Re: [Virtuoso-users] Two questions (tangent to maparent/virtuoso-python)

that maparent is maybe present on this list… From: Hugh Williams [mailto:hwilli...@openlinksw.com] Sent: Tuesday, November 21, 2017 10:11 AM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users@lists.sourceforge.net Subject: Re: [Virtuoso-users] Two questions Hi Daniel, A possible solution to this

[Virtuoso-users] Two questions

I am seeking to develop a new way to load updated/changed data into my Virtuoso graph. The current way I use involves a lot of churn - I load an NTriples file representing the data into an updates graph, and I delete all old triples and copy all new triples if the subject (owl:Thing) appears i

Re: [Virtuoso-users] Two questions

I wish also to clarify - I won't have blank nodes in any of the graphs I am considering, at least for now. From: Davis, Daniel (NIH/NLM) [C] Sent: Monday, November 20, 2017 4:04 PM To: virtuoso-users@lists.sourceforge.net Subject: Two questions I am seeking to develop a new way to load up

Re: [Virtuoso-users] client javascript

Carlo, Are you running in a browser or with nodejs? There are some minor differences. Here’s a tutorial for running in a browser: http://www.peej.co.uk/articles/http-auth-with-html-forms.html When you use jquery, you still need to use xhr methods: https://stackoverflow.com/questions/5507234/h

Re: [Virtuoso-users] how to pass as parameter the virtual graph IRI to a SPARQL statement ?

Here’s a brief example: -- -- Inserts triples of the form ?s meshv:active "true|false"^^xsd:boolean -- CREATE PROCEDURE meshrdf_insert_active(in graph_uri varchar, in active varchar) { DECLARE stmt varchar; IF (active <> 'false' AND active <> 'true') signal('INVALID', 'The argum

Re: [Virtuoso-users] Virtuoso Jena provider

NOTE: there are several editions of virt_jena: https://github.com/openlink/virtuoso-opensource/blob/develop/7/binsrc/jena/virt_jena.jar https://github.com/openlink/virtuoso-opensource/blob/develop/7/binsrc/jena2/virt_jena2.jar https://github.com/openlink/virtuoso-opensource/blob/develop/7/binsrc/j

Re: [Virtuoso-users] Mapping XML files to RDF graph using Virtuoso?

Eng.Bassam - you can take a look at https://github.com/HHS/meshrdf. We do something very similar - we've designed an OWLv1 ontology and then we have a fairly complicated XSLT transform that consumes MeSH XML and transforms it into RDF. It is unfair to say that RDF is schemaless - the vocabula

Re: [Virtuoso-users] Scope of log_enable and effect on deletes

. -Original Message- From: Hugh Williams [mailto:hwilli...@openlinksw.com] Sent: Tuesday, February 21, 2017 5:13 PM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users@lists.sourceforge.net Subject: Re: [Virtuoso-users] Scope of log_enable and effect on deletes Hi Daniel, What Virtuoso open

Re: [Virtuoso-users] Scope of log_enable and effect on deletes

set then proceed to re-enable the log. There might be better ways of doing it but that should work. -- Regards, Quentin Serrurier. GuidingHand.Solutions On 2017-02-22 02:01, Davis, Daniel (NIH/NLM) [C] wrote: I am not sure I understand the scope of the log_enable() procedure.If I cal

[Virtuoso-users] Scope of log_enable and effect on deletes

I am not sure I understand the scope of the log_enable() procedure.If I call log_enable(2,1); in a stored procedure, I am sure that it will affect the entire connection, but, will it affect other connections as well. Would it, for instance, persist until reboot and affect other connections

[Virtuoso-users] Understanding long start time

So, I have virtuoso, and I spend some time loading lots of ntriples files into it with TTLP, and then I wait for 2 minutes for checkpoint to complete, with CheckpointInterval = 60. Then, I restart it with +wait.It still has lots of I/O to do, doing a roll forward. The Database Administrat

Re: [Virtuoso-users] SPARQL Service Description

This is the bible - https://www.w3.org/TR/sparql11-service-description/, but it is rather complicated. I suggest instead you look at examples, too. Here’s mine - https://id.nlm.nih.gov/mesh/sparql. My intuition is to concentrate on the basics – the formats supported, the endpoints and urls.

