Re: Use LIMIT/OFFSET

2021-12-06 Thread Rob Vesse
Assuming the queries and the underlying data storage used remain the same then Jena will likely generate results in a consistent manner BUT you should never rely upon this. The only way to guarantee the behaviour you want is to provide an explicit ORDER BY clause For example adding an extra

Re: Spatial Index creation can fail , FIX proposed

2021-12-01 Thread Rob Vesse
Filed in JIRA as JENA-2202 [1] As always pull requests are welcome Regards, Rob [1] https://issues.apache.org/jira/browse/JENA-2202 On 01/12/2021, 08:59, "Jean-Marc Vanel" wrote: In the special case when latitude is present but not longitude, a null pointer exception is raised,

Re: Embedded Fuseki Cache

2021-11-23 Thread Rob Vesse
No it's not, no version of Fuseki, or any other Jena library, currently offers SPARQL Query Caching I presume there is some behaviour you are seeing that would lead you to suspect caching? There are a bunch of things going on both with the underlying TDB/TDB2 database layer that does include

Re: puzzling performance issue

2021-10-19 Thread Rob Vesse
Because it isn't a valid semantics preserving optimization. ARQ only applies optimizations that preserve the semantics of the query, the fact that this is ultimately a CONSTRUCT query doesn't change the semantics of the query evaluation itself, merely the final RDF produced. Making the

Re: puzzling performance issue

2021-10-19 Thread Rob Vesse
Not really This pattern of unconnected BGPs has legitimate use cases. A common one is doing similarity calculations where you use unconnected BGPs to create every possible combination of results and then use BIND and/or FILTER to compute some metric and use that to filter/rank the

Re: Jena hangs while reading HTTP stream

2021-07-05 Thread Rob Vesse
That's a really good suggestion. In the normal code flow do you ever call stream.close() ? And is createHttpClient() re-using an existing HttpClient object ? And is the hang only happening after some requests have succeeded ? It is possible what is happening is that you aren't closing the

Re: Unable to start embedded fuseki

2021-06-23 Thread Rob Vesse
Phil Without seeing your projects dependencies it is hard to say. The referenced method is from the Jetty web-app implementation. Running an embedded server will generally require that you have additional dependencies to provide the full server runtime, the jena-fuseki-main module is the

Re: Ordering results from oldest to newest

2021-05-14 Thread Rob Vesse
The difference is as Andy implied in the protocol definition. SPARQL as a protocol, is tied to HTTP, and does not expose any notion of cursors as a traditional RDBMS would. Once ARQ passes off a query to a remote SPARQL service it has no control over how that query is executed by the remote

Re: Compact won't execute on inference dataset

2021-05-10 Thread Rob Vesse
I think it depends on the underlying dataset. I know Andy made some improvements to that endpoint so that it tries to unwrap to the underlying TDB2 dataset to perform compaction on BUT this won't work for all possible datasets, especially non-trivial wrappers that potentially combine multiple

Re: Jena 4 and RDF/XML via Fuseki

2021-04-22 Thread Rob Vesse
What is the query? RDF/XML is a graph format and so only makes sense for CONSTRUCT/DESCRIBE queries ASK/SELECT queries are going to produce tabular results which uses the SPARQL XML Results format by default. Historically there was an ability to transcribe the tabular format into a graph but

Re: Multifactor authentication in Fuseki

2021-04-12 Thread Rob Vesse
Han The general approach to this kind of complex sign on scenario would be to use an external authentication service/protocol e.g. OAuth2/Open ID Connect which handles the multi-factor authentication and then configure your applications authentication layer to just validate the Json Web Tokens

Re: Adding auto-deletion to compact task?

