Re: Cannot get Fuseki 5 to run...

2024-05-02 Thread Andy Seaborne
Hi Phil, It's a bug. Fuseki uses the CORS filter from Eclipse Jetty by code-copy so as not to depend on Jetty. But at the last update, some Jetty code usage didn't get replaced and there are class references. Issue created: https://github.com/apache/jena/issues/2443 Andy On 02/05/2024

TDB3

2024-04-25 Thread Andy Seaborne
- finding the RDF terms that are currently in use in the database and recovering space indexes. RocksDB compaction is about the second case. Martynas On Wed, Apr 24, 2024 at 10:30 PM Andy Seaborne wrote: Hi Balduin, Thanks for the detailed report. It's useful to hear of the use case

Re: rdf:parseType="literal" vs. rdf:datatype="...XMLLiteral"

2024-04-25 Thread Andy Seaborne
On 25/04/2024 07:58, Thomas Francart wrote: Hello Andy Le lun. 22 avr. 2024 à 21:03, Andy Seaborne a écrit : On 22/04/2024 08:02, Thomas Francart wrote: Hello This is 3.17.0. Pretty old, due to other dependency with TopQuadrant SHACL API. It's not perfect in 5.0.0 either

Re: Java 21 support for Jena Fuseki 5.0.0

2024-04-24 Thread Andy Seaborne
The wording has been changed to "Jena5 requires Java 17, or a later version of Java." Thanks Andy On 24/04/2024 09:45, Balduin Landolt wrote: Hi list, me again... Does Jena Fuseki 5.0.0 support Java 21? On https://jena.apache.org/download/ all I can see is "Jena5 requires Java 17".

Re: Fuseki growing in size and need for compaction

2024-04-24 Thread Andy Seaborne
Hi Balduin, Thanks for the detailed report. It's useful to hear of the use case that occur and also the behaviour of specific deployments. On 22/04/2024 16:22, Balduin Landolt wrote: Hello, we're running Fuseki 5.0.0 (but previously the last 4.x versions behaved essentially the same) with

Re: Java 21 support for Jena Fuseki 5.0.0

2024-04-24 Thread Andy Seaborne
On 24/04/2024 10:41, Rob @ DNR wrote: Java versions are generally forwards compatible, so Fuseki should run fine on Java 21, unless any of our dependencies have some previously unreported issues with Java 21 If you do find any bugs then please file bugs as appropriate Thanks, Rob The

Re: rdf:parseType="literal" vs. rdf:datatype="...XMLLiteral"

2024-04-22 Thread Andy Seaborne
. I'd like to understand the usage to see which change is best). Andy BTW It's rdf:parseType="Literal" -- Jena 5.0.0 is not tolerant of lower case "literal" Thomas Le sam. 20 avr. 2024 à 18:06, Andy Seaborne a écrit : Hi Thomas, Which version of Jena is this? And

Re: rdf:parseType="literal" vs. rdf:datatype="...XMLLiteral"

2024-04-20 Thread Andy Seaborne
Hi Thomas, Which version of Jena is this? Andy On 19/04/2024 17:18, Thomas Francart wrote: Hello The RDF/XML parsing of the following succeeds: https://xx.xx.xx/PC"/> while the RDF/XML parsing of this gives an error : in that case the XML has simply be encoded with , and and the

Re: ModelExtract

2024-04-11 Thread Andy Seaborne
Hi Arne, hi Simon, It got removed because there wasn't evidence of use. 5.x.x was a chance It is opinionated and it doesn't feel like a good fit being in the central code for graph. It's more like a utility library feature. It can come back, maybe in a better form or better location. So to

Re: Performance question with joins

2024-04-01 Thread Andy Seaborne
Hi John, Yes, the join of two large subqueries is the issue. Optimization involves making pragmatic determination. Sometimes it isn't optimal for some data. Something to consider is detecting these independency of the (?X_i, ?X_j) and (?Y_i, ?Y_j) blocks because ia hash join is likely a

Re: Requesting advice on Fuseki memory settings

2024-03-25 Thread Andy Seaborne
and techniques for operation Fuseki/TDB. There is so much variety "out there" that all reports are helpful. Andy Best regards, Gaspar On Sun, Mar 24, 2024 at 5:00 PM Andy Seaborne wrote: On 21/03/2024 09:52, Rob @ DNR wrote: Gaspar This probably relates to https://access.

