Query Flattening and the Nested Data Parallelism Paradigm

This work is based on the observation that languages for two seemingly distant domains are closely related. Orthogonal query languages based on comprehension syntax admit various forms of query nesting to construct nested query results and express complex predicates. Languages for nested data parallelism allow to nest parallel iterators and thereby admit the parallel evaluation of computations that are themselves parallel. Both kinds of languages center around the application of side-effect-free functions to each element of a collection. The motivation for this work is the seamless integration of relational database queries with programming languages. In frameworks for language-integrated database queries, a host language's native collection-programming API is used to express queries. To mediate between native collection programming and relational queries, we define an expressive, orthogonal query calculus that supports nesting and order. The challenge of query flattening is to translate this calculus to bundles of efficient relational queries restricted to flat, unordered multisets. Prior approaches to query flattening either support only query languages that lack in expressiveness or employ a complex, monolithic translation that is hard to comprehend and generates inefficient code that is hard to optimize. To improve on those approaches, we draw on the similarity to nested data parallelism. Blelloch's flattening transformation is a static program transformation that translates nested data parallelism to flat data parallel programs over flat arrays. Based on the flattening transformation, we describe a pipeline of small, comprehensible lowering steps that translates our nested query calculus to a bundle of relational queries. The pipeline is based on a number of well-defined intermediate languages. Our translation adopts the key concepts of the flattening transformation but is designed with specifics of relational query processing in mind. Based on this translation, we revisit all aspects of query flattening. Our translation is fully compositional and can translate any term of the input language. Like prior work, the translation by itself produces inefficient code due to compositionality that is not fit for execution without optimization. In contrast to prior work, we show that query optimization is orthogonal to flattening and can be performed before flattening. We employ well-known work on logical query optimization for nested query languages and demonstrate that this body of work integrates well with our approach. Furthermore, we describe an improved encoding of ordered and nested collections in terms of flat, unordered multisets. Our approach emits idiomatic relational queries in which the effort required to maintain the non-relational semantics of the source language (order and nesting) is minimized. A set of experiments provides evidence that our approach to query flattening can handle complex, list-based queries with nested results and nested intermediate data well. We apply our approach to a number of flat and nested benchmark queries and compare their runtime with hand-written SQL queries. In these experiments, our SQL code generated from a list-based nested query language usually performs as well as hand-written queries

Reify Your Collection Queries for Modularity and Speed!

Modularity and efficiency are often contradicting requirements, such that programers have to trade one for the other. We analyze this dilemma in the context of programs operating on collections. Performance-critical code using collections need often to be hand-optimized, leading to non-modular, brittle, and redundant code. In principle, this dilemma could be avoided by automatic collection-specific optimizations, such as fusion of collection traversals, usage of indexing, or reordering of filters. Unfortunately, it is not obvious how to encode such optimizations in terms of ordinary collection APIs, because the program operating on the collections is not reified and hence cannot be analyzed. We propose SQuOpt, the Scala Query Optimizer--a deep embedding of the Scala collections API that allows such analyses and optimizations to be defined and executed within Scala, without relying on external tools or compiler extensions. SQuOpt provides the same "look and feel" (syntax and static typing guarantees) as the standard collections API. We evaluate SQuOpt by re-implementing several code analyses of the Findbugs tool using SQuOpt, show average speedups of 12x with a maximum of 12800x and hence demonstrate that SQuOpt can reconcile modularity and efficiency in real-world applications.Comment: 20 page

A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

A Survey on Array Storage, Query Languages, and Systems

Since scientific investigation is one of the most important providers of massive amounts of ordered data, there is a renewed interest in array data processing in the context of Big Data. To the best of our knowledge, a unified resource that summarizes and analyzes array processing research over its long existence is currently missing. In this survey, we provide a guide for past, present, and future research in array processing. The survey is organized along three main topics. Array storage discusses all the aspects related to array partitioning into chunks. The identification of a reduced set of array operators to form the foundation for an array query language is analyzed across multiple such proposals. Lastly, we survey real systems for array processing. The result is a thorough survey on array data storage and processing that should be consulted by anyone interested in this research topic, independent of experience level. The survey is not complete though. We greatly appreciate pointers towards any work we might have forgotten to mention.Comment: 44 page