2021-04-12 Thread Rob Vesse
Yes such a feature would be a valuable contribution. It's certainly something that other users have asked for. Your main issue is probably going to be verifying that there aren't open transactions against the old versions of the data, Andy might have some ideas/pointers to whether the

Re: updating persistent jena-fuseki dataset increases memory consumption in gigas

2021-03-31 Thread Rob Vesse
This script looks somewhat suspect. You start a compaction (which is an asynchronous background task) but then immediately start deleting files (which could still be in use by a running compaction) You really want to be polling the task status APIs to check that a compaction has actually

Re: About Parameterized SPARQL String

2021-03-26 Thread Rob Vesse
I have a question on ParameterizedSparqlString. I have been using SelectBuilder to build select queries. Is ParameterizedSparqlString any better or worse than SelectBuilder since they seem to do roughly the same thing. thanks graham On 25/03/21 10:05 pm, Rob V

Re: About Parameterized SPARQL String

2021-03-25 Thread Rob Vesse
ParameterizedSparqlString works by simple textual substitution into the provided query string so you get a more specific query with your parameters It does not have any relationship to joins. I guess what you may be asking is how it compares to other methods for providing initial bindings e.g.

Re: jena-fuseki's memory consumption keeps on growing

2021-03-22 Thread Rob Vesse
I assume that this is TDB 1? It is possible you are encountering the scenario detailed at https://jena.apache.org/documentation/tdb/faqs.html#fuseki-tdb-memory-leak If the queries are sufficiently frequent the server may never be able to flush the in-memory journal leading to continuous memory

Re: Suggestions for learning more about SPARQL query performance?

2021-03-18 Thread Rob Vesse
Realised I had linked the wrong version, correct link is below: https://www.dropbox.com/s/knudzewbiuqkqvy/SPARQL%20Optimisation%20101%20Tutorial.pptx?dl=0 Apologies for the confusion, Rob On 18/03/2021, 14:37, "Rob Vesse" wrote: Steve Think I've shared this before

Re: Suggestions for learning more about SPARQL query performance?

2021-03-18 Thread Rob Vesse
Steve Think I've shared this before on-list, I produced a slide deck a long time ago (2014) that covers this topic more focused on ARQ https://www.dropbox.com/s/ixetdcfesqse893/SPARQL%20Optimization%20101.pptx?dl=0 Some of the details have changed in the interim (e.g. new optimizations added,

Re: SPARQL query for matching exact phrase in elastic search

2021-01-18 Thread Rob Vesse
Also worth noting that historically the .Net ecosystem has massively lagged behind Lucene versions because the Lucene.Net project has been massively under-resourced. dotNetRDF always used to be Lucene 3.0.3 and I think only recently started looking at moving to Lucene 4.8 (which is the

Re: Java 8 or 11?

2021-01-12 Thread Rob Vesse
It's also worth noting that from a security perspective continuing to support Java 8 is increasingly going to become a problem for end users. In my $dayjob we see a lot of concern about outdated software versions, even and especially so, as we move to a more containerised model. A lot of

Re: Tried to compact a live TDB2 dataset using Lucene engine but failed

2020-12-08 Thread Rob Vesse
ples? I apologize if this sounds rude, we basically set this service by personal understanding of online docs from jena.apache.org, maybe there's some misinterpretation. Hope you could give us some hint, thank you. Regards, Huiling Lee -Original Message- From: Rob V

Re: Tried to compact a live TDB2 dataset using Lucene engine but failed

2020-12-07 Thread Rob Vesse
Online compaction will only work if the dataset is directly a TDB2 dataset, if it's wrapped in another dataset e.g. TextDataset as in this example then that won't work You would need to define another service that exposes the TDB2 dataset directly and then instead call /$/compact/ Rob On

Re: Construct Quads on Apache Jena Fuseki

2020-12-03 Thread Rob Vesse
The list does not permit attachments so we cannot see screenshots.  Please provide the example query that is failing and the error/log message(s) you see in relation to the failure Rob From: Ahmed Helal Reply to: Date: Thursday, 3 December 2020 at 06:26 To: "users@jena.apache.org"

Re: 3.17

2020-12-03 Thread Rob Vesse
Apache pushes to Central or Central pulls from Apache) so there can be a lag between a release being produced and it showing up on all the downstream mirrors. Rob Vesse On 02/12/2020, 19:53, "Jean-Marc Vanel" wrote: The announcement mail is here : https://lists.apache.org/t

Re: Fuseki Web UI does not consider Dataset Level Access Control Lists

2020-10-16 Thread Rob Vesse
Ideally you do this entirely on the API implementation side i.e. the server so that the UI doesn't need any changes. The browser will already be communicating the credentials the user provided to the server implicitly when authc is enabled (e.g. via the browser login prompt). If the UI is

Re: Could you tell me about 'EOL' of Apache Jena and Apache Jena Fuseki

2020-10-16 Thread Rob Vesse
As with most Apache projects we are entirely volunteer based. As a project we do not have any formal support/EOL policy. In practise our advice to users is always to use the latest versions released by the project. At the time of writing this is 3.16.0. Any bug fixes and changes we make

Re: How does one materialize an InfModel?

