TRANSFORMING DATABASES WITH RECURSIVE DATA STRUCTURES Anthony Kosky

187 Pages·2003·0.83 MB·English

TRANSFORMING DATABASES WITH RECURSIVE DATA
STRUCTURES
Anthony Kosky
A DISSERTATION
in
COMPUTER AND INFORMATION SCIENCE
Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the
Requirements for the Degree of Doctor of Philosophy.
1996
Susan Davidson— Supervisor of Dissertation
Peter Buneman— Supervisor of Dissertation
Peter Buneman— Graduate Group Chairperson
(cid:13)c Copyright 2003
by
Anthony Kosky
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To my parents.
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WARRANTY
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dissertation. Children under the age of five should not attempt to read this dissertation without
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Comments, suggestions and personal abuse are all welcome and should be sent to the author
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ACKNOWLEDGMENTS
This dissertation marks the end of six years which I spent engaged in studies and research
at the Department of Information and Computer Science of the University of Pennsylvania.
Though only a part of that time was spent directly on the work described in this dissertation,
it nevertheless reflects many influences, both from my time at Penn and from my studies prior
to that in England. There are many people to thank, both for their direct contributions to this
work, and also for their roles in developing my understanding and appreciation of theoretical
computer science, databases, programming languages, and many other subjects of relevance.
FirstlyIwouldliketothankmyadvisors,PeterBunemanandSusanDavidsonfortheirhelp,sug-
gestions,support,adviceandencouragement,andforintroducingmetothesubjectofdatabases.
Peter was also responsible for giving me the opportunity to enroll in a PhD program at Penn. I
would like to thank my committee members, Tim Griffin, Victor Markowitz, Carl Gunter, Val
Tannen and Chris Overton for their comments and advice. This work has also been influenced
greatly by the discussions of the “Tuesday afternoon group” including Leonid Libkin, Limsoon
Wong, Dan Suciu, Rona Machlin, Wenfei Fan and Kyle Hart. I would especially like to thank
Leonid for his many helpful comments and advice, and for his thorough reading of the proposal
for this dissertation. Barbara Eckman and Carmem Hara did much of the work on the trials
of the prototype transformation system described in part IV. Barbara also helped to explain
the Molecular Biology Databases and the database problems that inspired much of this work.
I am also grateful to Catriel Beeri, Jan Van den Bussche and Serge Abiteboul for their com-
ments on my other papers related to this work. Edward T. Bear gave consistent support and
encouragement,andhelpedwithsomeofthemoretechnicallydifficultproofsinthisdissertation.
One of the most enjoyable aspects of my research at Penn was the collaboration with members
of the computational biology group, not only because it gave me an opportunity to look at some
practical applications for my work, but also because it gave me a chance to learn a little about
the fascinating subjects of molecular biology and genetics. I would like to thank Chris Overton
and David Searls for sharing there enthusiasm for these subjects, and for their many impromptu
biology lessons.
There are also many people who have contributed to my development first as a mathematician
and then as a computer scientist. I would like to thank the lecturers of the Department of
Mathematics at the University of Kent at Canterbury, in particular John Earl, who helped me
to develop an appreciation for the beauty of pure mathematics. My introduction to computer
science came when I did a Masters degree at the Department of Computing at Imperial College
of Science and Technology. In particular I was introduced to the subjects of formal methods
and functional programming by the lectures of Samson Abramsky, Mike Smyth, Steve Vickers,
Pete Harrison, Chris Hankin and others. Samson Abramsky also supervised my masters thesis
and recommended me as a possible PhD student at the University of Pennsylvania, for which
I am especially grateful. My knowledge and appreciation of theoretical computer science has
been extended further while at the Penn, through the lectures Val Tannen, Carl Gunter, Scott
Weinstein, Peter Freyd and others.
viii ACKNOWLEDGMENTS
Many of the staff at the University of Pennsylvania have helped me in dealing with bureaucracy
and various administrative details. I would particularly like to thank Mike Felker who’s help
allowed me to finish off and co-ordinate this PhD while working in California. I would also like
to thank Karen Carter, Nan Blitz, Susan Deysher, Elaine Benedetto and Jackie Caliman, and
members of the computing staff Mark Foster, Mark-Jason Dominus and Alex Garthwaite.
There are also many people who helped in making my time at Penn enjoyable, and helping me
to maintain a semblance of sanity. I would like to thank the Old Quaker Computer Scientists
for some very bizarre and amusing times, the Penn Magic play-testers, the Saturday-morning
Reading Terminal crowd, and all at Bicycle Therapy for keeping my bikes running nicely.
Finally, butmostimportantlyofall, Iwouldliketothankmyparentsandmyfamily. Theirlove,
support and encouragement have been a constant comfort to me in spite of the long distances
between us, and I could not have achieved any of this without them.
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ABSTRACT
TRANSFORMING DATABASES WITH RECURSIVE DATA STRUCTURES
Anthony Kosky
Advisors: Susan Davidson and Peter Buneman.
This thesis examines the problems of performing structural transformations on databases in-
volving complex data-structures and object-identities, and proposes an approach to specifying
and implementing such transformations.
We start by looking at various applications of such database transformations, and at some of
the more significant work in these areas. In particular we will look at work on transformations
in the area of database integration, which has been one of the major motivating areas for this
work. We will also look at various notions of correctness that have been proposed for database
transformations, and show that the utility of such notions is limited by the dependence of
transformations on certain implicit database constraints. We draw attention to the limitations
of existing work on transformations, and argue that there is a need for a more general formalism
for reasoning about database transformations and constraints.
We will also argue that, in order to ensure that database transformations are well-defined and
meaningful, it is necessary to understand the information capacity of the data-models being
transformed. Tothisendwegiveathoroughanalysisoftheinformationcapacityofdata-models
supporting object identity, and will show that this is dependent on the operations supported by
a query language for comparing object identities.
We introduce a declarative language, WOL, based on Horn-clause logic, for specifying database
transformations and constraints. We also propose a method of implementing transformations
specified in this language, by manipulating their clauses into a normal form which can then be
translated into an underlying database programming language.
Finally we will present a number of optimizations and techniques necessary in order to build a
practical implementation based on these proposals, and will discuss the results of some of the
trials that were carried out using a prototype of such a system.
x ABSTRACT