Re: query performance on named graph vs. default graph

2024-03-24 Thread Andy Seaborne
Andy, On Mar 19, 2024, at 5:02 AM, Andy Seaborne wrote: Hi Jim, What happens if you use GRAPH rather than FROM? WHERE { GRAPH <http://example.org/ubergraph> { ?cell rdfs:subClassOf cell: . ?cell part_of: ?organ . ?organ rdfs:subClassOf organ: . ?organ part_of: a

Re: Requesting advice on Fuseki memory settings

2024-03-24 Thread Andy Seaborne
users@jena.apache.org Subject: Re: Requesting advice on Fuseki memory settings Hi Andy On Sat, Mar 16, 2024 at 8:58 PM Andy Seaborne wrote: On 12/03/2024 13:17, Gaspar Bartalus wrote: On Mon, Mar 11, 2024 at 6:28 PM Andy Seaborne wrote: On 11/03/2024 14:35, Gaspar Bartalus wrote: Hi Andy,

Re: [ANN] Apache Jena 5.0.0

2024-03-21 Thread Andy Seaborne
o write a value. "1"^^xsd:int is canonical; "+1"^^xsd:int is not canonical. Most published data uses canonical forms. Andy Shaw, Ryan schrieb am Mi., 20. März 2024, 13:32: On Mar 20, 2024, at 5:05 AM, Andy Seaborne wrote: ** Term graphs Graphs are now term graphs in t

[ANN] Apache Jena 5.0.0

2024-03-20 Thread Andy Seaborne
The Apache Jena development community is pleased to announce the release of Apache Jena 5.0.0. In Jena5: * Minimum Java requirement: Java 17 * Language tags are case-insensitive unique. * Term graphs for in-memory models * RRX - New RDF/XML parser * Remove support for JSON-LD 1.0 *

Re: [EXTERNAL] Re: Query Performance Degrade With Sorting In Subquery

2024-03-19 Thread Andy Seaborne
to those expressions may themselves be dynamically computed values that don’t exist in the underlying dataset directly. Rob From: Chirag Ratra Date: Tuesday, 19 March 2024 at 10:39 To: users@jena.apache.org , Andy Seaborne , dcchabg...@gmail.com Subject: Re: [EXTERNAL] Re: Query Performance

Re: query performance on named graph vs. default graph

2024-03-19 Thread Andy Seaborne
On 18/03/2024 17:46, Jim Balhoff wrote: Hi, I’m running a particular query in a Fuseki server which performs very differently if the data is in a named graph vs. the default graph. I’m wondering if it’s expected to have a large performance hit if a named graph is specified. The dataset

Re: Requesting advice on Fuseki memory settings

2024-03-16 Thread Andy Seaborne
On 12/03/2024 13:17, Gaspar Bartalus wrote: On Mon, Mar 11, 2024 at 6:28 PM Andy Seaborne wrote: On 11/03/2024 14:35, Gaspar Bartalus wrote: Hi Andy, On Fri, Mar 8, 2024 at 4:41 PM Andy Seaborne wrote: On 08/03/2024 10:40, Gaspar Bartalus wrote: Hi, Thanks for the responses. We

Re: Problems when querying the SPARQL with Jena

2024-03-12 Thread Andy Seaborne
On 12/03/2024 13:02, Anna P wrote: Hi Lorenz, Thank you for your reply. Yes, I used maven to build the project. Here are dependencies details: Hi Lorenz, Yes, I used maven to build the project. Here are the dependencies details: UTF-8 1.8 1.8 junit junit 4.11 test org.apache.jena

Re: Requesting advice on Fuseki memory settings

2024-03-11 Thread Andy Seaborne
On 11/03/2024 14:35, Gaspar Bartalus wrote: Hi Andy, On Fri, Mar 8, 2024 at 4:41 PM Andy Seaborne wrote: On 08/03/2024 10:40, Gaspar Bartalus wrote: Hi, Thanks for the responses. We were actually curious if you'd have some explanation for the linear increase in the storage, and why

Re: Requesting advice on Fuseki memory settings

2024-03-08 Thread Andy Seaborne
dataset and the size it uses on disk. (Changes between `df -h` and `du -lh`)? The heap memory has some very minimal peaks, saw-tooth, but otherwise it's flat. Regards, Gaspar On Thu, Mar 7, 2024 at 11:55 PM Andy Seaborne wrote: On 07/03/2024 13:24, Gaspar Bartalus wrote: Dear Jena support

Re: Requesting advice on Fuseki memory settings

2024-03-08 Thread Andy Seaborne
heap memory has some very minimal peaks, saw-tooth, but otherwise it's flat. At what amount of memory? Regards, Gaspar On Thu, Mar 7, 2024 at 11:55 PM Andy Seaborne wrote: On 07/03/2024 13:24, Gaspar Bartalus wrote: Dear Jena support team, We would like to ask you to help us in co

Re: Requesting advice on Fuseki memory settings

2024-03-07 Thread Andy Seaborne
On 07/03/2024 13:24, Gaspar Bartalus wrote: Dear Jena support team, We would like to ask you to help us in configuring the memory for our jena-fuseki instance running in kubernetes. *We have the following setup:* * Jena-fuseki deployed as StatefulSet to a k8s cluster with the resource

Re: RDFRemoteConnection to Shiro protected Fuseki

2024-02-17 Thread Andy Seaborne
m the web UI without issues > > Met Vriendelijke Groet / With Kind Regards > Bart van Leeuwen > > On 2024/02/16 10:49:38 Andy Seaborne wrote: > > Hi Bart, > > > > Do you have a complete, ideally runnable, example of how you are using > > RDFConnection and also th