Re: [Virtuoso-users] Better question on virt-jena.jar

, Kingsley Idehen wrote: > On 11/7/16 10:55 AM, Davis, Daniel (NIH/NLM) [C] wrote: >> >> Who is maintaining virt-jena? What is the process of maintaining >> this, e.g. is this portion of virtuoso purely contributed, or does OpenLink >> plan to update it and maintain it. >

Re: [Virtuoso-users] Better question on virt-jena.jar

@lists.sourceforge.net Cc: Hugh Williams ; Sergei Malinin Subject: Re: [Virtuoso-users] Better question on virt-jena.jar On 11/7/16 10:55 AM, Davis, Daniel (NIH/NLM) [C] wrote: Who is maintaining virt-jena? What is the process of maintaining this, e.g. is this portion of virtuoso purely contributed, or does

Re: [Virtuoso-users] Better question on virt-jena.jar

Ah, I see, there's a binsrc/jena, binsrc/jena2, and binsrc/jena3. I will look at the commits to this and try to answer my question on my own. It would be nice to hear clearly what the commitment of OpenLink is to this. From: Davis, Daniel (NIH/NLM) [C] Sent: Monday, November 07, 2016 10:

[Virtuoso-users] Better question on virt-jena.jar

Who is maintaining virt-jena? What is the process of maintaining this, e.g. is this portion of virtuoso purely contributed, or does OpenLink plan to update it and maintain it. My application depends on virt-jena. I will need to tell my boss where an upgrade to virt-jena is in an OpenLink road

Re: [Virtuoso-users] Using PREFIX in a prepared Statement

yway for me to preserve the convenience of prefixes: ... WHERE { mesh:?? %s ?l }; And then later bind the query argument? From: Kingsley Idehen [mailto:kide...@openlinksw.com] Sent: Friday, October 21, 2016 6:36 PM To: virtuoso-users@lists.sourceforge.net Subject: Re: [Virtuoso-users] Using PREFIX in a

[Virtuoso-users] Using PREFIX in a prepared Statement

So, I must run my application through a source code scanner, and it is reasonably complaining that I am using String.format() and stmt.executeQuery(query) with the Virtuoso JDBC connection. Yet, this is SPARQL. I see some discussion of prepared statements on this list in the past. What I wa

Re: [Virtuoso-users] VirtuosoDataSource fault-tolerance

Thanks, Hugh. We will almost certainly use that now that we have replication. From: Hugh Williams [mailto:hwilli...@openlinksw.com] Sent: Thursday, October 06, 2016 10:09 AM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users@lists.sourceforge.net Subject: Re: [Virtuoso-users

[Virtuoso-users] Restricting DBA logins by client IP

I've been hunting over the documentation, and I cannot see the way to restrict DBA logins by client IP. My security team doesn't allow me to use conductor, and so I do all my work from isql with the system tables. Even looking at DBEV_LOGIN and FIND_USER hooks, I don't see a way to do this.

[Virtuoso-users] VirtuosoDataSource fault-tolerance

I have a downstream project that uses Virtuoso JDBC against my server. I am wondering whether anyone out there has experience about the fault tolerance of VirtuosoDataSource. That is: *Does the open source VirtuosoDataSource have any fault tolerance features built-in to work with Vir

Re: [Virtuoso-users] Out of curiosity, some questions about OpenSource Virtuoso settings

Tangentially on JDBC/ODBC vs HTTP.HTTP is slow because of the transport, but JDBC/ODBC has more mature models of paging over results, pre-fetching, etc. I feel that RDF is mature as a Data format, but as a protocol it is not that mature. -Original Message- From: Hugh Williams [mai

Re: [Virtuoso-users] Java Melody with Virtuoso

So, the problem with this was within my web application, where I cast javax.sql.DataSource to virtuoso.jdbc4.VirtuosoDataSource. With that corrected, JavaMelody is able to monitor the data source. From: Davis, Daniel (NIH/NLM) [C] Sent: Tuesday, September 06, 2016 2:33 PM To: virtuoso-users

[Virtuoso-users] Java Melody with Virtuoso

Has anyone out there done a plugin so that Java Melody can monitor Virtuoso JDBC connections? I have a semantic web application using Virtuoso behind Jena behind Spring, and I have Java Melody monitoring it. It would be great to have Melody collect information on queries, but I'm not likely to

Re: [Virtuoso-users] Deleting large number of triples

deal with. From: Pantelis Natsiavas [mailto:natsia...@gmail.com] Sent: Wednesday, August 17, 2016 10:55 AM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users Subject: Re: [Virtuoso-users] Deleting large number of triples Thank you for your advice Daniel. Actually I want to delete only the

Re: [Virtuoso-users] Deleting large number of triples

So, this has nothing to do with the large vector size, but just to be sure the SPARQL is correct - do you wish to delete the subjects (and all their triples) where the subject has the predicate, or just the predicate itself? As far as avoiding the maximum vector size, I think your best approach

