Input and Output with Xquery and XML Databases
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SPARQL with Xquery-Based Filtering?
SPARQL with XQuery-based Filtering? Takahiro Komamizu Nagoya University, Japan [email protected] Abstract. Linked Open Data (LOD) has been proliferated over vari- ous domains, however, there are still lots of open data in various format other than RDF, a standard data description framework in LOD. These open data can also be connected to entities in LOD when they are as- sociated with URIs. Document-centric XML data are such open data that are connected with entities in LOD as supplemental documents for these entities, and to convert these XML data into RDF requires various techniques such as information extraction, ontology design and ontology mapping with human prior knowledge. To utilize document-centric XML data linked from entities in LOD, in this paper, a SPARQL-based seam- less access method on RDF and XML data is proposed. In particular, an extension to SPARQL, XQueryFILTER, which enables XQuery as a filter in SPARQL is proposed. For efficient query processing of the combination of SPARQL and XQuery, a database theory-based query optimization is proposed. Real-world scenario-based experiments in this paper showcase that effectiveness of XQueryFILTER and efficiency of the optimization. 1 Introduction Open data movement is a worldwide movement that data are published online with FAIR principle1. Linked Open Data (LOD) [4] started by Sir Tim Berners- Lee is best aligned with this principle. In LOD, factual records are represented by a set of triples consisting of subject, predicate and object in the form of a stan- dardized representation framework, RDF (Resource Description Framework) [5]. Each element in RDF is represented by network-accessible identifier called URI (Uniform Resource Identifier). -
Basex Server
BaseX Documentation Version 7.8 BaseX Documentation: Version 7.8 Content is available under Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0). Table of Contents 1. Main Page .............................................................................................................................. 1 Getting Started .................................................................................................................. 1 XQuery Portal .................................................................................................................... 1 Advanced User's Guide ..................................................................................................... 2 I. Getting Started ........................................................................................................................ 3 2. Command-Line Options ................................................................................................... 4 BaseX Standalone ..................................................................................................... 4 BaseX Server ............................................................................................................ 6 BaseX Client ............................................................................................................. 7 BaseX HTTP Server .................................................................................................. 9 BaseX GUI ............................................................................................................. -
Building Xquery Based Web Service Aggregation and Reporting Applications
TECHNICAL PAPER BUILDING XQUERY BASED WEB SERVICE AGGREGATION AND REPORTING APPLICATIONS TABLE OF CONTENTS Introduction ........................................................................................................................................ 1 Scenario ............................................................................................................................................ 1 Writing the solution in XQuery ........................................................................................................... 3 Achieving the result ........................................................................................................................... 6 Reporting to HTML using XSLT ......................................................................................................... 6 Sample Stock Report ......................................................................................................................... 8 Summary ........................................................................................................................................... 9 XQuery Resources ............................................................................................................................ 9 www.progress.com 1 INTRODUCTION The widespread adoption of XML has profoundly altered the way that information is exchanged within and between enterprises. XML, an extensible, text-based markup language, describes data in a way that is both hardware- and software-independent. As such, -
Declarative Access to Filesystem Data New Application Domains for XML Database Management Systems
