addis-core

ADDIS 2.x core

Before starting

The setup in this readme requires several components to already be installed and running. Please refer to the OVERALL-README.md in this folder for more information on how to do so, and for other readmes that might be relevant.

Required software:

• yarn
• compass (for changing css)
• postgresql >= 9.5
• maven
• karma (for testing)

Run yarn from the root of the repository to retrieve the javascript dependencies.

Run npm run build-dev from the root of the repository to build the webapp.

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"

The database structure is automatically created via liquibase maven plugin.

If you wish to allow programmatic access via the API, you can insert an API key into the addiscore database (note there should already be an account present to link the key to):

INSERT INTO applicationkey (secretkey, accountid, applicationname, creationdate, revocationdate) values ('[yourkey]', [accountid], '[yourname]', 'mm/dd/yyyy', 'mm/dd/yyyy');

It is assumed in the example environment settings below that instances of Patavi and Jena-ES are running on ports 3000 and 3030, respecively.

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 also depend on GeoTrust. Note that in most Java distributions this CA is trusted by default, in which case you do not need to generate and configure the trust store.

To add the geotrust CA to your trustfile:

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

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=googleSecret
export ADDIS_CORE_OAUTH_GOOGLE_KEY=googleKey
export CLINICALTRIALS_IMPORTER_URL=importservicelocation

Running

mvn tomcat7:run

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.

Running ADDIS as a docker container

• check out the (dockerfiles repository)[https://github.com/drugis/dockerfiles]
• build addis WAR, using mvn package. Or: download a recent stable version from from https://drugis.org/files/addis-core.war
• supply the WAR and SSL keystore and truststore to the tomcat/Dockerfile from the dockerfiles repository
• build and run the dockerfile.

Example run script

docker run -d --name addis \
  --link postgres:postgres \
  --link patavi-server:patavi-server \
  --link jena-es:jena-es \
  -e JAVA_OPTS=" \
  -DADDIS_CORE_DB=addiscore \
  -DtomcatProxyScheme=https \
  -DtomcatProxyName=localhost \
  -DtomcatProxyPort=443 \
  -DADDIS_CORE_DB_DRIVER=org.postgresql.Driver \
  -DADDIS_CORE_DB_HOST=postgres \
  -DADDIS_CORE_DB=addiscore \
  -DADDIS_CORE_DB_USERNAME=addiscore \
  -DADDIS_CORE_DB_PASSWORD=<password> \
  -e PATAVI_URI=https://patavi-server:3000 \
  -e ADDIS_CORE_OAUTH_GOOGLE_SECRET=<google-secret> \
  -e ADDIS_CORE_OAUTH_GOOGLE_KEY=<google-key> \
  -e TRIPLESTORE_BASE_URI=https://jena-es:3030 \
  -e KEYSTORE_PATH=/ssl/keystore.jks \
  -e KEYSTORE_PASSWORD=develop \
  -e EVENT_SOURCE_URI_PREFIX=https://jena-es:3030 \
  -e CLINICALTRIALS_IMPORTER_URL=https://nct.drugis.org \
  -p 8081:8080 \
  -p 2223:22 \
  -t addis-tomcat

Styling

ADDIS css is generated using SASS. If you wish to change the css, first make sure the SASS submodule is present:

git submodule init
git submodule update

Then run 'compass compile' from the root of the repository.