GitHub - RDFLib/sparqlwrapper: A wrapper for a remote SPARQL endpoint (original) (raw)

SPARQL Endpoint interface to Python

• About
• Installation & Distribution
• How to use
• SPARQL Endpoint Implementations
• Development

About

SPARQLWrapper is a simple Python wrapper around a SPARQL service to remotely execute your queries. It helps by creating the query invocation and, optionally, converting the result into more manageable formats.

Installation & Distribution

You can install SPARQLWrapper from PyPI:

$ pip install sparqlwrapper

You can install SPARQLWrapper from GitHub:

$ pip install git+https://github.com/rdflib/sparqlwrapper#egg=sparqlwrapper

You can install SPARQLWrapper from Debian:

$ sudo apt-get install python-sparqlwrapper

Note

Be aware that there could be a gap between the latest version of SPARQLWrapper and the version available as Debian package.

Also, the source code of the package can be downloaded in .zip and .tar.gz formats from GitHub SPARQLWrapper releases. Documentation is included in the distribution.

How to use

You can use SPARQLWrapper either as a Python command line script or as a Python package.

Command Line Script

To use as a command line script, you will need to install SPARQLWrapper and then a command line script called rqw (spaRQl Wrapper) will be available within the Python environment into which it is installed. run $ rql -h to see all the script's options.

Python package

Here are a series of examples of different queries executed via SPARQLWrapper as a python package.

SELECT examples

Simple use of this module is as follows where a live SPARQL endpoint is given and the JSON return format is used:

from SPARQLWrapper import SPARQLWrapper, JSON

sparql = SPARQLWrapper( "http://vocabs.ardc.edu.au/repository/api/sparql/" "csiro_international-chronostratigraphic-chart_geologic-time-scale-2020" ) sparql.setReturnFormat(JSON)

gets the first 3 geological ages

from a Geological Timescale database,

via a SPARQL endpoint

sparql.setQuery(""" PREFIX gts: http://resource.geosciml.org/ontology/timescale/gts#

SELECT *
WHERE {
    ?a a gts:Age .
}
ORDER BY ?a
LIMIT 3
"""

)

try: ret = sparql.queryAndConvert()

for r in ret["results"]["bindings"]:
    print(r)

except Exception as e: print(e)

This should print out something like this:

{'a': {'type': 'uri', 'value': 'http://resource.geosciml.org/classifier/ics/ischart/Aalenian'}} {'a': {'type': 'uri', 'value': 'http://resource.geosciml.org/classifier/ics/ischart/Aeronian'}} {'a': {'type': 'uri', 'value': 'http://resource.geosciml.org/classifier/ics/ischart/Albian'}}

The above result is the response from the given endpoint, retrieved in JSON, and converted to a Python object, ret, which is then iterated over and printed.

ASK example

This query gets a boolean response from DBPedia's SPARQL endpoint:

from SPARQLWrapper import SPARQLWrapper, XML

sparql = SPARQLWrapper("http://dbpedia.org/sparql") sparql.setQuery(""" ASK WHERE { http://dbpedia.org/resource/Asturias rdfs:label "Asturias"@es } """) sparql.setReturnFormat(XML) results = sparql.query().convert() print(results.toxml())

You should see something like:

CONSTRUCT example

CONSTRUCT queries return RDF, so queryAndConvert() here produces an RDFlib Graph object which is then serialized to the Turtle format for printing:

from SPARQLWrapper import SPARQLWrapper

sparql = SPARQLWrapper("http://dbpedia.org/sparql")

sparql.setQuery(""" PREFIX dbo: http://dbpedia.org/ontology/ PREFIX sdo: https://schema.org/

CONSTRUCT {
  ?lang a sdo:Language ;
  sdo:alternateName ?iso6391Code .
}
WHERE {
  ?lang a dbo:Language ;
  dbo:iso6391Code ?iso6391Code .
  FILTER (STRLEN(?iso6391Code)=2) # to filter out non-valid values
}
LIMIT 3

""")

results = sparql.queryAndConvert() print(results.serialize())

Results from this query should look something like this:

@prefix schema: https://schema.org/ .

http://dbpedia.org/resource/Arabic a schema:Language ; schema:alternateName "ar" .

http://dbpedia.org/resource/Aragonese_language a schema:Language ; schema:alternateName "an" .

http://dbpedia.org/resource/Uruguayan_Spanish a schema:Language ; schema:alternateName "es" .

