addis-core

ADDIS 2.x core

Make sure the SASS and Bower submodules are present:

git submodule init
git submodule update

Make sure you've run make in the src/main/webapp/resources directory first to generate the CSS.

Make sure you have the bower components needed by running bower update from the root of the repository

Running

Set up the database:

sudo -u postgres psql -c "CREATE USER addiscore WITH PASSWORD 'develop'"
sudo -u postgres psql -c "CREATE DATABASE addiscore ENCODING 'utf-8' OWNER addiscore"

sudo -u postgres psql -c "CREATE USER patavitask WITH PASSWORD 'develop'"
sudo -u postgres psql -c "CREATE DATABASE patavitask ENCODING 'utf-8' OWNER patavitask"

In addition to this, you will need an instance of Patavi and Jena-ES running. It is assumed here that Patavi is running on port 3000 and Jena-ES on port 3030.

To authenticate with Patavi, you need a client certificate signed by the Certificate Authority (CA) trusted by Patavi, in a JKS keystore.

If Patavi presents a certificate signed by your own CA, you need to trust that CA. To do this, generate a JKS truststore. This needs to contain the certificate of your own CA and (for OAuth) Google's CA (GeoTrust). The drugis.org domains are signed by StartCom. In that case, the trust store should contain:

keytool -importcert -file /etc/ssl/certs/GeoTrust_Global_CA.pem -alias geotrustCA -keystore <jks location>
keytool -importcert -file /etc/ssl/certs/StartCom_Certification_Authority.pem -alias startcomCA -keystore <jks location>

However, in most Java distributions these CAs are trusted by default, so you do not need to generate and configure the trust store in that case.

Set up the environment:

export KEYSTORE_PATH=/path/to/keyStore
export KEYSTORE_PASSWORD="develop"
export TRIPLESTORE_BASE_URI=http://localhost:3030
export PATAVI_URI=http://localhost:3000

export PATAVI_TASK_DB_DRIVER=org.postgresql.Driver
export PATAVI_TASK_DB_HOST=localhost
export PATAVI_TASK_DB=patavitask
export PATAVI_TASK_DB_USERNAME=patavitask
export PATAVI_TASK_DB_PASSWORD=develop

export ADDIS_CORE_DB_CHANGELOG=database.sql
export ADDIS_CORE_DB_DRIVER=org.postgresql.Driver
export ADDIS_CORE_DB_HOST=localhost
export ADDIS_CORE_DB=addiscore
export ADDIS_CORE_DB_USERNAME=addiscore
export ADDIS_CORE_DB_PASSWORD=develop
export ADDIS_CORE_OAUTH_GOOGLE_SECRET=HU_-JxoYUvMbvk4vVRMhHibI
export ADDIS_CORE_OAUTH_GOOGLE_KEY=201346854981-3pcdhh96orc3lcdr8k4i1u58pvepjme4.apps.googleusercontent.com
export CLINICALTRIALS_IMPORTER_URL=[importservicelocation]

Run the Tomcat server:

mvn tomcat7:run -Djavax.net.ssl.trustStore=/path/to/trust/store

To run integration tests:

mvn test -Dtest=*IT

Backup and restore

To back up the ADDIS data:

• stop the ADDIS application
• stop the Jena-ES server
• (if necessary) remove the tdb.lock file in the Jena-ES DB directory (it may remain after shutdown due to a bug)
• pg_dump the contents of the ADDIS database
• tdbdump --loc=DB > backup.n4 the contents of the Jena-ES database

To restore the ADDIS data:

• (if necessary) clear the SQL and Jena-ES databases
• \i backup.sql in the psql client
• tdbloader --loc=DB backup.n4

If not restoring to the same environment, use the util/changePrefix.sh script to change the triple store location.