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Virtuoso is a high-performance and scalable Multi-Model RDBMS, Data Integration Middleware, Linked Data Deployment, and HTTP Application Server Platform

Home Page: http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/

License: Other

Shell 2.42% CSS 1.59% JavaScript 4.64% XSLT 23.85% SQLPL 0.33% PLSQL 0.34% HTML 2.10% Java 8.75% PHP 1.42% Ruby 0.09% C 49.59% C# 1.84% Makefile 0.61% XQuery 0.01% Awk 0.11% C++ 1.96% PLpgSQL 0.05% Perl 0.15% Python 0.15% Inno Setup 0.01%
virtuoso-server databases sql sparql

virtuoso-opensource's Introduction

Virtuoso Open-Source Edition: Building

Copyright (C) 1998-2024 OpenLink Software [email protected]

Table of Contents

Introduction

This document explains steps to take after obtaining a Virtuoso source snapshot or git clone.

These sections explain how to compile, test and install and what components are produced by the make process and how one can interact with them.

Package Dependencies

To generate the configure script and all other build files necessary, please make sure the following packages and recommended versions are installed on your system.

Package Minimum Upto From
autoconf 2.57 2.69 http://www.gnu.org/software/autoconf/
automake 1.9 1.16.1 http://www.gnu.org/software/automake/
libtool 1.5 2.4.6 http://www.gnu.org/software/libtool/
flex 2.5.33 2.6.4 http://flex.sourceforge.net/
bison 2.3 3.5.1 http://www.gnu.org/software/bison/
gperf 3.0.1 3.1 http://www.gnu.org/software/gperf/
gawk 3.1.1 5.3.0 http://www.gnu.org/software/gawk/
m4 1.4.1 1.4.18 http://www.gnu.org/software/m4/
make 3.79.1 4.2.1 http://www.gnu.org/software/make/
OpenSSL 0.9.8e 3.2.x http://www.openssl.org/

and any GNU packages required by these. The autogen.sh and configure scripts check for the presence and right version of some of the required components.

The Minimum column contains the oldest known versions of these packages capable of building Virtuoso. Older versions of these packages can sometimes be used, but could cause build problems.

The Upto column contains the most recently tested version of these packages. Newer minor revisions of these packages can likely be used, but major version upgrades may cause build problems.

To check the version number of the tools installed on your system, use one of the following commands:

  • autoconf –version
  • automake –version
  • libtoolize –version
  • flex –version
  • bison –version
  • gperf –version
  • gawk –version
  • m4 –version
  • make –version
  • openssl version

If you have an older version than automake version 1.9 you can edit the configure.ac script around line 47 using the examples provided for each version.

If you have a problem porting Virtuoso in your platform, please open a Issue on Github so we can assist you.

Development packages

Note that many operating systems (particularly all Linux distibutions) split some of these packages into runtime and development packages, so users of these platforms may need to run e.g.:

apt-get install libssl-dev

or

yum install openssl-devel 

to get development headers & libraries for OpenSSL.

Diskspace Requirements

The build produces a demo database and Virtuoso application packages that are quite large. At least 800 MB of free space should be available in the build file system.

When running `make install’, the target file system should have about 400 to 600 MB free. By default, the install target directories are under /usr/local/, but you can specify

./configure --prefix=/path/to/dir

instead.

The minimum working configuration consists of the server executable and config files plus database, no more than a few MB for the server executable, depending on platform and options.

Make FAQ

In the root directory of the checkout perform the following commands:

./autogen.sh        # should only be needed in git clone
./configure
make

to produce the default binaries, VAD packages and demo database. This takes some time, principally due to building and filling the demo database, rendering the XML documentation into several target formats and composing various Virtuoso application packages. It takes about 30 minutes on a 2GHz machine.

The default configure does not enable most of the runtime-hosting and extension features. See the links on the building page for instructions on how to enable these and what additional software is required.

Some builds require additional C compiler and other environment flags to be set before running the configure command, especially when building 64-bit versions of the server. If your system is not in this list, please try to run the configure command without any environment settings.

Warning: if VAD or other packages fail to be built, especially on 64-bit Linux platforms, ensure you’re not using excessive optimization. CFLAGS=“-O2” is known to work but there are reports of -O3 failing.

If your system requires additional flags not listed below, please contact us at [email protected].

Recent systems

Linux 64-bit

CFLAGS="-O2 -m64"
export CFLAGS
./configure ...

Mac OS X 10.9-10.15 Intel 64-bit

CFLAGS="-O -arch x86_64 -mmacosx-version-min=10.9"
export CFLAGS
./configure ...

Mac OS X 11.x Universal

CFLAGS="-O -arch arm64 -arch x86_64 -mmacosx-version-min=10.9"
export CFLAGS
./configure --disable-dependency-tracking ...

Mac OS X 12.x Universal

CFLAGS="-O -arch arm64 -arch x86_64 -mmacosx-version-min=10.9"
export CFLAGS
./configure --disable-dependency-tracking ...

FreeBSD 64-bit

CFLAGS="-O2 -m64"
export CFLAGS
./configure ...

Legacy systems

AIX 4.x 64-bit

CC=cc_r7
CFLAGS="-O -q64"
LDFLAGS="-brtl"
OBJECT_MODE=64
export CC CFLAGS LDFLAGS OBJECT_MODE
./configure ...

AIX 5.x 64-bit

CC=cc_r
CFLAGS="-O -q64"
LDFLAGS="-brtl"
OBJECT_MODE=64
export CC CFLAGS LDFLAGS OBJECT_MODE
./configure ...

Digital Unix/OSF1 V5.0 64-bit

CFLAGS="-O"
export CFLAGS
./configure ...

HP/UX 11.00 64-bit

CFLAGS="-O -Ae +DA2.0W"
export CFLAGS
./configure ...

HP/UX 11.23 Itanium 64-bit

CFLAGS="-O -Ae +DD64"
export CFLAGS
./configure ...

Solaris 2.10 Opteron 64-bit

CC=cc
CFLAGS="-O -xtarget=opteron -xarch=amd64"
PATH=/opt/SUNWspro/bin:/usr/ccs/bin:$PATH
export CFLAGS CC PATH
./configure ...

Solaris 2.8 and above SPARC 64-bit

CC=cc
CFLAGS="-O -xtarget=ultra -xarch=v9"
PATH=/opt/SUNWspro/bin:/usr/ccs/bin:$PATH
export CFLAGS CC PATH
./configure ...

Generic build environment

CC=cc
CFLAGS="-O"
export CC CFLAGS
./configure
make
make install

Installation From Source Code

After running configure && make,

make install

at the root of the build tree copies the files to the locations specified by the –prefix option to configure. The default of –prefix is /usr/local/. You can override this by specifying `make install prefix=/opt/virtuoso’ instead, for example.

These subdirectories are all appended to the specified prefix, i.e. /usr/local/ by default:

  • share/virtuoso/doc/html
  • share/virtuoso/doc/pdf
  • share/virtuoso/vad - VAD packages BPEL, Conductor, tutorials, documentation
  • var/lib/virtuoso/db - Empty database
  • var/lib/virtuoso/demo - Demo database - obsolete as of version 5.0.3
  • bin/ - The virtuoso-t, isql, isqlw, virt_mail, virtuoso-sample-t, inifile executables
  • lib/ - libvirtuoso-t.a libvirtuoso-t.la virtodbc32.a virtodbc32.la virtodbc32 r.a virtodbc32_r.la virtodbc_r.so wikiv.so, plus any plugins that may be enabled.
  • lib/virtuoso - hosting sample.a hosting_sample.la hosting_sample.so plugin_sample.a plugin_sample.so

Note: as of version 5.0.2, the ./configure script supports different subdirectory structures with the –with-layout= parameter. If you’ve specified something other than the default, the above may differ accordingly.

As of version 5.0.3, the demo is a VAD package, not a separate directory.

Installer Packages

If installation from source code isn't for you, simply download and install using any of the following:

Test Suite

Optionally, you can run

make check

at the root of the build tree to start the automated test suite. This takes about an hour on a 2GHz machine and requires approximately 1 GB of free disk space.

Getting Started

Run

cd var/lib/virtuoso/db 
virtuoso-t -f &

to start the server in the background. It will not detach from the shell, so you see the startup messages.

By default, when no -c parameter is specified, virtuoso will use the virtuoso.ini file in this directory, which is generated as part of `make install’.

The first time it’s run, it will create the empty database (no special commands required) and install the Conductor VAD package. From here, you can access http://localhost:8890/ and http://localhost:8890/conductor/ and use the System Administration / Packages page to install other packages such as Demo and the ODS suite (addressbook, weblog, feeds manager and other applications) etc.

The default login is dba' with a password ofdba’ for the Conductor and isql (for DAV functions, the default login is dav' with a password ofdav’).

You will see a checkpoint in the terminal for each package selected:

15:33:54 INFO: Checkpoint made, log reused

To connect with the command line SQL tool,

isql 1112 dba dba

gives a SQL> prompt.

If you’ve installed the demo VAD above, type SQL> use Demo;

to switch to the demo database, containing the Microsoft Northwind sample tables. The `help’ command in isql gives further instructions.

