Should catch errors due to virtuoso being non-responsive

Question

Should catch errors due to virtuoso being non-responsive

Opened this issue 4 years ago · 0 comments

PARQL query:

PREFIX rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
PREFIX dcterms: http://purl.org/dc/terms/
PREFIX dc: http://purl.org/dc/elements/1.1/
PREFIX sbh: http://wiki.synbiohub.org/wiki/Terms/synbiohub#
PREFIX synbiohub: http://synbiohub.org#
PREFIX igem: http://wiki.synbiohub.org/wiki/Terms/igem#
PREFIX prov: http://www.w3.org/ns/prov#
PREFIX sbol2: http://sbols.org/v2#
PREFIX xsd: http://www.w3.org/2001/XMLSchema#
PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema#
PREFIX purl: http://purl.obolibrary.org/obo/
PREFIX ncbi: http://www.ncbi.nlm.nih.gov#

SELECT DISTINCT
?subject
?displayId
?version
?name
?description
?type
?graph
?role
?sboltype
FROM https://synbiohub.org/public
WHERE {
FILTER (?subject != ?subject)
?subject a ?type .
?subject sbh:topLevel ?subject .
OPTIONAL { ?subject sbol2:displayId ?displayId . }
OPTIONAL { ?subject sbol2:version ?version . }
OPTIONAL { ?subject dcterms:title ?name . }
OPTIONAL { ?subject dcterms:description ?description . }
OPTIONAL { ?subject sbol2:role ?role . }
OPTIONAL { ?subject sbol2:type ?sboltype . }
}
OFFSET 0 LIMIT 10000
[2021-03-04 20:50:55.298662] [ERROR] failed querying:http://virtuoso:8890/sparql?
[2021-03-04 20:50:55.298526] Virtuoso 42000 Error The estimated execution time 602 (sec) exceeds the limit of 400 (sec).

SPARQL query:

PREFIX rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
PREFIX dcterms: http://purl.org/dc/terms/
PREFIX dc: http://purl.org/dc/elements/1.1/
PREFIX sbh: http://wiki.synbiohub.org/wiki/Terms/synbiohub#
PREFIX synbiohub: http://synbiohub.org#
PREFIX igem: http://wiki.synbiohub.org/wiki/Terms/igem#
PREFIX prov: http://www.w3.org/ns/prov#
PREFIX sbol2: http://sbols.org/v2#
PREFIX xsd: http://www.w3.org/2001/XMLSchema#
PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema#
PREFIX purl: http://purl.obolibrary.org/obo/
PREFIX ncbi: http://www.ncbi.nlm.nih.gov#

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/flask/app.py", line 1813, in full_dispatch_request
rv = self.dispatch_request()
File "/usr/local/lib/python3.6/dist-packages/flask/app.py", line 1799, in dispatch_request
return self.view_functionsrule.endpoint
File "/SBOLExplorer/flask/explorer.py", line 165, in sparql_search_endpoint
response = jsonify(search.search(sparql_query, utils.get_uri2rank(), utils.get_clusters(), default_graph_uri))
File "/SBOLExplorer/flask/search.py", line 471, in search
criteria_response = query.query_parts(_from, similar_criteria)
File "/SBOLExplorer/flask/query.py", line 35, in query_parts
return memoized_query_sparql(query)
File "/SBOLExplorer/flask/query.py", line 39, in memoized_query_sparql
return query_sparql(query)
File "/SBOLExplorer/flask/query.py", line 57, in query_sparql
raise Exception("Endpoint not responding")
Exception: Endpoint not responding

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/flask/app.py", line 1813, in full_dispatch_request
rv = self.dispatch_request()
File "/usr/local/lib/python3.6/dist-packages/flask/app.py", line 1799, in dispatch_request
return self.view_functionsrule.endpoint
File "/SBOLExplorer/flask/explorer.py", line 165, in sparql_search_endpoint
response = jsonify(search.search(sparql_query, utils.get_uri2rank(), utils.get_clusters(), default_graph_uri))
File "/SBOLExplorer/flask/search.py", line 471, in search
criteria_response = query.query_parts(_from, similar_criteria)
File "/SBOLExplorer/flask/query.py", line 35, in query_parts
return memoized_query_sparql(query)
File "/SBOLExplorer/flask/query.py", line 39, in memoized_query_sparql
return query_sparql(query)
File "/SBOLExplorer/flask/query.py", line 57, in query_sparql
raise Exception("Endpoint not responding")