To run a full build of InterMine, you must use the
project_build script. This is a Perl program that reads a project.xml file and loads each source in turn. This makes multiple calls to Gradle to avoid memory problems encountered when running many Java task sequentially from Gradle. It also has the option of dumping the production database during the build and recovering from these dumps in case of problems.
This script requires the Expect and XML::Parser::PerlSAX Text::Glob perl modules - install with:
sudo cpan -i XML::Parser::PerlSAX Expect Text::Glob
Download the file from the intermine-scripts repository:
Run the build script from the mine directory:
server_name is hostname of the machine where the
pg_dump command should be run. If you are running
project_build on the same machine as PostgreSQL then you should specify
localhost as the server name. If the PostgreSQL server is on a remote machine, give its hostname. In that case the script will try to run
pg_dump on the remote machine using
ssh. This makes dumping a little faster and allows for the case where
/some/dump/location/dump_file_prefix is only visible on the remote machine.
Dumps are performed when a source has
dump=true in its
In this example, the dump will be made immediately after the
uniprot-malaria source has been ''successfully'' merged.
Once all sources are integrated
project_build will run any post-processing steps (also configured in the
It is also possible to run individual integrate and post-process steps separately, see below.
project_build script accepts the following flags:
|-v||is passed to ant to make it run in verbose mode, ant output can be seen in pbuild.log|
|-l||attempt to restart by reading the last dump file (see note below)|
|-b||run build-db before starting build and drop any existing backup databases (created when using the -t flag)|
|-V||set the release number to pass to gradle (as -Prelease=release_number)|
Dump files take the name
Running project_build with '''
-l''' will reload the latest dump (if any) with
dump_file_prefix and restart the build from that point.
You must use the full path to the dump file, e.g.
Before starting the build process you will need to set up the appropriate properties and then initialise your database with this command:
builddb target will drop the current database and create a new, blank database.
To run a data source, run this command in your mine directory, specifying the source name (as it appears in project.xml):
Most sources have multiple stages in retrieving data, to run just one stage use:
The stages are:
pre-processing that is done
load data from source database/files into an items database
read from a target items database and integrate into the production database
/system-requirements/software/gradle/index for the full list of common Gradle tasks, or run
./gradlew tasks to see the list of available tasks on the command line.
The build script expects the data source to be on the classpath already. If you are using a data source provided by InterMine, that parser will be put on the classpath for you. If you are using a custom source, you will need to put it on the classpath yourself. You can use the Gradle Maven plugin task
install to compile your Java code, build the JAR and put on your classpath.
install task will place the JAR in the Maven directory \"~/.m2/repository\".