To use the web admin interface, point the browser to:

http://localhost:8890/conductor

To read the documents online:

http://localhost:8890/doc/html

To experiment with online tutorials you can use the conductor to install the Tutorial vad package into your database, then point the browser to:

http://localhost:8890/tutorial

VAD Packages

The different VAD packages can be installed via ISQL using the following command (if the installation packages reside in the filesystem):

SQL> vad_install ('file/system/path/package-name.vad', 0);

Alternatively, you can copy VAD packages to Virtuoso’s DAV repository and then execute the following command (also from ISQL):

SQL> vad_install ('webdav/path>/package-name.vad', 1);

at the isql command line.

Note: The DirsAllowed parameter of the Parameters section of the ini-file must allow access to the directory where the package file is located.

virtuoso-opensource's People

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virtuoso-opensource's Issues

Undefined procedure DB.DBA.RDF_QM_DEFINE_LITERAL_CLASS_WITH_FIXED_LANG

It is not possible to add language statements like "lang 'fr'" to quad map patterns. This raises the following error during the creation of the quad map pattern:
42001 SR185: Undefined procedure DB.DBA.RDF_QM_DEFINE_LITERAL_CLASS_WITH_FIXED_LANG.

It seems like this procedure still needs to be defined.

Some code to reproduce the error during the creation of the quadmap:

create table "BEL"."DBA"."BEL_ADMINUNITS"
(
"ID" INTEGER,
"STATBEL_code" INTEGER,
"upperLevelUnit" INTEGER,
"NUTS_code" VARCHAR,
"AdminUnit_nl" VARCHAR,
"AdminUnit_fr" VARCHAR,
"Level" INTEGER
);

sparql
prefix ex: http://example.com/
prefix locn: http://www.w3.org/ns/locn#
create iri class ex:statbel_code_iri "http://location.testproject.eu/so/au/AdministrativeUnit/STATBEL/%d" (in CODE integer not null) .
alter quad storage virtrdf:DefaultQuadStorage
from "BEL"."DBA"."STATBEL_ADMINUNITS" as AU
{
create ex:map_belgian_location_pilot as graph iri ("http://location.testproject.eu/BEL")
{
ex:statbel_code_iri(AU."STATBEL_code") a locn:Location, ex:AdministrativeUnit as ex:map_statbel_code_iri ;
ex:upperLevelUnit ex:statbel_code_iri(AU."upperLevelUnit") as ex:map_upperLevelUnit_iri ;
locn:geographicName AU."AdminUnit_nl" lang 'nl' as ex:map_AdminUnit_nl ;
locn:geographicName AU."AdminUnit_fr" lang 'fr' as ex:map_AdminUnit_fr .
}
};

SPARQL: filter and optional clause influencing bug

It seems as if the current SPARQL parser has a bug wrt. same level co-existence
of FILTER and OPTIONAL clauses. In the following example i would expect to get
all ?p ?o candidates for Einstein where ?o is an IRI and ?t never bound (the OPTIONAL should be
unmatched).

SELECT * WHERE {
    dbpedia:Albert_Einstein ?p ?o.
    FILTER(isIRI(?o))
    OPTIONAL { ?o <http://example.com/foo> ?t. }
}

If you run this against http://dbpedia.org/sparql it returns nothing: 1
Seems as if the filter clause changed the optional clause to be mandatory.
If you leave the filter part away you get a results as expected.

Here is a workaround based on double brackets:

SELECT * WHERE {
    {
        dbpedia:Albert_Einstein ?p ?o.
        FILTER(isIRI(?o))
    }
    OPTIONAL { ?o <http://example.com/foo> ?t. }
} LIMIT 10

It's a mean bug in bigger queries though :-/

gawk 4.0 Seems To Break sql_to_c.awk

I'm using Virtuoso in Gentoo Unstable.After updating to 6.1.4-r1 it stopped working for the following query:

sparql select distinct ?r where { ?r http://www.semanticdesktop.org/ontologies/2007/08/15/nao#identifier "c8ae2fe2-0a63-429d-9ad4-b63a5fad8619"^^http://www.w3.org/2001/XMLSchema#string. } LIMIT 1

with an error on sparql.sql, line 770. I examined the sources and noticed that file is used to autogenerate another file using gawk, I checked my gawk installations and I installed gawk 4.0 on Feb 12 and Apr 28, after installing virtuoso-server 6.1.4 on Dec 11, but before installing virtuoso-server 6.1.4-r1 on May 16. I then downgraded my gawk to 3.1.8 and reinstalled virtuoso-server 6.1.4-r1 and it is working fine again.

The issue seems to be related to single quotes escaping but I couldn't get any info from gawk man pages about version 4.0 changes on that matter.

SPARQL 1.1 Update: Delete and Insert in one query does not work

The example from W3C:

PREFIX dc: http://purl.org/dc/elements/1.1/
DELETE DATA
{ GRAPH http://example/bookStore { http://example/book1  dc:title  "Fundamentals of Compiler Desing" } } ;

PREFIX dc: http://purl.org/dc/elements/1.1/
INSERT DATA
{ GRAPH http://example/bookStore { http://example/book1  dc:title  "Fundamentals of Compiler Design" } }

does not work:

Virtuoso 37000 Error SP030: SPARQL compiler, line 7: syntax error at 'PREFIX' before 'dc:'

Even if I remove the prefix redefinition (which nevertheless should work), it does not work:

Virtuoso 37000 Error SQ074: Line 7: syntax error at 'INSERT' before 'DATA'

Even if I remove the semicolon between the two clauses, it does not work.

Separately, the clauses work.

Virtuoso compiled from source develop/6 branch, 10.3.2013, version from 7.3.2013

Query answer taking too much time

I'm executing a query with the following structure:

PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema#
PREFIx example: http://my.issue.example#
select ?item
WHERE
{
?item a example:certainType .
?item rdfs:label ?name .
FILTER ( (regex(STR(?name),"^text1$"))||
(regex(STR(?name),"^text2$"))||
(regex(STR(?name),"^text3$"))||
(regex(STR(?name),"^text4$"))||
(regex(STR(?name),"^text5$"))||
(regex(STR(?name),"^text6$"))||
(regex(STR(?name),"^text7$"))||
(regex(STR(?name),"^text8$"))||
(regex(STR(?name),"^text9$"))
)
}

This query works fine in Virtuoso 6, it takes little time. But if I run the same query, over the same data, in Virtuoso 7 (developer branch build May, 7, 2013), it seems to have no end while getting the results. No time error is displayed or any other kind of error. Could be that there is no index created for the labels?

problem with version

Hi,
I have installed virtuoso version 6.1.5 and from the terminal when i type virtuoso-t -? i get Version 6.1.5.3127-pthreads as of Jul 18 2012 but from my conductor i see that i have Version: 06.01.3127. When i try to install certain vad packages such as rdfb2rdf_vad i get a message that tells me to upgrade my version.

SPARQL "LOAD … INTO …" doesn't work in recent git-version

Seems like Major Regression

I just recompiled my test-environment and noticed, that LOAD <file:///path/to/dataset.ttl> INTO <http://example.com/graph> command doesn't work anymore.

I do queries against http://127.0.0.1:8890/sparql/ and get confirmation of success:

Load <file:///path/to/dataset.ttl> into graph <http://example.com/graph> -- done but data doesn't appear in triplestore. If I use http://127.0.0.1:8890/sparql-graph-crud form than data is uploaded successfully

Both approaches worked fine in build from 2013-01-18, which I used until now.

I wonder if it is related to recent changes to /sparql/ endpoint. I'll do some digging and will add comments when I find something

VOS7: csv import issue

After following the instructions here, i get that error:

SQL> csv_register('/home/user/Virtuoso/import-data', '*.csv');

Done. -- 1 msec.
SQL> csv_loader_run ();

*** Error 22023: [Virtuoso Driver][Virtuoso Server]SR022: Type for make_array must be float, double, long or any
at line 2 of Top-Level:
csv_loader_run ()

Any idea?

Thank you,
George

develop/6: Unable to get a buffer for a new page

Recently, this keeps happening on the up-to-date version of develop/6 when running multiple more complex SPARQL queries:

17:27:39 Failed to get a buffer for a new page. Retrying. If the failure repeats, an out of disk error will be signalled. The cause of this is having too many buffers wired down for preread, flush or group by/hash join temp space. To correct, increase the number of buffers in the configuration file. If this repeats in spite of having hundreds of thousands of buffers, please report to support.

17:27:40 Signaling out of disk due to failure to get a buffer. This condition is not a case of running out of disk

Possible overflow in http_client.c

I am not particularly familiar with the code in question to say either way, but this warning sometimes indicates a potential security problem.

In function 'strncat', inlined from 'http_cli_negotiate_socks4' at http_client.c:426:15: /usr/include/bits/string3.h:152:3: warning: call to __builtin___strncat_chk might overflow destination buffer

Feature request: SPIN support

Looking at the mailing list, SPIN support is desired, and is claimed to be on the roadmap, which I can't seem to find on the OL wiki.

What is the plan for supporting this?

I am not much of a Java programmer: what can the community do to help support this coming to pass?

background

SPIN provides a much richer set of inference rules than SWRL, and, imho, lack of a solid SPIN implementation is one roadblock to widespread use of open source semantic web technology. The win here is being able to move more of your business logic into the data layer, and makes your constraints themselves inferrable... basically a mix between stored procedures, views and other handy things from RDBMS-land. One of the killer features is templates, which let you build reusable constraint bits.

