twinql API reference

Introduction

This document describes twinql, AllegroGraph's SPARQL implementation. Each of the following functions are exported from the db.agraph.sparql package. This package has sparql and twinql as nicknames.

For notes on twinql's conformance to the W3C specification please see this document.

You might also want to look at the reference guide for AllegroGraph and the AllegroGraph tutorial.

Conceptually, twinql has three layers:

a parser from the textual SPARQL surface syntax to s-expressions;
a query builder and planner that prepares the query for execution;
and an executor that runs the plan against a store to produce results.

Currently, input and output from each of these layers is limited (for example, the query plan is not available to user code, but parsed output is). This will change in a future release.

Queries can be executed by an extensible set of query engines (currently the engine first available in AllegroGraph 2, and another based on the SPARQL algebra). The engine is specified by the :engine keyword; acceptable values are returned by get-sparql-query-engines.

The default engine, used if the :engine argument is not supplied, is specified by the sparql:*default-sparql-query-engine* special variable. As of AllegroGraph 3.2, its value defaults to :algebra.

Valid result formats

There are three possible outputs from a SPARQL query:

a yes/no answer, in response to an ASK query;
a list of bindings, in response to a SELECT query; or
a new RDF graph, in response to a CONSTRUCT or DESCRIBE query.

twinql provides a number of different ways to serialize these results to a stream, provided as keyword symbols to the query functions. The results-format argument controls how ASK and SELECT query results are serialized; some possible formats are :sparql-xml, which serializes the result into the SPARQL XML result format, and :sparql-json, which uses the JSON format.

For CONSTRUCT and DESCRIBE, the value of the rdf-format argument applies.

The default formats are :sparql-xml and :rdf/xml respectively. Providing an unrecognized format will signal an error.

You can find out which formats are allowed for a particular verb by using get-allowed-results-formats and get-allowed-rdf-formats.

Exported functions

parse-sparql takes a string and parses it into an s-expression format. A parse error will result in a sparql-parse-error being raised.

This function is useful for three reasons: validation and inspection of queries, manual manipulation of query expressions without text processing, and performing parsing at a more convenient time than during query execution.

You do not need an open triple store in order to parse a query.

default-base and default-prefixes allow you to provide BASE and PREFIX arguments to the parser without inserting them textually into the query.

default-base should be nil or a string, and default-prefixes can either be a hash-table (string prefix to string expansion) or a list similar to db.agraph:*standard-namespaces*.

parse-sparql returns the s-expression representation of the query string.

run-sparql takes a SPARQL query as input and returns bindings or new triples as output.

Since AllegroGraph 3.0 it is a convenient wrapper for the db-run-sparql methods specialized on particular database classes and query engines. You might consider using those methods directly to gain more control over the execution of your queries.

You should consider specifying an engine argument in your invocations of run-sparql; the choice of default execution engine is not guaranteed to remain the same in future releases.

Allowable values for engine are keyword symbols returned by get-sparql-query-engines.

The precise arguments supplied to run-sparql vary according to the query engine. These are the typical arguments expected by the default engines.

SELECT and ASK query results will be presented according to the value provided for results-format, whilst the RDF output of DESCRIBE and CONSTRUCT will be serialized according to rdf-format. Both of these arguments take keyword values.

If the format is programmatic (that is, it is intended to return values rather than print a representation; :arrays is an example) then any results will be returned as the first value, and nothing will be printed on output-stream.

The query can be a string, which will be parsed by parse-sparql, or an s-expression as produced by parse-sparql. If you expect to run a query many times, you can avoid some parser overhead by parsing your query once and calling run-sparql with the parsed representation.
If query is a string, then default-base and default-prefixes are provided to parse-sparql to use when parsing the query. See the documentation for that function for details. Parser errors signaled within parse-sparql will be propagated onwards by run-sparql.
Results or new triples will be serialized to output-stream. If a programmatic format is chosen for output, the stream is irrelevant. An error will be signaled if output-stream is not a stream, t, or nil.
If limit, offset, from, or from-named are provided, they override the corresponding values specified in the query string itself. As FROM and FROM NAMED together define a dataset, and the SPARQL Protocol specification states that a dataset specified in the protocol (in this case, the programmatic API) overrides that in the query, if either from or from-named are non-nil then any dataset specifications in the query are ignored. You can specify that the contents of the query are to be partially overridden by providing t as the value of one of these arguments. This is interpreted as 'use the contents of the query'. from and from-named should be lists of URIs: future-parts, UPIs, or strings.
default-dataset-behavior controls how the query engine builds the dataset environment if FROM or FROM NAMED are not provided. Valid options are :all (ignore graphs; include all triples) and :default (include only the store's default graph).
default-graph-uris allows you to specify a list of resources which, when encountered in the SPARQL dataset specification, are to be treated as the default graph of the store. Each resource can be a resource UPI, resource future-part, or a URI string. For example, specifying '("http://example.com/default") will cause a query featuring

FROM FROM

to execute against the union of the contents of the named graph <http://example.com/baz> and the store's default graph, as determined by (default-graph-upi db).

with-variables should be an alist of variable names and values. The variable names can be strings (which will be interned in the package in which the query is parsed) or symbols (which should be interned in the package in which the query is to be, or was, parsed). The variable names can include or omit a leading '?'. Note that a query literal in code might be parsed at compile time. Using strings is the most reliable method for naming variables.