Declarative Access to Filesystem Data New application domains for XML database management systems Alexander Holupirek Dissertation zur Erlangung des akademischen Grades Doktor der Naturwissenschaften (Dr. rer. nat.) Fachbereich Informatik und Informationswissenschaft Mathematisch-Naturwissenschaftliche Sektion Universität Konstanz Referenten: Prof. Dr. Marc H. Scholl Prof. Dr. Marcel Waldvogel Tag der mündlichen Prüfung: 17. Juli 2012 Abstract XML and state-of-the-art XML database management systems (XML-DBMSs) can play a leading role in far more application domains as it is currently the case. Even in their basic configuration, they entail all components necessary to act as central systems for complex search and retrieval tasks. They provide language-specific index- ing of full-text documents and can store structured, semi-structured and binary data. Besides, they offer a great variety of standardized languages (XQuery, XSLT, XQuery Full Text, etc.) to develop applications inside a pure XML technology stack. Benefits are obvious: Data, logic, and presentation tiers can operate on a single data model, and no conversions have to be applied when switching in between. This thesis deals with the design and development of XML/XQuery driven informa- tion architectures that process formerly heterogeneous data sources in a standardized and uniform manner. Filesystems and their vast amounts of different file types are a prime example for such a heterogeneous dataspace. A new XML dialect, the Filesystem Markup Language (FSML), is introduced to construct a database view of the filesystem and its contents. FSML provides a uniform view on the filesystem’s contents and allows developers to leverage the complete XML technology stack on filesystem data. -
Xquery Tutorial
XQuery Tutorial Agenda • Motivation&History • Basics • Literals • XPath • FLWOR • Constructors • Advanced • Type system • Functions • Modules 2 Motivation • XML Query language to query data stores • XSLT for translation, not for querying • Integration language • Connect data from different sources • Access relational data represented as XML • Use in messaging systems • Need expressive language for integration 3 Design Goals • Declarative & functional language • No side effects • No required order of execution etc. • Easier to optimize • Strongly typed language, can handle weak typing • Optional static typing • Easier language • Non-XML syntax • Not a cumbersome SQL extension 4 History • Started 1998 as “Quilt” • Influenced by database- and document-oriented community • First W3C working draft in Feb 2001 • Still not a recommendation in March 2006 • Lots of implementations already available • Criticism: much too late • Current work • Full text search • Updates within XQuery 5 A composed language • XQuery tries to fit into the XML world • Based on other specifications • XPath language • XML Schema data model • various RFCs (2396, 3986 (URI), 3987 (IRI)) • Unicode • XML Names, Base, ID • Think: XPath 1.0 + XML literals + loop constructs 6 Basics • Literals • Arithmetic • XPath • FLWOR • Constructors 7 Basics - Literals • Strings • "Hello ' World" • "Hello "" World" • 'Hello " World' • "Hello $foo World" – doesn't work! • Numbers • xs:integer - 42 • xs:decimal – 3.5 • xs:double - .35E1 • xs:integer* - 1 to 5 – (1, 2, 3, 4, 5) 8 Literals (ctd.) -
Xpath and Xquery
XPath and XQuery Patryk Czarnik Institute of Informatics University of Warsaw XML and Modern Techniques of Content Management – 2012/13 . 1. Introduction Status XPath Data Model 2. XPath language Basic constructs XPath 2.0 extras Paths 3. XQuery XQuery query structure Constructors Functions . 1. Introduction Status XPath Data Model 2. XPath language Basic constructs XPath 2.0 extras Paths 3. XQuery XQuery query structure Constructors Functions . XPath XQuery . Used within other standards: Standalone standard. XSLT Main applications: XML Schema XML data access and XPointer processing XML databases . DOM . Introduction Status XPath and XQuery Querying XML documents . Common properties . Expression languages designed to query XML documents Convenient access to document nodes Intuitive syntax analogous to filesystem paths Comparison and arithmetic operators, functions, etc. Patryk Czarnik 06 – XPath XML 2012/13 4 / 42 Introduction Status XPath and XQuery Querying XML documents . Common properties . Expression languages designed to query XML documents Convenient access to document nodes Intuitive syntax analogous to filesystem paths Comparison and arithmetic operators, functions, etc. XPath XQuery . Used within other standards: Standalone standard. XSLT Main applications: XML Schema XML data access and XPointer processing XML databases . DOM . Patryk Czarnik 06 – XPath XML 2012/13 4 / 42 . XPath 2.0 . Several W3C Recommendations, I 2007: XML Path Language (XPath) 2.0 XQuery 1.0 and XPath 2.0 Data Model XQuery 1.0 and XPath 2.0 Functions and Operators XQuery 1.0 and XPath 2.0 Formal Semantics Used within XSLT 2.0 Related to XQuery 1.0 . Introduction Status XPath — status . XPath 1.0 . W3C Recommendation, XI 1999 used within XSLT 1.0, XML Schema, XPointer . -
Using Map and Reduce for Querying Distributed XML Data