Here is the reference API (note much of it is proprietary).

Unable to run Virtuoso 7 stable version

Hi,

I have downloaded the latest Virtuoso 7 Stable version, 1e7b4b7, and install it in an Ubuntu Server 12 64 bits edition.

Before the installation, I have downloaded all the dependencies needed and followed all the steps for the installation. When I run "make check" for ensuring that the installation process finished properly, test_server.sh script fails. In the console output, it's said that I should check some *.output files. In testall.output, it's indicated that some tests were aborted: nwxml.sh, trecov.sh, trecov_schema.sh, tnwords.sql and tsqlo.sql and one failed, thttp.sh:

nwxml.output:_ABORTED: nwxml.sh: nwxml.sql functions
thttp.output:
_FAILED: DBSCHEMA_COLUMNS : LAST[4]=Out_of_Bounds(0)
trecov.output:_ABORTED: trecov.sh: Connect failed after log roll forward
trecov_schema.output:
_ABORTED: trecov_schema.sh: Connect failed after -d roll forward
tsql.output:_ABORTED: nvarchar Wordtest -- tnwords.sql
tsqlo.output:
_ABORTED: tsqlo.sql: SQL optimizer functions

If I try to run the Virtuoso instance, an error is displayed on the screen "The VDBMS server process terminated prematurely after opening the database" but not in virtuoso.log file:

    Thu May 09 2013

13:20:13 { Loading plugin 1: Type plain', filewikiv' in /opt/virtuoso-7/default/lib/virtuoso/hosting' 13:20:13 WikiV version 0.6 from OpenLink Software 13:20:13 Support functions for WikiV collaboration tool 13:20:13 SUCCESS plugin 1: loaded from /opt/virtuoso-7/default/lib/virtuoso/hosting/wikiv.so } 13:20:13 { Loading plugin 2: Typeplain', file mediawiki' in/opt/virtuoso-7/default/lib/virtuoso/hosting'
13:20:13 MediaWiki version 0.1 from OpenLink Software
13:20:13 Support functions for MediaWiki collaboration tool
13:20:13 SUCCESS plugin 2: loaded from /opt/virtuoso-7/default/lib/virtuoso/hosting/mediawiki.so }
13:20:13 { Loading plugin 3: Type plain', filecreolewiki' in `/opt/virtuoso-7/default/lib/virtuoso/hosting'
13:20:13 CreoleWiki version 0.1 from OpenLink Software
13:20:13 Support functions for CreoleWiki collaboration tool
13:20:13 SUCCESS plugin 3: loaded from /opt/virtuoso-7/default/lib/virtuoso/hosting/creolewiki.so }
13:20:13 OpenLink Virtuoso Universal Server
13:20:13 Version 07.00.3201-pthreads for Linux as of May 9 2013
13:20:13 uses parts of OpenSSL, PCRE, Html Tidy
13:20:13 Database version 3126
13:20:13 SQL Optimizer enabled (max 1000 layouts)
13:20:14 Compiler unit is timed at 0.000801 msec
13:20:15 Roll forward started
13:20:15 Roll forward complete
13:20:16 PL LOG: Installing Virtuoso Conductor version 1.00.7920 (DAV)
13:20:16 Checkpoint started
13:20:17 Checkpoint finished, log reused

Any clue about the possible solution for this error or the error source?

Thanks in advance.

VOS7: Deadlock: Write wait on column page <number>. Waits should be on the index leaf page, except when col page is held for read by background write

I get this messages trying to load the LinkedGeoData data sets (especially the _.ways._ ones, that contain long linestrings) at

http://downloads.linkedgeodata.org/releases/2013-04-29/

Most of time it seems the DB can recover, but at some point it seems to result in a deadlock and only a kill -9 can bring the DB down.
Afterwards, I have to remove the transaction log, otherwise upon replay it will again run into the deadlock.
Seems like it is somehow related to large objects (e.g. polygons) exceeding page boundaries.

My virtuoso.ini is configured for 4 GB RAM and the virtuoso.db file is about 16GB; but I think the deadlock problem is rather independent of the db file size.

With point geometries this problem also happens, but much less frequent.

Note on loading the datasets: For Virtuoso, you need to do a little conversion (the awk part is there to experiment by filtering lines by length):

bzcat "$file" | ./convert-virtuoso.sh | ./discard-corrupted-geometries.sh | awk 'length<2048' > "$tmp"

The scripts (just sed - 1-liners) are available here:

http://downloads.linkedgeodata.org/releases/scripts/

UTF-8 Encoding Problem in SPARQL Select Results XML and RDF/XML

I'm using Version: 06.01.3127, Build: Aug 7 2012, compiled from version 6.1.6 available to download from SourceForge on a Debian.

I'm experiencing issues with some characters when performing SPARQL queries using the SPARQL endpoint using the XML or RDF/XML output. I have loaded a RDF/XML file using UTF8 and the SPARQL results are fine when output format is HTML but not when the output is XML or RDF/XML.

For instance, for the query:

http://omediadis.udl.cat:8890/sparql?default-graph-uri=http%3A%2F%2Fwww.diei.udl.cat%2F&query=SELECT+*+WHERE+%7B+%3Chttp%3A%2F%2Fwww.diei.udl.cat%2Fperson%2FClariaF%3E+%3Fp+%3Fo+%7D&format=application%2Fsparql-results%2Bxml

I get, among other things, the following:
<binding name="o"><literal>Clarià, F.</literal></binding>

Where the literal should be "Clariá".

It doesn't work either for RDF/XML but it works fine if the format is text/html.

This seems to be happening just for SELECT queries. For DESCRIBE queries like the following and RDF/XML output the UTF8 encoding is correct:

http://omediadis.udl.cat:8890/sparql?default-graph-uri=http%3A%2F%2Fwww.diei.udl.cat%2F&query=DESCRIBE+%3Chttp%3A%2F%2Fwww.diei.udl.cat%2Fperson%2FClariaF%3E&format=application%2Frdf%2Bxml

Error during the "isparql_dav.vad" installation step (branch develop/7)

Hi,

During the compilation of the develop/7 branch. I fall on this error (from the log file) :

Cleaning the vad directory
Creating the vad directory
Virtuoso.ini creation...
PASSED: virtuoso successfully started on port 1111
iSPARQL VAD sticker creation...

  • isql localhost:1111 dba dba ERRORS=STDOUT VERBOSE=OFF PROMPT=OFF EXEC=DB.DBA.VAD_PACK('make_isparql_vad.xml', '.', 'isparql_dav.vad')
    ***FAILED: starting DB.DBA.VAD_PACK('make_isparql_vad.xml', '.', 'isparql_dav.vad')
  • isql localhost:1111 dba dba ERRORS=STDOUT VERBOSE=OFF PROMPT=OFF EXEC=commit work
    ***FAILED: starting commit work
  • isql localhost:1111 dba dba ERRORS=STDOUT VERBOSE=OFF PROMPT=OFF EXEC=checkpoint
    ***FAILED: starting checkpoint
    Shutdown localhost:1111 ...
    Cleaning the vad directory

= Checking log file /home/julien-plu/virtuoso-opensource/binsrc/isparql/make_isparql_vad.log for statistics:

= Total number of tests PASSED : 1
= Total number of tests FAILED : 3

= Total number of tests ABORTED : 0

*** Not all tests completed successfully
*** Check the file /home/julien-plu/virtuoso-opensource/binsrc/isparql/make_isparql_vad.log for more information

  • egrep "**._FAILED:|_*.*ABORTED:" /home/julien-plu/virtuoso-opensource/binsrc/isparql/make_isparql_vad.log

= COMPLETED VAD PACKAGING

= Fri Apr 26 12:16:38 CEST 2013

Is-it normal ? Or is-it a bug ?

Best.

Julien.

erroneous 405 response code for invalid SPARQL syntax

$ cat query.sparql
INSERT IN GRAPH <http://example.org> {
    <http://example.org/cat> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2009/08/skos-reference/skos.html#Concept>
    <http://example.org/cat> <http://www.w3.org/2009/08/skos-reference/skos.html#related> <http://example.com/dog> .
}

$  curl -i -d @query.sparql -u "fnd:..." -H "Content-Type: application/sparql-query" http://myhost.com/DAV/home/fnd/query
HTTP/1.1 405 Method Not Allowed
Server: nginx/0.7.67
Date: Wed, 10 Oct 2012 06:08:15 GMT
Content-Type: text/html; charset=UTF-8
Connection: keep-alive
Accept-Ranges: bytes
Content-Length: 0

(note that the first triple is missing a trailing dot)

It seems like 405 is a misleading response here.

Specify "Base URI" in BulkLoader

Currently, there is no way to specify "base uri" for interpretation of rdf-file and BulkLoader just uses name of the graph as the base uri, which is not always desired.

Would be really good to have optional parameter to ld_dir and ld_dir_all for overriding the base-name

SPARQL: ORDER BY not working with DESCRIBE queries

When issuing queries against any graph, ORDER BY is ignored in DESCRIBE queries whereas it works with SELECT queries.

