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SPARQLWrapper does not work for CONSTRUCT and DESCRIBE queries on the UniProt SPARQL endpoint which is Virtuoso #234

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vemonet opened this issue Jun 5, 2024 · 3 comments
Open

SPARQLWrapper does not work for CONSTRUCT and DESCRIBE queries on the UniProt SPARQL endpoint which is Virtuoso #234

vemonet opened this issue Jun 5, 2024 · 3 comments

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@vemonet
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vemonet commented Jun 5, 2024

When running any CONSTRUCT or DESCRIBE query on the UniProt SPARQL endpoint https://sparql.uniprot.org/sparql/, whatever the return format asked (XML, turtle) SPARQLWrapper fails to resolve the query

Code to reproduce:

When asking for XML at least an error is thrown:

from SPARQLWrapper import TURTLE, XML, SPARQLWrapper

query = """PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
CONSTRUCT
{
	?protein a up:HumanProtein .
}
WHERE
{
	?protein a up:Protein .
	?protein up:organism taxon:9606
} LIMIT 10"""

sparql_endpoint = SPARQLWrapper("https://sparql.uniprot.org/sparql/")
sparql_endpoint.setReturnFormat(XML)
sparql_endpoint.setQuery(query)

results = sparql_endpoint.query().convert()
print(results)

Error message:

ExpatError                                Traceback (most recent call last)
Cell In[8], line 20
     17 # sparql_endpoint.setReturnFormat(TURTLE)
     18 sparql_endpoint.setQuery(query)
---> 20 results = sparql_endpoint.query().convert()
     21 print(results)

File ~/dev/.venv/lib/python3.10/site-packages/SPARQLWrapper/Wrapper.py:1190, in QueryResult.convert(self)
   1188 if _content_type_in_list(ct, _SPARQL_XML):
   1189     _validate_format("XML", [XML], ct, self.requestedFormat)
-> 1190     return self._convertXML()
   1191 elif _content_type_in_list(ct, _XML):
   1192     _validate_format("XML", [XML], ct, self.requestedFormat)

File ~/dev/.venv/lib/python3.10/site-packages/SPARQLWrapper/Wrapper.py:1073, in QueryResult._convertXML(self)
   1065 def _convertXML(self) -> Document:
   1066     """
   1067     Convert an XML result into a Python dom tree. This method can be overwritten in a
   1068     subclass for a different conversion method.
   (...)
   1071     :rtype: :class:`xml.dom.minidom.Document`
   1072     """
-> 1073     doc = parse(self.response)
   1074     rdoc = cast(Document, doc)
...
--> 211     parser.Parse(b"", True)
    212 except ParseEscape:
    213     pass

ExpatError: no element found: line 1, column 0

When asking for turtle, SPARQLWrapper does not even throw an error:

from SPARQLWrapper import TURTLE, XML, SPARQLWrapper

query = """PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
CONSTRUCT
{
	?protein a up:HumanProtein .
}
WHERE
{
	?protein a up:Protein .
	?protein up:organism taxon:9606
} LIMIT 10"""

sparql_endpoint = SPARQLWrapper("https://sparql.uniprot.org/sparql/")
# sparql_endpoint.setReturnFormat(XML)
sparql_endpoint.setReturnFormat(TURTLE)
sparql_endpoint.setQuery(query)

results = sparql_endpoint.query().convert()
print(results)

Printing results gives HTML: b'<!DOCTYPE html SYSTEM "about:legacy-compat">\n<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head><title>UniProt</title>......

UniProt uses OpenLink Virtuoso and supports the SPARQL 1.1 Standard.
@vemonet
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vemonet commented Jun 5, 2024

Using requests with the most logical config to request a SPARQL endpoint just works, so the problem is on SPARQLWrapper doing weird things internally:

import requests
from rdflib import Graph

query = """PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
CONSTRUCT
{
	?protein a up:HumanProtein .
}
WHERE
{
	?protein a up:Protein .
	?protein up:organism taxon:9606
} LIMIT 10"""

response = requests.post(
    "https://sparql.uniprot.org/sparql/",
    headers={
        "Accept": "text/turtle"
    },
    data={
        "query": query
    },
    timeout=60,
)
response.raise_for_status()
g = Graph()
g.parse(data=response.text, format="turtle")

print(response.text)
print(len(g))

In bonus we get basic features like timeout working! (the .setTimeout() option from SPARQLWrapper does not work at all, at least for UniProt endpoint, but this should go in another issue)

@JervenBolleman
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UniProt is not pure virtuoso and has some middleware that expects accept headers to ask for an rdf format if using describe and or construct.

@vemonet
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vemonet commented Jun 20, 2024

@JervenBolleman SPARQLWrapper also fails to run SELECT queries to SwissLipids https://beta.sparql.swisslipids.org/

Error 500 Internal Server Error</h1><p>The server was not able to handle your request.:

from SPARQLWrapper import XML, SPARQLWrapper, JSON

query = """PREFIX sh: <http://www.w3.org/ns/shacl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?comment ?query
WHERE
{
    ?sq a sh:SPARQLExecutable ;
        rdfs:label|rdfs:comment ?comment ;
        sh:select|sh:ask|sh:construct|sh:describe ?query .
}"""

sparql_endpoint = SPARQLWrapper("https://beta.sparql.swisslipids.org/")
sparql_endpoint.setReturnFormat(XML)
sparql_endpoint.setTimeout(60)
sparql_endpoint.setQuery(query)

results = sparql_endpoint.query().convert()
print(results)

With requests it works:

import requests

query = """PREFIX sh: <http://www.w3.org/ns/shacl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?comment ?query
WHERE
{
    ?sq a sh:SPARQLExecutable ;
        rdfs:label|rdfs:comment ?comment ;
        sh:select|sh:ask|sh:construct|sh:describe ?query .
}"""

response = requests.post(
    "https://beta.sparql.swisslipids.org/",
    headers={
        "Accept": "application/json",
        "User-agent": "sparqlwrapper 2.0.1a0 (rdflib.github.io/sparqlwrapper)"
    },
    data={
        "query": query
    },
    timeout=60,
)
try:
    response.raise_for_status()
    print(response.json())
except requests.exceptions.HTTPError as e:
    print(e)
    print(response.text)

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@JervenBolleman @vemonet