Hi Andy, I seem to have a configuration that's working, where my named graphs are persisting. See new config file below. However, it's horribly slow. I am running Java code which is reading 60,000 records and running SPARQL queries and updates viathe REST API. It will eventually will produce 5 million triples. The further along it gets, the slower it's working. It's about 1/3 done now and down to less than 1 update per second.
My ja:rdfsSchema file is large. It contains my full ontology and some reference data, which is large (about 90K axions). I'm not sure that's a factor, however, since the slowdown seems to be based on the number of triples loaded. But I still don't understand this schema stuff, since inferencing isn't going to work with my query unless I've also loaded the full ontology into a named graph that the query references. What really needs to be in the schema file? Appreciate any help. Thanks, Ted Theodore Hills Consultant | Research Phone: +1 212 296-1833 theodore.hi...@morganstanley.com ## Fuseki Server configuration file. PREFIX fuseki: <http://jena.apache.org/fuseki#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX tdb1: <http://jena.hpl.hp.com/2008/tdb#> PREFIX tdb2: <http://jena.apache.org/2016/tdb#> PREFIX ja: <http://jena.hpl.hp.com/2005/11/Assembler#> PREFIX : <#> <#service1> rdf:type fuseki:Service ; fuseki:name "msro" ; # http://host:port/msro fuseki:endpoint [ # http://host:port/msro/sparql?query= fuseki:operation fuseki:query ; fuseki:name "sparql" ] ; fuseki:endpoint [ # http://host:port/msro/query?query= # SPARQL query service (alt name) fuseki:operation fuseki:query ; fuseki:name "query" ] ; fuseki:endpoint [ # http://host:port/msro/update?query= # SPARQL update service fuseki:operation fuseki:update ; fuseki:name "update" ] ; fuseki:endpoint [ # SPARQL Graph Store Protocol (read) fuseki:operation fuseki:gsp_r ; fuseki:name "get" ] ; fuseki:endpoint [ # SPARQL Graph Store Protcol (read and write) # http://host:port/msro/data?default or http://host:port/msro/data?graph=<URL> fuseki:operation fuseki:gsp_rw ; fuseki:name "data" ] ; fuseki:dataset <#dataset> ; . <#dataset> rdf:type ja:DatasetRDFS ; ja:rdfsSchema <file:///c:/MSDE/hillsthe/msrows/eqr/msro/eqr.msro/resources/msRoAll.ttl> ; ja:dataset <#actualDataset> ; . <#actualDataset> rdf:type tdb2:DatasetTDB2; # for example. tdb2:location "C:\\Users\\hillsthe\\run\\data\\tdb2"; . -----Original Message----- From: Hills, Theodore (Research) Sent: Monday, October 17, 2022 6:02 PM To: Andy Seaborne <a...@apache.org> Cc: users@jena.apache.org Subject: RE: TDB2 Data Doesn't Persist Hi Andy, Thanks again for the reply. This seems quite odd to me, so let me check my understanding. When persistence is not an issue, RDFS inferencing without axioms works fine in a named graph--actually, across three named graphs. I use one of the named graphs for the vocabulary, and two for data. But if I want my named graph to persist, and because I am using inferencing, I have to define my named graph in the assembler (config file). Question: Do I need to put the named graph URL in the config file? If so, I can't tell from the documentation where to put that. Insights appreciated. Thanks, Ted Theodore Hills Consultant | Research Phone: +1 212 296-1833 theodore.hi...@morganstanley.com -----Original Message----- From: Andy Seaborne <a...@apache.org> Sent: Monday, October 17, 2022 4:25 PM To: Hills, Theodore (Research) <theodore.hi...@morganstanley.com> Cc: users@jena.apache.org Subject: Re: TDB2 Data Doesn't Persist Hi Theordore, <#dataset> rdf:type ja:RDFDataset; ja:defaultGraph <#inferenceModel> . defines a dataset with just a default graph. It does not pass down named graphs. They end up in a temporary holder. You can add the name graph to the ja:RDFDataset but you have to know it's name and define the inference. Inference is per-graph. There is https://jena.apache.org/documentation/rdfs/ # RDFS :rdfsDataset rdf:type ja:DatasetRDFS ; ja:rdfsSchema <file:vocabulary.ttl>; ja:dataset --- some TDB2 database --- . This applies RDFS - without axioms - so rdfs:subClassOf, rdf:subPropertyOf, rdfs:domain and rdfs:range - to all graphs in the ja:database. The schema is fixed at startup. Andy On 17/10/2022 14:39, theodore.hi...@morganstanley.com wrote: > Hi Andy, > > Thank you for the prompt reply. > > I deleted everything in my tdb2 directory in order to force Fuseki to > recreate the database from scratch so I knew I was working from a clean slate. > > I was able to duplicate your results, using my own D.ttl, which is below. > > <http://triples.ms.com/msro/dummy> <http://www.w3.org/2001/XMLSchema#string> > "dummy" . > > I then loaded the dummy triple into a named graph using the curl command > below. > > curl -T D.ttl --header 'Content-type: text/turtle' \ > > 'http://localhost:3030/msro/data?graph=https%3A%2F%2Ftriples.ms.com%2Fmsro%2F__dummy__' > > I was able to dump the named graph using the command below. > > curl > 'http://localhost:3030/msro/data?graph=https%3A%2F%2Ftriples.ms.com%2Fmsro%2F__dummy__' > > I then stopped and restarted Fuseki, and the triple in the named graph was > gone. The triple in the default graph was still there. > > Also, I monitored the size of