BioAssay Research Database (BARD)

To get the latest version of the source code, go to:

https://spotlite.nih.gov/ncats/bardweb/tree/master

Building and Installing BARD

Prerequisites

Before starting to build and installing BARD from source, you will need the following installed:

1. Grails 2.2.1 http://grails.org/
2. Maven http://maven.apache.org/ (Used to install 3rd party jars into a local repo)
3. An oracle database and an oracle user created with permissions to create views, triggers, stored procedures, function, and tables.
4. Redis 2.8.4 http://redis.io/
5. Tomcat 7.0.50 http://tomcat.apache.org/

Installation

Download and install the Oracle JDBC driver

The oracle java jdbc driver downloaded from http://www.oracle.com/technetwork/database/enterprise-edition/jdbc-112010-090769.html

The driver should be free, however, the license does not allow us to redistribute the driver, so you must download from oracle's site after agreeing to their license.

Install the oracle driver in your local maven repo with the following command:

mvn install:install-file -Dfile=ojdbc6-11.2.0.2.0.jar -DgroupId=com.oracle -DartifactId=ojdbc6 -Dversion=11.2.0.2.0 -Dpackaging=jar

Download instant JChem from ChemAxon and install jars into local maven repo

This will require you register with ChemAxon. Download instant JChem version 5.10.4, and specifically download the instantjchem-5_10_4.zip file. Extract the zip file and execute the following to import the needed jars into your repo.

mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans-concurrent.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans-concurrent -Dversion=5.10.4 -Dpackaging=jar
mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans-diverse-modules.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans-diverse-modules -Dversion=5.10.4 -Dpackaging=jar
mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans-formats-peptide.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans-formats-peptide -Dversion=5.10.4 -Dpackaging=jar
mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans-formats-smiles.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans-formats-smiles -Dversion=5.10.4 -Dpackaging=jar
mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans-formats.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans-formats -Dversion=5.10.4 -Dpackaging=jar
mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans-formats.cml.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans-formats.cml -Dversion=5.10.4 -Dpackaging=jar
mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans-formats.image.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans-formats.image -Dversion=5.10.4 -Dpackaging=jar
mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans-license.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans-license -Dversion=5.10.4 -Dpackaging=jar
mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans-plugin.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans-plugin -Dversion=5.10.4 -Dpackaging=jar
mvn install:install-file -Dfile=instantjchem/instantjchem/modules/ext/MarvinBeans.jar -DgroupId=ChemAxon -DartifactId=MarvinBeans -Dversion=5.10.4 -Dpackaging=jar

Check code out of github

Use git to clone the BARD repo locally.

git clone https://github.com/broadinstitute/BARD.git

In the following, I'll refer to the checked out directory (BARD) as $BARD_CHECKOUT

Build external lookup api for querying external ontologies and install jar in local maven repo

Change to the external-validation directory

cd $BARD_CHECKOUT/external-validation

copy gradle.properties_template to gradle.properties as follows

cp gradle.properties_template gradle.properties

copy eutils-java to your local mvn repository as follows

mvn install:install-file -Dfile=eutils-java-20130520.jar -DgroupId=edu.scripps -DartifactId=eutils-java -Dversion=20130520 -Dpackaging=jar

Then build the api jar as follows

./gradlew api:install

Create local configuration files

mkdir ~/.grails
mkdir ~/.grails/BARD
mkdir ~/.grails/dataExport
cp $BARD_CHECKOUT/sample_configs/BARD/BARD-production-config.groovy ~/.grails/BARD
cp $BARD_CHECKOUT/sample_configs/dataExport/dataExport-production-config.groovy ~/.grails/dataExport

Edit the file in ~/.grails/BARD replacing the following text with values for:

• DATABASE_HOST - The host the oracle database is running on
• DATABASE_SID - The oracle SID on that host to connect to
• USERNAME - The oracle user within the database which will hold the data for BARD
• PASSWORD - The oracle user password
• RESULTS_PATH - The path to a directory where results can be saved for transfering to the warehouse. The amount of space needed will depend on the volume of results loaded.
• WEB_SERVER_HOSTNAME - The name of the server which the webserver is running on.
• WAREHOUSE_API - The URL of the local warehouse API. (for example "http://bard.nih.gov/api" is the value used by public BARD)

Edit the file in ~/.grails/dataExport replacing the following text with values for:

• DATABASE_HOST - The host the oracle database is running on
• DATABASE_SID - The oracle SID on that host to connect to
• USERNAME - The oracle user within the database which will hold the data for BARD
• PASSWORD - The oracle user password
• RESULTS_PATH - The path to a directory where results can be saved for transfering to the warehouse. The amount of space needed will depend on the volume of results loaded.
• API_HASHED - a hashcode that will be used by client code to authenticate to the dataExport API. You can generate one with a command like "'foo' | md5sum".

Build and deploy BARD application

cd $BARD_CHECKOUT/BARD
grails compile -DuseBroadRepo=false

Set up database

The following will create all the necessary objects in the configured schema and populate reference data.

grails -Dgrails.env=production -DuseBroadRepo=false dbm-update --contexts=standard,insert-reference

You may see errors like "exception when trying to call bard_context.set_username" but these can be ignored. This happens when initializing an empty database because the package we use for auditing hasn't been installed yet. It will automatically be installed as part of the installation process. If the command's output ends with "Finished dbm-update" the set up process was successful and you can proceed to the next step.

Create BARD war and deploy

grails war -DuseBroadRepo=false BARD.war

Copy the BARD.war to your tomcat's webapp directory to deploy it.

Create dataExport API war and deploy

cd $BARD_CHECKOUT/dataExport
grails war -DuseBroadRepo=false dataExport.war

Copy the dataExport.war to your tomcat's webapp directory to deploy it

Set up environment variable for Tomcat

Add the following to the environment by editing your .bashrc file or simply executing the following before starting tomcat to increase the amount of memory that BARD is allowed to use.

export CATALINA_OPTS="-server -Djava.awt.headless=true -Xmx1024m -XX:MaxPermSize=512m"

With the WAR files in place, you can now start tomcat, and BARD should be accessible as "/BARD" once tomcat has finished starting.