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Comments (3)

vemonet avatar vemonet commented on July 22, 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)

from sparqlwrapper.

JervenBolleman avatar JervenBolleman commented on July 22, 2024

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.

from sparqlwrapper.

vemonet avatar vemonet commented on July 22, 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)

from sparqlwrapper.

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