Pharmacology API calls fail - estimated execution time -762693632 #15
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Updating to 07.20.3214-pthreads seems to fix it - but I am not sure if this is because I cleared the transaction log or the update :) |
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Updating virtuoso only fixed the SPARQL results But I still get error in apache: Puelia logs now say: PREFIX chembl: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX cheminf: <http://semanticscience.org/resource/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX qudt: <http://qudt.org/1.1/schema/qudt#>
PREFIX chembl: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX cheminf: <http://semanticscience.org/resource/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX qudt: <http://qudt.org/1.1/schema/qudt#>
SELECT DISTINCT ?item ?chembl_compound WHERE { VALUES ?chembl_target_uri {'No mappings found'} GRAPH <http://www.ebi.ac.uk/chembl> {
?assay_uri chembl:hasTarget ?chembl_target_uri .
?assay_uri chembl:hasActivity ?item .
?item chembl:hasMolecule ?chembl_compound .
?chembl_target_uri a ?target_type .
OPTIONAL { ?chembl_target_uri dcterms:title ?target_name_chembl }
OPTIONAL { ?chembl_target_uri chembl:organismName ?target_organism }
OPTIONAL { ?chembl_target_uri chembl:hasTargetComponent ?protein .
GRAPH <http://www.conceptwiki.org> {
?cw_target skos:exactMatch ?protein ;
skos:prefLabel ?protein_name
}
}
OPTIONAL { ?assay_uri chembl:organismName ?assay_organism }
OPTIONAL { ?assay_uri dcterms:description ?assay_description }
OPTIONAL { ?assay_uri chembl:assayTestType ?assay_type }
OPTIONAL { ?item chembl:publishedType ?published_type }
OPTIONAL { ?item chembl:publishedRelation ?published_relation }
OPTIONAL { ?item chembl:publishedValue ?published_value }
OPTIONAL { ?item chembl:publishedUnits ?published_unit }
OPTIONAL { ?item chembl:standardType ?activity_type }
OPTIONAL { ?item chembl:standardRelation ?activity_relation }
OPTIONAL { ?item chembl:standardValue ?standard_value .
BIND (xsd:decimal(?standard_value) as ?activity_value)}
OPTIONAL { ?item chembl:standardUnits ?activity_unit }
OPTIONAL { ?item chembl:hasQUDT ?qudt_uri }
OPTIONAL { ?item chembl:pChembl ?pChembl }
OPTIONAL { ?item chembl:activityComment ?act_comment }
OPTIONAL { ?item chembl:hasDocument ?doc_uri .
OPTIONAL { ?doc_uri owl:sameAs ?doi }
OPTIONAL { ?doc_uri bibo:pmid ?pmid }
}
}
OPTIONAL { GRAPH <http://ops.rsc.org> {
?ocrs_compound skos:exactMatch ?chembl_compound .
?ocrs_compound cheminf:CHEMINF_000396 ?inchi;
cheminf:CHEMINF_000399 ?inchi_key;
cheminf:CHEMINF_000018 ?smiles .
OPTIONAL { [] obo:IAO_0000136 ?ocrs_compound ;
a cheminf:CHEMINF_000484 ;
qudt:numericValue ?molweight . }
OPTIONAL { [] obo:IAO_0000136 ?ocrs_compound ;
a cheminf:CHEMINF_000367;
qudt:numericValue ?num_ro5_violations . }
OPTIONAL { GRAPH <http://www.conceptwiki.org> {
?cw_compound skos:exactMatch ?ocrs_compound ;
skos:prefLabel ?compound_name .
} }
} } } ORDER BY ?item LIMIT 10 OFFSET 0Executing this query gives a new Virtuoso error: |
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The clue is here: So actually my IMS instance was down - due to mySQL upgrade.. but the PHP API didn't fail over this. mysql_1 | 2015-10-26T16:46:08.845539Z 4 [Note] Aborted connection 4 to db: 'ims' user: 'ims' host: '172.17.0.121' (Got an error reading communication packets) |
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In the Docker install, the
target/pharmacology/pagesAPI calls like http://heater.cs.man.ac.uk:3002/target/pharmacology/pages?uri=http%3A%2F%2Fwww.uniprot.org%2Funiprot%2FP30542 fail with:logs/puelia.logsays the SPARQL query is:Trying this at the Virtuoso instance at http://heater.cs.man.ac.uk:3003/sparql I get the error:
I am not sure what a negative execution time means.. perhaps @ghard have any ideas?
(This is Virtuoso version 07.20.3212 - I'm updating the image to see if 7.2.1 does anything different)
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