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Easy and secure deployment
of Glowing Bear and tranSMART
Ewelina Grudzień - Software Engineer - The Hyve

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Agenda
1.Deployment methods overview
2.Why containers?
3.Glowing Bear and tranSMART with Docker - solution
overview

3.
▶ Directly on the server
▶ dependency conflicts
▶ Virtual machines
▶ high isolation, security
▶ deployment automation
▶ require more resources, each VM runs in its own OS
▶ long startup time
▶ Container deployment
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Deployment methods overview

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▶ consistent environment,
▶ isolation
▶ lightweight
▶ fast to launch
▶ scalable
Why containers?

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▶ fast deployment - development and production
▶ ensuring security
▶ standardization
▶ simplification of the configuration
▶ easy database population and updates
▶ solving dependency issues
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Our main deployment goals

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Data warehouse components

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Data warehouse components

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Dockerized components

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▶ tranSMART – Liquibase
( thehyve/transmart-core/transmart-schemas)
▶ create database on startup if does not exist
▶ updates - apply database schema changes
▶ Glowing Bear Backend - using Hibernate to automatically create the
database from the domain model
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Empty database population

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▶ single process = single container
▶ application - part of the image
▶ smallest images possible
▶ base images - alpine-based, official
▶ only necessary tools and libraries
- reduced number of vulnerabilities
▶ configuration - environment variables
▶ data - external volumes
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Following best practises

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Central public repository
▶ versioning
▶ documentation
▶ startall/stopall script
▶ configuration - “.env” file
▶ additional services:
▶ Identity provider - Keycloak + db
▶ Dockerfile for SSL proxy
thehyve/glowing-bear-docker

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Central repository - thehyve/glowing-bear-docker

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Image publishing process
Transmart-api-server image for tranSMART 17.x

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Extension example - transmart-packer (export)

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Extension example - Variant Store Connector

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Security - docker networks

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Security - proxy

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Security - SSL proxy

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Keycloak
▶ OpenID Connect security protocol support
▶ sync users from LDAP and Active Directory servers

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Multiple warehouses - one server

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Multiple warehouses - separate servers

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▶ stdout/stderr
▶ journald
▶ status endpoints - Health Check Actuator
○ sensu monitoring server
○ Grafana - visualization
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Logging and monitoring

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▶ glowing-bear-docker repository:
https://github.com/thehyve/glowing-bear-docker
▶ Loading tools:
transmart-copy: https://github.com/thehyve/transmart-core/tree/dev/transmart-copy
▶ TranSMART 17.2 & Glowing Bear documentation:
○ glowingbear.app
○ https://github.com/thehyve/transmart-core/docs
Visit our table to learn more!
Where to start?

24.
Acknowledgement
The development of the solution was funded by DIFUTURE consortium
and Eberhard Karls University Tübingen.