An error in the sparql query when processing with Python
Question
I am processing a sparql query with Python.
def query(var):
query_with_placeholder="""
SELECT ?same_context as ?context str(?context_label) as ?context_label ?same_s as ?s str(?s_label) as ?s_label ?s_type ?p "$ENTITY_CODE$" as ?gene str(?text) as ?text
WHERE {
?transcript <http://purl.obolibrary.org/obo/SO_transcribed_from> <http://rdf.ebi.ac.uk/resource/ensembl/$ENTITY_CODE$> .
?transcript <http://purl.obolibrary.org/obo/SO_translates_to> ?ensembl_protein .
?reflect_protein owl:sameAs ?ensembl_protein
graph ?event {
?s ?p ?reflect_protein .
}.
{
?s a <http://lcsb.uni.lu/biokb#Chemical> .
?s owl:sameAs ?same_s .
?same_s rdfs:label ?s_label .
} UNION {
?s a <http://lcsb.uni.lu/biokb#Protein> .
?s owl:sameAs ?same_s .
?ensembl_transcript <http://purl.obolibrary.org/obo/SO_translates_to> ?same_s .
?ensembl_transcript rdfs:label ?s_label
}
?s a ?s_type .
?sentence <http://lcsb.uni.lu/biokb#hasEvent> ?event .
?sentence <http://lcsb.uni.lu/biokb#containsEntity> ?context .
?sentence <http://lcsb.uni.lu/biokb#text> ?text .
?context a <http://lcsb.uni.lu/biokb#Tissue> .
?context owl:sameAs ?same_context .
?same_context rdfs:label ?context_label .
}"""
new_query=query_with_placeholder.replace("$ENTITY_CODE$",var)
sparql = SPARQLWrapper("http://biokb.lcsb.uni.lu/sparql")
sparql.setQuery(new_query)
sparql.setReturnFormat(JSON)
result_of_query = sparql.query().convert()
return result_of_query
Var is an element from a list I am iterating through. As a result of using this function I got a mistake
HTTPError: HTTP Error 404: File not found
and
EndPointNotFound: EndPointNotFound: it was impossible to connect with the endpoint in that address, check if it is correct.
Response:
b'<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">\n<html>\n <head>\n <title>Error HTTP/1.1 404 File not found</title>\n </head>\n <body>\n <h3>Error HTTP/1.1 404 File not found</h3><pre>\nThe requested URL was not found URI = \'/sparql\'\n </pre></body></html>\n'
And thus my query stops iterating at 65th element. But I still can run the query for that elements and further ones so I suppose it must work.
Where is the mistake? And how it could be corrected?
1 answers
solution1
1 ACCPTED 2018-03-11 11:24:28
This mistake appears when you run the query to DataBase too often during short period of time.
EndPointNotFound: EndPointNotFound: it was impossible to connect with the endpoint in that address, check if it is correct.
Response:
b'<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">\n<html>\n <head>\n <title>Error HTTP/1.1 404 File not found</title>\n </head>\n <body>\n <h3>Error HTTP/1.1 404 File not found</h3><pre>\nThe requested URL was not found URI = \'/sparql\'\n </pre></body></html>\n'
Add to python code the following:
import time
time.sleep(2)
Where 2 - time in seconds.
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