Version: Next

Gradle - Quick Start

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 FAQs for commonly asked questions about Gradle.

Below are common commands you will use when building InterMine databases and deploying webapps. See docs.gradle.org for the full list.

Data sources#

Previously, all third party JARs were kept in the InterMine code repository and the build compiled all InterMine dependencies. Now, Gradle, via the Maven plugin, manages and downloads all JARs and only your local project is compiled.

To use local data sources

~/git/flymine-bio-sources $ ./gradlew install

  • See the maven plugin docs on the install task for details.

  • Example: https://github.com/intermine/flymine-bio-sources - FlyMine-specific data sources.

  • When installed locally, the JAR that is produced is available in the

    maven repo located in ~/.m2/repository

  • The JARs downloaded as dependencies are available in the Gradle

    cache, ~/.gradle/caches/modules-2/files-2.1/.

Note The build is going to be looking at the resulting JAR created by this command. If you make any changes to your data sources, install again to update the JAR to make those changes visible to the build.

To use common data sources in the InterMine library

  • No action required. Use project XML file as normal.

The migration script you used already set up the dependency to the intermine-bio-sources project. This project includes uniprot and other data sources, and are on the classpath. During the build, the code will look for the uniprot jar, e.g. bio-source-uniprot-2.0.jar and find it on the classpath successfully. Maven will download it for you.

Database#

Delete and recreate all database tables

~/git/flymine $ ./gradlew buildDB

Delete and recreate all database tables using a specific property file.

~/git/flymine $ ./gradlew buildDB -Dorg.gradle.project.release=dev

To run a single source

~/git/flymine $ ./gradlew integrate -Psource=uniprot --stacktrace

Note You can try --info or --debug too

To run a single postprocess

~/git/flymine $ ./gradlew postprocess -Pprocess=do-sources --stacktrace

To run a full build

~/git/flymine $ ./project_build -b localhost /tmp/flymine-dump

We are using the same project build script, but we've moved it to the intermine-scripts repository with our other scripts.

Webapp#

To deploy your InterMine webapp you can use the cargo gradle plugin. Run ./gradlew tasks to see all the available tasks.

Deploy a webapp to a running Tomcat instance#

~/git/flymine $ ./gradlew cargoDeployRemote
~/git/flymine $ ./gradlew cargoRedeployRemote
~/git/flymine $ ./gradlew cargoUndeployRemote

Uses the config in the mine properties file, e.g. flymine.properties, to deploy the webapp, see below.

Property nameExampleDetermines
webapp.hostnamelocalhostname of host. If not set, tries to use webapp.deploy.url
webapp.pathflyminelocation of path of webapp
webapp.managerTOMCAT_USERtomcat username, needed to deploy webapp
webapp.passwordTOMCAT_PWDtomcat password, needed to deploy webapp
webapp.protocolhttpsOPTIONAL, defaults to http
webapp.port8081OPTIONAL, defaults to 8080

Note Cargo uses hot deployment which over time, fills up the PermGen memory of the JVM process running your container. Continuously deploying an artifact will inevitably lead to a java.lang.OutOfMemoryError

Deploy a webapp with embedded Tomcat#

Only on your local dev machines.

~/git/flymine $ ./gradlew cargoRunLocal
  • Embedded tomcat, uses port 8080.

Trying out BlueGenes#

note

This approach is only recommended for trying out the app. See BlueGenes for deploying to a production environment.

~/git/flymine $ ./gradlew blueGenesStart
  • The app will run at localhost on port 5000.
  • Will use systemProp.blueGenesVersion defined in gradle.properties file.
  • Uses the following parameters defined in the ~/.intermine/$MINE.properties file.
purposeparameterexample
base URL for mine's web serviceswebapp.baseurlhttp://www.flymine.org
path appended to the base URL and unique namespace for minewebapp.pathflymine
name of your mine as it will be displayed in BlueGenesproject.titleBioTestMine
location of JavaScript toolsbluegenes.toolLocation/intermine/tools/

Specify properties file#

To use a specific properties file, set the file suffix with the -Dorg.gradle.project.release parameter like so:

~/git/flymine $ ./gradlew builddb -Dorg.gradle.project.release=dev

That command will build the database set in the flymine.properties.dev file.

Gradle#

To see a list of command-line options, run:

./gradlew --help

To see what tasks are available, run:

./gradlew tasks

To get rid of compiled files, run:

./gradlew clean

To update your local packages, run:

./gradlew install

  • See Local installation for how to install InterMine locally. (You shouldn't do

    this normally, instead use the JARs available via Maven).

  • Always use ./gradlew instead of gradle. This is the wrapper that comes with InterMine and ensures that everyone is using the same version.

Daemons#

The updated Gradle version comes with daemons enabled by default. These are helper processes that exist in the background. This can speed up builds for example, but sometimes, under heavy development, can cause problems when InterMine does not properly dereference assets. We are working on fixing this! In the meantime, you should append -Dorg.gradle.daemon=false to your GRADLE_OPTS variable.

Further Reading#

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