Before the query is executed, the variables named after symbols will be bound to the provided values.

This allows you to use variables in your query which are externally imposed, or generated by other queries. The format expected by with-variables is the same as that used for each element of the list returned by the :alists results-format.

db (*db* by default) specifies the triple store against which queries should run.
destination-db (db by default) specifies the triple store against which Update modifications should take place. This is primarily of use when db is a read-only wrapper around a writable store, such as when reasoning has been applied.
If verbosep is non-nil, status information is written to *sparql-log-stream* (*standard-output* by default).

Three additional extensions are provided for your use.

If extendedp is true (or *use-extended-sparql-verbs-p* is true, and the argument omitted) some additional SPARQL verbs become available. SUM, AVERAGE, MEDIAN, STATS, CORRELATION, and COUNT can all be used in place of SELECT. These verbs are still experimental and undocumented, and can only be used with the :allegrograph-2 query engine. extendedp also controls other syntactic extensions in SPARQL queries, such as GEO syntax. Extensions are enabled by default in all versions of AllegroGraph after 3.2.
If memoizep is true (or *build-filter-memoizes-p* is true, and the argument omitted) calls to SPARQL query functions (such as STR, fn:matches, and extension functions) will be memoized for the duration of the query. For most queries this will yield speed increases when FILTER or ORDER BY are used, at the cost of additional memory consumption (and consequent GC activity). For some queries (those where repetition of function calls is rare) the cost of memoization will outweigh the benefits. In large queries which call SPARQL functions on many values, the size of the memos can grow large.

Memoization also requires that your extension functions do not depend on side-effects. The standard library is correct in this regard.

In some circumstances you can achieve substantial speed increases by sharing your memos between queries. Create a normal eql hash-table with (make-hash-table), passing it as the value of the memos argument to run-sparql. This hash-table will gradually fill with memos for each used query function.

If you wish to globally enable memoization, set the variables as follows:

(progn  
  (setf *build-filter-memoizes-p* t)  
  (setf *sparql-sop-memos* (make-hash-table)))

Be aware that the size of *sparql-sop-memos* could grow very large indeed. You might consider using a weak hash-table, or periodically discarding the contents of the hash-table.

load-function is a function with signature (uri db &optional type) or nil. If it is a function, it is called once for each FROM and FROM NAMED parameter making up the dataset of the query. The execution of the query commences once each parameter has been processed. The type argument is either :from or :from-named, and the uri argument is a part (ordinarily a future-part) naming a URI. The default value is taken from *dataset-load-function*. You can use this hook function to implement loading of RDF before the query is executed.

The values returned by run-sparql are dependent on the verb used. The first value is typically disregarded in the case of results being written to output-stream. If output-stream is nil, the first value will be the results collected into a string (similar to the way in which cl:format operates).

The second value is the query verb: one of :select, :ask, :construct, or :describe. Other values are possible in extended mode.

The third value, for SELECT queries only, is a list of variables. This list can be used as a key into the values returned by the :arrays and lists results formats, amongst other things.

Individual results formats are permitted to return additional values.

permitted-verbs is a keyword, either :all or :read-only. This defaults to :all, and will permit any kind of SPARQL or SPARQL/Update query. Use :read-only to allow only SELECT, ASK, DESCRIBE, and CONSTRUCT queries. Note that you must also enable extended mode (using :extendedp :update) to use SPARQL/Update operations.

Returns a list of keyword symbols that are valid when applied as values of results-format to a query with the given verb. if verb is not provided, the intersection of :ask and :select (the two permitted values) is returned. With AllegroGraph 3.0, an additional engine argument is available. In a similar manner to verb, omitting this restricts the returned values to those that apply to all built-in query engines.

Returns a list of keyword symbols that are valid when applied as values of rdf-format to a query with the given verb. if verb is not provided, the intersection of :construct and :describe (the two permitted values) is returned. With AllegroGraph 3.0, an additional engine argument is available. In a similar manner to verb, omitting this restricts the returned values to those that apply to all built-in query engines.