Using Map and Reduce for Querying Distributed XML Data Lukas Lewandowski Master Thesis in fulfillment of the requirements for the degree of Master of Science (M.Sc.) Submitted to the Department of Computer and Information Science at the University of Konstanz Reviewer: Prof. Dr. Marc H. Scholl Prof. Dr. Marcel Waldvogel Abstract Semi-structured information is often represented in the XML format. Although, a vast amount of appropriate databases exist that are responsible for efficiently storing semi- structured data, the vastly growing data demands larger sized databases. Even when the secondary storage is able to store the large amount of data, the execution time of complex queries increases significantly, if no suitable indexes are applicable. This situation is dramatic when short response times are an essential requirement, like in the most real-life database systems. Moreover, when storage limits are reached, the data has to be distributed to ensure availability of the complete data set. To meet this challenge this thesis presents two approaches to improve query evaluation on semi- structured and large data through parallelization. First, we analyze Hadoop and its MapReduce framework as candidate for our distributed computations and second, then we present an alternative implementation to cope with this requirements. We introduce three distribution algorithms usable for XML collections, which serve as base for our distribution to a cluster. Furthermore, we present a prototype implementation using a current open source database, named BaseX, which serves as base for our comprehensive query results. iii Acknowledgments I would like to thank my advisors Professor Marc H. Scholl and Professor Marcel Wald- vogel, who have supported me with advice and guidance throughout my master thesis. -
Xpath, Xquery and XSLT
XPath, XQuery and XSLT Timo Lilja February 25, 2010 Timo Lilja () XPath, XQuery and XSLT February 25, 2010 1 / 24 Introduction When processing, XML documents are organized into a tree structure in the memory All XML Query and transformation languages operate on this tree XML Documents consists of tags and attributes which form logical constructs called nodes The basic operation unit of these query/processing languages is the node though access to substructures is provided Timo Lilja () XPath, XQuery and XSLT February 25, 2010 2 / 24 XPath XPath XPath 2.0 [4] is a W3C Recomendation released on January 2007 XPath provides a way to query the nodes and their attributes, tags and values XPath type both dynamic and static typing if the XML Scheme denition is present, it is used for static type checking before executing a query otherwise nodes are marked for untyped and they are coerced dynamically during run-time to suitable types Timo Lilja () XPath, XQuery and XSLT February 25, 2010 3 / 24 XPath Timo Lilja () XPath, XQuery and XSLT February 25, 2010 4 / 24 XPath Path expressions Path expressions provide a way to choose all matching branches of the tree representation of the XML Document Path expressions consist of one or more steps separated by the path operater/. A step can be an axis which is a way to reference a node in the path. a node-test which corresponds to a node in the actual XML document zero or more predicates Syntax for the path expressions: /step/step Syntaxc for a step: axisname::nodestest[predicate] Timo Lilja () XPath, XQuery and XSLT February 25, 2010 5 / 24 XPath Let's assume that we use the following XML Docuemnt <bookstore> <book category="COOKING"> <title lang="it">Everyday Italian</title> <author>Giada De Laurentiis</author> <year>2005</year> <price>30.00</price> </book> <book category="CHILDREN"> <title lang="en">Harry Potter</title> <author>J K. -
Evolutionary Tree-Structured Storage: Concepts, Interfaces, and Applications
Evolutionary Tree-Structured Storage: Concepts, Interfaces, and Applications Dissertation submitted for the degree of Doctor of Natural Sciences Presented by Marc Yves Maria Kramis at the Faculty of Sciences Department of Computer and Information Science Date of the oral examination: 22.04.2014 First supervisor: Prof. Dr. Marcel Waldvogel Second supervisor: Prof. Dr. Marc Scholl i Abstract Life is subdued to constant evolution. So is our data, be it in research, business or personal information management. From a natural, evolutionary perspective, our data evolves through a sequence of fine-granular modifications resulting in myriads of states, each describing our data at a given point in time. From a technical, anti- evolutionary perspective, mainly driven by technological and financial limitations, we treat the modifications as transient commands and only store the latest state of our data. It is surprising that the current approach is to ignore the natural evolution and to willfully forget about the sequence of modifications and therefore the past state. Sticking to this approach causes all kinds of confusion, complexity, and performance issues. Confusion, because we still somehow want to retrieve past state but are not sure how. Complexity, because we must repeatedly work around our own obsolete approaches. Performance issues, because confusion times complexity hurts. It is not surprising, however, that intelligence agencies notoriously try to collect, store, and analyze what the broad public willfully forgets. Significantly faster and cheaper random-access storage is the key driver for a paradigm shift towards remembering the sequence of modifications. We claim that (1) faster storage allows to efficiently and cleverly handle finer-granular modifi- cations and (2) that mandatory versioning elegantly exposes past state, radically simplifies the applications, and effectively lays a solid foundation for backing up, distributing and scaling of our data. -
Applying Representational State Transfer (REST) Architecture to Archetype-Based Electronic Health Record Systems