See: http://dbpedia.org/sparql

This query delivers results in arbitrary order:

DESCRIBE ?s
WHERE
{
?s ?p ?o .
?s http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dbpedia.org/ontology/Place .
?s http://www.w3.org/2000/01/rdf-schema#label ?label .
?label bif:contains "Am" .
}
ORDER BY ?label
LIMIT 1000

Whereas this query delivers correctly ordered results:

SELECT ?s
WHERE
{
?s ?p ?o .
?s http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dbpedia.org/ontology/Place .
?s http://www.w3.org/2000/01/rdf-schema#label ?label .
?label bif:contains "Am" .
}
ORDER BY ?label
LIMIT 1000

unable to delete graph with URL-encoded characters

Following the HTTP POST examples, I managed to create a graph with the following name:

http://myhost.com:8890%2FDAV%2Fhome%2Ffnd%2Fquery

(as displayed in Virtuoso Conductor under RDF > Graphs)

Deleting this graph via the Conductor UI doesn't work, executing a SPARQL query (via /sparql) with this as Graph IRI returns an empty result set.

Presumably this is due to the URL-encoded characters in the graph name. However, escaping the percentage signs (to %25) in a manual CLEAR GRAPH query did not work either.

develop/7: Install on Ubuntu

Hello!

I am trying to install the branch develop7 locally on a ubuntu 13.04 32 bit, but i cant get it to work.

This is what i did:

  1. Download zip from here. Branch develop/7
  2. read the readme from here.
  3. ran ./autogen.sh from root folder, no errors (installed dependencies previously)
    -> "Bootstrap script completed successfully".
  4. ran ./configure then make then make install
    ./configure:
Virtuoso Open Source Edition (Column Store) 7.0.0-rc2 configuration summary
===========================================================================

Installation variables
  layout                  default
  prefix                  /usr/local/virtuoso-opensource
  exec_prefix             ${prefix}

Installation paths
  programs                ${exec_prefix}/bin
  include files           ${prefix}/include
  libraries               ${exec_prefix}/lib
  manual pages            ${datarootdir}/man
  vad packages            ${datarootdir}/virtuoso/vad
  database                ${prefix}/var/lib/virtuoso/db
  hosting                 ${exec_prefix}/lib/virtuoso/hosting

Options
  BUILD_OPTS               xml ssl imsg pldebug pthreads

make:

=  CREATING VAD PACKAGE FOR VIRTUOSO CONDUCTOR (mkvad.sh)
=  Tue Jun 4 15:52:39 CEST 2013

cp: omitting directory 'images/dav_browser'
cp: omitting directory 'images/icons'
cp: omitting directory 'help'
cp: omitting directory 'images'
cp: omitting directory 'syntax'
cp: omitting directory 'vad'
cp: cannot stat '/home/ds/Downloads/virtuoso-opensource-develop-7/binsrc/oat/toolkit/images/*': No such file or directory
VAD Sticker vad_fs.xml creation...
VAD Sticker vad_dav.xml creation...
Starting Virtuoso server ...
The VDBMS server process terminated prematurely
after opening the database.
***FAILED: Could not start Virtuoso Server within 120 seconds
make[2]: *** [conductor_dav.vad] Error 1
make[2]: Leaving directory `/home/ds/Downloads/virtuoso-opensource-develop-7/binsrc/yacutia'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/ds/Downloads/virtuoso-opensource-develop-7/binsrc'
make: *** [all-recursive] Error 1
  1. make install:

Making install in .
make[1]: Entering directory `/home/ds/Downloads/virtuoso-opensource-develop-7'
make[2]: Entering directory `/home/ds/Downloads/virtuoso-opensource-develop-7'
make[2]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/usr/local/virtuoso-opensource/share/virtuoso/doc'
/bin/mkdir: cannot create directory ‘/usr/local/virtuoso-opensource’: Permission denied
make[2]: *** [install-dist_docDATA] Error 1
make[2]: Leaving directory `/home/ds/Downloads/virtuoso-opensource-develop-7'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/ds/Downloads/virtuoso-opensource-develop-7'
make: *** [install-recursive] Error 1

any help appreciated :)

VOS develop/7 returns string instead of URI with ORDER BY

With the latest develop/7 sources (commit 8dc86c4) and under OS/X 10.6.8, string literals, instead of URIs, are returned from SPARQL queries. The query:

SELECT * FROM <http://www.openlinksw.com/schemas/virtrdf#>
WHERE { ?s a ?t }

correctly returns rows in the form:

result: [s=uri<http://www.openlinksw.com/virtrdf-data-formats#sql-varchar-literal-nullable>, t=uri<http://www.openlinksw.com/schemas/virtrdf#QuadMapFormat>]

However adding ORDER BY ?s, so the query becomes:

SELECT * FROM <http://www.openlinksw.com/schemas/virtrdf#>
WHERE { ?s a ?t }
ORDER BY ?s

returns the subject as a string:

result: [s=string("http://www.openlinksw.com/virtrdf-data-formats#sql-varchar-literal-nullable"), t=uri<http://www.openlinksw.com/schemas/virtrdf#QuadMapFormat>]

All is well if ORDER BY is followed by LIMIT.

Problem uploading files to DAV collection

I'm using Virtuoso 7, developer branch build May, 7, 2013.

I have created a DAV collection, with a specific user for that collection, with the proper permissions and I tried to upload files to that DAV collection. I made HTTP PUT requests to upload RDF files as it's described here [1]. It works fine when the file has a small size, less than 5-6 mb, but it doesn't for files greater. Those files are stored in the DAV collection created but they are not uploaded to the DDBB. No error is displayed in the log file and I get a HTTP 201 Created message after uploading the file.

I don't know whether is an error in the configuration of the user or in the Virtuoso parameters. I have checked user permissions and size limitation, unlimited for the user, and I haven't seen anything unsual.

[1] http://docs.openlinksw.com/virtuoso/rdfinsertmethods.html#rdfinsertmethodshttppost

virtuoso-t segfaults (page read with no key defd)

Virtuoso 6.1.6 doesn't start anymore on my system (Arch Linux).
Ask for any info you need, backtrace is attached.

$ virtuoso-t +foreground +wait 09:06:14 virtuoso-t() [0x443179] 09:06:14 GPF: insert.c:151 page read with no key defd GPF: insert.c:151 page read with no key defd [1] 19017 segmentation fault (core dumped) virtuoso-t +foreground

#1  0x00000000004aef51 in pg_make_map (buf=0x7ffff7f23808) at insert.c:151
#2  0x00000000004667db in buf_disk_read (buf=0x7ffff7f23808) at disk.c:1838
#3  0x000000000047ae09 in page_wait_access (itc=0x7fffffff6620, dp=3474, buf_from=0x7ffff7f8b808, buf_ret=0x7fffffff4fb8, mode=1, max_change=1) at gate.c:191
#4  0x000000000047d6db in itc_landed_down_transit (itc=0x7fffffff6620, buf_ret=0x7fffffff4fb8, to=3474) at gate.c:949
#5  0x000000000050c77a in itc_search (it=0x7fffffff6620, buf_ret=0x7fffffff4fb8) at search.c:1701
#6  0x000000000050ce65 in itc_next (it=0x7fffffff6620, buf_ret=0x7fffffff4fb8) at search.c:1826
#7  0x0000000000511852 in itc_sample_next (itc=0x7fffffff6620, buf_ret=0x7fffffff4fb8) at search.c:3407
#8  0x0000000000511bee in itc_sample_1 (it=0x7fffffff6620, buf_ret=0x7fffffff4fb8, n_leaves_ret=0x7fffffff4fc0, angle=-1) at search.c:3483
#9  0x00000000005124e5 in itc_local_sample (itc=0x7fffffff6620) at search.c:3633
#10 0x0000000000512978 in itc_sample (itc=0x7fffffff6620) at search.c:3678
#11 0x000000000057dee0 in sqlo_inx_sample_1 (tb_dfe=0x1a8a030, key=0x1561f10, lowers=0x7fffffff7e90, uppers=0x7fffffff7e60, n_parts=1, sop=0x7fffffff7d00,