2020-09-21 Thread Rob Vesse
I think your test assertions are faulty, from https://jena.apache.org/documentation/javadoc/jena/org/apache/jena/rdf/model/Model.html#size-- size will return the number of statements in a concrete model, for a virtualized model such as one created by an inference engine, it will return an

Re: RDF Delta/Zookeper freezing issue

2020-08-18 Thread Rob Vesse
Piotr Not used RDF Delta myself but the Zookeeper issues sound familiar When anything is trying to talk to Zookeeper if the ZK node they are trying to talk to stops responding then the ZK client code will fail and then re-establish a session to a diferent node. BUT this isn’t immediate for a

Re: Difference in query speed for rotating disk and SSD

2020-07-31 Thread Rob Vesse
I don’t have any specific queries to suggest since I have no familiarity with the database but an observation on the query shown Scanning the whole database and counting the triples inherently requires a full traversal of the B-Tree so what you have shown so far is a corner case extreme. 

Re: Fuseki behind a reverse proxy with sub-path

2020-07-23 Thread Rob Vesse
Sebastian Is this using Istio or some other service mesh? Could you show your VirtualService (or equivalent) definition? (YAML preferable for readability) This may well be an actual Fuseki bug with the JS, I know we have some production JS UIs where we explicitly have to set the base path so

Re: TDB2 parallel load on cloud SSD and other observations/questions

2020-06-22 Thread Rob Vesse
Isabel I think there might be a fundamental misunderstanding happening about batch sizes here. The batch sizes are fixed for a run and never changes, the "batch size" you refer to is a speed calculation e.g 19:03:24 INFO loader :: Add: 248,000,000 github_1_fixed.nq (Batch: 3,562 /

Re: Memory management with Fuseki

2020-04-17 Thread Rob Vesse
Okay, that's very helpful So one thing that jumps out at me looking at that Dockerfile and its associated entrypoint script is that it starts the JVM without any explicit heap size settings. When that is done the JVM will pick default heap sizes itself which normally would be fine. However

Re: Memory management with Fuseki

2020-04-16 Thread Rob Vesse
I find the implied figures hard to believe, as Lorenz has said you will need to share your findings via some other service since this mailing list does not permit attachments. Many people use Fuseki and TDB to host datasets in the hundreds of millions (if not billions) of triples in production

Re: Upgrading 3.0.1 to 3.13.1: ReaderRIOT

2020-03-27 Thread Rob Vesse
Martynas I don't see what bearing JAX-RS has on the HttpClient part of this discussion Jena needs something to manage the HTTP connections regardless of how it reads and writes data over those connections. A lot of users have use cases that require authenticating themselves to their remote

Re: JSONLD and base URL

2020-03-04 Thread Rob Vesse
This may be an upstream bug or it could be a bug in how we configure the underlying parser Jena's JSON-LD support is based upon the https://github.com/jsonld-java/jsonld-java library so you could try and reproduce your test case just using their library directly which would determine if it is

Re: Error org.apache.jena.tdb.transaction.TDBTransactionException: Not in a transaction

2020-03-02 Thread Rob Vesse
It's because you are trying to close the model after you've committed the transaction so the error message is quite correct in that you are no longer in a transaction at that point Put the dataset.commit() after the model.close() line and it will work Rob On 02/03/2020, 16:16, "Diptendu

Re: SPARQL performance question

2020-02-24 Thread Rob Vesse
To add to what else has been said Query execution in Apache Jena ARQ is based upon lazy evaluation wherever possible. Calling execSelect() simply prepares a ResultSet that is capable of delivering the results but doesn't actually evaluate the query and produce any results until you call