Re: RDFRemoteConnection to Shiro protected Fuseki

2024-02-16 Thread Andy Seaborne
Hi Bart, Do you have a complete, ideally runnable, example of how you are using RDFConnection and also the client side auth setup. Andy On 15/02/2024 19:27, Bart van Leeuwen wrote: Hi, I'm running Fuseki 4.9.0. on linux with OpenJDK 17 I've protected it with the shiro configuration and

[ANN] Apache Jena 5.0.0-rc1

2024-02-14 Thread Andy Seaborne
The Apache Jena development community is pleased to announce the release of Apache Jena 5.0.0-rc1 In Jena5: * Minimum: Java 17 * Language tags are case-insensitive unique. * Term graphs for in-memory models * RRX - New RDF/XML parser * Remove support for JSON-LD 1.0 * Turtle/Trig Output :

Re: Database Migrations in Fuseki

2024-02-09 Thread Andy Seaborne
Hi Balduin, On 07/02/2024 11:05, Balduin Landolt wrote: Hi everyone, we're storing data in Fuseki as a persistence for our application backend, the data is structured according to the application logic. Whenever something changes in our application logic, we have to do a database migration, so

Re: jena-fuseki UI in podman execution (2nd effort without attachments)

2024-02-09 Thread Andy Seaborne
Hi Jaana, Glad you got it sorted out. The Fuseki UI does not do anything special about browser caches. There was a major UI update with implementing it in Vue and all the HTML assets that go with that. Andy On 09/02/2024 05:37, jaa...@kolumbus.fi wrote: Hi, I just noticed that it's

Re: Restart during Fuseki compaction

2024-02-07 Thread Andy Seaborne
Recorded as https://github.com/apache/jena/issues/2254 On 06/02/2024 23:06, Andy Seaborne wrote: Hi Samuel, This is when the server exists for some reason? (If it's an internal exception, there should be a stack trace in the log file.) What operating system are you running on? What's

Re: Restart during Fuseki compaction

2024-02-06 Thread Andy Seaborne
Hi Samuel, This is when the server exists for some reason? (If it's an internal exception, there should be a stack trace in the log file.) What operating system are you running on? What's in the new Data-0002 directory? It does look like some defensive measures are needed to not choose to

Re: question about FROM keyword

2024-02-05 Thread Andy Seaborne
This is a combination of things happening. In the one case of no data (grph or dataset) provided, Jena does read the URL. If there is supplied data, FROM refers the dataset. The URL is coming back from www.learningsparql.com as explicitly "Content-Type: text/plain", not "text/turtle". Jena

Re: ARQInternalErrorException during query execution in Jena 4.10.0

2024-01-04 Thread Andy Seaborne
https://github.com/apache/jena/discussions/2150 The query shows is not the one generated by the update builder.

Re: ARQInternalErrorException during query execution in Jena 4.10.0

2024-01-04 Thread Andy Seaborne
On 03/01/2024 20:58, Dhamotharan, Kishan wrote: Hi all, We are attempting to upgrade from Jena 3.5 to Jena 4.10.0. We are using “RDFConnection.connect(TDBFactory.createDataset());” for unit tests. The below query works totally fine in Jena 3.5 but fails with the following exception in

Jena5: what to expect

2023-12-30 Thread Andy Seaborne
Jena5 is the next planned release for Apache Jena. ** All issues for Jena5: https://github.com/apache/jena/issues?q=is%3Aissue+label%3AJena5 ** Java Requirement Java 17 or later is required. Java 17 language constructs now are used in the codebase. ** Language tags Language tags become are

Re: Parallel requests on multiple fuseki

2023-12-14 Thread Andy Seaborne
Jorge, Have you looked at https://jena.apache.org/documentation/query/service_enhancer.html It might have features of use to you. Andy On 14/12/2023 08:25, George News wrote: Hi, I have deployed several Fuseki instances. This email scenario is just for 2. I was testing the SERVICE

Re: Checking that SPARQL Update will not validate SHACL constraints

2023-12-13 Thread Andy Seaborne
On 13/12/2023 15:49, Arne Bernhardt wrote: Hello Martynas, I have no experience with implementing a validation layer for Fuseki. But I might have an idea for your suggested approach: Instead of loading a copy of the graph and modifying it, you could create an

Re: Unable to build the below query using jena query builder

2023-12-08 Thread Andy Seaborne
On 08/12/2023 02:08, Dhamotharan, Kishan wrote: Hello Lorenz, Thanks for your response. ... Since query builder 3.5 does not have addWhereValueVar is there any other way to build the query ? It’s a very painful process to pull in three party / open source libraries, requires multiple

Re: Problem running AtomGraph/fuseki-docker

2023-12-07 Thread Andy Seaborne
[2023-12-06 22:19:53] INFO Server :: Path = /'/ds' Not good. Shell quoting didn't happen. That's a URL path component called '/ds' in the server root. Andy On 06/12/2023 23:55, Steve Vestal wrote: I was using bash.  When I run it in command prompt, it works. Thanks!