ic=0x7fffffff8100) at sqlcost.c:1359

#12 0x000000000057ec7d in sqlo_inx_sample (tb_dfe=0x1a8a030, key=0x1561f10, lowers=0x7fffffff7e90, uppers=0x7fffffff7e60, n_parts=1, ic=0x7fffffff8100) at sqlcost.c:1647
#13 0x00000000005807c4 in dfe_table_cost_ic_1 (dfe=0x1a8a030, ic=0x7fffffff8100, inx_only=0) at sqlcost.c:2083
#14 0x0000000000581251 in dfe_table_cost_ic (dfe=0x1a8a030, ic=0x7fffffff8100, inx_only=0) at sqlcost.c:2209
#15 0x0000000000593255 in sqlo_choose_index (so=0x1a80658, tb_dfe=0x1a8a030, col_preds=0x7fffffff81e8, after_preds=0x7fffffff8200) at sqldf.c:3145
#16 0x0000000000595a26 in sqlo_tb_col_preds (so=0x1a80658, tb_dfe=0x1a8a030, preds=0x1a8c068, nj_preds=0x0) at sqldf.c:3703
#17 0x00000000005a0207 in sqlo_place_table (so=0x1a80658, tb_dfe=0x1a8a030) at sqldf.c:4615
#18 0x00000000005a44be in sqlo_try (so=0x1a80658, ot=0x1a80b68, dfes=0x1a8a160, in_loop_ret=0x7fffffff84a0, score_ret=0x7fffffff8480) at sqldf.c:5772
#19 0x00000000005a49ee in sqlo_layout_1 (so=0x1a80658, ot=0x1a80b68, is_top=1) at sqldf.c:5870
#20 0x00000000005a5d56 in sqlo_layout (so=0x1a80658, ot=0x1a80b68, is_top=1, super=0x1a8ba00) at sqldf.c:6138
#21 0x000000000058f897 in sqlo_place_dt_leaf (so=0x1a80658, tb_dfe=0x1a88520, dt_dfe=0x1a89dc0, preds=0x0) at sqldf.c:2253
#22 0x000000000058fc4d in sqlo_place_dt_set (so=0x1a80658, tb_dfe=0x1a88520, dt_dfe=0x1a89dc0, preds=0x0) at sqldf.c:2316
#23 0x000000000058fcf7 in sqlo_place_dt_set (so=0x1a80658, tb_dfe=0x1a88520, dt_dfe=0x1a88668, preds=0x0) at sqldf.c:2323
#24 0x000000000059189b in sqlo_place_dt (so=0x1a80658, tb_dfe=0x1a88520, preds=0x0) at sqldf.c:2726
#25 0x000000000059ffea in sqlo_place_table (so=0x1a80658, tb_dfe=0x1a88520) at sqldf.c:4567
#26 0x00000000005a44be in sqlo_try (so=0x1a80658, ot=0x1a80970, dfes=0x1a88650, in_loop_ret=0x7fffffff8980, score_ret=0x7fffffff8960) at sqldf.c:5772
#27 0x00000000005a49ee in sqlo_layout_1 (so=0x1a80658, ot=0x1a80970, is_top=1) at sqldf.c:5870
#28 0x00000000005a5d56 in sqlo_layout (so=0x1a80658, ot=0x1a80970, is_top=1, super=0x1a8b510) at sqldf.c:6138
#29 0x000000000058f897 in sqlo_place_dt_leaf (so=0x1a80658, tb_dfe=0x1a88168, dt_dfe=0x1a88168, preds=0x0) at sqldf.c:2253
#30 0x000000000059185b in sqlo_place_dt (so=0x1a80658, tb_dfe=0x1a88168, preds=0x0) at sqldf.c:2721
#31 0x000000000059ffea in sqlo_place_table (so=0x1a80658, tb_dfe=0x1a88168) at sqldf.c:4567
#32 0x00000000005a44be in sqlo_try (so=0x1a80658, ot=0x1a80778, dfes=0x1a88298, in_loop_ret=0x7fffffff8da0, score_ret=0x7fffffff8d80) at sqldf.c:5772
#33 0x00000000005a49ee in sqlo_layout_1 (so=0x1a80658, ot=0x1a80778, is_top=2) at sqldf.c:5870
#34 0x00000000005a5d56 in sqlo_layout (so=0x1a80658, ot=0x1a80778, is_top=2, super=0x0) at sqldf.c:6138
#35 0x00000000005a7362 in sqlo_top_2 (so=0x1a80658, sc=0x7fffffff99c0, ptree=0x7fffffff9830) at sqldf.c:6531
#36 0x00000000005a881d in sqlo_top_1 (so=0x1a80658, sc=0x7fffffff99c0, ptree=0x7fffffff9830) at sqldf.c:6782
#37 0x00000000005a92c5 in sqlo_top_select (sc=0x7fffffff99c0, ptree=0x7fffffff9830) at sqldf.c:6926
#38 0x0000000000570db1 in sql_stmt_comp (sc=0x7fffffff99c0, ptree=0x7fffffff9830) at sqlcomp2.c:934
#39 0x0000000000572b2d in sql_compile_1 (

string2=0x1a762b8 "select DB.DBA.VECTOR_AGG (\nvector (\nid_to_iri ("jclass"),\nid_to_iri ("jinst"),\ncoalesce ("s", "jinst") ) )\nfrom ( sparql\ndefine output:valmode "LONG"\ndefine input:storage ""\nselect ?jclass ?jinst ?s\nw"..., cli=0x13a5060, err=0x7fffffffae78, cr_type=0, the_parse_tree=0x0, view_name=0x0) at sqlcomp2.c:1542

#40 0x00000000005735d2 in sql_compile (

string2=0x1a762b8 "select DB.DBA.VECTOR_AGG (\nvector (\nid_to_iri ("jclass"),\nid_to_iri ("jinst"),\ncoalesce ("s", "jinst") ) )\nfrom ( sparql\ndefine output:valmode "LONG"\ndefine input:storage ""\nselect ?jclass ?jinst ?s\nw"..., cli=0x13a5060, err=0x7fffffffae78, cr_type=0) at sqlcomp2.c:1710

#41 0x0000000000560063 in bif_exec (qst=0x7fffffffb6a0, err_ret=0x7fffffffafa0, args=0x1a764d8) at sqlbif.c:12359
#42 0x00000000005c81be in ins_call_bif (ins=0x1a765d0, qst=0x7fffffffb6a0, code_vec=0x1a76578) at sqlintrp.c:178
#43 0x00000000005cdd80 in code_vec_run_1 (code_vec=0x1a76578, qst=0x7fffffffb6a0, offset=0) at sqlintrp.c:1896
#44 0x000000000060164f in qn_input (xx=0x1a767a0, inst=0x7fffffffb6a0, state=0x7fffffffb6a0) at sqlrun.c:680
#45 0x000000000060bc00 in qr_subq_exec (cli=0x13a5060, qr=0x1a75f00, caller=0x7fffffffc0c0, auto_qi=0x7fffffffb6a0, auto_qi_len=792, lc=0x0, parms=0x7fffffffb4d8,

opts=0x0) at sqlrun.c:3544

#46 0x00000000005c9305 in ins_call (ins=0x1a74d28, qst=0x7fffffffc0c0, code_vec=0x1a74cc8) at sqlintrp.c:453
#47 0x00000000005cdd49 in code_vec_run_1 (code_vec=0x1a74cc8, qst=0x7fffffffc0c0, offset=0) at sqlintrp.c:1892
#48 0x000000000060164f in qn_input (xx=0x1a75720, inst=0x7fffffffc0c0, state=0x7fffffffc0c0) at sqlrun.c:680
#49 0x000000000060bc00 in qr_subq_exec (cli=0x13a5060, qr=0x1a738a0, caller=0x7fffffffcae0, auto_qi=0x7fffffffc0c0, auto_qi_len=792, lc=0x0, parms=0x7fffffffbef8,

opts=0x0) at sqlrun.c:3544

#50 0x00000000005c9305 in ins_call (ins=0x1a71790, qst=0x7fffffffcae0, code_vec=0x1a716f8) at sqlintrp.c:453
#51 0x00000000005cdd49 in code_vec_run_1 (code_vec=0x1a716f8, qst=0x7fffffffcae0, offset=0) at sqlintrp.c:1892
#52 0x000000000060164f in qn_input (xx=0x1a71820, inst=0x7fffffffcae0, state=0x7fffffffcae0) at sqlrun.c:680
#53 0x000000000060bc00 in qr_subq_exec (cli=0x13a5060, qr=0x1a71170, caller=0x7fffffffd500, auto_qi=0x7fffffffcae0, auto_qi_len=792, lc=0x0, parms=0x7fffffffc918,

opts=0x0) at sqlrun.c:3544

#54 0x00000000005c9305 in ins_call (ins=0x1a79530, qst=0x7fffffffd500, code_vec=0x1a794c8) at sqlintrp.c:453
#55 0x00000000005cdd49 in code_vec_run_1 (code_vec=0x1a794c8, qst=0x7fffffffd500, offset=0) at sqlintrp.c:1892
#56 0x000000000060164f in qn_input (xx=0x1a79590, inst=0x7fffffffd500, state=0x7fffffffd500) at sqlrun.c:680
#57 0x000000000060bc00 in qr_subq_exec (cli=0x13a5060, qr=0x1a70e40, caller=0x1a4f9d8, auto_qi=0x7fffffffd500, auto_qi_len=792, lc=0x0, parms=0x7fffffffd338, opts=0x0)

at sqlrun.c:3544

#58 0x00000000005c9305 in ins_call (ins=0x1a601d8, qst=0x1a4f9d8, code_vec=0x1a601d8) at sqlintrp.c:453
#59 0x00000000005cdd49 in code_vec_run_1 (code_vec=0x1a601d8, qst=0x1a4f9d8, offset=0) at sqlintrp.c:1892
#60 0x000000000060164f in qn_input (xx=0x1a64810, inst=0x1a4f9d8, state=0x1a4f9d8) at sqlrun.c:680
#61 0x000000000060a2fb in qr_exec (cli=0x13a5060, qr=0x1a64b10, caller=0x1, cr_name=0x0, stmt=0x0, lc_ret=0x0, parms=0x1a3e528, opts=0x0, named_params=1)

at sqlrun.c:3184

#62 0x000000000060c8c6 in qr_quick_exec (qr=0x1a64b10, cli=0x13a5060, id=0xa0642a "", lc_ret=0x0, n_pars=0) at sqlrun.c:3742
#63 0x000000000045688b in ddl_ensure_table (name=0xb75006 "do this always", text=0xb74f00 "DB.DBA.RDF_INIT_SINGLE_SERVER ()\n") at ddlrun.c:1823
#64 0x00000000006d62bd in sqls_define_sparql_init () at sql_code_sparql_init.c:1455
#65 0x0000000000618848 in srv_global_init (mode=0xa03350 "") at sqlsrv.c:3929
#66 0x00000000004489f6 in main (argc=3, argv=0x130f770) at viunix.c:668```