Re: super slow filter

2020-01-22 Thread Rob Vesse
Comments inline: On 22/01/2020, 10:27, "Élie Roux" wrote: Thanks a lot, after some investigation, here are a few results: - the problem was that I had no .opt file and that the default behavior was fixed.opt (or so it seems), when adding a none.opt (or a stats.opt) the

Re: tdbquery on UnionGraph

2020-01-22 Thread Rob Vesse
See https://jena.apache.org/documentation/tdb/datasets.html#special-graph-names You may need to use (not sure, not a feature I ever use myself) though not sure if tdbquery allows for overriding the default graph Rob On 22/01/2020, 09:58, "Élie Roux" wrote: Dear all, I'm trying

Re: super slow filter

2020-01-22 Thread Rob Vesse
See https://jena.apache.org/documentation/tdb/optimizer.html#running-tdbstats Which describes the various options for optimization. Rob On 22/01/2020, 09:32, "Élie Roux" wrote: Thanks for your answers! I'm trying to understand why tdbquery doesn't return any result but in the

Re: Jena fails to parse valid RDF

2019-12-16 Thread Rob Vesse
The server does not appear to be sending an appropriate Content-Type header. Note that if you read the stack trace you can see that Jena thinks the URI is returning JSON/LD and invoking its JSON/LD parser hence why you hit a parsing error. I would consider filing a bug report with the server

Re: Graph status?

2019-09-09 Thread Rob Vesse
Playing Devil's advocate: I am always curious when folks complain about a "huge" dependency stack (for a start the term huge is inherently subjective). This is pretty much the reality of the modern OSS ecosystem, people (yourself included) try to avoid reinventing the wheel and want to focus

Re: TDBTransactionException: Not in a transaction

2019-07-08 Thread Rob Vesse
This looks like a simpler variation upon JENA-1667 [1] which is a Known Bug that is not currently resolved in any version of Jena Although not sure why this worked in past versions of Fuseki, may be a side effect of other Fuseki refactoring that has happened Rob [1]

Re: ERROR Impossibly large object

2019-07-04 Thread Rob Vesse
guess what could cause this? On 04/07/2019 12:18, Rob Vesse wrote: > Impossibly Large Object means the database has been corrupted (more specifically the Node Table). This is non-recoverable although it may not affect the entire database i.e. any query that tries to access the affe

Re: ERROR Impossibly large object

2019-07-04 Thread Rob Vesse
Impossibly Large Object means the database has been corrupted (more specifically the Node Table). This is non-recoverable although it may not affect the entire database i.e. any query that tries to access the affected portion of the node table will fail but other queries may continue to

Re: Debugging corrupted TDB?

2019-07-04 Thread Rob Vesse
What do you mean by a re-index? i.e. what were the sequence of operations that preceded this error Rob On 03/07/2019, 20:40, "Matthew Holt" wrote: Hi all, Upon trying to access a TDB instance that was just re-indexed, we are getting the following error:

Re: tdb2.tdbsync

2019-06-13 Thread Rob Vesse
b2.tdbsync tool that automatically updates a tdb dataset with only the changes (instead of reloading everything). > Sent: Thursday, June 13, 2019 at 10:26 AM > From: "Rob Vesse" > To: users@jena.apache.org > Subject: Re: tdb2.tdbsync > >

Re: tdb2.tdbsync

2019-06-13 Thread Rob Vesse
Can you not just do a fresh TDB load into a new dataset from the data file? This would be much faster and more performant than what you are proposing (in particular the delete handling would be very expensive) Rob On 13/06/2019, 05:27, "Laura Morales" wrote: This is only a potential

Re: Batching federated calls using VALUES block

2019-06-10 Thread Rob Vesse
oint is > across the unreliable internet. > > As Rob says, batching for SERVICE calls would be good to have. > > Andy > > On 01/05/2019 09:40, Rob Vesse wrote: > > Dave > > > > Yes this is what is happening. This ste

Re: Why QueryExecution blocks when another QueryExecution not close?