Re: Text indexing stopped working

2023-11-30 Thread Andy Seaborne
There isn't much information to go. On 29/11/2023 09:50, Mikael Pesonen wrote: No idea? On 16/11/2023 13.11, Mikael Pesonen wrote: What could be the reason why new data is suddenly not added to text index and not found with Jena text queries? The newest files in Jena text index folder are

Re: Querying URL with square brackets

2023-11-25 Thread Andy Seaborne
at 1:34 PM Andy Seaborne wrote: On 24/11/2023 10:05, Marco Neumann wrote: (side note) preferably the local name of a URI should not start with a number but a letter or underscore. It's a hangover from XML QNames. Turtle doesn't care. Style-wise, yes, avoid an initial number. What d

Re: Querying URL with square brackets

2023-11-25 Thread Andy Seaborne
On 24/11/2023 10:05, Marco Neumann wrote: (side note) preferably the local name of a URI should not start with a number but a letter or underscore. It's a hangover from XML QNames. Turtle doesn't care. Style-wise, yes, avoid an initial number. What do you mean by human-readable here?

Re: Querying URL with square brackets

2023-11-25 Thread Andy Seaborne
On 24/11/2023 08:55, Marco Neumann wrote: Laura, see jena issue #2102 https://github.com/apache/jena/issues/2102 It's specific to []. Because data formats accept these bad URIs (with a warning), the fact SPARQL generates errors is a bug to be fixed. Andy Marco On Fri, Nov 24,

Re: Querying URL with square brackets

2023-11-25 Thread Andy Seaborne
On 24/11/2023 10:40, Marco Neumann wrote: The URI syntax is defined by the Internet Engineering Task Force (IETF) in RFC 3986. W3C RDF is just a rule-taker here ;) https://datatracker.ietf.org/doc/html/rfc3986 We've drafted a non-normative section:

RDF URI references [Was: Querying URL with square brackets]

2023-11-25 Thread Andy Seaborne
Another option is the HTTP query string - think of it as asking a question of resource "http://example.org/book; Andy On 24/11/2023 11:03, Martynas Jusevičius wrote: On Fri, Nov 24, 2023 at 11:46 AM Laura Morales wrote: in the case that I want to use these URLs with a web browser. I

Re: Implicit default-graph-uri

2023-11-19 Thread Andy Seaborne
On 18/11/2023 08:21, Laura Morales wrote: I've tried this option too using the following configuration fuseki:dataset [ a ja:RDFDataset; ja:defaultGraph [ a ja:UnionModel ; ja:subModel [ a tdb2:GraphTDB2 ; tdb2:dataset [

Re: Implicit default-graph-uri

2023-11-17 Thread Andy Seaborne
On 16/11/2023 11:35, Laura Morales wrote: I would like to configure Fuseki such that I can use 2 datasets from 2 different locations, as if they were a single dataset. This is my config.ttl: <#> a fuseki:Service ; fuseki:endpoint [ fuseki:operation fuseki:query ] ;

Re: Delete Dataset with fuseki

2023-11-16 Thread Andy Seaborne
On 15/11/2023 09:19, Steven Blanchard wrote: Dear Jena Users, When i delete a dataset with fuseki, only the configuration file are removing and not the tdb2 folder According to the documentation this is expected behaviour  :

Re: Issues importing Jena to Eclipse after clean install

2023-11-16 Thread Andy Seaborne
https://stackoverflow.com/questions/77490993/importing-jena-to-eclipse-compile-problems On 15/11/2023 21:35, Paul Jarski wrote: I believe I've followed the instructions from https://jena.apache.org/tutorials/using_jena_with_eclipse.html: I ran mvn clean install with apparently no issues, but

Re: Semantics of SPARQL Update Delete

2023-11-10 Thread Andy Seaborne
On 10/11/2023 20:35, Marco Neumann wrote: On Fri, Nov 10, 2023 at 5:51 PM Andy Seaborne wrote: On 10/11/2023 12:33, Marco Neumann wrote: Should DELETE {URI URI * } not update all matching graph patterns? No. (and that's bad syntax) I had a case where only DELETE {URI URI NODE } did

Re: Semantics of SPARQL Update Delete

2023-11-10 Thread Andy Seaborne
On 10/11/2023 18:19, Marco Neumann wrote: On Fri, Nov 10, 2023 at 5:51 PM Andy Seaborne wrote: On 10/11/2023 12:33, Marco Neumann wrote: Should DELETE {URI URI * } not update all matching graph patterns? No. (and that's bad syntax) DELETE { ?x } is bad syntax? "*" is