DESCRIBE example

Like CONSTRUCT queries, DESCRIBE queries also produce RDF results, so this example produces an RDFlib Graph object which is then serialized into the JSON-LD format and printed:

from SPARQLWrapper import SPARQLWrapper

sparql = SPARQLWrapper("http://dbpedia.org/sparql") sparql.setQuery("DESCRIBE http://dbpedia.org/resource/Asturias")

results = sparql.queryAndConvert() print(results.serialize(format="json-ld"))

The result for this example is large but starts something like this:

[ { "@id": "http://dbpedia.org/resource/Mazonovo", "http://dbpedia.org/ontology/subdivision": [ { "@id": "http://dbpedia.org/resource/Asturias" } ], ...

SPARQL UPDATE example

UPDATE queries write changes to a SPARQL endpoint, so we can't easily show a working example here. However, if https://example.org/sparql really was a working SPARQL endpoint that allowed updates, the following code might work:

from SPARQLWrapper import SPARQLWrapper, POST, DIGEST

sparql = SPARQLWrapper("https://example.org/sparql") sparql.setHTTPAuth(DIGEST) sparql.setCredentials("some-login", "some-password") sparql.setMethod(POST)

sparql.setQuery(""" PREFIX dbp: http://dbpedia.org/resource/ PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema#

WITH <http://example.graph>
DELETE {
   dbo:Asturias rdfs:label "Asturies"@ast
}
"""

)

results = sparql.query() print results.response.read()

If the above code really worked, it would delete the tripledbo:Asturias rdfs:label "Asturies"@ast from the graphhttp://example.graph.

SPARQLWrapper2 example

There is also a SPARQLWrapper2 class that works with JSON SELECT results only and wraps the results to make processing of average queries even simpler.

from SPARQLWrapper import SPARQLWrapper2

sparql = SPARQLWrapper2("http://dbpedia.org/sparql") sparql.setQuery(""" PREFIX dbp: http://dbpedia.org/resource/ PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema#

SELECT ?label
WHERE {
    dbp:Asturias rdfs:label ?label
}
LIMIT 3
"""
            )

for result in sparql.query().bindings: print(f"{result['label'].lang}, {result['label'].value}")

The above should print out something like:

en, Asturias ar, أشتورية ca, Astúries

Return formats

The expected return formats differs per query type (SELECT, ASK, CONSTRUCT, DESCRIBE...).

Note

From the SPARQL specification,The response body of a successful query operation with a 2XX response is either:

• SELECT and ASK: a SPARQL Results Document in XML, JSON, or CSV/TSV format.
• DESCRIBE and CONSTRUCT: an RDF graph serialized, for example, in the RDF/XML syntax, or an equivalent RDF graph serialization.

The package, though it does not contain a full SPARQL parser, makes an attempt to determine the query type when the query is set. This should work in most of the cases, but there is a possibility to set this manually, in case something goes wrong.

Automatic conversion of the results

To make processing somewhat easier, the package can do some conversions automatically from the return result. These are:

• for XML, the xml.dom.minidom is used to convert the result stream into a Python representation of a DOM tree.
• for JSON, the json package to generate a Python dictionary.
• for CSV or TSV, a simple string.
• For RDF/XML and JSON-LD, the RDFLib package is used to convert the result into a Graph instance.
• For RDF Turtle/N3, a simple string.

There are two ways to generate this conversion:

• use ret.convert() in the return result from sparql.query() in the code above
• use sparql.queryAndConvert() to get the converted result right away, if the intermediate stream is not used

For example, in the code below:

try : sparql.setReturnFormat(SPARQLWrapper.JSON) ret = sparql.query() d = ret.convert() except Exception as e: print(e)

the value of d is a Python dictionary of the query result, based on the SPARQL Query Results JSON Format.