Examples:

Get RDF formats for the default query engine that apply to both CONSTRUCT and DESCRIBE queries.
(get-allowed-rdf-formats nil :allegrograph-2)
Get formats for CONSTRUCT queries executed by the algebra query engine.
(get-allowed-rdf-formats :construct :algebra)

Returns a list of keyword symbols that are valid when applied as values of the engine argument to run-sparql or db-run-sparql.

In AllegroGraph 3.0, to prepare for future extension to different query engines and databases, the db-run-sparql generic function was introduced. You can continue to use run-sparql in your code.

A generic function to dispatch query execution across different SPARQL engines and database types.

N.B., if you request a results-format of :cursor, you should yield bindings from it within a (sparql:with-stable-xquery-environment) form, or avoid the use of filter functions that rely on the implicit environment (such as fn:currentDate).

Serialized results formats are provided with a managed environment; only returned cursors need this.

Extension functions

SPARQL allows for query engines to associate extension functions with URIs, and call them from within queries.

You can define your own URI functions in twinql through defurifun, or associate existing functions with a URI through associate-function-with-uri. defurifun does some manipulation of the arguments, so you should use it whenever possible.

Assert a mapping between uri, which is a string or a valid part, and the provided function, which is a symbol or a function. If cache-now-p, and function is a symbol, its function binding is stored instead of the symbol itself.

Print all mappings between URIs and functions to stream (*standard-output* by default).

Define a new function, name, and associate it with uri as with associate-function-with-uri. args is not evaluated, exactly as with defun.

Here's an example: a function that will do an HTTP HEAD request against the provided URL, returning the HTTP status code as an integer literal, or 0 if there's a problem.

(The built-in functions are quite robust, so a Lisp integer will be treated as an RDF literal with data type xsd:integer.)

(defurifun ex-head-request !<http://example.com/fn/head> (uri)  
  (or  
    (when uri  
      (ignore-errors  
        (format t "~&Performing HTTP HEAD request on <~A>...~%"  
                  (upi->value uri))  
        (second  
          (multiple-value-list  
            (net.aserve.client:do-http-request (upi->value uri)  
                                               :method :head)))))  
    0))

You can use this function in a query exactly as you would a built-in function.

Using this data as an example:

<http://ex.com/a> <http://ex.com/foo> "200"^^<http://www.w3.org/2001/XMLSchema#integer> .

we can run a query like so:

sparql(54): (run-sparql  
"  
PREFIX f: <http://example.com/fn/>  
SELECT ?x {  
  ?x <http://ex.com/foo> ?y .  
  FILTER ( ?y = f:head("http://franz.com\") )  
}"  
  :results-format :count)

which produces this output:

Performing HTTP HEAD request on <http://franz.com>...  
1  
:select  
(?x)

… we know, then, that franz.com is returning a 200 status code.

Note that these filter functions can be called an arbitrary number of times during the execution of a query. It's not a good idea to actually perform expensive operations like HTTP requests in your queries.

`SELECT` bindings and `ASK` results

run-sparql allows you programmatic access to results in a number of ways.

Any of the following results-formats are suitable as arguments to SELECT or ASK queries:

:sparql-xml, which serializes the results as XML to output-stream.
:sparql-json, which does the same in the JSON encoding.
:sparql-ttl, which does the same in the SPARQL results Turtle encoding.
:table, a simple debugging format that concisely prints the results in a table. See *sparql-table-width*.

The following results-formats are suitable as arguments to SELECT queries:

:arrays, which returns a list of arrays, each with one entry for each results variable.
:lists, which is the same but with lists instead of arrays.
:hashes, which returns a list of eq hash-tables. Each hash table maps from results variables (interned as symbols; see below) to values.
:alists, which is the same but with association lists instead of hash tables.
:count, which returns the number of results rows.

The following results-formats are suitable as arguments to ASK queries:

:boolean, which returns t or nil for true and false respectively.

Returning triples from `CONSTRUCT` and `DESCRIBE` queries

Any of the following rdf-formats are suitable as arguments to CONSTRUCT or DESCRIBE queries:

:ntriples, which serializes the triples as N-Triples to output-stream.
:rdf/xml, which does the same in RDF/XML.
:rdf-n3, which does the same in the Turtle subset of Notation-3.

The following rdf-format is suitable for DESCRIBE queries:

:hash, which returns a upi-hash-table from nodes to their Concise Bounded Descriptions. The union of the values in the upi-hash-table makes up the output of the DESCRIBE query. This method is unsupported and internal.
:triples, which returns a list of AllegroGraph triples.

The following rdf-format is suitable for CONSTRUCT queries:

:arrays, which returns a list of three-element arrays. The elements of the array are the subject, predicate, and object of a constructed triple, and can be UPIs or future-parts.

