Open danidi opened 10 years ago
This is timing out (I assume) with a 500 Internal Server Error
is only on the beta.openphacts.org
deployment - but it works on ops2. Perhaps OpenLink can check the configuration for talking to the 1.4 PHP? (Is it a RewriteRule?)
stain@biggie-mint ~ $ curl 'http://ops2.few.vu.nl/target/tree/pharmacology/pages?uri=http%3A%2F%2Fpurl.uniprot.org%2Fenzyme%2F2.-.-.-&app_id=XXX&app_key=XXX&target_organism=Homo+sapiens&min-pChembl=7&_pageSize=all' > /tmp/1
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 114M 0 114M 0 0 144k 0 --:--:-- 0:13:26 --:--:-- 3217k
(13 minutes there for enzyme/2
- enzyme/1
took less than 2 minutes and then got cached)
btw probably unrelated: - http://purl.uniprot.org/enzyme/1 and http://purl.uniprot.org/enzyme/1.-.-.- in real life gives a 400 Bad Request
with Can't handle namespace: enzyme
.
Assigning to @ghard @yrjana for OpenLink to have a look if the nginx config for 1.4 differs from 1.3 with regards to timeouts.
The resulting SPARQL query returns 251478 rows from 1.4 virtuoso instance. No error on the backend. @antonisloizou we should cross-check with ops2.
I cannot re-create this error on either 1.3 or 1.4 using the 3-scale interface (with out the pagesize=all)
There are 13012 activites that should be returned here. https://ops2.few.vu.nl/target/tree/pharmacology/pages?uri=http%3A%2F%2Fpurl.uniprot.org%2Fenzyme%2F1.-.-.-&app_id=be7ce5a9&app_key=77069eed83fceb8bb23f031c05193151&target_organism=Homo+sapiens&min-pChembl=7&_pageSize=all
It currently times out across all 1.4, 1.5 and develop, so at least its consistent.
Up until _pageSize=4000 you get results back, after that we run into :
Endpoint returned 400 Virtuoso 37000 Error SP030: SPARQL compiler, line 105: Too many arguments of a standard built-in function in operator()
The final CONSTRUCT query hasn't returned in over an hour on virtuoso, and the timeout is at 15mins. The SELECT version of it however , takes only 30s
Maybe OL, @ghard can take a look at these queries, but they are pretty expensive by definition:
SELECT:
PREFIX chembl: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX ops: <http://www.openphacts.org/api#>
PREFIX obo_goa: <http://www.semantic-systems-biology.org/ontology/rdf/OBO#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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 {
{
SELECT DISTINCT ?item ?chembl_compound ?chembl_target ?assay_uri ?target_type ?assay_organism ?assay_description ?assay_type ?target_name ?target_organism ?protein ?protein_name ?published_type ?published_relation ?published_value ?published_unit ?activity_type ?activity_relation ?activity_value ?activity_unit ?qudt_uri ?pChembl ?act_comment ?document ?doi ?pmid WHERE {
{
SELECT DISTINCT ?chembl_target WHERE {
?chembl_target chembl:hasProteinClassification|chembl:hasTargetComponent/chembl:targetCmptXref|chembl:hasTargetComponent/skos:exactMatch/obo_goa:C|chembl:hasTargetComponent/skos:exactMatch/obo_goa:F|chembl:hasTargetComponent/skos:exactMatch/obo_goa:P ?class .
VALUES ?node_uri {
<http://purl.uniprot.org/enzyme/1.-.-.->
} GRAPH ?g {
?class rdfs:subClassOf ?node_uri .
}
}
}
GRAPH <http://www.ebi.ac.uk/chembl> {
{
?item <http://rdf.ebi.ac.uk/terms/chembl#pChembl> ?pChembl FILTER( ?pChembl >= 7 )
} {
?chembl_target<http://rdf.ebi.ac.uk/terms/chembl#organismName> "Homo sapiens".
}
?item a chembl:Activity ;
chembl:hasAssay ?assay_uri ;
chembl:hasMolecule ?chembl_compound .
?assay_uri chembl:hasTarget ?chembl_target .
?chembl_target a ?target_type .