2019-06-05 Thread Rob Vesse
Well you don't specify what kind of QueryExecution you use but given the described behaviour I assume you are querying a SPARQL service via HTTP Jena uses Apache HTTP Client as our HTTP Client library which uses a connection pool with a maximum number of simultaneous connections to a given

Re: sparql.org allows invalid Turtle

2019-04-09 Thread Rob Vesse
Just to close the loop on this Yes sparql.org (and more specifically the data validator included in Fuseki) was not configuring the underlying parser for strict mode which meant it would allow some syntax errors through. Andy has a PR open to address this -

Re: Storing a lot of strings in TDB store

2019-02-22 Thread Rob Vesse
stick to that option, but TDB storage logic was quite unclear to me. Would be great if it was mentioned in official documentation since I couldn't find it. Thanks again for your help On Tue, 19 Feb 2019 at 20:40, Rob Vesse wrote: > Since I don't think anyone

Re: Storing a lot of strings in TDB store

2019-02-19 Thread Rob Vesse
Since I don't think anyone answered your specific original question TDB and TDB2 both use dictionary encoding (and in fact most RDF stores use some variation on this). Basically they map each unique RDF term (whether URI, string, blank node etc) to a consistent internal identifier and use this

Re: Out of memory

2019-02-05 Thread Rob Vesse
/jvmtop - as an open source command line based JVM profiler Rob On 05/02/2019, 15:44, "Rob Vesse" wrote: -Xms and -Xmx do two different things (the previous email in the thread mentioned -Xmx but then you referenced -Xms in your question). The former sets the minimum heap

Re: Out of memory

2019-02-05 Thread Rob Vesse
you have maybe 8GB ram?I'd try > 16GB and see how it does; watch the total memory usage. > > > > On Tue, Jan 29, 2019 at 9:43 AM Mikael Pesonen > wrote: > >> >> >> On 29/01/2019 16:28, Rob Vesse wrote: >>> Th

Re: wrong content-types in s-get | Re: Export named graph from TDB to several ntriples files

2019-01-31 Thread Rob Vesse
No the content types aren't wrong you're just using them for the wrong things. Per application/json several people have already commented that there is no serialization directly linked to application/json. There are specific MIME types for specific variants of JSON e.g. application/ld+json for

Re: Out of memory

2019-01-29 Thread Rob Vesse
This may be partly a case of a simple looking query having unexpected execution semantics. Strictly speaking your query says select all triples in the specific graph then join them with these list of values for ?s. Now the optimiser should, and does appear, to do the right thing and flip the

Re: Out of memory

2019-01-29 Thread Rob Vesse
Comments inline: On 29/01/2019, 11:34, "Mikael Pesonen" wrote: I'm not able to run a basic read-only script without running out of memory on the server. Consumption goes to 7+gigs (VM 10+ gigs), then system kills Fuseki when running out of memory. All I'm

Re: Altering ARQ query to accept non-executed pattern

2018-11-30 Thread Rob Vesse
Assuming you are accessing over HTTP you can create an instance of QueryEngineHTTP directly passing in the query as a string and ARQ won't attempt to parse the query e.g. QueryExecution qe = new QueryEngineHTTP("http://someserver/query;, yourQueryString); Rob On 29/11/2018, 17:52, "Dan

Re: update INSERT on TDB2 results in org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction

2018-11-13 Thread Rob Vesse
Fuseki is properly managing transactions for the underlying datasets update is a general purpose command that doesn't have awareness of transactions (though it probably could/should) Use tdb2.tdbupdate to run updates on TDB2, note that in the command line tools there are a variety of tools

Re: riot json-ld library version

2018-11-07 Thread Rob Vesse
You can look up dependency versions in the top level pom.xml Specifically for JSON-LD - https://github.com/apache/jena/blob/master/pom.xml#L59-L63 - we are currently at 0.12.1 As noted on the JSON-LD libraries repository - https://github.com/jsonld-java/jsonld-java - they implement the

Re: SPARQL-Generate

2018-11-06 Thread Rob Vesse
No On 06/11/2018, 12:52, "Laura Morales" wrote: Do Jena/Fuseki support this thing called "SPARQL-Generate"? https://ci.mines-stetienne.fr/sparql-generate/tutorial.html

Re: Transaction error with Fuseki REST API + TDB2

2018-10-09 Thread Rob Vesse
tdb2:location "PIPPO"; tdb2:unionDefaultGraph true ; . Unfortunately I can't provide the data in the KB.I'm trying to reproduce the problem with other neutral data.Meanwhile, please let me know if you have any idea.Thanks a lotBye Il martedì 9 ottobre 2018, 1

