Bio4j + Statika: Managing module dependencies on the type level

Bio4j bioinformatics graph database is modular and customizable, allowing you to import just the data you are interested in. There exist, though, dependencies among these resources that must be taken into account and that's where Statika enters the picture; a set of Scala libraries which allows you to declare dependencies between components of any modular system and track their correctness using Scala type system. Thanks to this, it's possible now to deploy only selected components of the integrated data sets, with Amazon Web Services deployments on hardware specifically configured for them.

These are the slides of the talk, given by Alexey Alekhin at FOSDEM 2014:
https://fosdem.org/2014/schedule/event/graphdevroom_bio4j_1/

Transcript

1. BIO4J + STATIKA ALEXEY ALEKHIN GRAPH DEVROOM @ FOSDEM 2014
2. BIO4J MODULES
3. BIO4J DATA SOURCES
4. BIO4J MODULES HIERARCHY
5. BIO4J CUSTOM RELEASES
6. BIO4J CUSTOM RELEASES
7. GOALS Flexible module system Simple import process Dependencies management Easy and robust deployment
8. STATIKA
9. WHAT IS STATIKA
10. ABSTRACT MODULE SYSTEM Modules as Scala types — bundles They can depend on each other! It’s validated by compiler — i.e. statically Linearizing types graph to get them in the right order
11. MANAGING ARTIFACTS Packing bundles into versioned artifacts (jars) Reusing (Simple Build Tool) infrastructure Standardizing settings and release process with the SBT sbt-statika plugin
12. DEPLOYMENT + Amazon Web Services aws-statika lib Bundles can be applied, i.e. deployed it to an EC2 instance Statika distributions — an abstraction for the cloud infrastructure specifics
13. BIO4J + STATIKA
14. DEFINING BIO4J MODULES Raw data Node/relations type defs Importing process Exposing some API
15. INNER BUNDLES LAYOUT
16. INNER BUNDLES LAYOUT EXAMPLE
17. INCREMENTAL IMPORT Incremental import of data to existing Bio4j distributions Not repeating already done work Easy to describe abstractly
18. INCREMENTAL IMPORT EXAMPLE
19. CUSTOM RELEASE OF BIO4J create a release-bundle with needed modules be sure not to spend resources on a wrong configuration — compile it! use tools for easy release and deployment: + sbt-statika statika-cli
20. SUMMARY
21. BIO4J + STATIKA = WIN! Abstract layout of bundles Hierarchy of concrete modules Tracking deps on all levels Doing it at compile time Using AWS cloud infrastructure for the actual work