Partial interpretation of the results

Further help is to offer an extra, partial interpretation of the results, again to cover most of the practical use cases. Based on the SPARQL Query Results JSON Format, the :class:`SPARQLWrapper.SmartWrapper.Bindings` class can perform some simple steps in decoding the JSON return results. If :class:`SPARQLWrapper.SmartWrapper.SPARQLWrapper2`is used instead of :class:`SPARQLWrapper.Wrapper.SPARQLWrapper`, this result format is generated. Note that this relies on a JSON format only, ie, it has to be checked whether the SPARQL service can return JSON or not.

Here is a simple code that makes use of this feature:

from SPARQLWrapper import SPARQLWrapper2

sparql = SPARQLWrapper2("http://example.org/sparql") sparql.setQuery(""" SELECT ?subj ?prop WHERE { ?subj ?prop ?obj } """ )

try: ret = sparql.query() print(ret.variables) # this is an array consisting of "subj" and "prop" for binding in ret.bindings: # each binding is a dictionary. Let us just print the results print(f"{binding['subj'].value}, {binding['subj'].type}") print(f"{binding['prop'].value}, {binding['prop'].type}") except Exception as e: print(e)

To make this type of code even easier to realize, the [] and in operators are also implemented on the result of :class:`SPARQLWrapper.SmartWrapper.Bindings`. This can be used to check and find a particular binding (ie, particular row in the return value). This features becomes particularly useful when the OPTIONAL feature of SPARQL is used. For example:

from SPARQLWrapper import SPARQLWrapper2

sparql = SPARQLWrapper2("http://example.org/sparql") sparql.setQuery(""" SELECT ?subj ?obj ?opt WHERE { ?subj http://a.b.c ?obj . OPTIONAL { ?subj http://d.e.f ?opt } } """ )

try: ret = sparql.query() print(ret.variables) # this is an array consisting of "subj", "obj", "opt" if ("subj", "prop", "opt") in ret: # there is at least one binding covering the optional "opt", too bindings = ret["subj", "obj", "opt"] # bindings is an array of dictionaries with the full bindings for b in bindings: subj = b["subj"].value o = b["obj"].value opt = b["opt"].value # do something nice with subj, o, and opt

# another way of accessing to values for a single variable:
# take all the bindings of the "subj"
subjbind = ret.getValues("subj")  # an array of Value instances
...

except Exception as e: print(e)

GET or POST

By default, all SPARQL services are invoked using HTTP GET verb. However,POST might be useful if the size of the query extends a reasonable size; this can be set in the query instance.

Note that some combinations may not work yet with all SPARQL processors (e.g., there are implementations where POST + JSON return does not work). Hopefully, this problem will eventually disappear.

SPARQL Endpoint Implementations

Introduction

From SPARQL 1.1 Specification:

The response body of a successful query operation with a 2XX response is either:

• SELECT and ASK: a SPARQL Results Document in XML, JSON, or CSV/TSV format.
• DESCRIBE and CONSTRUCT: an RDF graph serialized, for example, in the RDF/XML syntax, or an equivalent RDF graph serialization.

The fact is that the parameter key for the choice of the output format is not defined. Virtuoso uses format, Fuseki uses output, rasqual seems to use results, etc... Also, in some cases HTTP Content Negotiation can/must be used.

ClioPatria

OpenLink Virtuoso

• Parameter value, like directly: "text/html" (HTML), "text/x-html+tr" (HTML (Faceted Browsing Links)), "application/vnd.ms-excel", "application/sparql-results+xml" (XML), "application/sparql-results+json" (JSON), "application/javascript" (Javascript), "text/turtle" (Turtle), "application/rdf+xml" (RDF/XML), "text/plain" (N-Triples), "text/csv" (CSV), "text/tab-separated-values" (TSV)
• Parameter value, like indirectly: "HTML" (alias text/html), "JSON" (alias application/sparql-results+json), "XML" (alias application/sparql-results+xml), "TURTLE" (alias text/rdf+n3), JavaScript (alias application/javascript) See http://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/VOSSparqlProtocol#AdditionalHTTPResponseFormats--SELECT
• For a SELECT query type, the default return mimetype (if Accept: */* is sent) is application/sparql-results+xml
• For a ASK query type, the default return mimetype (if Accept: */* is sent) is text/html
• For a CONSTRUCT query type, the default return mimetype (if Accept: */* is sent) is text/turtle
• For a DESCRIBE query type, the default return mimetype (if Accept: */* is sent) is text/turtle