Re: Semantics of SPARQL Update Delete

2023-11-10 Thread Andy Seaborne
On 10/11/2023 12:33, Marco Neumann wrote: Should DELETE {URI URI * } not update all matching graph patterns? No. (and that's bad syntax) I had a case where only DELETE {URI URI NODE } did execute the update in the dataset/graph/query fuseki UI. To be precise it is a DELETE INSERT

Re: Ever-increasing memory usage in Fuseki

2023-11-02 Thread Andy Seaborne
Hi Hugo, On 01/11/2023 19:43, Hugo Mills wrote: Hi, We’ve got an application we’ve inherited recently which uses a Fuseki database. It was originally Fuseki 3.4.0, and has been upgraded to 4.9.0 recently. The 3.4.0 server needed regular restarts (once a day) in order to keep working; the

[ANN] Apache Jena 4.10.0

2023-11-01 Thread Andy Seaborne
The Apache Jena development community is pleased to announce the release of Apache Jena 4.10.0 In this release: * Prepare for Jena5 Check use of deprecated API calls These are largely being removed in Jena5. Jena5 will require Java17 jena5 Fuseki will switch from javax.servlet to

Re: HTTP QueryExecution has been closed

2023-10-29 Thread Andy Seaborne
It's not clear from the information so far. Complete, minimal, verifiable example please. Also - what's the stacktrace you are seeing and which Jena version are you running? Andy On 27/10/2023 22:18, Martynas Jusevičius wrote: Hi, I'm trying to understand in which circumstances can

Re: qparse but preserve comments

2023-10-29 Thread Andy Seaborne
On 27/10/2023 17:58, Justin wrote: Hello, Is it possible to allow qparse to preserve comments? No - the parser skips them. e.g. it currently does not: ``` justin@parens:/tmp$ cat a.rq select * where { ?s ?p ?o # comment here } justin@parens:/tmp$ ~/Downloads/apache-jena-4.7.0/bin/qparse

Re: How to reconstruct a Literal from a SPARQL SELECT row element?

2023-10-26 Thread Andy Seaborne
On 26/10/2023 10:17, Steve Vestal wrote: What is the best way to reconstruct a typed Literal from a SPARQL SELECT result? I have a SPARQL SELECT query issued against an OntModel in this way: QueryExecution structureRowsExec = QueryExecutionFactory.create(structureRowsQuery,

Re: pellet version

2023-10-19 Thread Andy Seaborne
On 19/10/2023 14:46, Taras Petrenko wrote: Hi, I would like to know which Pellet implementation is the most consistent with Jena? or which one is currently used in Protege ? Now I am using the openllet-jena, version 2.6.3: To finf the version of jena to go with a release of openllet-jena,

Re: In using RIOT I encounter the "64000" entity expansions error.

2023-10-13 Thread Andy Seaborne
.     Andy On 10/12/2023 1:42 PM, Andy Seaborne wrote: Thanks. It parses OK. On Thu, 12 Oct 2023, 19:36 Jim Balhoff, wrote: On Oct 6, 2023, at 3:46 AM, Andy Seaborne wrote: On 28/06/2023 09:26, Damion Dooley wrote: I’m using RIOT to parse a large food ontology in owl rdf/xml format.

Re: In using RIOT I encounter the "64000" entity expansions error.

2023-10-12 Thread Andy Seaborne
Thanks. It parses OK. On Thu, 12 Oct 2023, 19:36 Jim Balhoff, wrote: > > On Oct 6, 2023, at 3:46 AM, Andy Seaborne wrote: > > > > > > On 28/06/2023 09:26, Damion Dooley wrote: > >> I’m using RIOT to parse a large food ontology in owl rdf/xml format. >

Re: In using RIOT I encounter the "64000" entity expansions error.

2023-10-06 Thread Andy Seaborne
On 28/06/2023 09:26, Damion Dooley wrote: I’m using RIOT to parse a large food ontology in owl rdf/xml format. Damion, Is that data publicly available? There's a new RDF/XML parser for Jena in the pipeline and I'd like to try it out on real data. Andy

Re: Encountering the error "org.apache.thrift.protocol.TProtocolException: Unrecognized type 0" in different scenarios

2023-09-28 Thread Andy Seaborne
s happening. On Tue, 19 Sept 2023 at 23:05, Andy Seaborne wrote: Hi Jan, Thanks for the update. On 18/09/2023 19:49, Jan Eerdekens wrote: Hi Andy, Sorry for the late answer, but I was quite busy. The database was as far as I can tell generated in version 4.7.0 and then upgrades to 4.8.0

Normalizing language tags

2023-09-28 Thread Andy Seaborne
An active issue in the RDF 1.2 Working Group is whether to mandate the syntactic form of language tags. Currently, in RDF, it says that language tags are compared case insensitively and also that "Lexical representations of language tags MAY be converted to lower case." Its actually in RDF