Applying representational state transfer (REST) architecture to archetype-based electronic health record systems Erik Sundvall, Mikael Nyström, Daniel Karlsson, Martin Eneling, Rong Chen and Håkan Örman Linköping University Post Print N.B.: When citing this work, cite the original article. Original Publication: Erik Sundvall, Mikael Nyström, Daniel Karlsson, Martin Eneling, Rong Chen and Håkan Örman, Applying representational state transfer (REST) architecture to archetype-based electronic health record systems, 2013, BMC Medical Informatics and Decision Making, (13), 57. http://dx.doi.org/10.1186/1472-6947-13-57 Licensee: BioMed Central http://www.biomedcentral.com/ Postprint available at: Linköping University Electronic Press http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-87696 Sundvall et al. BMC Medical Informatics and Decision Making 2013, 13:57 http://www.biomedcentral.com/1472-6947/13/57 SOFTWARE Open Access Applying representational state transfer (REST) architecture to archetype-based electronic health record systems Erik Sundvall1*, Mikael Nyström1, Daniel Karlsson1, Martin Eneling1, Rong Chen1,2 and Håkan Örman1 Abstract Background: The openEHR project and the closely related ISO 13606 standard have defined structures supporting the content of Electronic Health Records (EHRs). However, there is not yet any finalized openEHR specification of a service interface to aid application developers in creating, accessing, and storing the EHR content. The aim of this paper is to explore how the Representational State Transfer (REST) architectural style can be used as a basis for a platform-independent, HTTP-based openEHR service interface. Associated benefits and tradeoffs of such a design are also explored. Results: The main contribution is the formalization of the openEHR storage, retrieval, and version-handling semantics and related services into an implementable HTTP-based service interface. -
Polishing Structural Bulk Updates in a Native XML Database
Polishing Structural Bulk Updates in a Native XML Database Master thesis presented by Lukas Kircher Submitted to the Department of Computer and Information Science at the University of Konstanz Reviewers Prof. Dr. Marc H. Scholl Prof. Dr. Marcel Waldvogel October 2013 Abstract BaseX is a native XML database on the foundation of a fixed-length, sequen- tial document encoding. Built with a strong focus on reading performance, this thesis shows that the Pre/Dist/Size encoding is yet perfectly capable of handling massive bulk update transactions. Despite its theoretical limi- tations regarding structural changes of the tree, we show that performance is indeed restricted by the document order and disk access patterns. Dur- ing tests with the XQuery Update Facility (XQUF), we delete 1.8 million nodes in 22.4 seconds, evenly distributed over a 1.1GB XMark document in- stance. Compared to the prior approach, this equals a reduction of processing time by 99.99%. To achieve this, we extend the obligatory implementation of the XQUF pending update list with an additional low-level layer, that pre-calculates tree structure adjustments in-memory. This layer adds little overhead and further enables us to merge update operations and curb frag- mentation that finds its origin at the user level. To not violate the document order, the XQUF is only arduously brought together with the concept of effi- cient bulk updates. A method is introduced that imposes an order on update primitives to finally get a ready-to-apply sequence of atomic updates. The reviewed implementation is fully consistent with the XQUF specification and has already proven rock-solid efficiency in production use. -
Efficient and Failure-Aware Replication of an XML Database
Efficient and failure-aware replication of an XML database Master thesis presented by Dirk Kirsten (01/775833) Submitted to the Department of Computer and Information Science at the University of Konstanz 1st Referee Prof. Dr. Marc Scholl 2nd Referee Prof. Dr. Marcel Waldvogel Mentor Dr. Christian Grün September 2014 ABSTRACT english BaseX is a native XML database with a single point of failure. If the database server fails, the data is unreachable. Therefore, we introduce the concept of replication to BaseX to achieve high availability. We explore sev- eral update management strategies and introduce an update management suitable for the specific requirements of BaseX. As a primary is needed as updating location within our replication architecture, we present several leader election algorithms and show and implement a modified version thereof to fit our requirements. To detect failures, a probabilistic accrual failure detector is used, which is able to detect failures fast and reliably. The thesis shows a favorable performance of the systems in terms of repli- cation and transaction latency of the replication system. Hence, the used replication system high availability with a minimal performance impact in terms of transaction runtimes. deutsch BaseX ist eine native XML Datenbank, welche momentan über einen Single Point of Failure verfügt. Wenn ein einzelner Datenbankserver ausfällt, sind alle Daten nicht verfügbar. Daher wird BaseX in dieser Arbeit derart erweit- ert, indem wir das Konzept der Replikation einführen und somit Hochver- fügbarkeit erreichen. Wir präsentieren eine Übersicht über diverse Update- Management-Strategien und führen eine geeignete Strategie für BaseX ein, um die angestrebten Designziele zu erreichen.