Fuseki

• Fuseki 1 - Short names for "output=" : "json", "xml", "sparql", "text", "csv", "tsv", "thrift"
• Fuseki 2 - Short names for "output=" : "json", "xml", "sparql", "text", "csv", "tsv", "thrift"
• If a non-expected short name is used, the server returns an "Error 400: Can't determine output serialization"
• Valid alias for SELECT and ASK: "json", "xml", csv", "tsv"
• Valid alias for DESCRIBE and CONSTRUCT: "json" (alias for json-ld ONLY in Fuseki 2), "xml"
• Valid mimetype for DESCRIBE and CONSTRUCT: "application/ld+json"
• Default return mimetypes: For a SELECT and ASK query types, the default return mimetype (if Accept: / is sent) is application/sparql-results+json
• Default return mimetypes: For a DESCRIBE and CONTRUCT query types, the default return mimetype (if Accept: / is sent) is text/turtle
• In case of a bad formed query, Fuseki 1 returns 200 instead of 400.

Eclipse RDF4J

• SELECT
  • application/sparql-results+xml (DEFAULT if Accept: */* is sent))
  • application/sparql-results+json (also application/json)
  • text/csv
  • text/tab-separated-values
  • Other values: application/x-binary-rdf-results-table
• ASK
  • application/sparql-results+xml (DEFAULT if Accept: */* is sent))
  • application/sparql-results+json
  • Other values: text/boolean
  • Not supported: text/csv
  • Not supported: text/tab-separated-values
• CONSTRUCT
  • application/rdf+xml
  • application/n-triples (DEFAULT if Accept: */* is sent)
  • text/turtle
  • text/n3
  • application/ld+json
  • Other acceptable values: application/n-quads, application/rdf+json, application/trig, application/trix, application/x-binary-rdf
  • text/plain (returns application/n-triples)
  • text/rdf+n3 (returns text/n3)
  • text/x-nquads (returns application/n-quads)
• DESCRIBE
  • application/rdf+xml
  • application/n-triples (DEFAULT if Accept: */* is sent)
  • text/turtle
  • text/n3
  • application/ld+json
  • Other acceptable values: application/n-quads, application/rdf+json, application/trig, application/trix, application/x-binary-rdf
  • text/plain (returns application/n-triples)
  • text/rdf+n3 (returns text/n3)
  • text/x-nquads (returns application/n-quads)

RASQAL

Uses roqet as RDF query utility (see http://librdf.org/rasqal/roqet.html) For variable bindings, the values of FORMAT vary upon what Rasqal supports but include simple for a simple text format (default), xml for the SPARQL Query Results XML format, csv for SPARQL CSV, tsv for SPARQL TSV, rdfxml and turtle for RDF syntax formats, and json for a JSON version of the results.

For RDF graph results, the values of FORMAT are ntriples (N-Triples, default), rdfxml-abbrev (RDF/XML Abbreviated), rdfxml (RDF/XML), turtle (Turtle), json (RDF/JSON resource centric), json-triples (RDF/JSON triples) or rss-1.0 (RSS 1.0, also an RDF/XML syntax).

Marklogic

You can use following methods to query triples:

• SPARQL mode in Query Console. For details, see Querying Triples with SPARQL
• XQuery using the semantics functions, and Search API, or a combination of XQuery and SPARQL. For details, see Querying Triples with XQuery or JavaScript.
• HTTP via a SPARQL endpoint. For details, see Using Semantics with the REST Client API.