Re: Literal term equality - cannonizalise / normalize

2023-09-28 Thread Andy Seaborne
On 25/09/2023 15:35, Arne Bernhardt wrote: Hello, in order to use the GraphMem2 graphs in Jena 4.9, we are planning to switch to "literal term equality" in our projects. Currently we are discussing the following two approaches: 1. simple RDF standard compatibility. We treat object literal

Re: Encountering the error "org.apache.thrift.protocol.TProtocolException: Unrecognized type 0" in different scenarios

2023-09-19 Thread Andy Seaborne
, but I'll check with our OPS people to see if they can identify something on the OS level that might access the files or if they have setup a backup process. Currently we're only running 1 Jena instance per environment. regards, Jan On Wed, 30 Aug 2023 at 23:08, Andy Seaborne wrote: Hi Jan

Re: read-only Fuseki TDB2

2023-09-19 Thread Andy Seaborne
. tdb2.tdbquery --loc DATABASE 'ASK{}' TDB1 is different; read-transactions can do some completion actions. The journal is more heavily used. Andy On 18/09/2023 16:35, Jim Balhoff wrote: On Sep 18, 2023, at 11:09 AM, Andy Seaborne wrote: On 18/09/2023 15:35, Jim Balhoff wrote: Thanks

Re: read-only Fuseki TDB2

2023-09-18 Thread Andy Seaborne
On 18/09/2023 15:35, Jim Balhoff wrote: Thanks, I think that’s basically what I’ve got. The only operation I have enabled is 'fuseki:query’. But Fuseki still complains if the filesystem is read-only. The database is opened before the configuration is processed. Also, there is only one

Re: read-only Fuseki TDB2

2023-09-18 Thread Andy Seaborne
The TDB2 database is open for general use (i.e. write). You can get read-only by restricting the operations on the dataset to only query and the read functions of the Graph Store Protocol. Being SPARQL, query operations and write (update) operations are separate by syntax and there are

Re: Jena hangs on deleted files

2023-09-09 Thread Andy Seaborne
: Just on a command line (dev system) /usr/bin/java -Xmx8G -jar fuseki-server.jar --update --port 3030 --config=../jena_config/fuseki_config.ttl On 08/09/2023 11.47, Andy Seaborne wrote: In a container? As a VM? On 08/09/2023 07:36, Mikael Pesonen wrote: We are using Ubuntu. On Thu, 7 Sept

Re: Jena hangs on deleted files

2023-09-08 Thread Andy Seaborne
In a container? As a VM? On 08/09/2023 07:36, Mikael Pesonen wrote: We are using Ubuntu. On Thu, 7 Sept 2023 at 16:33, Andy Seaborne wrote: Are the database files on a MS Windows filesystem? There is a long-standing Java issue that memory mapped files on MS Windows do not get freed until

Re: Use rdf:ID in RDF/XML generated file

2023-09-07 Thread Andy Seaborne
On 07/09/2023 15:54, mbk wrote: Hi! We generate a RDF/XML file which has all its resources with the 'rdf:about' attribute. We would like to replace this attribute with 'rdf:id' Using apache-jena 3.17.0 We create ressource with model.createResource(uri,res) where uri is an UUID with prefix

Re: Jena hangs on deleted files

2023-09-07 Thread Andy Seaborne
Are the database files on a MS Windows filesystem? There is a long-standing Java issue that memory mapped files on MS Windows do not get freed until the JVM exists. Various bugs in the OpenJDK bug database such as: https://bugs.openjdk.org/browse/JDK-4715154 Andy On 07/09/2023 13:06,

Re: Problem with federated queries

2023-08-31 Thread Andy Seaborne
On 31/08/2023 08:58, Simon Bin wrote: On Wed, 2023-08-30 at 21:36 +0100, Andy Seaborne wrote: The query editor in the UI is a 3rd party compoent (from @zazuco/yasqe - it has security bug fixes from the original). It is has a SPARQL 1.1 grammar engine which determines the synatx checking

Re: Encountering the error "org.apache.thrift.protocol.TProtocolException: Unrecognized type 0" in different scenarios

2023-08-30 Thread Andy Seaborne
Hi Jan, On 30/08/2023 14:58, Jan Eerdekens wrote: Hi, We've been evaluating an using Jena for about 1,5 years now, but are recently running into a perplexing issue. In a lot of different scenarios, ways of using Jena, we are getting the exceptions like the one below: Caused by:

Re: Java 11 vs Java 17

2023-08-30 Thread Andy Seaborne
On 29/08/2023 12:26, Andy Seaborne wrote: Which result format is this? JSON? XML? Thanks - the fact the impact on JSON and XML results writers is suggestive that the difference is in that area. Andy No suggestion that our case is representative of any broader pattern. Dave

Re: Problem with federated queries

2023-08-30 Thread Andy Seaborne
determines the synatx checking. It would benefit from a contribution to update the parser. LATERAL is not implemented by several engines. Andy Orange Restricted -Message d'origine- De : Andy Seaborne Envoyé : mardi 29 août 2023 22:10 À : users@jena.apache.org Objet : Re: Problem

