Hi Brandon,
The configuration is quite complex - it's likely due to the inference
layer but it would be worth trying without the text index to confirm
that especially for the loading.
Do you need all that
<http://jena.hpl.hp.com/2003/OWLMicroFBRuleReasoner>
offers or is all you want RDFS subclass?
Because there is
https://jena.apache.org/documentation/rdfs/
(give ICD10CM as both data and also in a file to be the schema).
The schema is assumed to be fixed which might not work for you long term
but it is another data point to understand the situation.
About ICD10CM itseld - are you wanting to navigate its structure or use
it with data for inference? If it is to navigate its structure do you
even want inference?
Andy
On 14/09/2021 00:42, Brandon Sara wrote:
I have been able to create an easily reproducible scenario that others can use
to replicate and test the issues that I’m seeing:
1. Start fuseki using the config that I’ve listed below.
2. Attempt to load the latest version of ICD-10 CM as provided freely by
BioPortal: https://bioportal.bioontology.org/ontologies/ICD10CM
If inference is enabled, then I can’t even get the turtle file to load in its
entirety. If I load the turtle file without inference, then the load completes,
but upon restarting the server and submitting a request, the service doesn’t
finish processing the request in any reasonable amount of time, no matter how
simple the query of the request is (one that actually queries data from the
dataset at least).
Config:
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX fuseki: <http://jena.apache.org/fuseki#>
PREFIX ja: <http://jena.hpl.hp.com/2005/11/Assembler#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX tdb2: <http://jena.apache.org/2016/tdb#>
PREFIX text: <http://jena.apache.org/text#>
[] rdf:type fuseki:Server ;
fuseki:pingEP true ;
fuseki:statsEP true ;
fuseki:metricsEP true ;
fuseki:compactEP true ;
ja:context [
ja:cxtName "arq:queryTimeout" ;
ja:cxtValue "10000,60000" ;
] ;
.
<#kgService> a fuseki:Service ;
fuseki:name "kg" ;
fuseki:dataset <#kgIndexedDataset> ;
fuseki:endpoint [ fuseki:operation fuseki:query; ] ;
fuseki:endpoint [ fuseki:operation fuseki:update; ] ;
fuseki:endpoint [ fuseki:operation fuseki:gsp_r; ] ;
fuseki:endpoint [ fuseki:operation fuseki:gsp_rw; fuseki:name "data"; ] ;
.
<#kgIndexedDataset> rdf:type text:TextDataset ;
text:dataset <#kgInferredDataset> ;
text:index <#kgIndex> ;
.
<#kgIndex> a text:TextIndexLucene ;
text:directory <file:/fuseki/databases/kg.index> ;
text:entityMap <#kgEntityMap> ;
text:storeValues true ;
text:queryParser [ a text:ComplexPhraseQueryParser ]
.
<#kgEntityMap> a text:EntityMap ;
text:defaultField "label" ;
text:entityField "uri" ;
text:uidField "uid" ;
text:langField "lang" ;
text:graphField "graph" ;
text:map (
[ text:field "id" ;
text:predicate dcterms:identifier ]
[ text:field "label" ;
text:predicate rdfs:label ]
) ;
.
<#kgInferredDataset> a ja:RDFDataset ;
ja:defaultGraph <#kgInferenceModel> ;
.
<#kgInferenceModel> a ja:InfModel ;
ja:baseModel <#kgTdbGraph> ;
ja:reasoner [
ja:reasonerURL <http://jena.hpl.hp.com/2003/OWLMicroFBRuleReasoner>
] ;
.
<#kgTdbGraph> a tdb2:GraphTDB2 ;
tdb2:dataset <#kgTdbDataset> ;
.
<#kgTdbDataset> a tdb2:DatasetTDB2 ;
tdb2:location "/fuseki/databases/kg" ;
.
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