Re: [Virtuoso-users] Debugging JDBC Virtuoso connection

, 2016 9:47 AM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users Subject: Re: [Virtuoso-users] Debugging JDBC Virtuoso connection Hi Daniel, So the same application using the same JDBC connect string work on localhost where Virtuoso runs, but not from remote client ? I once had same problem when

[Virtuoso-users] Debugging JDBC Virtuoso connection

I've done my UI using Java Spring, but so far, I've been doing it as an old dinosaur, running my build and my changes on the Linux host where Virtuoso is running. Now, I'm trying to use Virtuoso remotely from another host. >From Python, I can connect to port , but when I try to connect to Vi

[Virtuoso-users] CREATE TABLE IF NOT EXISTS

What is the best way to run some SQL statements to create tables if they do not exists? I'm trying to achieve (at last), true automated deployment. Dan Davis, Systems/Applications Architect (Contractor), Office of Computer and Communications Systems, National Library of Medicine, NIH ---

[Virtuoso-users] Release memory without restart

Virtuoso-opensource in my environment is using 79% - 83% of memory after several weeks of nightly TTLP and daily queries. When I restart it, it is using 26% of memory (on a 16GB machine). I cannot restart it in my nightly data processing jobs, because that requires root, and my jobs do not run a

Re: [Virtuoso-users] Replication on a schedule

e a license for Virtuoso Cluster - this email was a product of research towards that decision. -Original Message- From: Hugh Williams [mailto:hwilli...@openlinksw.com] Sent: Friday, June 10, 2016 5:36 PM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users Subject: Re: [Virtuoso-users] R

Re: [Virtuoso-users] Replication on a schedule

I should probably rewack my stored procedures and systems architecture so that my update jobs run efficiently with transaction isolation. From: Davis, Daniel (NIH/NLM) [C] Sent: Friday, June 10, 2016 10:55 AM To: virtuoso-users Subject: [Virtuoso-users] Replication on a schedule Hi, does anyone out

[Virtuoso-users] Replication on a schedule

Hi, does anyone out there with the Cluster edition of Virtuoso replicate on a schedule rather than as deltas are flushed? Is this desirable? The issue is that in a star topology, replication represents an increased risk of the replicant failing. It may therefore be better to replicate only dur

Re: [Virtuoso-users] System setup guidelines

Thanks, Hugh. From: Hugh Williams [hwilli...@openlinksw.com] Sent: Wednesday, April 06, 2016 7:26 PM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users Subject: Re: [Virtuoso-users] System setup guidelines Hi Dan, The main places Virtuoso setup and

[Virtuoso-users] System setup guidelines

Maybe I'm missing something, but is there any place in the documentation I simple list of the things you should do to setup Virtuoso: *Don't use NFS *If you do use NFS, don't use soft mounts *The change to add "vm.swappiness = 10" to /etc/sysctl.conf that is mentioned i

Re: [Virtuoso-users] Temporary DB size and server restart

my install script enough, and most people use puppet/chef or other tools. From: Hugh Williams [mailto:hwilli...@openlinksw.com] Sent: Wednesday, March 30, 2016 4:53 PM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users Subject: Re: [Virtuoso-users] Temporary DB size and server restart Hi

Re: [Virtuoso-users] Temporary DB size and server restart

It looks like this is merely a cache, and it's OK for it to be bigger.It doesn't look like it has anything to do with my Virtuoso shutdown issues. From: Davis, Daniel (NIH/NLM) [C] Sent: Wednesday, March 30, 2016 12:09 PM To: virtuoso-users Subject: Temporary DB size and server

[Virtuoso-users] Temporary DB size and server restart

I have a strange failure condition somewhere in my deployment.Virtuoso goes down, and whenever I restart it, I see something like this in the log: Unlinked the temp db file /usr/nlm/virtuoso/db/virtuoso-temp.db as its size (8180MB) was greater than TempDBSize INI (10MB) Now, that is a big d

[Virtuoso-users] Making REGEX filters fast

Is there a way to make FILTER(REGEX(?label, 'Insurance, Health/utilization', 'I')) queries fast? I can see that REGEX is going to require a linear scan of the data, and that there are stored functions that do the matching. Will STRSTARTS be able to work quickly? Does the database collation al

[Virtuoso-users] Restrict dba login to localhost

Is there any way to restrict DBA login to requests originating from localhost? We have an application that would like to use the JDBC interface, and we've exposed port on the network, but we are a little paranoid about security and want to restrict DBA login to the localhost. In our env

Re: [Virtuoso-users] uploade TTl big file?