Additionally, the :allegrograph-2 engine allows the :triples format. The slots in these triples will be mostly empty: you should use only subject, predicate, and object. More importantly, you should be aware that parts included by a CONSTRUCT query might not be dereferenceable, depending on the current triple store: AllegroGraph triples, by their nature, contain only UPIs, but a CONSTRUCT query can include new URIs and literals that have not been added to the open triple store's string dictionary. The :arrays format is wholeheartedly recommended as a replacement.

Finally, the :algebra engine can return results from CONSTRUCT and DESCRIBE queries as in-memory triple stores, using the :in-memory format.

These stores are an experimental addition, but the ability to treat the results of a query as an independent triple store can be very useful. Such a store can be queried or serialized so long as a reference to it exists.

You can use get-allowed-results-formats and get-allowed-rdf-formats to access these allowed values dynamically at run-time.

Variables

Programmatic results associate values with variables. Variables are parsed into symbols by the query parser.

The mapping from variables to symbols is straightforward, and best illustrated by example:

?x → '|?x|
?X → '?X
$foo → '|?foo|

If you provide variables in a with-variables argument, a leading ? is prepended to the variable name. Your queries will run correctly if you provide them as s-expressions and do not prepend ?, but:

variables that share a name with a self-evaluating symbol, such as most-positive-fixnum, t, or nil, will cause your query to fail
bindings you provide using with-variables will not apply, because they are always preprocessed.

All variables created by the parser are interned in the current package, as if by a call to cl:intern. You should adhere to these rules when processing results or providing bindings using with-variables.

SPARQL and first-class triples

AllegroGraph permits you to make assertions about triple IDs (UPIs of type triple-id). SPARQL offers no support for this: only named graphs are supported. First-class triples are entirely outside the scope of both RDF and SPARQL.

SPARQL queries against stores using first-class triples are not supported. twinql makes only limited provisions for such queries:

programmatic output is likely to work in most situations. Certain FILTER and ORDER BY operations will fail, however; typically these will result in an internal SPARQL type error, which will cause the FILTER to fail for all triple-id values.
output in one of the provided results formats will, under normal circumstances, fail when a triple-id is encountered. The SPARQL XML writer exports a variable, sparql.results:*strict-sparql-xml-output*, which toggles triple-id output. If this is set to nil, triple-id values are printed in a <triple> element, analogous to <literal>. A similar variable is exported for the JSON format: *strict-sparql-json-output*. The Turtle results format will always treat the triple-id as an integer.

It bears repeating that SPARQL is not intended to work with first-class triples; any queries that run successfully are little more than accidents, and named graphs are a better choice in all cases.

Datasets

Dataset loading

It is sometimes useful to be able to process the SPARQL dataset — the set of URIs provided as FROM and FROM NAMED parameters — when a query is executed. AllegroGraph provides a dataset load hook for your convenience.

You may bind a function to *dataset-load-function* to specify a default, or pass one as the :load-function argument to run-sparql. Passing nil disables the hook for that query. The argument list of the function is described in *dataset-load-function*.

Default dataset handling

When no dataset (FROM and FROM NAMED) are provided to a query, the actual dataset against which the query is run is not defined by the SPARQL specification. twinql provides you with two options: :default, meaning that the default part of the dataset contains only the default graph of the store; and :all, whereby both the default and named parts of the dataset contain every graph in the store.

You can control the default behavior by setting *sparql-default-graph-behavior*, and set the behavior for specific queries by passing the :default-dataset-behavior argument to run-sparql.

Verbose output

Logging output when queries are run in verbose mode is written to sparql.logging:*sparql-log-stream*. This is *standard-output* by default.

SPARQL and encoded values

AllegroGraph offers the ability to directly encode a range of literal values — numbers, geospatial values, and more — directly within a UPI, without the overhead of a string representation as an RDF literal. Whenever these encoded values are encountered by AllegroGraph's printing functions, and in many other situations, they are seamlessly treated as RDF literals, but with significant time and space savings.

twinql's implementations of most SPARQL and XQuery operators also handle encoded values transparently.

TODO

Variables

The log stream to which SPARQL verbose output is written.

This variable specifies how wide to draw the results table in characters.

Set this to :default to have SPARQL queries with no FROM parts use only the default graph for queries. Set it to :all to have the store run the queries on all triples in the store.

Set this to a function of two or three arguments, (uri db &optional type), to load dataset parameters before a query is executed.

twinql API reference

Table of Contents

Introduction

Valid result formats

Exported functions

Extension functions

SELECT bindings and ASK results

Returning triples from CONSTRUCT and DESCRIBE queries

Variables

SPARQL and first-class triples

Datasets

Dataset loading

Default dataset handling

Verbose output

SPARQL and encoded values

Variables

Function index

`SELECT` bindings and `ASK` results

Returning triples from `CONSTRUCT` and `DESCRIBE` queries