}
GRAPH <http://www.ebi.ac.uk/chembl> {
{
?assay_uri chembl:organismName ?assay_organism
}
UNION {
?assay_uri dcterms:description ?assay_description
}
UNION {
?assay_uri chembl:assayTestType ?assay_type
}
UNION {
?chembl_target dcterms:title ?target_name
}
UNION {
?chembl_target chembl:organismName ?target_organism
}
UNION {
?chembl_target chembl:hasTargetComponent ?protein .
OPTIONAL {
GRAPH <http://www.conceptwiki.org> {
?cw_target skos:exactMatch ?protein ;
skos:prefLabel ?protein_name
}
}
}
UNION {
?item chembl:publishedType ?published_type
}
UNION {
?item chembl:publishedRelation ?published_relation
}
UNION {
?item chembl:publishedValue ?published_value
}
UNION {
?item chembl:publishedUnits ?published_unit
}
UNION {
?item chembl:standardType ?activity_type
}
UNION {
?item chembl:standardRelation ?activity_relation
}
UNION {
?item chembl:standardValue ?std_value .
BIND (xsd:decimal(?std_value) as ?activity_value)
}
UNION {
?item chembl:standardUnits ?activity_unit
}
UNION {
?item chembl:hasQUDT ?qudt_uri
}
UNION {
?item chembl:pChembl ?pChembl
}
UNION {
?item chembl:activityComment ?act_comment
}
UNION {
?item chembl:hasDocument ?document .
{
?document owl:sameAs ?doi
}
UNION {
?document bibo:pmid ?pmid
}
}
}
}
}
OPTIONAL {
GRAPH <http://ops.rsc.org> {
{
?ocrs_compound skos:exactMatch ?chembl_compound ;
cheminf:CHEMINF_000396 ?inchi;
cheminf:CHEMINF_000399 ?inchi_key;
cheminf:CHEMINF_000018 ?smiles .
} UNION {
[] obo:IAO_0000136 ?ocrs_compound ;
a cheminf:CHEMINF_000484 ;
qudt:numericValue ?molweight .
}
UNION {
[] 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 .
}
}
}
}
}
CONSTRUCT :
PREFIX chembl: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX ops: <http://www.openphacts.org/api#>
PREFIX obo_goa: <http://www.semantic-systems-biology.org/ontology/rdf/OBO#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX cheminf: <http://semanticscience.org/resource/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX qudt: <http://qudt.org/1.1/schema/qudt#>
CONSTRUCT { ?item chembl:hasMolecule ?chembl_compound;
chembl:publishedType ?published_type ;
chembl:publishedRelation ?published_relation ;
chembl:publishedValue ?published_value ;
chembl:publishedUnits ?published_unit ;
chembl:standardType ?activity_type;
chembl:standardRelation ?activity_relation;
chembl:standardValue ?activity_value;
chembl:hasQUDT ?qudt_uri;
chembl:hasAssay ?assay_uri ;
chembl:pChembl ?pChembl ;
chembl:activityComment ?act_comment ;
chembl:hasDocument ?doi ;
bibo:pmid ?pmid ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?qudt_uri skos:prefLabel ?activity_unit .
?assay_uri chembl:hasTarget ?chembl_target ;
chembl:assayTestType ?assay_type ;
dcterms:description ?assay_description ;
chembl:assayOrganismName ?assay_organism ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?chembl_target dcterms:title ?target_name;
chembl:targetOrganismName ?target_organism ;
ops:classifiedUnder ?class ;
chembl:hasTargetComponent ?protein ;
a ?target_type ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?chembl_compound skos:exactMatch ?ocrs_compound ;
skos:exactMatch ?cw_compound ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?ocrs_compound ops:smiles ?smiles ;
ops:inchi ?inchi ;
ops:inchikey ?inchi_key;
ops:molweight ?molweight ;
ops:ro5_violations ?num_ro5_violations ;
void:inDataset <http://ops.rsc.org> .
?protein skos:exactMatch ?cw_target .
?cw_target skos:prefLabel ?protein_name ;
void:inDataset <http://www.conceptwiki.org> .
?cw_compound skos:prefLabel ?compound_name ;
void:inDataset <http://www.conceptwiki.org> .