Re: Problem with federated queries

2023-08-29 Thread Andy Seaborne
There is also the service enhancer https://jena.apache.org/documentation/query/service_enhancer.html which provides various ways to control federated query. Andy On 29/08/2023 19:22, Simon Bin wrote: You could use the "LATERAL" extension of Jena (not standard Sparql 1.1): PREFIX wd:

Re: Java 11 vs Java 17

2023-08-29 Thread Andy Seaborne
On 29/08/2023 08:46, Dave Reynolds wrote: Hi Andy, On 27/08/2023 10:36, Andy Seaborne wrote: On 25/08/2023 15:18, Dave Reynolds wrote: [1]  > We've being testing some of our troublesome queries on 4.9.0 on java  > 11 vs java 17 and see a 10-15% performance hit on java 17 (even after

Java 11 vs Java 17

2023-08-27 Thread Andy Seaborne
On 25/08/2023 15:18, Dave Reynolds wrote: [1] > We've being testing some of our troublesome queries on 4.9.0 on java > 11 vs java 17 and see a 10-15% performance hit on java 17 (even after > we take control of the GC by forcing both to use the old parallel GC > instead of G1). No idea why,

Re: TDB2 Exception in initialisation

2023-08-25 Thread Andy Seaborne
On 25/08/2023 09:04, Enrico.Daga wrote: Hi, I am having a strange error while attempting to initialise a TDB2 dataset: TDB2Factory.connectDataset(tdb2location); tdb2location existing. However, I am getting the error below, which I don't understand. It seems related to some file system

Re: Transactions over http (fuseki)

2023-08-25 Thread Andy Seaborne
On 18/08/2023 07:38, Gaspar Bartalus wrote: Hi, We would like to execute queries (construct) and updates (insert/delete data) in one transaction. Very similar I think to what Andy described here: https://github.com/w3c/sparql-dev/issues/83 Something that has not quite ever managed to

Re: RSIterator deprecation

2023-08-25 Thread Andy Seaborne
ps://github.com/spdx/tools/blob/bc35e25dacb728bf8332b82b509bb3efacd6c64e/src/org/spdx/rdfparser/SPDXDocument.java#L1225-L1235 On 16 Aug 2023, at 18:18, Andrii Berezovskyi wrote: Thanks Andy, On 15 Aug 2023, at 10:12, Andy Seaborne wrote: That's quite a long method! Yes, not proudest part of

Re: Mystery memory leak in fuseki

2023-08-25 Thread Andy Seaborne
On 03/07/2023 14:20, Dave Reynolds wrote: We have a very strange problem with recent fuseki versions when running (in docker containers) on small machines. Suspect a jetty issue but it's not clear. From the threads here, it does seem to be Jetty related. I haven't managed to reproduce the

Re: How to log the client ip address?

2023-08-15 Thread Andy Seaborne
If you turn on the NCSA logging, there is a standard format logging line output. In the provided log4j2.properties, it is switched off by default: logger.fuseki-request.level = OFF so comment out that line and a NCSA log line is generated which include X-Forwarded-For. You

Re: RSIterator deprecation

2023-08-15 Thread Andy Seaborne
On 14/08/2023 19:46, Andrii Berezovskyi wrote: Hello, I just noticed that .listReifiedStatements() ReifiedStatement, and RSIterator, which we use [1], That's quite a long method! What is reification used for in Lyo? Do quoted triples provide the same capability? have been deprecated in

JSON-LD framing

2023-08-15 Thread Andy Seaborne
Jena uses jsonld-java for JSON-LD 1.0 and titanium-json-ld for JSON-LD 1.1 Rob describes the framing support for passing information to jsonld-java for JSON-LD 1.0. At Jena5, support for JSON-LD 1.0 is planned for removal. The jsonld-java project does not appear to be active. The project

Re: Help with incremental loading of TTL files

2023-07-26 Thread Andy Seaborne
Hi Robert, On 26/07/2023 12:44, Robert Alexander wrote: Dear friends, I am using Apache Jena Fuseki from a Docker image  https://hub.docker.com/r/secoresearch/fuseki and all works so well. Love Jena/Fuseki! The problem I’m grappling with though is that after an initial mass loading from RDF

Required Java version

2023-07-20 Thread Andy Seaborne
A reminder that Jena will move from requiring Java11 to requiring Java17. The project aims to support for 2 LTS versions of Java. Java21 is scheduled for September 19 this year and is LTS. Some time after that date that Jena will switch, with a major version bump to Jena 5.x.y For Fuseki,

Re: CVE-2023-32200

2023-07-20 Thread Andy Seaborne
On 20/07/2023 17:18, Brandon Sara wrote: I just came across CVE-2023-32200 and was wondering, is it different than CVE-2023-22665 and, if so, how is it different? Jena 4.8.0 addresses CVE-2023-22665 by requiring the Java system property "jena:scripting" to enable scripting. Jena 4.9.0

