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project_build script

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 ant to avoid memory problems encountered when running many Java task sequentially from ant. It also has the option of dumping the production database during the build and recovering from these dumps in case of problems.

Note

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:

flymine $ wget https://raw.githubusercontent.com/intermine/intermine-scripts/master/project_build

Run the build script from the mine directory:

flymine $ ./project_build -b -v server_name /some/dump/location/dump_file_prefix

The 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 project.xml definition:

<source name="uniprot-malaria" type="uniprot" dump="true">
  <property name="uniprot.organisms" value="36329"/>
  <property name="src.data.dir" location="/data/flyminebuild/malaria/uniprot/7.7/36329"/>
</source>

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 project.xml).

It is also possible to run individual integrate and post-process steps separately, see below.

Command line options

The 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 ant (as -Drelease=release_number) [1]_.

Dump files take the name dump_file_prefix.final.

Running project_build with ‘’‘-l‘’’ will reload the latest dump (if any) with dump_file_prefix and restart the build from that point.

Note

You must use the full path to the dump file, e.g. /some/dump/location/dump_file_prefix

Running a Single Datasource

Before starting the build process you will need to set up the appropriate properties and then initialise your database with this command:

flymine $ ./gradlew builddb

Warning

Running the 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):

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

Most sources have multiple stages in retrieving data, to run just one stage use:

flymine $ ./gradlew integrate -Psource=uniprot -Paction=load --stacktrace

The stages are:

preretrieve
pre-processing that is done
retrieve
load data from source database/files into an items database
load
read from a target items database and integrate into the production database

See /system-requirements/software/gradle/ for the full list of common Gradle tasks, or run ./gradlew tasks to see the list of available tasks on the command line.

Running a Custom Datasource

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.

# run the install task to build your JAR
flymine-bio-sources $ ./gradlew install
# you can install a single source
flymine-bio-sources $ ./gradlew rnai:install

The install task will place the JAR in the Maven directory “~/.m2/repository”.