Formats are specified as part of the HTTP Accept headers of the REST request.When you query the SPARQL endpoint with REST Client APIs, you can specify the result output format (See https://docs.marklogic.com/guide/semantics/REST#id_54258. The response type format depends on the type of query and the MIME type in the HTTP Accept header.

This table describes the MIME types and Accept Header/Output formats (MIME type) for different types of SPARQL queries. (See https://docs.marklogic.com/guide/semantics/REST#id_54258 and https://docs.marklogic.com/guide/semantics/loading#id_70682)

• SELECT
  • application/sparql-results+xml
  • application/sparql-results+json
  • text/html
  • text/csv
• ASK queries return a boolean (true or false).
• CONSTRUCT or DESCRIBE
  • application/n-triples
  • application/rdf+json
  • application/rdf+xml
  • text/turtle
  • text/n3
  • application/n-quads
  • application/trig

AllegroGraph

• SELECT
  • application/sparql-results+xml (DEFAULT if Accept: / is sent)
  • application/sparql-results+json (and application/json)
  • text/csv
  • text/tab-separated-values
  • OTHERS: application/sparql-results+ttl, text/integer, application/x-lisp-structured-expression, text/table, application/processed-csv, text/simple-csv, application/x-direct-upis
• ASK
  • application/sparql-results+xml (DEFAULT if Accept: / is sent)
  • application/sparql-results+json (and application/json)
  • Not supported: text/csv
  • Not supported: text/tab-separated-values
• CONSTRUCT
  • application/rdf+xml (DEFAULT if Accept: / is sent)
  • text/rdf+n3
  • OTHERS: text/integer, application/json, text/plain, text/x-nquads, application/trix, text/table, application/x-direct-upis
• DESCRIBE
  • application/rdf+xml (DEFAULT if Accept: / is sent)
  • text/rdf+n3

4store

• SELECT
  • application/sparql-results+xml (alias xml) (DEFAULT if Accept: / is sent))
  • application/sparql-results+json or application/json (alias json)
  • text/csv (alias csv)
  • text/tab-separated-values (alias tsv). Returns "text/plain" in GET.
  • Other values: text/plain, application/n-triples
• ASK
  • application/sparql-results+xml (alias xml) (DEFAULT if Accept: / is sent))
  • application/sparql-results+json or application/json (alias json)
  • text/csv (alias csv)
  • text/tab-separated-values (alias tsv). Returns "text/plain" in GET.
  • Other values: text/plain, application/n-triples
• CONSTRUCT
  • application/rdf+xml (alias xml) (DEFAULT if Accept: / is sent)
  • text/turtle (alias "text")
• DESCRIBE
  • application/rdf+xml (alias xml) (DEFAULT if Accept: / is sent)
  • text/turtle (alias "text")

Blazegraph

• SELECT
  • application/sparql-results+xml (alias xml) (DEFAULT if Accept: / is sent))
  • application/sparql-results+json or application/json (alias json)
  • text/csv
  • text/tab-separated-values
  • Other values: application/x-binary-rdf-results-table
• ASK
  • application/sparql-results+xml (alias xml) (DEFAULT if Accept: / is sent))
  • application/sparql-results+json or application/json (alias json)
• CONSTRUCT
  • application/rdf+xml (alias xml) (DEFAULT if Accept: / is sent)
  • text/turtle (returns text/n3)
  • text/n3
• DESCRIBE
  • application/rdf+xml (alias xml) (DEFAULT if Accept: / is sent)
  • text/turtle (returns text/n3)
  • text/n3