Re: Mystery memory leak in fuseki

2023-07-19 Thread Andy Seaborne
Conal, Thanks for the information. Can you see if metaspace is growing as well? All, Could someone please try running Fuseki main, with no datasets (--empty) with some healthcheck ping traffic. Andy On 19/07/2023 14:42, Conal McLaughlin wrote: Hey Dave, Thank you for providing an in

Re: java.lang.Error: Maximum lock count exceeded

2023-07-17 Thread Andy Seaborne
ttp://jmvanel.free.fr/jmv.rdf%23me> +33 (0)6 89 16 29 52 Le dim. 16 juil. 2023 à 21:53, Andy Seaborne a écrit : https://github.com/apache/jena/issues/1499 Are you are using 4.6.0? Andy On 16/07/2023 14:54, Jean-Marc Vanel wrote: Every few weeks, I get this stack, and the database is un

Re: java.lang.Error: Maximum lock count exceeded

2023-07-16 Thread Andy Seaborne
https://github.com/apache/jena/issues/1499 Are you are using 4.6.0? Andy On 16/07/2023 14:54, Jean-Marc Vanel wrote: Every few weeks, I get this stack, and the database is unusable afterwards. Is there some "purge" to call now and then ? java.lang.Error: Maximum lock count exceeded

Re: error on tdb2.tdbbackup: "Caused by: org.apache.thrift.protocol.TProtocolException: Unrecognized type 0"

2023-07-14 Thread Andy Seaborne
to just do a complete rebuild? Yes, that is safer. Andy Many thanks, jw On Thu, Jul 13, 2023 at 3:55 PM Andy Seaborne wrote: Hi Jeff, There were fixes to compaction in 4.6.0. On 12/07/2023 23:53, Jeffrey C. Witt wrote: Dear List, I ran into an unusual error today when I tried

Re: OOM Killed

2023-07-14 Thread Andy Seaborne
Hi Laura, It hadn't occurred to me that the GC choice might be involved. Also, I though G1 was the default GC but it seems at java11 it isn't that simple. It's build dependent. I use the Ubuntu build of OpenJDK. Java11 has Shenandoah Java17 has G1 -- and I think java21 will be G1. Could you

Re: Dataset management API

2023-07-13 Thread Andy Seaborne
clashes. Andy Martynas On Sun, 2 Jul 2023 at 19.03, Andy Seaborne wrote: On 02/07/2023 13:23, Martynas Jusevičius wrote: Hi, Can I see an example of the data that needs to be POSTed to /$/datasets in order to create a new dataset+service? The API is documented here but the data

Re: OOM Killed

2023-07-13 Thread Andy Seaborne
RAM when running a lot of simple queries in series (not in parallel). One thing that I want to try, but so far haven't, is to restart Fuseki halfway through the job. Sent: Monday, July 10, 2023 at 1:18 PM From: "Andy Seaborne" To: users@jena.apache.org Subject: Re: OO

Re: error on tdb2.tdbbackup: "Caused by: org.apache.thrift.protocol.TProtocolException: Unrecognized type 0"

2023-07-13 Thread Andy Seaborne
Hi Jeff, There were fixes to compaction in 4.6.0. On 12/07/2023 23:53, Jeffrey C. Witt wrote: Dear List, I ran into an unusual error today when I tried to backup (and also compact) my TDB instance. I first encountered the error when trying to compact and backup up using fuseki 4.3.2 I ran

CVE-2023-32200: Apache Jena: Exposure of execution in script engine expressions.

2023-07-11 Thread Andy Seaborne
Severity: important Affected versions: - Apache Jena 3.7.0 through 4.8.0 Description: There is insufficient restrictions of called script functions in Apache Jena versions 4.8.0 and earlier. It allows a remote user to execute javascript via a SPARQL query. This issue affects Apache Jena:

Re: OOM Killed

2023-07-10 Thread Andy Seaborne
On 10/07/2023 12:18, Andy Seaborne wrote: Laura, Dave, This doesn't sound like the same issue but let's see. Sorry for the confusion - these questions are for Laura. - Is it in a container? If so:   Is it the container being killed OOM or     Java throwing an OOM exception?   Much

Re: OOM Killed

2023-07-10 Thread Andy Seaborne
Laura, Dave, This doesn't sound like the same issue but let's see. Dave - your situation isn't under high load is it? - Is it in a container? If so: Is it the container being killed OOM or Java throwing an OOM exception? Much RAM does the container get? How many threads? - If not a

[ANN] Apache Jena 4.9.0

2023-07-08 Thread Andy Seaborne
The Apache Jena development community is pleased to announce the release of Apache Jena 4.9.0. In this release: * New in-memory graph implementations * Important update to Fuseki UI. Switch from TriplyDB/(yasr,yasqe) to zazuko/(yasr,yasqe) This changes picks up some security fixes in yasr

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