Re: Transaction error with Fuseki REST API + TDB2

2018-10-09 Thread Rob Vesse
Brad The stack trace looks like you have configured a dataset with some inference. It is possible that the inference layer is not using transactions on the underlying dataset properly, and/or caching some data that is tied to a specific transaction. For further help we would likely need to

Re: statement identifiers

2018-09-18 Thread Rob Vesse
None of the Jena provided implementations use statement IDs, that includes both TDB1 and TDB2 which both just store quads directly Rob On 18/09/2018, 13:15, "ajs6f" wrote: >> >> Not in general, no, although some specific DatasetGraph implementations may. > > Any idea where

Re: How to use ORDER BY in a query built by the ARQ API?

2018-09-18 Thread Rob Vesse
Use one of the .addOrderBy() methods on the Query object - https://jena.apache.org/documentation/javadoc/arq/org/apache/jena/query/Query.html#addOrderBy-org.apache.jena.sparql.expr.Expr-int- If you are building lots of queries programmatically the higher level Query Builder API may be more

Re: Updating large amounts of data

2018-09-13 Thread Rob Vesse
.2018 um 11:41 schrieb Rob Vesse : > > Markus > > Comments inline: > > On 12/09/2018, 16:09, "Markus Neumann" wrote: > >Hi, > >we are running a Fuseki server that will hold about 2.2 * 10^9 triple

Re: Updating large amounts of data

2018-09-13 Thread Rob Vesse
Markus Comments inline: On 12/09/2018, 16:09, "Markus Neumann" wrote: Hi, we are running a Fuseki server that will hold about 2.2 * 10^9 triples of meteorological data eventually. I currently run it with "-Xmx80GB" on a 128GB Server. The database is TDB2 on a 900GB SSD.

Re: Updating large amounts of data

2018-09-13 Thread Rob Vesse
I am not sure tdbloader/tbdloader2 scripts help in this case. This is an online update of a running Fuseki instance backed by TDB from what has been described. Since a TDB instance can only be safely used by a single JVM at a time using those scripts would not be a viable option here unless

Re: fuseki text:query : strange results + Lucene configuration

2018-09-12 Thread Rob Vesse
Well the order of triple patterns shouldn't matter too much when you have a pure BGP (albeit the optimiser might pick a bad order in some cases) But we aren't talking about pure BGPs here, having the text:query triples results in the BGP being broken up into joins of several property functions

Re: Question about indexing in text search

2018-08-07 Thread Rob Vesse
tches: var ?root -> > http://localhost/jena_example/#text_dataset, > file:///home/alysson/Documents/PUC-Rio/TestJena/tdb-citation-data-en-fuseki-index/index.ttl#dataset > > > Em qui, 19 de jul de 2018 às 13:13, Rob Vesse > escreveu: > &

Re: Question about indexing in text search

2018-07-19 Thread Rob Vesse
de 2018 às 10:04, Rob Vesse escreveu: > Thanks, so your problem was as I suspected > > You use tdbquery which does not understand text indexes using it as you > do. By using --loc you are only querying your base dataset, this does not > include your te

Re: Question about indexing in text search

2018-07-18 Thread Rob Vesse
(file index.ttl) but to facility it, follow the image: I'm using the same queries of the previous mail. Case has something wrong, please indicate it some solution. Em qua, 18 de jul de 2018 às 10:12, Rob Vesse escreveu: This is a misunderstanding, not a bug. Property functions use

Re: Question about indexing in text search

2018-07-18 Thread Rob Vesse
This is a misunderstanding, not a bug.  Property functions use the SPARQL collection syntax i.e. ( “David”) to pass arguments to the function which is given as the predicate, in this case text:query. The rdf:first/rdf:rest you see in the logs is simply the

Re: reading a ttl file from remote location for quering

2018-07-13 Thread Rob Vesse
FileInputStream is used for accessing local files, this is a standard Java component. It cannot be used to read remote URLs. There is actually no need to explicitly specify a stream here, you can simply provide the URL as a string and Jena will do the right thing i.e.

