PB138 — XML databases, NoSQL databases

(C) 2019 Masaryk University -- Tomáš Pitner, Luděk Bártek, Adam Rambousek

NoSQL databases

  • non relational databases, flexible schema

  • often used for big data applications, clusters

  • different storage structure than SQL databases

  • give up constraints/transactions to improve performance

  • low-level interface

NoSQL types

  • key-value

    • Redis, Memcached, Amazon SimpleDB…​

  • document (JSON, XML…​)

    • CouchDB, Elasticsearch, MongoDB…​

  • graph / RDF triple

    • Virtuoso, Neo4j…​

  • object

    • Caché, GemStone…​

RDF databases / triple store

  • standard data model (RDF)

  • standardized interchange format (N-Triples, N-Quads, XML,…​)

  • query language (SPARQL), Linked Data

  • native

    • Apache Jena, Sesame/RDF4J…​

  • RDF layer to relational database

    • Virtuoso, IBM DB2…​

SPARQL

  • SPARQL Protocol and RDF Query Language

  • W3C Recommendation SPARQL 1.1, March 2013

  • SELECT - values as table

  • CONSTRUCT - extract RDF

  • ASK - true/false

  • DESCRIBE - extract RDF graph

  • inferencing

SPARQL example

Ontology
ex1:FullProfessor  rdf:subClassOf  ex1:Professor.
ex1:AssistantProfessor  rdf:subClassOf  ex1:Professor.
ex1:Professor  owl:equivalentClass  ex2:Teacher
Data
ex1:Bob  rdf:type  ex1:FullProfessor .
ex1:Alice  rdf:type  ex1:AssistantProfessor .
ex2:Mary  rdf:type  ex2:Teacher

SPARQL example

Data
ex1:Bob  rdf:type  ex1:FullProfessor .
ex1:Alice  rdf:type  ex1:AssistantProfessor .
ex2:Mary  rdf:type  ex2:Teacher
SPARQL query
SELECT ?x
 WHERE {
 ?x rdf:type ex1:Professor
 }

  • noone is Professor, but inferencing will find Bob, Alice, Mary

XML databases, when to use

  • working with documents or metadata in XML format

  • data format/schema changes over time

  • complex and variable schema

  • structure queries

XML database concepts

  • basic element = document

  • documents gathered in collections ("tables")

  • query on document structure

  • output is document, document fragment, or constructed XML

XML database types

  • XML-enabled databases

    • mapping XML data to own data model (relational, object…​)

      • character large object

      • fragmented to series of tables/objects

      • stored in XML Type

    • ISO SQL/XML - element construction, data mapping, enhanced SQL with XQuery

    • Oracle, IBM DB2, MS SQL, PostgreSQL

XML database types

  • native XML databases

    • using XML data model directly

  • open-source

    • eXist, Sedna, BaseX, MonetDB, Oracle/Berkeley DB XML

  • commercial

    • MarkLogic, Virtuoso, Qizx

Interface

XQuery
<titles>{
for $book in collection("books")/book where $book/year="1990"
return $book/title
}</titles>

Interface

XQuery Update
update delete collection("books")/book/isbn
update insert <title>XQuery Guide</title>
 into collection("books")/book[isbn="42"]

Interface

SQL/XML (result-table)
SELECT
   id, vol,
   xmlquery('$j/name', passing journal as "j") as name
FROM
   journals
WHERE
   xmlexists('$j[licence="CreativeCommons"]',
     passing journal as "j")

Interface

SQL/XML (result-XML)
SELECT XMLELEMENT (NAME "saleProducts",
     XMLNAMESPACES (DEFAULT 'http://posample.org'),
     XMLAGG (XMLELEMENT (NAME "prod",
        XMLATTRIBUTES (p.Pid AS "id"),
        XMLFOREST (p.name AS "name",
        i.quantity AS "numInStock"))))
FROM PRODUCT p, INVENTORY i
WHERE p.Pid = i.Pid

  • XSLT - output transformation

  • XML Schema - input validation

Interface

  • XQJ - XQuery API for Java

    • unified query layer between application and XML Datasource

    • prepared statements

    • binding variables

Interface

XQDataSource xqs = new ExistXQDataSource();
XQDataSource xqs = new SednaXQDataSource();
xqs.setProperty("serverName", "localhost");
XQConnection conn = xqs.getConnection();
XQExpression xqe = conn.createExpression();
String xqueryString =  "for $x in doc('books.xml')//book
   return $x/title/text()";
XQResultSequence rs = xqe.executeQuery(xqueryString);
while(rs.next())
  System.out.println(rs.getItemAsString(null));
conn.close();

Interface

  • XML:DB

  • similar concept to JDBC, abstract interface to XML database

    • Driver - access to given database

    • Collection - document collection in database

    • Services - support database features, e.g. XPathQueryService, XUpdateQueryService

    • Resource - data stored in database

    • ResourceSet - data as result of query

Storage

  • intact document storage

    • unique identifier for document

    • preferably parse and index on storage

    • on query: fast, if application need access to whole document and index can select the right document

    • slow, if additional parsing needed

Storage

  • parsing documents

    • document parsed on save and stored in own data model (eg. DOM)

    • addressable numbered nodes - some operations faster based on numbers

    • no need for parsing on query, more efficient

    • retrieved document not 100% same

    • fine granularity for addressing

    • partial modifications

Indexing

  • index scope - collection, database, document

  • index target - document, node

  • value index

    • store all combinations of element/attribute values

  • substring index

    • for contains() etc., store n-grams

Indexing

  • structural index

    • track existing paths, enriched tree, trie, DataGuide etc.

XML database index example

Benchmark

  • compare database performance

  • mostly XQuery speed, less often Update

  • data generator (up to GBs) and a set of XQueries

  • XMark, XBench, XMach-1

  • TPoX - complex database testing, XQuery and SQL/XML, indexing, XML Schema, XQuery Update