openspecimen BIBBOX application

This container can be installed as BIBBOX APP or standalone.

After the docker installation follow these instructions.

Standalone Installation

Clone the github repository. If necessary change the ports in the environment file .env and the volume mounts in docker-compose.yml.

git clone https://github.com/bibbox/app-openspecimen
cd app-openspecimen
docker network create bibbox-default-network
docker-compose up -d

The main App can be opened and set up at:

http://localhost:9000

Install within BIBBOX

Visit the BIBBOX page and find the App by its name in the store. Click on the symbol and select install. Then fill the parameters below and name your App, click install again.

Docker Images used

• mysql
• bibbox/openspecimen

Install Environment Variables

• MYSQL_DATABASE_USER = The User of the DB created for OpenSpecimen
• MYSQL_DATABASE_PASSWORD = The Password of the DB User created for OpenSpecimen

The default values for the standalone installation are:

• MYSQL_DATABASE_USER = openspecimen
• MYSQL_DATABASE_PASSWORD = openspecimen

Mounted Volumes

mysql Container

• ./data/mysql:/var/lib/mysql
• ./configs/openspecimen.cnf:/etc/mysql/conf.d/openspecimen.cnf:ro

  bibbox/openspecimen Container

• ./data/os-data:/var/lib/tomcat9/openspecimen/data
• ./data/os-plugins:/var/lib/tomcat9/openspecimen/plugins
• ./configs/openspecimen/ROOT:/var/lib/tomcat9/webapps/ROOT
• ./configs/openspecimen/scripts/entrypoint.sh:/opt/scripts/entrypoint.sh

In case the installation process reccurently shows the following information message

INFO liquibase.executor.jvm.JdbcExecutor- SELECT LOCKED FROM openspecimen.DATABASECHANGELOGLOCK WHERE ID=1 INFO liquibase.lockservice.StandardLockService- Waiting for changelog lock....

and the installationis not proceeding, do the following:

• Enter your mysql:8.0.26 container (Attach Shell to it) and execute the commands listed below:

  mysql -uroot -p'openspecimen' (or your set MYSQL_ROOT_PASSWORD)

USE openspecimen

SELECT * from DATABASECHANGELOGLOCK;

UPDATE DATABASECHANGELOGLOCK SET LOCKED=FALSE, LOCKGRANTED=null, LOCKEDBY=null where ID=1;

• and rerun docker-compose up in the root folder of the project.