} WHERE {
{ SELECT DISTINCT ?item ?chembl_compound ?chembl_target ?assay_uri ?target_type ?assay_organism ?assay_description ?assay_type ?target_name ?target_organism ?protein ?protein_name ?published_type ?published_relation ?published_value ?published_unit ?activity_type ?activity_relation ?activity_value ?activity_unit ?qudt_uri ?pChembl ?act_comment ?document ?doi ?pmid WHERE {
{ SELECT DISTINCT ?chembl_target WHERE {
?chembl_target chembl:hasProteinClassification|chembl:hasTargetComponent/chembl:targetCmptXref|chembl:hasTargetComponent/skos:exactMatch/obo_goa:C|chembl:hasTargetComponent/skos:exactMatch/obo_goa:F|chembl:hasTargetComponent/skos:exactMatch/obo_goa:P ?class .
VALUES ?node_uri { <http://purl.uniprot.org/enzyme/1.-.-.-> } GRAPH ?g {
?class rdfs:subClassOf ?node_uri .
}
} }
GRAPH <http://www.ebi.ac.uk/chembl> { { ?item <http://rdf.ebi.ac.uk/terms/chembl#pChembl> ?pChembl FILTER( ?pChembl >= 7 ) } { ?chembl_target<http://rdf.ebi.ac.uk/terms/chembl#organismName> "Homo sapiens". }
?item a chembl:Activity ;
chembl:hasAssay ?assay_uri ;
chembl:hasMolecule ?chembl_compound .
?assay_uri chembl:hasTarget ?chembl_target .
?chembl_target a ?target_type .
}
GRAPH <http://www.ebi.ac.uk/chembl> {
{ ?assay_uri chembl:organismName ?assay_organism }
UNION { ?assay_uri dcterms:description ?assay_description }
UNION { ?assay_uri chembl:assayTestType ?assay_type }
UNION { ?chembl_target dcterms:title ?target_name }
UNION { ?chembl_target chembl:organismName ?target_organism }
UNION { ?chembl_target chembl:hasTargetComponent ?protein .
OPTIONAL {
GRAPH <http://www.conceptwiki.org> {
?cw_target skos:exactMatch ?protein ;
skos:prefLabel ?protein_name
}
}
}
UNION { ?item chembl:publishedType ?published_type }
UNION { ?item chembl:publishedRelation ?published_relation }
UNION { ?item chembl:publishedValue ?published_value }
UNION { ?item chembl:publishedUnits ?published_unit }
UNION { ?item chembl:standardType ?activity_type }
UNION { ?item chembl:standardRelation ?activity_relation }
UNION { ?item chembl:standardValue ?std_value .
BIND (xsd:decimal(?std_value) as ?activity_value)
}
UNION { ?item chembl:standardUnits ?activity_unit }
UNION { ?item chembl:hasQUDT ?qudt_uri }
UNION { ?item chembl:pChembl ?pChembl }
UNION { ?item chembl:activityComment ?act_comment }
UNION { ?item chembl:hasDocument ?document .
{ ?document owl:sameAs ?doi }
UNION { ?document bibo:pmid ?pmid }
}
}
} }
OPTIONAL {
GRAPH <http://ops.rsc.org> {
{ ?ocrs_compound skos:exactMatch ?chembl_compound ;
cheminf:CHEMINF_000396 ?inchi;
cheminf:CHEMINF_000399 ?inchi_key;
cheminf:CHEMINF_000018 ?smiles .
} UNION {
[] obo:IAO_0000136 ?ocrs_compound ;
a cheminf:CHEMINF_000484 ;
qudt:numericValue ?molweight .
}
UNION {
[] 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 .
}
}
}
} }
https://beta.openphacts.org/1.4/target/tree/pharmacology/pages?uri=http%3A%2F%2Fpurl.uniprot.org%2Fenzyme%2F1.-.-.-&app_id=XXX&app_key=XXX&target_organism=Homo+sapiens&min-pChembl=7&_pageSize=all returns an internal server error after approx. 1min 30s. The same query on 1.3 gives results in a bit less than 2min. Are there any changes in the restrictions or time-outs on 1.4?