess/gradle.properties

Currently set to 2.1+

You can overwrite this value and set these values in your mine’s gradle.properties file.

I got a different error! Help!

Please send a detailed stacktrace to the dev mailing list, or pop onto our discord – chat.intermine.org.

Common issues:

  • Always use the wrapper provided. ./gradlew and NOT gradle.
  • Using a daemon. Update your GRADLE_OPTS with the no-daemon flag.

See Troubleshooting tips for common error messages.