A gentle introduction to the HypergraphDB database.

1. HypergraphDB
NDBI040
Jan Drozen
http://www.ms.mff.cuni.cz/~drozenj

2. HypergraphDB (HGDB)
• open-source
• graph-oriented database
• embedded
• higher-order relationships
• queries and traversals
• indices
• transactions
• distribution

3. Hypergraph
• „is a family of sets over a universal set of vertices V“
• undirected graph where an edge can connect ANY number of
vertices

4. Data model
• basic unit is an atom
• each atom has associated tuple of atoms called target set
• the size of target set is arity
• arity 0 atoms are nodes, otherwise links
• let x is an atom then a set of atoms having x in target set is
incidence set of x
• set of links pointing to x
• each atom has its value
• each value has its type

5. Storage architecture
• physical storage independent
• needs key-value indexing storage
• uses BerkeleyDB
• two layers
• primitive storage layer
• model layer

6. Primitive storage layer
• low-level storage
• graph of identities and raw data
• consists of two key-value stores
• LinkStore: ID->List<ID>
• DataStore: ID->List<Byte>
• ID is cryptographically strong UID
• eliminating collisions
• type 4 UUID

7. Model layer
• atoms, type system, caching, indexing, queries
• formalizing layout of the primitive storage
• AtomID -> [type,value,{target set}]
• ValueID -> List<ID> | List<Byte>
• ValueID can form complex structures
• core indices needed – UUID -> SortedSet<UUID>
• IncidenceIndex
• maps hypergraph atom to set of all links pointing to it
• TypeIndex
• maps type atom to set of all its instance atoms
• ValueIndex
• maps a top-level value structure to the set of atoms with this value

8. Architecture

9. Types
• programming language neutral
• maps data values to/from permanent storage
• type is an atom too
• capable of storing, constructing and removing instances to/from
storage
• subtype/supertype relationships

10. Type system
• is bootstrapped from basic types
• predefined numbers, strings, records, lists, maps
• HGAtomType interface
• each type atom implements this one
• has an Object make(…) method
• type constructor is a type atom which make method returns an
HGAtomType instance
• records type constructor is managing records
• single record‘s parts are managed recursively
• as atoms
• as values

11. Java typing

12. Indices
• we are able to create indices
• maintained at primitive layer
• handled by type implementation
• and at model layer too
• are always associated with atom types (and sub-types)
• interface HGIndexer
• instances are atoms
• produces a key for given atom
• predefined indexers
• ByPartIndexer, ByTargetIndexer, CompositeIndexer, LinkIndexer,
TargetToTargetIndexer

13. Queries
• traversal
• DF or BF
• adjacency
• depending on atom type, traversal direction
• predicate match
• not necessarily linked atoms
• pattern matching of graph structures
• special query language needed (SPARQL)

14. Predicate match
• set-oriented queries
• set of query primitives:
• eq(x), lt(x), eq(“name“,x) compare atom‘s value
• target(LinkID) atom belongs to the target set of LinkID
• incident(TargetID) atom points to TargetID
• arity(n) arity of the atom is n
• and, or, not
• …
• lazy evaluation

15. Transactions
• multiversion consistency check
• ACI by default
• upon failure commited data may be lost
• transaction nesting
• auto-transactions (for updates)

16. Distribution
• implemented at model layer
• peer-to-peer
• Agent Communication Language
• propose, accept, inform, request, query,…
• not total availability
• eventually consistent
• upon startup each agent broadcasts interest in certain atoms (sending subscribe)
• each peer listens to atom events. After update, additon or removal notifies interested
peers (sending inform)
• local transactions are lineary ordered by a version number and logged (ensures
consistency, can reach all interested peers)
• a peer that received transaction notification must acknowledge it and decide whether
to enact the transaction locally or not

17. DEMO
• assume we have following situation:
• library containing some books, every book has an author, someone
could borrow some books, there can be friendships between people
Human
Book writen by Author
Name First name
Page count Last name
lent
Nationality friendship
Reader
First name
Last name

18. Queries
• we can now query the database:
• set-oriented queries:
• for all books of an author X
• for all books are currently lent to a friend of a person X
• traversal-oriented:
• get all people are connected with me via my friends

19. References
• http://www.hypergraphdb.org
• official website
• http://code.google.com/p/hypergraphdb/
• official Google code repository and Wiki

20. Thank you!