VOS6: Compilation issue

Hi,
I have compiled VOS7 successfully ("develop/7" branch) in Ubuntu 13.04 amd64 but the "develop/6" branch fails with the following error during make (after running make clear, configure, autogen):

libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../libsrc/Dk -fno-strict-aliasing -O2 -Wall -DNDEBUG -DPOINTER_64 -I/home/user/Virtuoso/virtuoso-opensource/libsrc/Xml.new -DOPENSSL_NO_KRB5 -Dlinux -D_GNU_SOURCE -DFILE64 -D_LARGEFILE64_SOURCE -D_GNU_SOURCE -DGLOBALREF=extern -D_USRDLL -I../../libsrc -I../../libsrc/Dk -I../../libsrc/zlib -I../../libsrc/langfunc -I../../libsrc/plugin -I../../libsrc/Xml.new -I../../libsrc/Wi -I../../libsrc/odbcsdk/include -O2 -m64 -MT libplugin_la-export_gate_virtuoso.lo -MD -MP -MF .deps/libplugin_la-export_gate_virtuoso.Tpo -c export_gate_virtuoso.c  -fPIC -DPIC -o .libs/libplugin_la-export_gate_virtuoso.o
In file included from ../Wi/rdf_mapping_jso.h:26:0,
             from ../Wi/rdf_core.h:29,
             from export_gate_virtuoso.c:53:
../Wi/jso.h:89:43: warning: 'struct jso_rtti_s' declared inside parameter list [enabled by default]
../Wi/jso.h:89:43: warning: its scope is only this definition or declaration, which is probably not what you want [enabled by default]
export_gate_virtuoso.c:91:6: error: 'bif_arg_unrdf_ext' undeclared here (not in a function)
export_gate_virtuoso.c:97:6: error: 'bif_dc_arg' undeclared here (not in a function)
export_gate_virtuoso.c:160:6: error: 'box_strong_equal' undeclared here (not in a function)
export_gate_virtuoso.c:299:6: error: 'mp_box_double' undeclared here (not in a function)
export_gate_virtuoso.c:303:6: error: 'mp_box_float' undeclared here (not in a function)
export_gate_virtuoso.c:349:6: error: 'sqlr_set_cbk_name_and_proc' undeclared here (not in a function)
make[1]: *** [libplugin_la-export_gate_virtuoso.lo] Error 1
make[1]: Leaving directory `/home/user/Virtuoso/virtuoso-    opensource/libsrc/plugin'
make: *** [all] Error 2

Also, i run make under /home/user/Virtuoso/virtuoso-opensource/libsrc/plugin but there is no logfile i can look at. Any ideas?

Thank you,
George

FILTER concatenation doesn't work with sameTerm

If you import the following minimal model to virtuoso

@prefix ex: <http://example.com/> .

ex:a a ex:A .
ex:b a ex:B .

and run this query

SELECT ?i
WHERE {
    ?i a ?class.
    FILTER (sameTerm(?class, <http://example.com/A>) || sameTerm(?class, <http://example.com/B>))
}

the expected result would be that ?i is bound to ex:a and ex:b but the result set will be empty.

While the following queries are working as expected

SELECT ?i
WHERE {
    ?i a ?class.
    FILTER (sameTerm(?class, <http://example.com/A>))
}

SELECT ?i
WHERE {
    ?i a ?class.
    FILTER (?class = <http://example.com/A> || ?class = <http://example.com/B>)
}

Faceted Browser Raw Data extracts data only from a single named graph

fct 1.13.11

When trying to download displayed data by clicking on Raw Data on the bottom of the faceted browser, only data from one graph is present. Data from other graphs which are displayed by the fct browser is missing.

Suggested fix: Add support for TRIG and in formats without named graph support merge all displayed data into the raw data output (maybe this could be optional).

Not able to load large Turtle files in V7

Virtuoso 7
commit a9356b9c8a52d5ce7ac1864df922ce46c67acd2f (April 25)

When loading large files (2GB) using DB.DBA.TTLP_MT (file_to_string_output ('filename'), '', 'graphname');
virtuoso eventually either hangs (CPU usage 100% for a looong time but nothing happens) or it says Transaction deadlocked.

In virtuoso.ini:

;; Uncomment next two lines if there is 8 GB system memory free
       NumberOfBuffers          = 680000
       MaxDirtyBuffers          = 500000

the machine has 8GB of RAM.

In the log:

21:41:29 Write wait on column page 69382.  Waits should be on the index leaf page, except when col page is held for read by background write
21:41:39 Failed to get a buffer for a new page. Retrying.  If the failure repeats, an out of disk error will be signalled.  The cause of this is having too many buffers wired down for preread, flush or group by/hash join temp space.  To correct, increase the number of buffers in the configuration file.  If this repeats in spite of having hundreds of thousands  of buffers, please report to support.
21:41:50 Write wait on column page 4355.  Waits should be on the index leaf page, except when col page is held for read by background write
21:41:50 Write wait on column page 66409.  Waits should be on the index leaf page, except when col page is held for read by background write
21:41:50 Write wait on column page 69420.  Waits should be on the index leaf page, except when col page is held for read by background write
21:41:50 Failed to get a buffer for a new page. Retrying.  If the failure repeats, an out of disk error will be signalled.  The cause of this is having too many buffers wired down for preread, flush or group by/hash join temp space.  To correct, increase the number of buffers in the configuration file.  If this repeats in spite of having hundreds of thousands  of buffers, please report to support.
21:41:50 Failed to get a buffer for a new page. Retrying.  If the failure repeats, an out of disk error will be signalled.  The cause of this is having too many buffers wired down for preread, flush or group by/hash join temp space.  To correct, increase the number of buffers in the configuration file.  If this repeats in spite of having hundreds of thousands  of buffers, please report to support.
21:41:50 Failed to get a buffer for a new page. Retrying.  If the failure repeats, an out of disk error will be signalled.  The cause of this is having too many buffers wired down for preread, flush or group by/hash join temp space.  To correct, increase the number of buffers in the configuration file.  If this repeats in spite of having hundreds of thousands  of buffers, please report to support.
21:41:56 Write wait on column page 66408.  Waits should be on the index leaf page, except when col page is held for read by background write
21:41:56 Write wait on column page 69410.  Waits should be on the index leaf page, except when col page is held for read by background write
21:41:56 Write wait on column page 98049.  Waits should be on the index leaf page, except when col page is held for read by background write
21:41:56 Failed to get a buffer for a new page. Retrying.  If the failure repeats, an out of disk error will be signalled.  The cause of this is having too many buffers wired down for preread, flush or group by/hash join temp space.  To correct, increase the number of buffers in the configuration file.  If this repeats in spite of having hundreds of thousands  of buffers, please report to support.
21:41:56 Failed to get a buffer for a new page. Retrying.  If the failure repeats, an out of disk error will be signalled.  The cause of this is having too many buffers wired down for preread, flush or group by/hash join temp space.  To correct, increase the number of buffers in the configuration file.  If this repeats in spite of having hundreds of thousands  of buffers, please report to support.
21:42:08 Write wait on column page 45307.  Waits should be on the index leaf page, except when col page is held for read by background write
21:42:14 Write wait on column page 4377.  Waits should be on the index leaf page, except when col page is held for read by background write
21:42:14 Write wait on column page 4620.  Waits should be on the index leaf page, except when col page is held for read by background write
21:42:14 Write wait on column page 69486.  Waits should be on the index leaf page, except when col page is held for read by background write
21:42:14 Write wait on column page 98100.  Waits should be on the index leaf page, except when col page is held for read by background write
21:42:14 Write wait on column page 105993.  Waits should be on the index leaf page, except when col page is held for read by background write
21:42:14 Write wait on column page 66423.  Waits should be on the index leaf page, except when col page is held for read by background write
21:42:14 Write wait on column page 69425.  Waits should be on the index leaf page, except when col page is held for read by background write

develop/7 missing implementation for clrdf.c/cl_id_to_iri

I loaded a million or so skos triples and then trying to index them with:

SQL> RDF_OBJ_FT_RULE_ADD(null,'http://www.w3.org/2004/02/skos/core#altLabel','alt label');
SQL> RDF_OBJ_FT_RULE_ADD(null,'http://www.w3.org/2004/02/skos/core#prefLabel','pref label');

results in:

16:46:27 0 virtuoso-t 0x000000010aef1038 gpf_notice + 56
16:46:27 1 virtuoso-t 0x000000010aa5d587 cl_id_to_iri + 23
16:46:27 2 virtuoso-t 0x000000010acf95db bif_rdf_obj_ft_rule_add + 187
16:46:27 3 virtuoso-t 0x000000010ac49506 ins_call_bif + 166
16:46:27 4 virtuoso-t 0x000000010ac4fe5a code_vec_run_1 + 1498
16:46:27 5 virtuoso-t 0x000000010ac7a912 qn_input + 546
16:46:27 6 virtuoso-t 0x000000010ac7edea qr_subq_exec + 1306
16:46:27 7 virtuoso-t 0x000000010ac4ce04 ins_call + 2644
16:46:27 8 virtuoso-t 0x000000010ac4fe3d code_vec_run_1 + 1469
16:46:27 9 virtuoso-t 0x000000010ac7a912 qn_input + 546
16:46:27 10 virtuoso-t 0x000000010ac80606 qr_exec + 2758
16:46:27 11 virtuoso-t 0x000000010ac80d9d qr_quick_exec + 445
16:46:27 12 virtuoso-t 0x000000010aa99475 ddl_ensure_table + 277
16:46:27 13 virtuoso-t 0x000000010aba0674 sqls_define_sparql + 6052
16:46:27 14 virtuoso-t 0x000000010ac823b2 sql_code_global_init + 50
16:46:27 15 virtuoso-t 0x000000010ac897ad srv_global_init + 2957
16:46:27 16 virtuoso-t 0x000000010aa0e71a main + 1514
16:46:27 17 libdyld.dylib 0x00007fff8d9237e1 start + 0
16:46:27 18 ??? 0x0000000000000002 0x0 + 2
16:46:27 GPF: clrdf.c:680 internal error
GPF: clrdf.c:680 internal error
'

Tracking that down in the source gives:

caddr_t
cl_id_to_iri (query_instance_t * qi, caddr_t id)
{
GPF_T;
return NULL;
}

Error SQ156: Internal Optimized compiler error

Virtuoso develop/6 e8adecc
When executing the query below, this error is returned:

Virtuoso 37000 Error SQ156: Internal Optimized compiler error : Unplaced predicate in select layout in sqldf.c:6058.
Please report the statement compiled.

The query has two parts and we use MINUS (it does the same error with FILTER NOT EXIST). The two parts executed separately work OK, when the two MINUS clauses are switched, it runs, but returns something else, obviously.

Query:
PREFIX sukl: http://linked.opendata.cz/ontology/sukl/
PREFIX sukl1: http://linked.opendata.cz/ontology/sukl/drug/
PREFIX atc: http://linked.opendata.cz/resource/ATC/
PREFIX mesh: http://linked.opendata.cz/ontology/mesh/
PREFIX dbank: http://linked.opendata.cz/ontology/drugbank/
PREFIX ndf: http://linked.opendata.cz/ontology/ndfrt/
PREFIX spc: http://linked.opendata.cz/ontology/spc/

SELECT DISTINCT(?concept) AS ?interacting_concept
WHERE
{
{
http://linked.opendata.cz/resource/sukl/medicinal-product/0011064 sukl:hasATCCode/skos:broaderTransitive/skos:broaderTransitive ?atc2 .
?alternative sukl:hasATCCode/skos:broaderTransitive/skos:broaderTransitive ?atc2 .
?alternative sukl:hasActiveIngredient ?ai .
?ai mesh:hasConcept ?concept .
}
MINUS
{
#SUKL
http://linked.opendata.cz/resource/sukl/medicinal-product/0188638 sukl:hasActiveIngredient ?ingr .
http://linked.opendata.cz/resource/sukl/medicinal-product/0188638 sukl:hasATCCode ?atc .
?ingr mesh:hasConcept ?ingr_concept .
?ingr_concept mesh:parent ?descriptor .
#DBANK
?drug_same_dbank sukl1:hasATCCode ?atc .
#NDF
?ingr_same_ndf mesh:hasDescriptor ?descriptor .
?drug_ingr_same_ndf ndf:has_Ingredient ?ingr_same_ndf .
{
?interaction dbank:interactionDrug1 ?drug_same_dbank .
?interaction dbank:interactionDrug2 ?drug .
?drug mesh:hasConcept ?concept .
}
UNION
{
?interaction dbank:interactionDrug1 ?drug .
?interaction dbank:interactionDrug2 ?drug_same_dbank .
?drug mesh:hasConcept ?concept .
}
UNION
{
?interaction_ndf ndf:ingredient ?drug_ingr_same_ndf .
?interaction_ndf ndf:ingredient ?drug_ingr_ndf .
?drug_ingr_ndf ndf:has_Ingredient ?drug .
?drug mesh:hasDescriptor ?descriptor1 .
?descriptor1 mesh:prefChildConcept ?concept .
}
UNION
{
?interaction_spc spc:hasIngredient ?ingr .
?interaction_spc spc:hasIngredient ?drug .
?drug mesh:hasConcept ?concept .
}
}
}

Bootstrap with automake-1.13 - configure.in:39: error: 'AM_CONFIG_HEADER': this macro is obsolete.

  1. install automake-1.13.1
  2. unpack virtuoso-opensource-6.1.6.tar.gz
  3. run ./autogen.sh

Checking build environment ...
Using aclocal (GNU automake) 1.13.1
Using autoconf (GNU Autoconf) 2.69
Using autoheader (GNU Autoconf) 2.69
Using automake (GNU automake) 1.13.1
Using libtoolize (GNU libtool) 2.4.2
Using bison (GNU Bison) 2.7.12-4996
Using flex 2.5.37
Using GNU Awk 4.0.2
Using GNU gperf 3.0.4
Using OpenSSL 1.0.1e 11 Feb 2013

Generating build scripts ...
Running libtoolize ...
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, binsrc/config'. libtoolize: copying filebinsrc/config/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, binsrc/config'. libtoolize: copying filebinsrc/config/libtool.m4'
libtoolize: copying file binsrc/config/ltoptions.m4' libtoolize: copying filebinsrc/config/ltsugar.m4'
libtoolize: copying file binsrc/config/ltversion.m4' libtoolize: copying filebinsrc/config/lt~obsolete.m4'
Running aclocal ...

** ERROR **
configure.in:39: the top level
autom4te-2.69: /usr/bin/m4 failed with exit status: 1
aclocal-1.13: error: echo failed with exit status: 1

Bootstrap script aborting (see autogen.log for details) ...

$ cat autogen.log
am-wrapper: aclocal: warning: auto-detected versions not found (1.10); falling back to latest available
aclocal-1.13: warning: autoconf input should be named 'configure.ac', not 'configure.in'
configure.in:39: error: 'AM_CONFIG_HEADER': this macro is obsolete.
You should use the 'AC_CONFIG_HEADERS' macro instead.
/usr/share/aclocal-1.13/obsolete-err.m4:12: AM_CONFIG_HEADER is expanded from...
configure.in:39: the top level
autom4te-2.69: /usr/bin/m4 failed with exit status: 1
aclocal-1.13: error: echo failed with exit status: 1

See also:
https://bugs.gentoo.org/show_bug.cgi?id=466954

Faceted browser: does not preserve &lang parameter

When browsing using faceted browser (/fct), it show labels in the language preferred by the web browser. When I want to see a different language, I can use the &lang=cs (for Czech) parameter in URL. Problem is that this parameter is not preserved when clicking in the browser, it resets to default with each click. I think it should prefer the &lang=cs parameter and if it is different from the preferred browser language, it should generate the clickable links with this parameter so the selected language is preserved. Alternatively, put this in preferences or put a switch (language selection) somewhere.

SPARQL 1.1 VALUES clause takes very long

It seems as if the values clause in virtuoso isn't really working yet.
The following query takes forever to complete on dbpedia 1:

SELECT *
WHERE {
  ?uri rdfs:label ?label.
  VALUES (?uri) { (dbpedia:Berlin) (dbpedia:Kaiserslautern) }
}

If you run the same query with a single entity only it works 2:

SELECT *
WHERE {
  ?uri rdfs:label ?label.
  VALUES (?uri) { (dbpedia:Berlin) }
}

A workaround is constructing a filter clause 3 which works fast as usual:

SELECT *
WHERE {
  ?uri rdfs:label ?label.
  FILTER (?uri=dbpedia:Berlin || ?uri=dbpedia:Kaiserslautern)
}

Inference in combination with rdfs_rule_set and isIRI/isBlank not working

The functions isIRI/isBLANK always return true/false for inferred
bindings whether the bound value is a BNode or not.

This behaviour was observed with the Windows (Windows XP) and
the Linux version (Ubuntu 10.04) of Virtuoso 6.1.4.

Steps to reproduce the problem:

1. Insert some test data:

PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX test: <http://example/inferencetest#>

insert into <http://example/inferencetest#> {
    test:Tree a owl:Class ;
    rdfs:subClassOf [
        a owl:Restriction ;
        owl:onProperty test:hasChildren ;
        owl:allValuesFrom test:Node
    ] .
    test:Node a owl:Class .
    test:TheTree a test:Tree
}

2. Create rule set:

rdfs_rule_set('http://example/inferencetest#', 'http://example/inferencetest#')

3. Execute SPARQL query with inference rules:

define input:inference 'http://example/inferencetest#'

select *
from <http://example/inferencetest#>
where {
    ?s a ?o filter (isIRI(?s) && isIRI(?o))
}

4. Observations:

The restriction BNode is filtered in the case when it occurs
as asserted ?s but not in the case when it is an inferred ?o.

develop/7. minor installation issues

There are some notices from cp during installation (vad packaging). These should be either fixed or deliberately muted.

