openspecimen-fair BIBBOX application

This container can be installed as BIBBOX APP or standalone.

After the docker installation follow these instructions.

• initial user: ** admin **

• initial password: ** Login@123 **

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-fair
cd app-openspecimen-fair
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

• bibbox/openspecimen
• mysql
• jupyter/datascience-notebook
• fairdata/fairdatapoint
• fairdata/fairdatapoint-client
• mongo
• metaphacts/blazegraph-basic
• neo4j

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
• JUPYTER_TOKEN =
• FDP_TITLE =
• FDP_DESCRIPTION =
• CATALOG_TITLE =
• CATALOG_DESCRIPTION =
• VERSION =
• PUBLISHERNAME =
• PUBLISHEREMAIL =
• PUBLISHERUID = Unique id of Publisher e.g. ORCID
• LANGUAGE = Language of Catalog and Dataset in IRI format. e.g. http://id.loc.gov/vocabulary/iso639-1/en

The default values for the standalone installation are:

• MYSQL_DATABASE_USER = user
• MYSQL_DATABASE_PASSWORD = changethisdatabasepasswordinproductionenvironments
• JUPYTER_TOKEN = token
• FDP_TITLE = fdp title
• FDP_DESCRIPTION = enter description
• CATALOG_TITLE = catalog title
• CATALOG_DESCRIPTION = catalog description
• VERSION = enter version
• PUBLISHERNAME = publisher name
• PUBLISHEREMAIL = [email protected]
• PUBLISHERUID = uid
• LANGUAGE = language

Mounted Volumes

bibbox/openspecimen Container

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

mysql Container

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

jupyter/datascience-notebook Container

• ./data/jupyter/home/jovyan/work:/home/jovyan/work

fairdata/fairdatapoint Container

• ./data/application.yml:/fdp/application.yml:ro

mongo Container

• ./data/mongo/data:/data/db

metaphacts/blazegraph-basic Container

• ./data/blazegraph:/blazegraph-data

neo4j Container

• ./data/neo4j/conf:/conf
• ./data/neo4j/data:/data
• ./data/neo4j/import:/import
• ./data/neo4j/logs:/logs
• ./data/neo4j/plugins:/plugins

Troubleshooting

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'

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.