My experience was that I needed explicit SQL: DELETE FROM load_list; I didn't see anything else. I also didn't experience any acceleration from TTLP_MT vs TTLP even though I had multiple cores. I only had 2 cores, and so I don't know whether it reflects on the product. __

Re: [Virtuoso-users] deadlocks in bulk loading using rdf_loader_run function

One way to achieve this is to use RDF Graph Groups and read-only users, e.g. users in the SPARQL_SELECT group. The idea is to load data into a graph that your normal, read-only user will not see due to RDF Graph

Re: [Virtuoso-users] output:format "NT" question

ped. -Dan From: Hugh Williams [hwilli...@openlinksw.com] Sent: Saturday, November 21, 2015 8:37 PM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users@lists.sourceforge.net Subject: Re: [Virtuoso-users] output:format "NT" question Hi Daniel, A default vir

Re: [Virtuoso-users] federated SPARQL queries?

Communications Systems, National Library of Medicine, NIH From: Davis, Daniel (NIH/NLM) [C] Sent: Monday, November 16, 2015 11:04 AM To: 'Hugh Williams' ; Eng.Bassam Cc: virtuoso-users@lists.sourceforge.net Subject: RE: [Virtuoso-users] federated SPARQL queries? Bassam, As a professional in thi

Re: [Virtuoso-users] output:format "NT" question

l. From: Davis, Daniel (NIH/NLM) [C] Sent: Monday, November 16, 2015 1:09 PM To: virtuoso-users@lists.sourceforge.net Subject: output:format "NT" question I have a simple script to export triples, but it seems not to get all triples, but only about 10,000.I cannot guess what may be t

[Virtuoso-users] output:format "NT" question

I have a simple script to export triples, but it seems not to get all triples, but only about 10,000.I cannot guess what may be the problem. Any advice is appreciated. isql dba "$PASSWORD" BANNER=OFF BLOBS=ON VERBOSE=OFF ECHO=OFF PROMPT=OFF TIMEOUT=0 >fullmesh.nt

Re: [Virtuoso-users] federated SPARQL queries?

Bassam, As a professional in this field, I want to suggest that SPARQL Federated Query is not widely used in the field. Think about how this affects inferencing - unless the federating server has some way of knowing which vocabulary to associate with a remote graph, there is no way to do infe

[Virtuoso-users] How can I profile stored procedures?

How can I profile SQL or SPARQL statements when running this statements within a stored procedure? I've refactored my versioning algorithm to use more complicated single queries, for example: LOG_ENABLE(2, 1); DELETE FROM RDF_QUAD WHERE g = __target_graph AND EXIST

Re: [Virtuoso-users] log_enable(2,1) - how long?

same changes to the graph, will that cause the transaction logging to be less of an issue for performance (and failure as it exceeds its maximum size)? From: Hugh Williams [mailto:hwilli...@openlinksw.com] Sent: Tuesday, October 27, 2015 11:20 PM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users Su

[Virtuoso-users] log_enable(2,1) - how long?

When I execute log_enable(2,1) in a session, does it just affect statements made by that statement, or the whole server? When the session closes, does it revert to logging transactions? What if I move log_enable(2,1) to a stored procedure called by a session? Dan Davis, Systems/Applications Arch

[Virtuoso-users] power user problems

I guess I am turning into more of a power-user. Nonetheless, I have had some problems using exec() with SPARQL statements where the GRAPH URI is a variable. In this case, I must use { GRAPH ?? { ?? mesh:altLabel ?? } } for instance as below. I also see no way to specify the language code w

[Virtuoso-users] Validate graph based on rules

So, I have a rule set (vocabulary) for a graph that includes certain object properties, some with a domain and range, and some with only domain. I also have object properties.How can a go forward and validate such a schema using Virtuoso?Can I declare the graph as not validating, and t

[Virtuoso-users] virtuoso crash during nightly reload

Virtuoso's load via TTLP of a N-triples file failed for me last night. I am running 7.2.1 + the memory leak patch I posted about earlier. The back-trace doesn't have that many symbols in it (optimized, stripped). So, I'm skipping a lot: ... 11:20:25 /usr/nlm/virtuoso/bin/virtuoso-t(table_sourc

Re: [Virtuoso-users] Automating RDF data imports in VIrtuoso

> What is the best option for automating the import and update of RDFa/HTML > data on a regular basis into the virtuoso DB? Jason, Are you running virtuoso on a Windows system or on a UNIX/Linux system? In either case, I suggest you: - Write a script that talks to the server on port 11