Re: problem with SPARQL query with GROUP_CONCAT

2018-06-22 Thread Rob Vesse
On 22/06/2018, 10:04, "turb...@disp.uniroma2.it" wrote: I do not understand what do you mean with the last sentence: "Connection reset by peer" is something to take up with the operators of the service as is the different behaviour from different places This is a low-level error

Re: How ro restore from backup?

2018-06-21 Thread Rob Vesse
I believe so, if the data is corrupted then the backup process will encounter the corruption when it tries to read out the corrupted entries in order to output them and should fail accordingly The same should hold true of trying to use tbddump on a database, essentially the Fuseki backup is

Re: Long response times on TDB queries

2018-06-15 Thread Rob Vesse
large dent in the time the query took to execute. Adam From: Rob Vesse Sent: 15 June 2018 13:48 To: users@jena.apache.org Subject: Re: Long response times on TDB queries Adam Did you try generating the

Re: Long response times on TDB queries

2018-06-15 Thread Rob Vesse
Just tried re-ordering it as you suggested, and this was exactly the improvement that I needed. Now getting returns in 0.1 seconds rather than 200+. Much appreciated, Adam From: Rob Vesse Sent: 15 June 2018 12:12

Re: Long response times on TDB queries

2018-06-15 Thread Rob Vesse
On 15/06/2018, 11:46, "Adam Ladly" wrote: 22:18:21 INFO exec :: Reorder/generic ?node ?id ?node ?p "http://www.ncbi.nlm.nih.gov/gene/1956; So it looks like TDB is using a generic execution ordering and for your data this is clearly

Re: huge fuseki memory usage; NIO errors; heap NOT running out

2018-06-15 Thread Rob Vesse
Dan Is there any chance you could try grabbing a JVM thread dump next time you notice this happening? There are multiple ways to do this depending on your environment, the simplest and most portable is just to send a SIGQUIT to the JVM process which will cause a thread dump to be output to

Re: Fuseki and changing passwords

2018-06-06 Thread Rob Vesse
You can set up a shiro.ini where authentication is handled by external authentication service like LDAP. Then if uses change their passwords with that service those changes are automatically reflected by consumers of the service e.g. Fuseki For LDAP configuration in Shiro see

Re: Comparison method violates its general contract!

2018-05-23 Thread Rob Vesse
A stack trace would be helpful... Rob On 23/05/2018, 11:15, "Mikael Pesonen" wrote: Hi, I'm geting this Java error with following query (prefixes omitted) with Jena Fuseki 3.6.0 . Query works if every ?property_type is collected instead of

Re: Fuseki service vs. webapp

2018-04-26 Thread Rob Vesse
Sorin Thanks for the report, unfortunately the lack of reproducible detail means I can only speculate on the source of the issues. The Jena project has only recently added a template service file for Fuseki so presumably when you say you are setting it up as a service either you define your

Re: Apache Jena installation issues with JENAROOT (on Mac)

2018-04-24 Thread Rob Vesse
On 24/04/2018, 14:37, "Cumulative Knowledge" wrote: When adding the classpath I did so with: export CLASSPATH=$CLASSPATH:$JENA_HOME/bin/\* You should be adding $JENA_HOME/lib/\* to the CLASSPATH rather than the bin/ subdirectory Rob

Re: limit on resultset from a select query?

2018-04-20 Thread Rob Vesse
18 at 1:20 PM, Andy Seaborne <a...@apache.org<mailto:a...@apache.org>> wrote: There is no specific limitation in the Fseki code but every intermediate proxy can truncate output. Is there anything in the Fuseki log file? Is Fuseki running as a WAR file or standalone server? Andy On 20/04/18

Re: limit on resultset from a select query?

2018-04-20 Thread Rob Vesse
Paul Can you get a Java thread dump for the Fuseki process to see what it is doing when it is hung? Rob On 20/04/2018, 11:42, "Paul Hermans" wrote: It is 160MB downloaded CSV. Paul On 20 Apr 2018, at 11:31, Laura Morales

Re: Limit memory usage of Fuseki server?