GraphDB

• SELECT
  • application/sparql-results+xml, application/xml (.srx file)
  • application/sparql-results+json, application/json (.srj file)
  • text/csv (DEFAULT if Accept: / is sent)
  • text/tab-separated-values
• ASK
  • application/sparql-results+xml, application/xml (.srx file)
  • application/sparql-results+json (DEFAULT if Accept: / is sent), application/json (.srj file)
  • NOT supported: text/csv, text/tab-separated-values
• CONSTRUCT
  • application/rdf+xml, application/xml (.rdf file)
  • text/turtle (.ttl file)
  • application/n-triples (.nt file) (DEFAULT if Accept: / is sent)
  • text/n3, text/rdf+n3 (.n3 file)
  • application/ld+json (.jsonld file)
• DESCRIBE
  • application/rdf+xml, application/xml (.rdf file)
  • text/turtle (.ttl file)
  • application/n-triples (.nt file) (DEFAULT if Accept: / is sent)
  • text/n3, text/rdf+n3 (.n3 file)
  • application/ld+json (.jsonld file)

Stardog

• SELECT
  • application/sparql-results+xml (DEFAULT if Accept: / is sent)
  • application/sparql-results+json
  • text/csv
  • text/tab-separated-values
  • Other values: application/x-binary-rdf-results-table
• ASK
  • application/sparql-results+xml (DEFAULT if Accept: / is sent)
  • application/sparql-results+json
  • Other values: text/boolean
  • Not supported: text/csv
  • Not supported: text/tab-separated-values
• CONSTRUCT
  • application/rdf+xml
  • text/turtle (DEFAULT if Accept: / is sent)
  • text/n3
  • application/ld+json
  • Other acceptable values: application/n-triples, application/x-turtle, application/trig, application/trix, application/n-quads
• DESCRIBE
  • application/rdf+xml
  • text/turtle (DEFAULT if Accept: / is sent)
  • text/n3
  • application/ld+json
  • Other acceptable values: application/n-triples, application/x-turtle, application/trig, application/trix, application/n-quads

Ontop

• SELECT
  • application/sparql-results+json (DEFAULT if Accept: / is sent)
  • application/sparql-results+xml
  • text/csv (versions before Ontop 5.2 returned text/sparql-results+csv)
  • text/tab-separated-values (versions before Ontop 5.2 returned text/sparql-results+tsv)
• ASK
  • application/sparql-results+json (DEFAULT if Accept: / is sent)
  • application/sparql-results+xml
  • Other values: text/boolean
• CONSTRUCT
  • text/turtle (DEFAULT if Accept: / is sent)
  • application/rdf+xml
  • text/n3
  • application/ld+json
  • Other acceptable values: application/n-triples, application/n-quads, rdf+json, rdf+xml
• DESCRIBE
  • text/turtle (DEFAULT if Accept: / is sent)
  • application/rdf+xml
  • application/rdf+json
  • text/n3
  • application/ld+json
  • Other acceptable values: application/n-triples, application/n-quads

Development

Requirements

The RDFLib package is used for RDF parsing.

This package is imported in a lazy fashion, i.e. only when needed. If the user never intends to use the RDF format, the RDFLib package is not imported and the user does not have to install it.

Source code

The source distribution contains:

• SPARQLWrapper: the Python package. You should copy the directory somewhere into your PYTHONPATH. Alternatively, you can also run the distutils scripts: python setup.py install
• test: some unit and integrations tests. In order to run the tests some packages have to be installed before. So please install the dev packages:pip install '.[dev]'
• scripts: some scripts to run the package against some SPARQL endpoints.
• docs: the documentation.

Community

Community support is available through the RDFlib developer's discussion group rdflib-dev. The archives. from the old mailing list are still available.

Issues

Please, report any issue to github.

Documentation

The SPARQLWrapper documentation is available online.

Other interesting documents are the latest SPARQL 1.1 Specification (W3C Recommendation 21 March 2013)and the initial SPARQL Specification (W3C Recommendation 15 January 2008).

License

The SPARQLWrapper package is licensed under W3C license.

Acknowledgement

The package was greatly inspired by Lee Feigenbaum's similar package for Javascript.

Developers involved:

• Ivan Herman <http://www.ivan-herman.net>
• Sergio Fernández <http://www.wikier.org>
• Carlos Tejo Alonso <http://www.dayures.net>
• Alexey Zakhlestin <https://indeyets.ru/>

Organizations involved:

• World Wide Web Consortium
• Salzburg Research
• Foundation CTIC