Data-0001\nodes-data.obj at every step. Upon > creation of a fresh database, it was 0 KB. It remained 0 KB even if I loaded > my dummy triple into a named graph. Only when I loaded my dummy triple into > the default graph did it grow to 1 KB. It remained 1KB across restarts. > > So, the problem seems to be that triples in the default graph persist, but > triples in named graphs do not. > > The only inferencing I need is subclass inferencing in order for a query of > this form to work: > ?s rdfs:subClassOf+ ?c . > > Once I layered in the TransitiveReasoner in the config file, the above query > worked fine in the midst of a complicated and well-tested query that runs > fine on Stardog and MarkLogic. As mentioned, I was getting the desired > results on Fuseki TDB2 as well. The only problem seems to be the lack of > persistence for named graphs. > > Thanks so much for your attention to this problem! > > Theodore Hills > Consultant | Research > Phone: +1 212 296-1833 > theodore.hi...@morganstanley.com > -----Original Message----- > From: Andy Seaborne <a...@apache.org> > Sent: Saturday, October 15, 2022 5:41 AM > To: users@jena.apache.org > Subject: Re: TDB2 Data Doesn't Persist > > Hi Theodore, > > I tried your configuration and got persisted data. > > I tried: > > curl -T D.ttl --header 'Content-type: text/turtle' \ > 'http://localhost:3030/msro/data?default' > > this appeared in the file: > > [2022-10-15 10:36:19] Fuseki INFO [3] Body: Content-Length=338, > Content-Type=text/turtle, Charset=null => Turtle : Count=4 Triples=4 > Quads=0 > > (reformatted for email). > > then I stopped the server, restarted it and did > > curl 'http://localhost:3030/msro/data?default' > > and got the data with inference output. > > > How are you loading the data? > > Looking in "C:\\Users\\hillsthe\\run\\data\\tdb2", there is a file > Data-0001/nodes-data.obj. How big it is it after loading the data? You can > look while the server is running. Does it shrink when the server is stopped? > It's zero bytes for an empty database, non-zero otherwise. > > ---- > > Also - for general information - you're using the transitive reasoner What > inferences are you hoping to generate? > > Andy > > On 14/10/2022 15:09, theodore.hi...@morganstanley.com wrote: >> Hello, >> >> I have Apache Jena Fuseki running on my localhost with TDB2 configured with >> inferencing. See entire config file below. I am running Fuseki server under >> Windows 10 with the following command line issued from a CMD prompt. >> >> C:\Users\hillsthe\apache-jena-fuseki-4.6.1\fuseki-server.bat --conf >> C:\Users\hillsthe\config.ttl >> >> I can do updates and queries and everything works as expected. However, if I >> stop the Fuseki server with a Control-C, and restart it with the above >> command, my graphs are empty. Any insights? >> >> Theodore Hills >> Consultant | Research >> Phone: +1 212 296-1833 >> theodore.hi...@morganstanley.com<mailto:Theodore.Hills@morganstanley. >> c >> om> >> >> ## Fuseki Server configuration file. >> >> PREFIX fuseki: http://jena.apache.org/fuseki# >> PREFIX rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# >> PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema# >> PREFIX tdb1: http://jena.hpl.hp.com/2008/tdb# >> PREFIX tdb2: http://jena.apache.org/2016/tdb# >> PREFIX ja: http://jena.hpl.hp.com/2005/11/Assembler# >> PREFIX : <#> >> >> >> <#service1> rdf:type fuseki:Service ; >> fuseki:name "msro" ; # http://host:port/msro >> fuseki:endpoint [ # http://host:port/msro/sparql?query= >> fuseki:operation fuseki:query ; >> fuseki:name "sparql" >> ] ; >> fuseki:endpoint [ # http://host:port/msro/query?query= >> # SPARQL query service (alt name) >> fuseki:operation fuseki:query ; >> fuseki:name "query" >> ] ; >> >> fuseki:endpoint [ # http://host:port/msro/update?query= >> # SPARQL update service >> fuseki:operation fuseki:update ; >> fuseki:name "update" >> ] ; >> >> fuseki:endpoint [ >> # SPARQL Graph Store Protocol (read) >> fuseki:operation fuseki:gsp_r ; >> fuseki:name "get" >> ] ; >> fuseki:endpoint [ >> # SPARQL Graph Store Protcol (read and write) >> # http://host:port/msro/data?default or >> http://host:port/msro/data?graph=<URL<http://host:port/msro/data?graph=%3cURL>> >> fuseki:operation fuseki:gsp_rw ; >> fuseki:name "data" >> ] ; >> >> fuseki:dataset <#dataset> ; >> . >> >> <#dataset> rdf:type ja:RDFDataset; >> ja:defaultGraph <#inferenceModel> >> . >> >> <#inferenceModel> rdf:type ja:InfModel; >> ja:reasoner [ ja:reasonerURL >> http://jena.hpl.hp.com/2003/TransitiveReasoner ]; >> ja:baseModel <#baseModel>; >> . >> >> <#baseModel> rdf:type tdb2:GraphTDB2; >> tdb2:dataset <#actualDataset> . >> >> <#actualDataset> rdf:type tdb2:DatasetTDB2; >> tdb2:location "C:\\Users\\hillsthe\\run\\data\\tdb2"; >> . >> >> >> ________________________________ >> >> For important information including analyst certification and disclosures >> regarding specific companies, derivatives, or other instruments discussed in >> this email, please refer to the latest report, if attached and/or >> hyperlinked to this email, or by logging on to the Morgan Stanley Matrix >> Platform at http://matrix.ms.com/eqr/research . 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