2018-04-10 Thread Rob Vesse
The OOM killer is a Linux feature designed to prevent one program monopolising the system. I've never seen it hitting Fuseki before but have seen it hit other database processes in the past because in-memory/aggressively cached databases like Fuseki do tend to be large memory consumers. See

Re: Splitting data into graphs vs datasets

2018-03-21 Thread Rob Vesse
You can run many datasets by using the --config argument and specifying an appropriate configuration file. This should be used instead of the --loc argument which is a convenience short cut to run a server with a single dataset.

Re: Speed issue while processing query resultSets on various ontology models

2018-03-14 Thread Rob Vesse
mercredi 14 mars 2018 à 16:41 +, Rob Vesse a écrit : > You've made a common error that people trying to benchmark Jena > make. execSelect() simply prepares a result set backed by an > iterator that is capable of answering the query, until you are > consume that re

Re: Speed issue while processing query resultSets on various ontology models

2018-03-14 Thread Rob Vesse
You've made a common error that people trying to benchmark Jena make. execSelect() simply prepares a result set backed by an iterator that is capable of answering the query, until you are consume that result set no execution actually takes place. All query execution in Jena is lazy, if you

Re: ParameterizedSparqlString strange behavior

2018-03-05 Thread Rob Vesse
; <agate.m...@gmail.com> wrote: On 2018/03/05 10:24:46, Rob Vesse <rve...@dotnetrdf.org> wrote: > FYI your second example has mismatched brackets in the FILTER which leads to a SPARQL parser error once the underlying ParameterizedSparlString bug is fixed > &g

Re: ParameterizedSparqlString strange behavior

2018-03-05 Thread Rob Vesse
FYI your second example has mismatched brackets in the FILTER which leads to a SPARQL parser error once the underlying ParameterizedSparlString bug is fixed Rob On 04/03/2018, 22:07, "agate.m...@gmail.com" wrote: Here is a piece of code that illustrates the issue

Re: NullPointerExceptions in v3.6.0

2018-02-28 Thread Rob Vesse
28 February 2018 at 14:54, Rob Vesse <rve...@dotnetrdf.org> wrote: > Two things look odd: > > - You never call dataset.begin() to start the transaction yet you later > try to commit() it > - Calling SystemTDB.setFileMode() after opening a dataset p

Re: NullPointerExceptions in v3.6.0

2018-02-28 Thread Rob Vesse
Two things look odd: - You never call dataset.begin() to start the transaction yet you later try to commit() it - Calling SystemTDB.setFileMode() after opening a dataset probably doesn't have any effect on already open datasets though I could be wrong on this point Rob On 28/02/2018, 13:08,

Re: TDB2 - text indexing error on rebuilding indexes with jena.textindexer

2018-02-12 Thread Rob Vesse
Filed as JENA-1486: https://issues.apache.org/jira/browse/JENA-1486 Rob On 12/02/2018, 14:11, "Rob Vesse" <rve...@dotnetrdf.org> wrote: This is probably a bug in the command line tool textindexer, looking at the source code it just attempts to access the Dataset given i

Re: TDB2 - text indexing error on rebuilding indexes with jena.textindexer

2018-02-12 Thread Rob Vesse
This is probably a bug in the command line tool textindexer, looking at the source code it just attempts to access the Dataset given in the descriptor without attempting to use a transaction. Since TDB2 requires transactions it will not be possible to use this tool until the bug is fixed Rob

Re: Extending Sparql with New Keywords

2018-02-07 Thread Rob Vesse
the file doesn't have any extension. Many Thanks 2018-02-06 11:53 GMT+02:00 Rob Vesse <rve...@dotnetrdf.org>: > This is entirely possible but it is not at all trivial. We have been doing > this for several years to add several extensions to the language.

Re: Extending Sparql with New Keywords

2018-02-06 Thread Rob Vesse
This is entirely possible but it is not at all trivial. We have been doing this for several years to add several extensions to the language. The extent of the necessary changes Will vary depending on what your extensions are intended to do. To start with the grammar. You can find the input

Re: Assembler for GenericRuleEngine Custom Builtin

2017-12-12 Thread Rob Vesse
See the documentation on Other Assembler directives: http://jena.apache.org/documentation/assembler/assembler-howto.html#other-assembler-directives Using ja:loadClass to load in a class that sets up any custom assemblers via static initializer blocks in that class should be sufficient and

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