Re: [Virtuoso-users] Automating RDF data imports in VIrtuoso

Hi Paul, We haven't had problem with data corruption, but the fix for the load memory leak is indeed a patch on top of 7.2.1. If you download 7.2.1 and expand it, then you can apply the patch as follows: - Take attached patch file and save to system - Apply with Unix/Linux patc

Re: [Virtuoso-users] Vituoso API for generating triples from C++ program

My experience is that you are better off loading the schema/vocabulary from Turtle (TTL) or RDF rather than OWL. Aside from that, it does load the vocabulary/schema from RDF, and it does load the triples from RDF, and if you later add triples through a program, then you can export them all tog

Re: [Virtuoso-users] saving results to a file

on, and Management Technology Providers > On 9 Sep 2015, at 20:49, Davis, Daniel (NIH/NLM) [C] > wrote: > > When I run the statement below in an ISQL command prompt, I get as a result a > BLOB of 225899 chars. > > SPARQL define output:format "NT" CONSTRUCT { ?s ?

[Virtuoso-users] saving results to a file

When I run the statement below in an ISQL command prompt, I get as a result a BLOB of 225899 chars. SPARQL define output:format "NT" CONSTRUCT { ?s ?p ?o } FROM WHERE { ?s ?p ?o }; I'm not quite sure how to use string_to_file() with a query like this... Dan Da

Re: [Virtuoso-users] Parameterizing SPARQL in Virtuoso/PL

hwilli...@openlinksw.com] Sent: Sunday, September 06, 2015 8:56 PM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users@lists.sourceforge.net Subject: Re: [Virtuoso-users] Parameterizing SPARQL in Virtuoso/PL Hi Daniel, Details on passing parameters in SPARQL queries can be found at:

[Virtuoso-users] Parameterizing SPARQL in Virtuoso/PL

I'm trying to implement a versioning policy our linked data, and when I see , located at http://id.nlm.nih.gov/mesh. We currently load the triples each night, and we want to start being sensitive to which subjects no longer appear in the graph, updating the triples of subjects that exist in th

[Virtuoso-users] Question on graph replication

I want to confirm my assumption - is it true that the RDF Graph Replication feature is only available in virtuoso professional? I was surprised to see that the stored procedures are there: SQL> db.dba.rdf_repl_start(); Done. -- 8 mse

[Virtuoso-users] Birthday problem - RDF_64BIT_UPGRADE()

http://docs.openlinksw.com/virtuoso/rdfdatarepresentation.html states that: Virtuoso supports a native IRI_ID data type, internally an unsigned 32 bit or unsigned 64 bit integer value. Small databases can use 32 bit values but if database becomes big then the administrator should executeDB.DBA

Re: [Virtuoso-users] Memory leaks with virtuoso 7.2.0

Hugh Williams wrote: > Hi Daniel, > > Thanks, I have been able to recreate and reported to development to fix: > Thank you very much. I will continue to monitor the mailing list to see if there is a fix, but it is VOS, so perhaps 7.2.2. There are still many things that may be done on my end –

Re: [Virtuoso-users] Memory leaks with virtuoso 7.2.0

nih.gov/mesh again and again (I used 15 seconds delay) with DB.DBA.ttlp(). From: Hugh Williams [mailto:hwilli...@openlinksw.com] Sent: Sunday, August 16, 2015 8:52 PM To: Davis, Daniel (NIH/NLM) [C] Cc: virtuoso-users@lists.sourceforge.net Subject: Re: [Virtuoso-users] Memory leaks with virtuos

Re: [Virtuoso-users] Memory leaks with virtuoso 7.2.0

Hugh Williams wrote: > Also, note the following 2 parameters: ThreadCleanupInterval, > ResourcesCleanupInterval which can both be set to 1 in order to reduce memory > leaking: > > > http://docs.openlinksw.com/virtuoso/databaseadmsrv.html#ex_threadcleanupinterval > > although as this wa

Re: [Virtuoso-users] Memory leaks with virtuoso 7.2.0

Hugh Williams wrote: > How is this "process to convert MeSH XML to MeSH RDF" which uses lots of > memory performed, is this done in Virtuoso or by some external process ? It's really converting to triples - https://github.com/HHS/meshrdf contains the conversion code, which is basically an XSLT p

[Virtuoso-users] Memory leaks with virtuoso 7.2.0

MeSH RDF in production (front-end is http://id.nlm.nih.gov/) is experiencing Virtuoso memory leaks of virtuoso during our nightly reload of all the MeSH triples.We noticed these first because virtuoso was being killed by the OOM killer, either when the process to convert MeSH XML to MeSH RDF