Here's relevant log:

Making install in yacutia
PATH="/private/tmp/virtuoso-ck6p/binsrc/virtuoso:/private/tmp/virtuoso-ck6p/binsrc/tests:.:$PATH" PORT=1111 HOME="/private/tmp/virtuoso-ck6p" HOST=localhost sh ./mkvad.sh

=====================================================================
=  CREATING VAD PACKAGE FOR VIRTUOSO CONDUCTOR (mkvad.sh)
=  Mon Jun 3 17:36:52 MSK 2013
=====================================================================

cp: images/dav_browser is a directory (not copied).
cp: images/icons is a directory (not copied).
cp: help is a directory (not copied).
cp: images is a directory (not copied).
cp: syntax is a directory (not copied).
cp: vad is a directory (not copied).
cp: /private/tmp/virtuoso-ck6p/binsrc/oat/toolkit/images/*: No such file or directory
VAD Sticker vad_fs.xml creation...
VAD Sticker vad_dav.xml creation...
Starting Virtuoso server ...
Virtuoso server started
PASSED: DB.DBA.VAD_PACK('vad_dav.xml', '.', 'conductor_dav.vad')
PASSED: DB.DBA.VAD_PACK('vad_fs.xml', '.', 'conductor_filesystem.vad')
PASSED: checkpoint
PASSED: shutdown

=====================================================================
=  Checking log file mkvad.output for statistics:
=
=  Total number of tests PASSED  :        4
=  Total number of tests FAILED  :        0
=  Total number of tests ABORTED :        0
=====================================================================


=====================================================================
=  COMPLETED VAD PACKAGING
=  Mon Jun 3 17:37:17 MSK 2013
=====================================================================

make[3]: Nothing to be done for `install-exec-am'.
 ../../binsrc/config/install-sh -c -d '/opt/homebrew/Cellar/virtuoso/HEAD/share/virtuoso/vad'
 /usr/bin/install -c -m 644 conductor_dav.vad '/opt/homebrew/Cellar/virtuoso/HEAD/share/virtuoso/vad'

Dereferencing URIs with Greek Characters in Faceted Browser

We're having a problem with URIs that contain greek characters. It seems that Virtuoso messes up the encoding in a way that when using /describe/?uri={someURI} the query uses a scrambled version of the original URI that does not correspond to any actual resource.
Is there any workaround, maybe by tweaking the code in description.vsp/description.sql?
Some additional information: In virtuoso.ini the character encoding is "utf-8" and we have set "set http_charset='UTF-8' ;" in description.vsp.

SPARQL compiler error (bad syntax)

We generated a query with the part

"FROM <http://purl.org/example#20130418-poc> "

When we execute this query against a OpenLink Virtuoso Server (Version 05.08.3034), we received the error message:

HttpException: 400 Bad Request
37000 Error SP030: SPARQL compiler, line 5: syntax error at '20130418' before '-'

We have tried other endpoints (different versions of Virtuoso), and we have no error at all.

We think that somehow, Virtuoso change URIs to CURIEs and the compiler treat them as QNAMEs. But this is just a assumption.

Deletes are are not cascaded if a row references 2 different rows.

I discovered a bug in RDBMS. I have a table a with a single column a.id. Table b has two different columns, both referencing a.id. In case a row from b contains references to two different rows in a, delete of referenced row from a does not cascade to row in b.

My virtuoso version:
Virtuoso Open Source Edition (Row Store) (multi threaded)
Version 6.1.7-rc1.3127-pthreads as of May 25 2013
Compiled for Linux (x86_64-unknown-linux-gnu)

Steps to reproduce:

CREATE TABLE a
(
  id INTEGER IDENTITY,
  PRIMARY KEY (id)
);

CREATE TABLE b
(
  id INTEGER IDENTITY,
  id1 INTEGER,
  id2 INTEGER,
  PRIMARY KEY (id)
);

ALTER TABLE b
  ADD CONSTRAINT b_a_id_id1 FOREIGN KEY (id1)
    REFERENCES a (id)
    ON UPDATE CASCADE ON DELETE CASCADE;

ALTER TABLE b
  ADD CONSTRAINT b_a_id_id2 FOREIGN KEY (id2)
    REFERENCES a (id)
    ON UPDATE CASCADE ON DELETE CASCADE;


INSERT INTO a(id) VALUES(1);
INSERT INTO a(id) VALUES(2);
INSERT INTO b(id,id1,id2) VALUES(1,1,2);

-- so far so good
-- lets truncate table a -> all rows in b should be deleted as well
DELETE FROM a;

-- however select still returns a row referencing nonexistent rows!
SELECT * FROM b;

I can provide more details if needed. Note that if I change the insert to INSERT INTO b(id,id1,id2) VALUES(1,1,1);, everything works fine.

Possible overflow in isql.c

This warning can sometimes indicate a potential security problem:

In function ‘wcsncpy’, inlined from ‘debug_command’ at isql.c:5742:19: /usr/include/bits/wchar2.h:201:2: warning: call to ‘__wcsncpy_chk_warn’ declared with attribute warning: wcsncpy called with length bigger than size of destination buffer

VOS7: Feature request: Add flag to TTLP/TTLP_MT to only warn on invalid geometries.

TTLP will stop loading data if it encounters invalid geometries such as

<http://linkedgeodata.org/geometry/way100237274> <http://www.opengis.net/ont/geosparql#asWKT> "LINESTRING(0 0)"^^<http://www.openlinksw.com/schemas/virtrdf#Geometry>

Would be very convenient if such errors could be turned into warnings by explicitely specifying a flag.

Faceted Browser Installation Fails

On develop/6 and develop/7 branches, when installing a fresh version, fct cannot be enabled. When clicking on Install in conductor, I get the following error:
00000 Errors detected
00000 Installation of "Faceted Browser" was unsuccessful.
The installation of this VAD package has failed.
Please delete the transaction file /data/virtuoso/db01/virtuoso.trx
and then restart your database server.
Note: Your database will be in its pre VAD installation state after you restart.
00000 FATAL

In virtuoso.log:
10:47:04 PL LOG: SR185: Undefined procedure DB.DBA.dpipe_define.
while executing the following statement:
--no_c_escapes-
dpipe_define ('IRI_RANK', 'DB.DBA.RDF_IRI_RANK', 'RDF_IRI_RANK', 'DB.DBA.IR_SRV', 128)
in file
10:47:04 PL LOG: SR185: Undefined procedure DB.DBA.dpipe_define.
while executing the following statement:
--no_c_escapes-
dpipe_define ('DB.DBA.IRI_RANK', 'DB.DBA.RDF_IRI_RANK', 'RDF_IRI_RANK', 'DB.DBA.IR_SRV', 128)

10:47:04 PL LOG: Errors where detected during installation of "Faceted Browser".
10:47:04 PL LOG: The installation of this VAD package has failed.
10:47:04 PL LOG: Please delete the transaction file
10:47:04 PL LOG: /data/virtuoso/db01/virtuoso.trx
10:47:04 PL LOG: and then restart your database server.
10:47:04 PL LOG: Note: Your database will be in its pre VAD installation
10:47:04 PL LOG: state after you restart.
10:47:07 Server shutdown complete

On v6 this can be worked around by installing stable/6, enabling fct and then updating to develop/6.

I am running debian,
Linux xrg13 2.6.32-5-amd64 #1 SMP Sun Sep 23 10:07:46 UTC 2012 x86_64 GNU/Linux

and configuring virtuoso like this:
./configure --prefix=/usr/local/ --with-readline --program-transform-name="s/isql/isql-v/" --with-layout=Debian --enable-fct-vad

Builld error (develop/7, OSX, clang)

/bin/sh ../../bin/libtool.macosx  --tag=CC   --mode=compile cc -DHAVE_CONFIG_H -I. -I../../libsrc/Dk    -fno-strict-aliasing -O2  -Wall  -DNDEBUG -DPOINTER_64   -I/private/tmp/virtuoso-9q7P/libsrc/Xml.new  -DOPENSSL_NO_KRB5    -I../../libsrc -I../../libsrc/Dk -I../../libsrc/zlib -I. -I../../libsrc/langfunc -I../../libsrc/plugin -I../../libsrc/Tidy -I../../libsrc/Xml.new -I../../libsrc/odbcsdk/include -DVAD -DDBP -DBIF_XPER -DOPSYS=\"Darwin\" -DHOST=\"x86_64-apple-darwin12.3.0\" -g -O2 -c -o libwi_la-colins.lo `test -f 'colins.c' || echo './'`colins.c
col.c:5309:45: error: use of unknown builtin '__builtin_ia32_loadups' [-Wimplicit-function-declaration]
      __builtin_ia32_storeups ((float *) t, __builtin_ia32_loadups ((float *) s));
                                            ^
col.c:5309:45: note: did you mean '__builtin_ia32_storeups'?
      __builtin_ia32_storeups ((float *) t, __builtin_ia32_loadups ((float *) s));
                                            ^~~~~~~~~~~~~~~~~~~~~~
                                            __builtin_ia32_storeups
col.c:5309:45: error: passing 'int' to parameter of incompatible type '__attribute__((__vector_size__(4 * sizeof(float)))) float'
      __builtin_ia32_storeups ((float *) t, __builtin_ia32_loadups ((float *) s));
                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2 errors generated.
make[3]: *** [libwi_la-col.lo] Error 1
$ cc --version
Apple LLVM version 4.2 (clang-425.0.28) (based on LLVM 3.2svn)
Target: x86_64-apple-darwin12.3.0
Thread model: posix

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