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Should catch errors due to virtuoso being non-responsive #98

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cjmyers opened this issue Mar 5, 2021 · 0 comments
Open

Should catch errors due to virtuoso being non-responsive #98

cjmyers opened this issue Mar 5, 2021 · 0 comments
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@cl117

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cjmyers commented Mar 5, 2021

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#

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 20:50:55.299271] [ERROR] failed querying:http://virtuoso:8890/sparql?
[2021-03-04 20:50:55.299451] [ERROR] Returning error Endpoint not responding
Traceback:
Traceback (most recent call last):
File "/SBOLExplorer/flask/query.py", line 54, in query_sparql
results.extend(page_query(query, endpoint))
File "/SBOLExplorer/flask/query.py", line 123, in page_query
new_results = send_query(full_query, endpoint)
File "/SBOLExplorer/flask/query.py", line 153, in send_query
raise Exception(url + ' is not responding')
Exception: http://virtuoso:8890/sparql?query=%0A++++PREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0A++++PREFIX+dcterms%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0A++++PREFIX+dc%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Felements%2F1.1%2F%3E%0A++++PREFIX+sbh%3A+%3Chttp%3A%2F%2Fwiki.synbiohub.org%2Fwiki%2FTerms%2Fsynbiohub%23%3E%0A++++PREFIX+synbiohub%3A+%3Chttp%3A%2F%2Fsynbiohub.org%23%3E%0A++++PREFIX+igem%3A+%3Chttp%3A%2F%2Fwiki.synbiohub.org%2Fwiki%2FTerms%2Figem%23%3E%0A++++PREFIX+prov%3A+%3Chttp%3A%2F%2Fwww.w3.org%2Fns%2Fprov%23%3E%0A++++PREFIX+sbol2%3A+%3Chttp%3A%2F%2Fsbols.org%2Fv2%23%3E%0A++++PREFIX+xsd%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2001%2FXMLSchema%23%3E%0A++++PREFIX+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0A++++PREFIX+purl%3A+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2F%3E%0A++++PREFIX+ncbi%3A+%3Chttp%3A%2F%2Fwww.ncbi.nlm.nih.gov%23%3E%0A++++%0A++++SELECT+DISTINCT%0A++++++++%3Fsubject%0A++++++++%3FdisplayId%0A++++++++%3Fversion%0A++++++++%3Fname%0A++++++++%3Fdescription%0A++++++++%3Ftype%0A++++++++%3Fgraph%0A++++++++%3Frole%0A++++++++%3Fsboltype%0A++++FROM+%3Chttps%3A%2F%2Fsynbiohub.org%2Fpublic%3E+%0A++++WHERE+%7B%0A++++FILTER+%28%3Fsubject+%21%3D+%3Fsubject%29%0A++++++++%3Fsubject+a+%3Ftype+.%0A++++++++%3Fsubject+sbh%3AtopLevel+%3Fsubject+.%0A++++++++OPTIONAL+%7B+%3Fsubject+sbol2%3AdisplayId+%3FdisplayId+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+sbol2%3Aversion+%3Fversion+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+dcterms%3Atitle+%3Fname+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+dcterms%3Adescription+%3Fdescription+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+sbol2%3Arole+%3Frole+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+sbol2%3Atype+%3Fsboltype+.+%7D%0A++++%7D+%0A++++OFFSET+0+LIMIT+10000&default-graph-uri= is 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")
Exception: Endpoint not responding

[2021-03-04 20:50:55.300089] [ERROR] Returning error Endpoint not responding
Traceback:
Traceback (most recent call last):
File "/SBOLExplorer/flask/query.py", line 54, in query_sparql
results.extend(page_query(query, endpoint))
File "/SBOLExplorer/flask/query.py", line 123, in page_query
new_results = send_query(full_query, endpoint)
File "/SBOLExplorer/flask/query.py", line 153, in send_query
raise Exception(url + ' is not responding')
Exception: http://virtuoso:8890/sparql?query=%0A++++PREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0A++++PREFIX+dcterms%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0A++++PREFIX+dc%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Felements%2F1.1%2F%3E%0A++++PREFIX+sbh%3A+%3Chttp%3A%2F%2Fwiki.synbiohub.org%2Fwiki%2FTerms%2Fsynbiohub%23%3E%0A++++PREFIX+synbiohub%3A+%3Chttp%3A%2F%2Fsynbiohub.org%23%3E%0A++++PREFIX+igem%3A+%3Chttp%3A%2F%2Fwiki.synbiohub.org%2Fwiki%2FTerms%2Figem%23%3E%0A++++PREFIX+prov%3A+%3Chttp%3A%2F%2Fwww.w3.org%2Fns%2Fprov%23%3E%0A++++PREFIX+sbol2%3A+%3Chttp%3A%2F%2Fsbols.org%2Fv2%23%3E%0A++++PREFIX+xsd%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2001%2FXMLSchema%23%3E%0A++++PREFIX+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0A++++PREFIX+purl%3A+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2F%3E%0A++++PREFIX+ncbi%3A+%3Chttp%3A%2F%2Fwww.ncbi.nlm.nih.gov%23%3E%0A++++%0A++++SELECT+DISTINCT%0A++++++++%3Fsubject%0A++++++++%3FdisplayId%0A++++++++%3Fversion%0A++++++++%3Fname%0A++++++++%3Fdescription%0A++++++++%3Ftype%0A++++++++%3Fgraph%0A++++++++%3Frole%0A++++++++%3Fsboltype%0A++++FROM+%3Chttps%3A%2F%2Fsynbiohub.org%2Fpublic%3E+%0A++++WHERE+%7B%0A++++FILTER+%28%3Fsubject+%21%3D+%3Fsubject%29%0A++++++++%3Fsubject+a+%3Ftype+.%0A++++++++%3Fsubject+sbh%3AtopLevel+%3Fsubject+.%0A++++++++OPTIONAL+%7B+%3Fsubject+sbol2%3AdisplayId+%3FdisplayId+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+sbol2%3Aversion+%3Fversion+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+dcterms%3Atitle+%3Fname+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+dcterms%3Adescription+%3Fdescription+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+sbol2%3Arole+%3Frole+.+%7D%0A++++++++OPTIONAL+%7B+%3Fsubject+sbol2%3Atype+%3Fsboltype+.+%7D%0A++++%7D+%0A++++OFFSET+0+LIMIT+10000&default-graph-uri= is 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")
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